@article {pmid40743911,
year = {2025},
author = {Luo, Z and Lin, J and Ji, J and Zhang, M},
title = {Molecular Characterization of Two Hypertension Pedigrees Carrying Mitochondrial tRNA[Gln] 4386T>C Mutation.},
journal = {Human heredity},
volume = {90},
number = {1},
pages = {41-50},
pmid = {40743911},
issn = {1423-0062},
mesh = {Humans ; Pedigree ; Female ; *Hypertension/genetics ; DNA, Mitochondrial/genetics ; *Mutation ; Male ; *RNA, Transfer, Gln/genetics ; Phylogeny ; Maternal Inheritance ; Genome, Mitochondrial ; Mitochondria/genetics ; RNA, Mitochondrial ; Adult ; Middle Aged ; Essential Hypertension/genetics ; Asian People/genetics ; Base Sequence ; },
abstract = {UNLABELLED: <p>Introduction: The aim of this study was to explore the relationships between mitochondrial tRNA (mt-tRNA) mutations and essential hypertension (EH), and providing the valuable information for molecular diagnosis of EH.<br><br>METHODS: We reported here clinical, genetic and molecular characterizations of two Han Chinese pedigrees with maternally inherited EH. We first amplified the mitochondrial genomes of the matrilineal relatives with EH, furthermore, Sanger sequencing was used to screen mitochondrial DNA (mtDNA) mutations. Phylogenetic conservation, mt-tRNA structural analyses, as well as mitochondrial functional evaluations were performed to assess the potential pathogenicity of mtDNA mutations.<br><br>RESULTS: EH-1 and EH-2 pedigrees exhibited typically maternal transmission; analysis of mitochondrial genomes revealed the co-existence of tRNAGln 4386T>C mutation in both families. Moreover, members of EH-2 pedigree carried the tRNAAla 5601C>T mutation. The m.4386T>C and m.5601C>T mutations were very conserved and implicated to have impact on mitochondrial functions. Compared with the control cells and cells with only the m.4386T>C mutation, cells carrying both m.4386T>C and m.5601C>T mutations exhibited much lower levels of ATP, membrane potential and mtDNA copy number, whereas reactive oxygen species increased significantly. Thus, the m.5601C>T and m.4386T>C mutations caused mitochondrial dysfunctions and involved in EH progression.<br><br>CONCLUSION: The m.5601C>T may be a secondary variant that increase the penetrance and expressivity of hypertension-associated tRNAGln 4386T>C mutation. </p>.},
}
@article {pmid42840963,
year = {2026},
author = {Chan, MKS and Skutella, T and Thomas, FM and Lakey, JRT and Mutto, A and Fukuda, K and Baochi, L and Wong, MBF},
title = {Enhancing immune resilience in swine: a comprehensive meta-review of preventive and host-directed strategies against African swine fever and swine influenza.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1919982},
pmid = {42840963},
issn = {2297-1769},
abstract = {African swine fever (ASF) and swine influenza (SI) are among the most consequential infectious threats to global swine production because they combine major economic burden with fundamentally different transmission ecology, tissue tropism, and immune-pathological behavior. ASF is a highly lethal systemic disease characterized by macrophage tropism, immune dysregulation, environmental persistence, and severe trade and production consequences, whereas SI is a highly transmissible respiratory infection associated with recurrent herd-level morbidity, viral evolution, and zoonotic significance. Although these diseases differ markedly in biology and field presentation, both highlight the limitations of isolated pathogen-centered control strategies when implemented without integrated herd-level resilience measures. This meta-review synthesizes the cited literature into an evidence-based framework encompassing epidemiology, pathogenesis, surveillance, vaccination, biosecurity, herd management, supportive care, nutritional and immune-supportive measures, and host-directed regenerative approaches. Across the reviewed literature, the strongest field-supported evidence remains centered on surveillance, vaccination where applicable, biosecurity, and production-system management. At the same time, regenerative and host-supportive biologic strategies, including mitochondria-targeted peptides, thymic and organ-derived peptides, extracellular vesicle-based approaches, and stem cell-related therapies, demonstrate growing translational and immunomodulatory relevance within the broader context of immune resilience and recovery support. Comparative analysis further demonstrates that intervention priorities must remain aligned with disease biology: ASF control depends primarily on preventing viral introduction and limiting outbreak dissemination, whereas SI management benefits from integrated vaccination strategies, environmental optimization, mitigation of secondary bacterial disease, and continual adaptation to antigenic evolution. Within this framework, immune resilience is best understood not as a replacement for conventional disease control, but as a layered outcome arising from reduced infection pressure, preserved immune competence, regulated inflammatory responses, tissue recovery capacity, and supportive production practices.},
}
@article {pmid42843676,
year = {2026},
author = {Zhang, M and Cai, Y and Zeng, Q and Yi, Y and Liu, J and Lei, F and Huang, R and Cai, Z and Chen, Y and Deng, Y},
title = {Mitochondria-associated ferroptosis in ischemic stroke: Pathophysiological evolution, interorganelle crosstalk, and therapeutic targeting.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {109662},
doi = {10.1016/j.phrs.2026.109662},
pmid = {42843676},
issn = {1096-1186},
abstract = {Ischemic stroke (IS) results from an acute interruption of cerebral blood flow and the ensuing collapse of energy metabolism. Although vascular recanalization can salvage the ischemic penumbra, its overall benefit remains constrained by a narrow therapeutic window and reperfusion injury. Ferroptosis, an iron-dependent form of regulated cell death driven by lipid peroxidation, contributes to neuronal injury after IS and can amplify ischemia/reperfusion injury. By integrating energy metabolism, iron homeostasis, and redox balance, mitochondria can shape ferroptosis susceptibility within the energy-depleted, iron-dysregulated, and oxidatively stressed ischemic brain. However, most studies have examined iron metabolism and lipid peroxidation at the whole-cell level, leaving the temporal and interorganelle dimensions of mitochondrial regulation of ferroptosis insufficiently integrated. Here, we organize mitochondria-associated ferroptosis across the pathological course of IS, from metabolic reprogramming and substrate accumulation during ischemia to the reverse electron transport-associated reactive oxygen species burst during early reperfusion and subsequent disruption of mitochondrial quality control. We further examine mitochondrial crosstalk with the endoplasmic reticulum, lysosomes, lipid droplets, and nucleus, compare ferroptosis susceptibility across neurovascular unit cell populations, and map these mechanisms onto pharmacological interventions and mechanistically plausible therapeutic windows. Finally, we assess barriers to the clinical translation of mitochondria-targeted therapies and provide a stage-resolved framework for developing neuroprotective strategies in IS.},
}
@article {pmid42315408,
year = {2026},
author = {Cabrera-Alarcón, JL and Enríquez, JA},
title = {Rethinking mitochondrial metabolism: Intraindividual variability meets population constraints.},
journal = {Trends in genetics : TIG},
volume = {42},
number = {10},
pages = {881-884},
doi = {10.1016/j.tig.2026.05.011},
pmid = {42315408},
issn = {0168-9525},
mesh = {*DNA, Mitochondrial/genetics ; *Mitochondria/genetics/metabolism ; Animals ; Humans ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Oxidative Phosphorylation ; },
abstract = {Recent advances integrating high-resolution 3D structures with population genetics and comparative evolutionary analyses indicate that mitochondrial DNA (mtDNA) acts as a primary evolutionary engine driving nuclear coadaptation. This process reflects a trade-off between individual heterozygosity and mtDNA-driven variability, which together expand the mitonuclear haplotype pool within species.},
}
@article {pmid42828706,
year = {2026},
author = {Shan, Z and Jiao, N and Ding, D and Liu, G and Zeng, X and Zhan, C and Chen, X},
title = {Multi-level metabolic engineering for squalene production: from pathway optimization to systematic regulation.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828706},
issn = {1573-0972},
mesh = {*Squalene/metabolism ; *Metabolic Engineering/methods ; Biosynthetic Pathways ; Metabolic Networks and Pathways ; Lipid Metabolism ; },
abstract = {Squalene is a high-value unsaturated triterpene extensively used in pharmaceuticals, cosmetics, and health products. Traditional extraction methods of squalene from shark oil are environmentally unfriendly, making it imperative to explore better production approaches. Microbial engineering for squalene production has drawn much attention due to its environmentally friendly nature, sustainability, and high efficiency. However, the capacity of squalene biosynthesis is still limited by many challenges, including insufficient precursor supply, metabolic flux competition, product toxicity, and extracellular transport. To address these issues, this review systematically summarizes various metabolic engineering strategies to enhance squalene production at three hierarchies, including pathway, organelle, and cell. At the pathway level, we discuss several common metabolic engineering strategies to improve the biosynthetic pathways of squalene, including enhancing precursor supply, regulating cofactor levels, and inhibiting competing metabolic pathways. At the organelle level, we underscore the application of organelle engineering in peroxisomes, mitochondria, and endoplasmic reticulum to achieve compartmentalized storage of squalene, alleviate product cytotoxicity, reduce distribution of precursor metabolic flux, and improve catalytic efficiency. At the cell level, cellular production capacity can be comprehensively improved to achieve high-level production of squalene by regulating lipid metabolism, promoting squalene secretion, modulating transcription factors, and combining mutagenesis and evolution. These metabolic engineering strategies not only offer comprehensive guidance for the efficient squalene biosynthesis but also establish a theoretical and technical foundation for the microbial production of other high-value terpenoids.},
}
@article {pmid42154823,
year = {2026},
author = {Piñeros, L and Heald, R},
title = {Beyond Kleiber's Law: Variation and Mechanisms of Metabolic Scaling.},
journal = {Annual review of cell and developmental biology},
volume = {42},
number = {1},
pages = {59-82},
doi = {10.1146/annurev-cellbio-101323-015244},
pmid = {42154823},
issn = {1530-8995},
mesh = {Animals ; *Energy Metabolism/physiology ; Humans ; Biological Evolution ; Models, Biological ; Mitochondrial Dynamics ; Mitochondria/metabolism ; Cell Size ; },
abstract = {The scaling relationship between metabolic rate and body mass is a foundational principle in biology that links physiology, ecology, and evolution. From early empirical studies-most notably Kleiber's observation of 3/4 power law scaling-to contemporary theoretical frameworks, decades of research have sought to explain why organismal metabolic rate increases more slowly than body mass. This review examines variation in scaling exponents across the tree of life and explores how cellular features, including cell size, mitochondrial dynamics, and energy storage, shape whole-organism metabolism. We describe how dynamic metabolic rates during embryonic development reveal patterns of energy use during growth, while deviations in metabolic scaling across species and disease states indicate how biological systems balance energy constraints with adaptive flexibility. Together, these insights position cells as the critical interface linking molecular bioenergetics to organismal function, evolution, and ecology.},
}
@article {pmid42212533,
year = {2026},
author = {Zhu, L and Togashi, Y},
title = {Mitochondrial transfer-driven immune evasion in the tumor microenvironment.},
journal = {International immunology},
volume = {38},
number = {10},
pages = {603-609},
pmid = {42212533},
issn = {1460-2377},
support = {//Japan Society for the Promotion of Science (JSPS)/ ; //Japan Agency for Medical Research and Development (AMED)/ ; JP23ama221325h0001//Promotion of Cancer Research and Therapeutic Evolution/ ; JP24fk0210158h0001//Research Program for Hepatitis/ ; },
mesh = {Humans ; *Mitochondria/immunology/metabolism ; *Tumor Microenvironment/immunology ; Animals ; *Neoplasms/immunology ; *Tumor Escape/immunology ; T-Lymphocytes/immunology ; T-Cell Exhaustion ; *Immune Evasion ; },
abstract = {The tumor microenvironment (TME) is a complex landscape where metabolic interactions significantly dictate antitumor immunity. Immune evasion in cancer is typically discussed in terms of inhibitory receptors and ligands, suppressive cytokines, defective antigen presentation, and metabolic competition. However, recent evidence reveals that intercellular mitochondrial transfer adds a new mechanism of immune evasion in the TME. The mitochondrial fitness of T cells is central to sustained effector function, memory formation, and responsiveness to immune-checkpoint blockade. Tumor cells can act as pathogenic mitochondrial donors, transferring functional or dysfunctional mitochondria to neighboring T cells via tunneling nanotubes and extracellular vesicles. This process involves a mitophagy imbalance that leads to the homoplasmic replacement of endogenous mitochondria, thereby driving T-cell senescence, impairing memory formation and long-term antitumor function, and ultimately weakening cancer immunosurveillance. Overall, mitochondrial transfer should be considered a new part of the tumor immune evasion framework. It also provides new therapeutic opportunities for improving cancer immunotherapy.},
}
@article {pmid42817631,
year = {2026},
author = {Labbadia, J},
title = {More than the 'master regulator of cytosolic proteostasis': new roles for HSF1 in promoting tissue health.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1960},
pages = {},
pmid = {42817631},
issn = {1471-2970},
support = {BB/W104980/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RPG-2025-061//Leverhulme Trust/ ; },
mesh = {*Proteostasis ; Animals ; *Heat Shock Transcription Factors/metabolism/genetics ; *Cytosol/metabolism ; Humans ; *Heat-Shock Response ; },
abstract = {Maintaining protein homeostasis (proteostasis) is crucial for long-term tissue health. This requires the action of stress response pathways and protein quality control mechanisms that act within or across different sub-cellular compartments to preserve proteome integrity. Within the cytosol/nucleus, the loss of proteostasis induces a transcriptional programme known as the heat-shock response (HSR) through activation of heat-shock factor 1 (HSF1). The HSR rapidly elevates levels of molecular chaperones, co-chaperones and protein degradation factors that restore proteostasis in the cytosol/nucleus. As a result, the ability of HSF1 to promote tissue health has long been attributed to its capacity to safeguard the cytosolic/nucleosolic proteome. However, over the past 15 years, it has become apparent that HSF1 activity is also intimately coupled with the biogenesis and maintenance of other organelles, including mitochondria, peroxisomes, the endoplasmic reticulum, lysosomes and chloroplasts. This suggests that HSF1 promotes tissue health in plants and animals through mechanisms beyond the maintenance of cytosolic/nucleosolic proteostasis. In this opinion piece, I will discuss advances in our understanding of the interplay between HSF1 and organelle homeostasis and make the case that the existing model for the relationship between HSF1 and tissue health should be expanded to encompass these additional roles. This article is part of the Theo Murphy meeting issue 'ProteostaSys: a systems view of proteostasis'.},
}
@article {pmid42822419,
year = {2026},
author = {Vacas, AF and Solayman, M and Calvo, SE and Nguyen, K and Lian, CG and Rivera, KD and Chen, MZ and , and Udeshi, ND and Mootha, VK and Aphasizhev, R and Aphasizheva, I},
title = {Lineage-specific innovations expand mitochondrial proteomes in kinetoplastids.},
journal = {Molecular cell},
volume = {86},
number = {19},
pages = {4058-4074.e8},
doi = {10.1016/j.molcel.2026.08.032},
pmid = {42822419},
issn = {1097-4164},
mesh = {*Proteome/genetics/metabolism ; DNA, Kinetoplast/genetics/metabolism ; *Trypanosoma brucei brucei/genetics/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; *Mitochondria/metabolism/genetics ; *Leishmania/genetics/metabolism ; *Protozoan Proteins/metabolism/genetics ; Animals ; Proteomics/methods ; RNA Editing ; Phylogeny ; Evolution, Molecular ; },
abstract = {Trypanosoma brucei and Leishmania tarentolae are model kinetoplastids whose mitochondria contain a unique DNA network, kinetoplast DNA (kDNA), and exhibit specialized features, including developmental remodeling and RNA editing. By integrating mass spectrometry-based protein correlation profiling with published datasets, we assembled inventories of 1,666 mitochondrial proteins in T. brucei and 1,594 in L. tarentolae. These include 124 polypeptides not previously recognized as mitochondrial. Despite their phylogenetic distance, trypanosomes and leishmanias maintain highly conserved mitoproteomes, including about 700 components with no detectable homologs in other eukaryotes. Comparison of T. brucei insect and mammalian stages revealed similar mitoproteome compositions but globally reduced mitochondrial protein abundance in the latter, except for components of calcium homeostasis and the alternative oxidase pathway. We also detected ten kDNA-encoded proteins, including products of pan-edited transcripts. These inventories establish a framework for functional analysis of previously uncharacterized mitochondrial factors and illuminate innovations that have shaped kinetoplastid evolution.},
}
@article {pmid42822422,
year = {2026},
author = {Stairs, CW and Gawryluk, RMR},
title = {Mitochondria before we knew them.},
journal = {Cell},
volume = {189},
number = {20},
pages = {6214-6216},
doi = {10.1016/j.cell.2026.09.003},
pmid = {42822422},
issn = {1097-4172},
mesh = {*Mitochondria/metabolism/genetics ; Animals ; Phylogeny ; *Mitochondrial Proteins/genetics/metabolism ; *Proteome ; Humans ; Evolution, Molecular ; },
abstract = {In this issue of Cell, Chen et al. chart mitochondrial proteome diversity across eukaryotes, revealing an unexpectedly complex ancestral proteome alongside extensive lineage-specific innovation. Their broad phylogenetic reconstruction provides new insights into the mitochondrial proteome of the last eukaryotic common ancestor while unearthing a wealth of unexplored mitochondrial biology outside of traditional model systems.},
}
@article {pmid42822423,
year = {2026},
author = {Mootha, VK and Calvo, SE},
title = {Decoding mitochondrial proteomes of diverse eukaryotes.},
journal = {Cell},
volume = {189},
number = {20},
pages = {6243-6245},
doi = {10.1016/j.cell.2026.09.007},
pmid = {42822423},
issn = {1097-4172},
mesh = {Animals ; *Proteome/analysis ; *Mitochondrial Proteins/metabolism/analysis/genetics ; *Mitochondria/metabolism/chemistry ; Humans ; *Eukaryota/metabolism/genetics ; Proteomics ; },
abstract = {Our textbook view of mitochondria, which has been shaped by studies in animals and yeast, fails to do justice to the organelle's broader eukaryotic diversity. While most mitochondria retain a tiny genome, the overwhelming majority of their proteins are nuclear-encoded and vary extensively across lineages. To map this diversity, the MitoCarta Tree of Life Consortium developed experimental and computational workflows to generate high-accuracy mitochondrial proteomes across diverse eukaryotes-helping to lay a foundation for comparative mitochondrial biology with broad implications for physiology, evolution, and disease.},
}
@article {pmid42822426,
year = {2026},
author = {Chen, MZ and Stefely, JA and Bardon, EG and , and Calvo, SE and Mootha, VK},
title = {Comparative analysis of mitochondrial proteomes across the tree of life.},
journal = {Cell},
volume = {189},
number = {20},
pages = {6285-6306.e13},
doi = {10.1016/j.cell.2026.08.029},
pmid = {42822426},
issn = {1097-4172},
mesh = {*Proteome/analysis ; *Mitochondrial Proteins/metabolism/genetics ; *Mitochondria/metabolism ; *Eukaryota/metabolism/classification/genetics ; Phylogeny ; Animals ; Evolution, Molecular ; Humans ; },
abstract = {Mitochondria arose from the endosymbiosis of a bacterium with an archaea-related host cell about 2 billion years ago. To understand their origins and evolution, we compared experimentally defined mitoproteomes from the MitoCarta Tree of Life project. Across eight organisms, we identified 8,619 distinct mitochondrial proteins within 3,199 families, of which 43% lack Pfam domains. We report 33 protein families conserved in eukaryotic pathogens yet absent in humans, representing promising candidate targets for protozoan infectious diseases. Leveraging our experimentally defined mitoproteomes, we retrained a classifier based on a protein language model to predict mitoproteomes of ∼200 eukaryotes. From this expanded set, we detail the evolutionary trajectories of mitochondria, ranging from clade-specific gene family expansions to extreme mitoproteome reductions seemingly en route to complete organelle loss. Finally, we reconstruct the last eukaryotic common ancestor (LECA) mitoproteome, revealing that LECA possessed a complex mitochondrion capable of both aerobic and anaerobic metabolism.},
}
@article {pmid42822427,
year = {2026},
author = {Fry, MY and Luce, BE and Stefely, JA and Chen, MZ and Deng, FG and Issa, TM and , and Calvo, SE and Samuelson, J and Mootha, VK and Chao, LH},
title = {Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS.},
journal = {Cell},
volume = {189},
number = {20},
pages = {6307-6324.e7},
doi = {10.1016/j.cell.2026.08.057},
pmid = {42822427},
issn = {1097-4172},
mesh = {*Oxidative Phosphorylation ; *Citric Acid Cycle ; *Acanthamoeba castellanii/enzymology/metabolism ; Cryoelectron Microscopy ; *Mitochondrial Proton-Translocating ATPases/chemistry/metabolism ; Models, Molecular ; Protozoan Proteins/chemistry/metabolism ; Mitochondria/metabolism ; Malate Dehydrogenase/metabolism/chemistry ; },
abstract = {Oxidative phosphorylation (OXPHOS) is a key metabolic process that couples redox energy to ATP production. While some core OXPHOS complex subunits are found across all domains of life, many have diverged or expanded across evolution-as seen in the protozoan pathogen Acanthamoeba castellanii. By integrating cryo-electron microscopy of unenriched mitochondrial lysate with mass spectrometry proteomics, we resolved the structures of endogenous mitochondrial ATP synthase (complex V), Hsp60, and respiratory complex III from Acanthamoeba. We capture Acanthamoeba ATP synthase in an IF1-inhibited state and reveal how Acanthamoeba-specific subunits and extensions stabilize the molecular machine, which includes a β subunit extension that interfaces with the peripheral stalk. Additionally, we characterize an active malate dehydrogenase (MDH) dimer structurally integrated within the ATP synthase peripheral stalk, thus revealing a direct protein tether between OXPHOS and the tricarboxylic acid cycle. Together, these findings provide structural insight into lineage-specific adaptations in Acanthamoeba that may tune protozoan metabolism.},
}
@article {pmid42822458,
year = {2026},
author = {Betsinger, CN and Calvo, SE and Mian, SY and Bauer, NC and Paul, AS and Batzli, DL and Lian, CG and Boyle, BW and Rivera, KD and Sreenivasamurthy, SK and McCoy, JG and Chen, MZ and Issa, TM and Stefely, JA and , and Dvorin, JD and Udeshi, ND and Duraisingh, MT and Mootha, VK},
title = {Mitochondrial proteome of the apicomplexan Babesia divergens.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.08.072},
pmid = {42822458},
issn = {1879-0445},
abstract = {Babesia are tick-transmitted apicomplexan parasites of widespread medical and veterinary importance. Although atovaquone, a first-line therapy for human babesiosis, targets one of the three proteins encoded by mitochondrial DNA, a full characterization of the nuclear-encoded mitochondrial proteome is lacking. Here, we combined organelle immunoprecipitation and density gradient separation to enrich mitochondria from Babesia divergens. Using protein mass spectrometry and protein correlation profiling, we generated B. divergens MitoCarta (BdMitoCarta), a high-confidence inventory of 525 mitochondrial proteins. The B. divergens mitoproteome is broadly conserved across Apicomplexa, which, as a clade, have undergone reductive evolution. As seen in other apicomplexans, metabolite transport and the TCA cycle have diverged, with loss of the pyruvate dehydrogenase complex, presence of malate:quinone oxidoreductase, and a class I fumarate hydratase. Specific to Babesia is the presence of two mitochondrial isocitrate dehydrogenase homologs. Using isolated mitochondria, we performed blue native PAGE complexome analysis and detected previously uncharacterized proteins co-migrating with the ATP synthase and mitochondrial ribosome. Our work has yielded the first mitochondrial proteome and complexome for Babesia, which we expect to be a valuable resource for understanding the evolution of apicomplexan parasites for future therapeutic development.},
}
@article {pmid42636980,
year = {2026},
author = {Loveridge, KM and Olsen, OD and Scherer, SR and Espino-Sanchez, TJ and Wienkers, H and Hill, CP and Kay, MS and Sigala, PA},
title = {A Divergent Mitochondrial Cytochrome c in Malaria Parasites With an Anomalously Low Redox Potential.},
journal = {Journal of molecular biology},
volume = {438},
number = {21},
pages = {169996},
pmid = {42636980},
issn = {1089-8638},
support = {R21 AI185746/AI/NIAID NIH HHS/United States ; R35 GM161383/GM/NIGMS NIH HHS/United States ; },
mesh = {Oxidation-Reduction ; *Cytochromes c/metabolism/genetics/chemistry ; *Plasmodium falciparum/metabolism/genetics ; *Mitochondria/metabolism ; Heme/metabolism ; Protozoan Proteins/metabolism/chemistry ; Phylogeny ; Electron Transport ; },
abstract = {Eukaryotic cytochrome (cyt) c is a highly conserved mitochondrial protein central to cellular respiration, featuring a covalently attached heme with hexacoordinate iron whose redox potential is tuned by axial His/Met ligands and surrounding residues to support electron transport chain (ETC) function. We have identified a previously unrecognized lineage of eukaryotic cyt c homologs in Apicomplexa, a phylum of intracellular pathogens that includes Plasmodium falciparum malaria parasites. P. falciparum cyt c-2 (Pfcyt c-2) exemplifies this divergent lineage and displays heterogeneous heme coordination despite conservation of His/Met ligands. We determined that Pfcyt c-2 has a redox potential of -278 ± 6 mV that is over 500 mV lower than canonical mitochondrial cyt c homologs (+250 mV) and contradicts a conserved ETC role. This anomalous redox potential is lower than any natural monoheme c-type cyt and reveals exceptional evolutionary tuning for a eukaryotic cyt c. Although Pfcyt c-2 displays signs of structural heterogeneity, it retains low-level peroxidase activity and global protein thermostability comparable to canonical cyt c proteins. These results reveal a new clade of eukaryotic cyt c proteins with divergent biochemical properties and biological roles, opening new scaffolds for mechanistic discovery and redox engineering of natural and abiological functions.},
}
@article {pmid42802190,
year = {2026},
author = {Couée, I},
title = {Involvement of cytokinin response factor 6 in the integration of abiotic stress responses with metabolism and growth in Arabidopsis thaliana.},
journal = {Planta},
volume = {264},
number = {5},
pages = {},
pmid = {42802190},
issn = {1432-2048},
mesh = {*Arabidopsis/growth &amp; development/metabolism/genetics/physiology ; *Stress, Physiological ; *Arabidopsis Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; Cytokinins/metabolism ; Signal Transduction ; *Transcription Factors/metabolism/genetics ; Plant Growth Regulators/metabolism ; },
abstract = {This review highlights the importance of the CYTOKININ RESPONSE FACTOR 6 transcription factor as a plant regulatory nexus integrating responses to multiple abiotic stresses with metabolism, growth and development. Cytokinin Response Factors constitute a subfamily of plant transcription factors that have been identified as cytokinin-responsive APETALA2/ethylene-responsive element binding proteins and further characterised as components of cytokinin signalling. Besides being involved in the canonical cytokinin signalling pathway, they are part of complex networks of interactive regulation. Their mode of action, their interactions and their functions however remain to be fully understood. Among cytokinin response factors that are currently identified and characterised in Arabidopsis thaliana, CYTOKININ RESPONSE FACTOR 6 has been extensively studied as it is related to numerous developmental, nutritional, hormonal, abiotic stress and biotic stress processes. CYTOKININ RESPONSE FACTOR 6 was thus recently shown to be part of a SNF1-related kinase1/Jumonji C domain-containing JMJ15 regulatory axis involved in energy, oxidative stress and growth co-regulation. This review focusses on involvement of CYTOKININ RESPONSE FACTOR 6 in the integration of abiotic stress responses with metabolism, growth and development, and on the underlying mechanisms of this integration. The characterisation of CYTOKININ RESPONSE FACTOR 6 as a stress-growth nexus will be highlighted in terms of regulatory processes and mechanisms. The essential roles of this stress-growth nexus will be discussed in the context of multiple stresses and global changes with potential implications for plant biodiversity dynamics and agricultural sustainability.},
}
@article {pmid42803112,
year = {2026},
author = {Hadjadji, C and Ohse, M and Stier, A and Bize, P},
title = {High-throughput mitochondrial aerobic metabolism measurement: assessing a plate-reader approach using avian blood cells.},
journal = {Biology open},
volume = {},
number = {},
pages = {},
doi = {10.1242/bio.062712},
pmid = {42803112},
issn = {2046-6390},
support = {212971//Schweizerischer Nationalfonds zur Furderung der Wissenschaftlichen Forschung/ ; //Centre National de la Recherche Scientifique/ ; },
abstract = {Mitochondria power biological processes, driving interest in measuring mitochondrial aerobic metabolism to understand individual variation in performance and fitness. High-resolution respirometry (HRR) is the gold standard for its sensitivity and versatility, but is time-consuming and low throughput, limiting large-scale studies. We assessed the validity of a high-throughput, fluorescence-based plate reader by comparing it to HRR. In a first experiment, we measured mitochondrial respiration in blood cells from two bird species (quails and chicken) across three temperatures (hypo-, normo-, and hyperthermia). The two methods were moderately correlated and revealed similar species effects; however, temperature effects differed between approaches, particularly under hyperthermic conditions, indicating that the plate-reader approach is best suited to stable, normothermic conditions. In a second experiment on sex differences in quail at normothermia, the two methods agreed quantitatively for proton leak and oxidative control efficiency and qualitatively for oxidative phosphorylation, although the plate-reader estimate was marginally significant (p=0.060 vs. p=0.046 for HRR). The plate reader's main limitation is lower sensitivity and greater measurement error, which could be offset by increasing sample sizes. Following protocol optimisation for each study system, this approach may offer a useful high-throughput complement to HRR for studies prioritising larger sample sizes.},
}
@article {pmid42803785,
year = {2026},
author = {Havird, JC},
title = {Molas have mighty mitochondria: intensified purifying selection on mtDNA despite presumed "low-energy" lifestyles in ocean sunfishes (family Molidae).},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag178},
pmid = {42803785},
issn = {1558-5646},
abstract = {Ocean sunfish (family Molidae) are often perceived as "low-energy" drifters composed largely of connective tissue with noticeably missing fins and even cited as "mistakes" of natural selection. Because locomotory capacity has been identified as a driver of evolution in animal mitochondrial genomes (mtDNA), ocean sunfish are expected to show signatures of relaxed selection on mtDNA compared to closely related, more energetic species. Contrary to expectations, ocean sunfish showed lower dN/dS ratios (the ratio of non-synonymous to synonymous substitution rates) in all mitochondrial-encoded genes and further analyses strongly suggest this is due to increased purifying selection on mtDNA within Molidae. Population genetic data also support more intense selection on ocean sunfish mtDNA. These results agree with recent studies recharacterizing ocean sunfish as active swimmers with a complex lifestyle including extreme vertical migrations, behavioral thermoregulation, and extreme fecundity. Finally, across 64 diverse fishes, mtDNA evolutionary rates did not correlate with swimming speed. More broadly, this study highlights how predicting selection on mitochondrial genes is not straightforward. Assuming different selective pressures on mtDNA given locomotion or different perceived "lifestyles" may be an oversimplification, analogous to regarding an unusual species as an evolutionary "mistake".},
}
@article {pmid42469540,
year = {2026},
author = {Murugaiah, C},
title = {Mitochondrial cytochrome b motif architecture predicts host-specific genomic vulnerability across vertebrate species.},
journal = {Virus genes},
volume = {62},
number = {5},
pages = {684-689},
pmid = {42469540},
issn = {1572-994X},
mesh = {Animals ; *Cytochromes b/genetics ; *DNA, Mitochondrial/genetics ; *Vertebrates/genetics ; *Host Specificity ; Cattle ; Phylogeny ; Evolution, Molecular ; Polymorphism, Restriction Fragment Length ; Swine ; *Mitochondria/genetics ; Rabbits ; Amino Acid Motifs ; },
abstract = {Mitochondrial DNA (mtDNA) plays a pivotal role in cellular bioenergetics, immune regulation, and evolutionary adaptation, making it a uniquely informative genomic system for studying host-pathogen interactions. The cytochrome b (cyt b) gene, one of the most conserved mitochondrial protein-coding loci, is widely recognized for its utility in species identification, phylogenetics, and molecular evolution [1-3]. However, its potential role in shaping comparative host susceptibility to infectious diseases remains underexplored. In this study, we re-analyzed PCR-RFLP-derived mitochondrial cyt b restriction profiles targeting CCNNGG, GTAC, AGCT, TTAA, and CGCG motifs across seven vertebrate hosts: cattle, buffalo, pig, goat, rabbit, chicken, and quail. These motif architectures were compared with documented susceptibility patterns for Pasteurellosis, foot-and-mouth disease (FMD), Rinderpest, and Sarcoptes scabiei infestation [4, 6, 7]. The integrated motif matrix revealed distinct host-specific restriction profiles and four comparative genomic vulnerability clades. The findings support a model in which conserved mitochondrial motif architecture may reflect evolutionary genomic signatures relevant to pathogen-host range and susceptibility. The study is intended as a comparative genomic framework and does not claim direct causality between single restriction motifs and disease outcome.},
}
@article {pmid42794633,
year = {2026},
author = {Anvari, E and Daryabor, G and Sedigh, A and Rashidi, S and Nguewa, P},
title = {Evolution and Adaptation of the Mitochondrial Protein Import Machinery in Parasitic Protists: Beyond the Canonical TOM Complex.},
journal = {International journal of molecular sciences},
volume = {27},
number = {18},
pages = {},
doi = {10.3390/ijms27188205},
pmid = {42794633},
issn = {1422-0067},
support = {MICIU/AEI/10.13039/501100011033 (grant number PID2023-147765OB-C21, -C22)//Ministerio de Ciencia e Innovaci&#xf3;n from Spain/ ; 2026//Fundaci&#xf3;n Roviralta (Chair "Maria Francisca de Roviralta of Molecular Parasitology, Leishmaniasis and One Health")/ ; },
mesh = {Protein Transport ; *Mitochondrial Proteins/metabolism/genetics ; Mitochondria/metabolism ; *Evolution, Molecular ; Animals ; *Parasites/metabolism ; *Mitochondrial Membrane Transport Proteins/metabolism/genetics ; },
abstract = {The translocase of the outer membrane (TOM) complex is the primary entry gate for nucleus-encoded mitochondrial proteins and is conserved across eukaryotes; however, parasitic protists exhibit remarkable adaptations. This review synthesizes current knowledge on the composition, structure, and function of TOM and related import systems in apicomplexans, kinetoplastids, and anaerobic protists with reduced mitochondrion-related organelles (MROs). We highlight major evolutionary innovations, including the bacterial-origin ATOM complex in trypanosomes-comprising core channel ATOM40, receptors ATOM46/69, structural subunit ATOM19, and multifunctional pATOM36 linking protein import to mitochondrial DNA inheritance-alongside lineage-specific receptors such as Tom60 in Entamoeba histolytica and extreme reductive streamlining in microsporidian mitosomes. Beyond its canonical role in biogenesis, we explore how parasites co-opt the host TOM complex for intracellular survival and how the import machinery integrates with broader cellular processes, including immune signaling, stress responses, and organelle dynamics. Notably, the essential nature of these adapted systems, coupled with their significant divergence from host machinery, highlights their potential as targets for developing novel therapeutic strategies against major parasitic diseases. This work underscores that understanding the diversity of mitochondrial protein import pathways not only provides insights into eukaryotic evolution but may also open new avenues for the development of antiparasitic drugs.},
}
@article {pmid42797851,
year = {2026},
author = {Rosas-Rodríguez, JA and Muñoz-Bacasehua, C and González-Ochoa, G and Ruiz, EA and Mancilla-Morales, MD and Zamora-Alvarez, LA and Soñanez-Organis, JG},
title = {Regulation of Glycerol-3-Phosphate Dehydrogenase by Hypoxia-Inducible Factor-1 in WSSV-Infected White Shrimp Litopenaeus vannamei.},
journal = {Viruses},
volume = {18},
number = {9},
pages = {},
doi = {10.3390/v18091020},
pmid = {42797851},
issn = {1999-4915},
support = {USO513007035//Universidad de Sonora/ ; },
mesh = {Animals ; *Penaeidae/virology/enzymology/genetics ; *White spot syndrome virus 1/physiology ; *Glycerolphosphate Dehydrogenase/genetics/metabolism ; Phylogeny ; Mitochondria/enzymology ; Hepatopancreas/enzymology/virology ; *Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; },
abstract = {Hypoxia-inducible factor-1 (HIF-1) induces the Warburg effect in the Litopenaeus vannamei shrimp infected with white spot syndrome virus (WSSV) to satisfy the energetic and biosynthetic demands required for viral replication. Glycerol-3-phosphate dehydrogenase (GPDH) is a key enzyme linking carbohydrate metabolism, lipid biosynthesis, and cellular redox balance; however, its role during WSSV infection remains poorly understood. In this study, the complete coding sequences of the cytoplasmic (LvGPDHc) and mitochondrial (LvGPDHm) GPDH isoforms were characterized from the hepatopancreas of L. vannamei, and their regulation by HIF-1α during WSSV infection was investigated. Sequence and phylogenetic analyses revealed that both proteins are highly conserved among crustaceans and contain the characteristic domains required for catalytic activity. WSSV infection decreases the mRNA expression of both GPDH isoforms and increases the cytoplasmic GPDH activity. In contrast, HIF-1α silencing increases the mRNA expression of both GPDH isoforms and increases the mitochondrial GPDH activity. The concentrations of glycerol-3-phosphate and citrate increase with WSSV infection and return to basal levels upon HIF-1α silencing. Results suggest that WSSV infection in white shrimp is associated with increased lipid biosynthesis via cytoplasmic GPDH, which contributes to viral replication, whereas mitochondrial GPDH may help maintain cellular redox status. Furthermore, these results demonstrate that the expression of GPDH isoforms is regulated by HIF-1, contributing to metabolic reprogramming in shrimp during WSSV infection.},
}
@article {pmid42789308,
year = {2026},
author = {Li, C and Zhou, Z and Wu, T and Wang, Z and Ji, Z and Lu, B and Zhang, X and Lynch, M and Yan, Y},
title = {Cellular remodeling during reversible life-stage transition in sessile ciliates: Genomic and transcriptomic insights.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {40},
pages = {e2536061123},
doi = {10.1073/pnas.2536061123},
pmid = {42789308},
issn = {1091-6490},
support = {DBI-2119963//NSF (NSF)/ ; DEB-1927159//NSF (NSF)/ ; 32270558//MOST | National Natural Science Foundation of China (NSFC)/ ; 2025M772643//China Postdoctoral Science Foundation ()/ ; Grant 735927//Simons Foundation (SF)/ ; 2R35GM122566//HHS | NIH (NIH)/ ; },
mesh = {*Ciliophora/genetics/growth &amp; development/metabolism ; *Transcriptome ; Genomics ; *Genome, Protozoan ; Mitochondria/metabolism/genetics ; Cilia/genetics/metabolism ; *Life Cycle Stages/genetics ; Gene Expression Profiling ; },
abstract = {Unraveling mechanisms driving dramatic life-stage transitions in response to environmental stress is central to understanding cellular adaptation. We studied a distinctive group of sessile ciliates that undergo profound morphological and organellar remodeling when transitioning from sessile trophonts to motile telotrochs. We generated chromosome-level genomes for two colonial species (Campanella sinica, Epistylis hentscheli) and one solitary species (Vorticella campanula), revealing genome sizes of 41.30 to 60.37 Mb. Notably, minichromosomes (10 to 100 kb) represent a shared, distinct chromosomal architecture across all three species. We constructed a transcriptional atlas by profiling five transitional stages, revealing core gene sets linked to transcriptional regulation, cilia, cytoskeletal dynamics, and metabolism. Intermediate stages converge on conserved genes driving structural and energetic turnover, including polyubiquitin and the mitochondrial regulator CHCHD2. Furthermore, we uncovered metabolic reprogramming and active spatial mobilization of mitochondria tailored to fuel these extreme morphological shifts. During structural remodeling, the mitochondrial genome exhibits asymmetric regulation-coordinating the upregulation of translational and early respiratory machineries with the downregulation of terminal electron transport potentially mitigating oxidative stress. Crucially, in vivo imaging physically corroborates this transcriptomic priming, revealing a marked increase in mitochondrial density and their targeted redistribution to regions of high ATP demand. Conversely, during stalk biosynthesis, organellar regulation selectively upregulates the mitochondrial protein ymf66 to sustain prolonged translational and energetic demands. Ultimately, our findings highlight how ciliates integrate global transcriptomic shifts with organelle-specific spatial and metabolic fine-tuning to meet the precise mechanical requirements of complex life-cycle transitions.},
}
@article {pmid42400034,
year = {2026},
author = {Husin, NA and Low, VL and AbdulRahim, MHS and Abdullah Halim, MR and AbdulHalim, AA and Mohd-Redzuan, MAA and Jiliun, EA and Mohd Kharip Shah, AK and Makepeace, BL and Ya'cob, Z},
title = {Mitochondrial COI and 16S rDNA barcoding improve species delimitation of ixodid ticks in Peninsular Malaysia.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42400034},
issn = {1756-3305},
support = {Sub-program MO002A-2021//Dana Langganan Sukuk Pakej Rangsangan Ekonomi Prihatin Rakyat (SUKUK PRIHATIN), Malaysia Ministry of Finance through the Ministry of Higher Education, Malaysia/ ; },
mesh = {Animals ; Malaysia ; *DNA Barcoding, Taxonomic/methods ; *Electron Transport Complex IV/genetics ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/genetics/classification ; DNA, Ribosomal/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {BACKGROUND: Hard ticks (Acari: Ixodidae) are major vectors of zoonotic pathogens affecting humans and animals. Accurate species identification is essential for surveillance and disease risk assessment but is often hindered by morphological similarity and intraspecific variation. In Malaysia, tick studies have largely relied on morphology or single-gene barcoding, with limited taxonomic and geographic coverage.<br><br>METHODS: This study applied a multilocus mitochondrial approach using cytochrome c oxidase I (COI) and 16S ribosomal DNA (rDNA) to evaluate species boundaries among ixodid ticks from Peninsular Malaysia. Ticks were collected from wild and domestic hosts between 2022 and 2023. A total of 319 specimens representing 14 morphologically defined species were analysed using COI and 16S rDNA sequencing, with additional reference sequences retrieved from GenBank for comparative analyses. Phylogenetic reconstruction, barcode gap assessment, and four species delimitation methods (ASAP, ABGD, bPTP, and GMYC) were employed to assess genetic divergence and identification accuracy.<br><br>RESULTS: Molecular analyses were largely congruent with morphological identification. Distance-based delimitation methods (ASAP and ABGD) recovered operational taxonomic units (OTUs) largely consistent with morphologically defined species, whereas tree-based approaches (bPTP and GMYC) inferred substantially higher numbers of OTUs, reflecting sensitivity to intraspecific mitochondrial structuring. These additional subdivisions are interpreted conservatively as population-level genetic differentiation rather than evidence of distinct species. Clear barcode gaps were observed for COI and the concatenated COI&#x2009;+&#x2009;16S rDNA datasets, whereas partial overlap occurred with 16S rDNA alone. COI demonstrated the highest and most consistent performance for routine species identification, while concatenated datasets improved phylogenetic resolution but reduced assignment clarity under strict barcoding criteria.<br><br>CONCLUSIONS: Overall, COI remains the most effective mitochondrial marker for routine species identification of ixodid ticks in Peninsular Malaysia. These findings highlight the value of integrative approaches combining morphology and molecular data to strengthen tick taxonomy and support surveillance of tick-borne pathogens in the region.},
}
@article {pmid42725482,
year = {2026},
author = {Laizé, M and Marques, JP and Geniez, P and Mochales-Riaño, G and Kaliontzopoulou, A and Muyle, A and Pinho, C and Crochet, PA},
title = {Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards.},
journal = {Genome biology and evolution},
volume = {18},
number = {9},
pages = {},
doi = {10.1093/gbe/evag228},
pmid = {42725482},
issn = {1759-6653},
support = {//FCT/FEDER/ ; //EXPL/BIA-EVF/1283/2012/ ; //French Minist&#xe8;re de l'Enseignement Sup&#xe9;rieur et de la Recherche through GAIA doctoral school/ ; },
mesh = {Animals ; *Lizards/genetics ; *DNA, Mitochondrial/genetics ; *Oxidative Phosphorylation ; Phylogeny ; Cell Nucleus/genetics ; *Genetic Introgression ; Evolution, Molecular ; Genome, Mitochondrial ; },
abstract = {In this study, we took advantage of the previously reported instances of mitochondrial DNA (mtDNA) capture in the Podarcis Iberian group, a speciose group of Iberian wall lizards, to test the hypothesis that nuclear genes from the OXPHOS (oxidative phosphorylation) chain can co-introgress with the mitochondria as an evolutionary response to mitigate the costs of mitonuclear incompatibilities. Using dense population sampling and transcriptome data, we generated capture-sequence datasets for nuclear OXPHOS chain genes (nucOXPHOS), random nuclear loci (nucControl) and the complete mitochondrial genome. Phylogenetic analyses of nuclear and mitochondrial genes confirmed two previously identified events of mitochondrial introgression in the Podarcis Iberian group and revealed two new cases. Three of these cases have led to complete local mtDNA replacements, where the introgressed mitotypes have replaced the native ones in several populations, and involve a currently unknown and presumably extinct donor species, so-called "ghost lineage." Detecting introgression from ghost lineages, whose genomes are not accessible, remains challenging. To overcome this issue, we designed or adapted several tests aimed at detecting differential signals of introgression between our nucOXPHOS and nucControl gene sets. One of these tests, based on the effects of introgression on branch lengths in phylogenetic trees, uncovered a weak but consistently significant signal of partial co-introgression of nucOXPHOS genes compared to the genomic background (represented by the nucControl gene set) in three out of four cases of mtDNA introgression.},
}
@article {pmid42128920,
year = {2026},
author = {Tatarczuch, A and Kotarska, K and Polański, Z and Ptak, A},
title = {A PFAS mixture at environmental relevant concentration induces DNA damage and compromises the in vitro maturation of mouse oocytes.},
journal = {Archives of toxicology},
volume = {100},
number = {10},
pages = {4705-4716},
pmid = {42128920},
issn = {1432-0738},
support = {2022/45/B/NZ7/00254//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Oocytes/drug effects/metabolism/pathology ; *DNA Damage/drug effects ; Female ; Reactive Oxygen Species/metabolism ; Mice ; Mitochondria/drug effects/metabolism ; *Environmental Pollutants/toxicity ; *Fluorocarbons/toxicity ; Meiosis/drug effects ; Glutathione/metabolism ; Oxygen Consumption/drug effects ; Oxidative Stress/drug effects ; In Vitro Oocyte Maturation Techniques ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants that can accumulate in the human body, including follicular fluid (FF), potentially affecting the function of reproductive cells. We used the mixture of these chemicals at concentrations previously reported in human FF to assess their effects on in vitro maturation, DNA integrity, and mitochondrial function of mouse oocytes. Exposure to PFAS led to meiotic abnormalities, manifested by an increase in the percentage of oocytes arrested at the germinal vesicle breakdown (GVBD) stage and a decrease in the number of oocytes reaching the metaphase II (MII) stage. We demonstrated that arrest at GVBD is associated with Spindle Assembly Checkpoint (SAC) activation as experimental inhibition of SAC restores normal maturation to MII. In addition, we observed increased DNA damage and changes in oxidative balance, including an increase in reduced glutathione (GSH) and a decrease in reactive oxygen species (ROS) levels. However, we found an increase in mitochondrial activity, basal oxygen consumption (OCR), and mitochondrial respiration intensity in immature GV stage oocytes, indicating disturbances in bioenergetic homeostasis. These findings show for the first time that PFAS mixtures, at concentrations relevant to human exposure, interfere with oocyte maturation, genome integrity, and mitochondrial function. The data obtained highlight the need for further research on the toxicity of PFAS mixtures, especially at doses mirroring their environmental presence, and their potential impact on female fertility.},
}
@article {pmid42387401,
year = {2026},
author = {Kang, SW and Shin, H and Kim, SJ and Lee, J and Cheon, KS},
title = {The first complete assembly and analysis of mitochondrial genome of Pinus thunbergii in Pinaceae.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {},
pmid = {42387401},
issn = {1471-2229},
support = {FG0400-2022-01-2026//National Institute of Forest Science/ ; },
mesh = {*Genome, Mitochondrial/genetics ; *Pinus/genetics ; Phylogeny ; Genome, Plant ; },
abstract = {BACKGROUNDS: The Korean black pine (Pinus thunbergii) is a coastal conifer native to East Asia, including Korea, China, and Japan. Mitochondria and chloroplast in plants are semi-autonomous organelle that encode a small set of proteins and modulate nuclear genome expressions with retrograde signaling to coordinate stress responses and photosynthesis. Although the chloroplast genome of P. thunbergii has been previously characterized, a complete mitochondrial genome has not yet been reported, limiting genomic insights into the evolutionary dynamics of the genus Pinus.<br><br>RESULTS: We assembled the mitogenome using a hybrid sequencing approach that integrates Nanopore long reads with Illumina short reads. The mitogenome comprises two distinct chromosomes-a circular chromosome (~&#x2009;2.24&#xa0;Mb) and a linear chromosome (~&#x2009;0.31&#xa0;Mb)-with a total length of 2,553,981&#xa0;bp (46.86% of GC), which is two times larger than mitogenome of P. taeda (1.2&#xa0;Mb). These genomes encode 41 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. Based on these PCGs, we predicted 861 potential C-to-U RNA editing sites. Relative synonymous codon usage (RSCU) analysis identified that 30 codon values exceed 1; among these, 86.6% of codons ended with A/T bases, except UUG (Leu), UCC (Ser), ACC (Thr), and UAG (Ter). Only atp1 is exposed to purifying selection (Ka/Ks&#x2009;<&#x2009;1). Comparative genomics revealed that 15 fragments were transferred to chromosome 1 and two fragments were transferred to chromosome 2 from the chloroplast of P. thunbergii (Accession number MW599991.31). Moreover, collinearity analysis showed that 217 fragments were similar to the mitogenome of P. taeda, which accounts for 23.92% of the P. thunbergii mitogenome. Phylogenetic analysis with 15 PCGs confirmed the taxonomic position within the family Pinaceae. Notably, rps3 showed a similar distribution to the phylogenetic tree of 30 PCGs.<br><br>CONCLUSIONS: In this study, we present the first complete mitogenome of P. thunbergii, analyze mitochondrial genomic characters, confirm horizontal gene transfer from the chloroplast genome, and reveal similarity and close phylogenetic affinity with P. taeda. This study expands the current organellar genomic resources and provides a foundation for evolutionary research in the genus Pinus. Moreover, the discovery of a multi-chromosomal architecture opens new avenues for investigating genome rearrangement and complex evolutionary dynamics across gymnosperm lineages.},
}
@article {pmid42750666,
year = {2026},
author = {Tan, SL and Vera-Vives, AM and Wang, H and Huang, X and Beraldo, C and Alboresi, A and Morosinotto, T},
title = {Essential mitochondrial activity in Physcomitrium patens relies on complementary cytochrome and alternative oxidase pathways.},
journal = {The Plant journal : for cell and molecular biology},
volume = {127},
number = {5},
pages = {e71127},
pmid = {42750666},
issn = {1365-313X},
support = {2022B25BKC//Ministero dell'Universit&#xe0; e della Ricerca/ ; //Chinese Scholarship Council/ ; },
mesh = {Alternative Oxidase ; *Oxidoreductases/metabolism/genetics ; *Plant Proteins/metabolism/genetics ; *Bryopsida/metabolism/genetics/enzymology/physiology ; *Mitochondrial Proteins/metabolism/genetics ; *Mitochondria/metabolism ; *Cytochromes/metabolism ; Electron Transport ; Photosynthesis ; Oxidation-Reduction ; Cell Respiration ; Adenosine Triphosphate/metabolism ; },
abstract = {Mitochondrial respiration catalyses the transfer of electrons from NADH to oxygen through the activity of five multiprotein complexes. In plants, mitochondria also possess additional alternative electron transport pathways, including the alternative oxidase (AOX) pathway, which transfers electrons from ubiquinol to O2, bypassing the cytochrome-dependent electron transport chain. This study investigates the functional role of AOX during plant evolution by analysing Physcomitrium patens plants that lack or overexpress AOX. In the moss P. patens, AOX exhibits a remarkably high electron transport capacity, sufficient to fully compensate for the inactivation of the cytochrome pathway. Despite the high potential activity of AOX, aox knockout lines did not show significant defects in growth under various abiotic stresses. This suggests that the cytochrome pathway can compensate for AOX loss and effectively support the consumption of reducing power produced by photosynthesis even under stressful conditions. Although photosynthetically active cells can produce ATP in chloroplasts under illumination independently of mitochondrial electron transport, respiration is shown to be essential for the conversion of reducing power into ATP for distribution throughout the cell. Simultaneous inactivation of AOX and CIII was lethal, indicating that AOX and the complementary cytochrome pathway contribute to the essential role of mitochondrial respiration in the redox and energy balance in P. patens cells.},
}
@article {pmid42751568,
year = {2025},
author = {Miller, E and Bambakidis, P and Templin, P and Paul, BD and Pieper, AA},
title = {Emerging roles of the ciliary-mitochondrial axis in cellular homeostasis and neuroprotection.},
journal = {Molecular neurodegeneration advances},
volume = {1},
number = {1},
pages = {5},
pmid = {42751568},
issn = {3059-4944},
abstract = {Primary cilia and mitochondria, long studied as separate cellular players, are now recognized as a tightly coupled signaling and metabolic hub whose interplay powerfully shapes cell fate. The bidirectional ciliary-mitochondrial axis integrates extracellular sensing, calcium dynamics, bioenergetics, and organelle quality control to drive adaptive responses to stress and sustain neuronal resilience. Recent studies reveal compelling associations that merit further investigation, such as the impact of primary cilium-initiated signaling cascades on mitochondrial dynamics and mitophagy, and the effects on cilia of shifting mitochondrial metabolic states. Dysfunction at any node in this axis has potential to trigger neurodegeneration. Framing primary cilia and mitochondria as a coordinated physiologic axis enables reconsideration of neurodegeneration and reveals novel, tractable entry points for therapeutic restoration of brain homeostasis. This review traces the field's evolution, synthesizes key molecular mechanisms, and highlights exciting translational opportunities to harness the ciliary-mitochondrial axis for neuroprotection.},
}
@article {pmid42738339,
year = {2026},
author = {Morabito, F and Martino, EA and Bruzzese, A and Amodio, N and Vigna, E and Gentile, M},
title = {Mitochondrial Fitness as a Functional Immune Checkpoint in Cancer: Metabolic Plasticity, Tumor Evolution, and Immunotherapy.},
journal = {Cancers},
volume = {18},
number = {17},
pages = {},
pmid = {42738339},
issn = {2072-6694},
abstract = {Mitochondria are increasingly recognized as dynamic regulators of cancer-cell adaptation, immune function, and therapeutic response. Beyond their canonical role in energy production, mitochondrial metabolism, dynamics, quality control, and stress signaling influence tumor-cell survival and the capacity of immune effector cells to sustain antitumor activity within the tumor microenvironment. In this narrative review, we examine mitochondrial fitness as a multidimensional functional property encompassing bioenergetic capacity, metabolic flexibility, redox homeostasis, mitochondrial quality control, and adaptation to cellular and therapeutic stress. We propose the mitochondrial functional immune checkpoint as a conceptual framework linking mitochondrial fitness in malignant and immune cells to tumor-immune interactions and immunotherapy response. We discuss how mitochondrial metabolic plasticity, mitochondrial stress and mtDNA signaling, reactive oxygen species, mitochondrial dynamics, and intercellular mitochondrial transfer contribute to immune escape and treatment resistance. We further examine the relevance of mitochondrial fitness to immune checkpoint blockade, CAR-T-cell therapy, and T-cell-redirecting bispecific antibodies, with particular attention to hematological malignancies, including acute myeloid leukemia and multiple myeloma, while incorporating selected evidence from solid tumors to highlight shared mitochondrial mechanisms and their broader oncologic relevance. Finally, we discuss emerging strategies for mitochondrial targeting and functional mitochondrial profiling and their potential integration with established molecular and measurable residual disease assessments. Current evidence supports mitochondrial biology as a complementary dimension of precision oncology, although important challenges remain regarding context dependence, biomarker standardization, therapeutic selectivity, and preservation of immune-cell fitness. Prospective studies are needed to determine whether functional mitochondrial profiling can improve patient stratification and guide rational therapeutic combinations that selectively exploit tumor mitochondrial vulnerabilities while preserving effective antitumor immunity.},
}
@article {pmid42733965,
year = {2026},
author = {Chakraborty, A and Rodríguez, E and Bettinazzi, S and Stroila, S and Lane, N and Camus, MF},
title = {Mitochondrial genetic effects mediate the response to stress through development, but not adult metabolic rate in Drosophila.},
journal = {The Journal of experimental biology},
volume = {},
number = {},
pages = {},
doi = {10.1242/jeb.253155},
pmid = {42733965},
issn = {1477-9145},
support = {BB/S003681/1//BBSRC/ ; //London Interdisciplinary Doctoral Programme/ ; //Research Experience Placement Award by the London Interdisciplinary Doctoral Programme/ ; },
abstract = {Energy expenditure is fundamental to physiology, behaviour, ecology, and life history, yet the mechanisms that regulate metabolic rate remain poorly understood. At the cellular level, incompatibilities between the maternally inherited mitochondrial genome and the nuclear genome can impair energy production, signalling and gene expression, with potential to disrupt a wide range of physiological processes. However, how these often-subtle genomic mismatches influence whole-organism traits such as metabolic rate, activity, and fitness remains unclear. Here, we generated mitonuclear-mismatched fly lines to test how early-life dietary and metabolic stress affect larval and adult physiology. Our results revealed sex and line-specific physiological effects, with larval development, survival and female fertility strongly contingent on the haplotypes and treatment, while adult resting metabolic rate and activity were not influenced by mitochondrial haplotype, nor by developmental stress.},
}
@article {pmid42734359,
year = {2026},
author = {Brittain, KS and Delfino, LM and Thiemann, OH and Cortines, JR and Parent, KN},
title = {The organization and dynamics of viral factories.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0089226},
doi = {10.1128/jvi.00892-26},
pmid = {42734359},
issn = {1098-5514},
abstract = {Viral factories (VFs) are dynamic, virus-induced microcompartments that serve as centralized hubs in the host cell for viral genome replication, transcription, and virion assembly. These structures employ unique viral mechanisms for remodeling cellular architecture to create specialized replication organelles and improve the efficiency of viral propagation. VFs exhibit striking structural and functional diversity among RNA and DNA viruses, from reoviruses and poxviruses to the Nucleocytoviricota phylum. Some are enclosed by host-derived membranes, while others exist as biomolecular condensates from liquid-liquid phase separation. VFs recruit host lipids, cytoskeletal elements, and metabolic enzymes, effectively reprogramming the intracellular environment to favor viral replication. This review provides a comprehensive examination of the molecular composition, ultrastructure, and biogenesis of viral factories across a wide range of viral lineages and host systems. We describe membrane-bound and phase-separated VFs and the mechanisms by which they hijack host machinery to create these replication organelles and explore viral strategies to shield replication intermediates from host immune responses. Additional emphasis is placed on the complex VFs formed by giant viruses in the Nucleocytoviricota, whose ability to spatially compartmentalize replication and transcription, exclude ribosomes, and recruit host mitochondria and membranes blurs the line between viral and cellular organization. By integrating findings from cell biology and evolutionary virology, this review proposes that viral factories offer a conceptual framework for understanding virus-host coevolution and provides new insights into how their organization may have shaped the emergence of eukaryotic complexity.},
}
@article {pmid42734362,
year = {2026},
author = {Hancks, DC and Baker, SF},
title = {The factory enters the fray: how mitochondrial protein trafficking shapes the host response to infection.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0174625},
doi = {10.1128/jvi.01746-25},
pmid = {42734362},
issn = {1098-5514},
abstract = {Beyond textbook functions in homeostatic metabolism, mitochondria are now recognized as central coordinators of cell-intrinsic and cell-extrinsic immune responses to infection. Directed trafficking of proteins and other molecules between mitochondria and the rest of the cell underlies a growing catalog of these activities. Some are pro-host; others are antagonized by viral effectors or co-opted by viruses entirely. How host and viral factors rewire the mitochondrial proteome during infection to shape these outcomes remains incompletely understood. The evolutionary history of this system adds another dimension: mitochondria retain biochemical signatures of their α-proteobacterial endosymbiotic origin, and ongoing co-evolution between viral, host, and mitochondrial genomes continues to shape the proteins that traffic to and from the organelle. Using published examples, we highlight general principles, mechanisms, and consequences of host and viral protein localization to and from the mitochondria. To support discovery, we present integrated gene lists identifying host mitochondrial factors with evidence for type I interferon stimulation, interactions with viral proteins, and signatures of positive selection. Together, these resources and the principles within offer a framework for understanding mitochondria not as passive metabolic machinery but as actively contested cellular territory whose protein composition is continuously negotiated between the host and the pathogen.},
}
@article {pmid42209703,
year = {2026},
author = {Yu, J and Xu, M and Wu, XR and Kang, WB and Zou, WY and Liu, Q and Zhang, DF and Yao, YG},
title = {Convergent mitochondrial impairment and apoptosis driven by simultaneous down-regulation of multiple genes at 11p11.2 in Alzheimer's disease.},
journal = {Molecular psychiatry},
volume = {31},
number = {10},
pages = {5862-5878},
pmid = {42209703},
issn = {1476-5578},
support = {32230021//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300826//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M763353//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Alzheimer Disease/genetics/metabolism ; Apoptosis/genetics/physiology ; Mitochondria/metabolism/genetics ; Humans ; Down-Regulation/genetics ; Mice ; Reactive Oxygen Species/metabolism ; Mice, Transgenic ; Disease Models, Animal ; Genome-Wide Association Study/methods ; Neurons/metabolism ; Male ; NADH Dehydrogenase/genetics/metabolism ; },
abstract = {Genome-wide association studies (GWAS) and multi-omics analyses have identified numerous risk loci and thousands of potential causal genes associated with Alzheimer's disease (AD). However, the synergistic pathogenic contributions of multiple low-risk causal genes within a single locus remain poorly understood. Polygenic synergism at the 11p11.2 locus was systematically examined in AD pathogenesis. Three causal genes (MTCH2, NDUFS3, and PSMC3) exhibited coordinated down-regulation in both AD patients and AD mouse models. Individual knockdown in cultured cells altered mitochondrial function and disrupted AD-associated pathways, as revealed by transcriptomic profiling. Integrated RNA-seq analysis and experimental validation demonstrated that the concurrent down-regulation of all three genes synergistically enhanced mitochondrial reactive oxygen species (ROS) generation and activated the caspase-7-mediated apoptotic pathway. Notably, pharmacological caspase inhibition with Q-VD-OPh attenuated neuronal apoptosis, ameliorated memory deficits, and reduced Aβ plaque deposition in APP/PS1 mice. Simultaneous down-regulation of multiple genes at the 11p11.2 locus contributed to mitochondrial dysfunction and apoptosis in AD, highlighting polygenic synergism as a key pathogenic mechanism.},
}
@article {pmid42657789,
year = {2026},
author = {Fang, R and Tian, X and Liang, D and Zhang, P},
title = {Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.},
journal = {Molecular biology and evolution},
volume = {43},
number = {9},
pages = {},
doi = {10.1093/molbev/msag221},
pmid = {42657789},
issn = {1537-1719},
support = {//Outstanding Youth Team/ ; 2023B1515040002//Natural Science Foundation of Guangdong Province/ ; 32370541//National Natural Science Foundation of China/ ; 32370477//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Butterflies/genetics ; Cell Nucleus/genetics ; Phylogeny ; Evolution, Molecular ; Genome, Mitochondrial ; Selection, Genetic ; Mitochondria/genetics ; Biological Evolution ; Diet ; },
abstract = {Mitochondrial function depends on tight coordination between mitochondrial and nuclear genomes, which requires long-term coevolution to maintain mitonuclear coadaptation. While mitonuclear incompatibility is typically studied in the context of hybridization, other evolutionary scenarios that may disrupt coadaptation between the two genomes remain less explored. Here, we propose that extreme ecological niche shifts may disrupt mitonuclear coadaptation, which we test in carnivorous Miletinae butterflies with an extreme dietary transition. By generating high-quality genome assemblies, we found that Miletinae exhibit extensive chromosomal rearrangements. Comparative phylogenomic analyses revealed a striking asymmetric mitonuclear evolutionary response: Miletinae exhibit elevated mitochondrial nucleotide substitution rates compared to phytophagous relatives, whereas nuclear rates remain stable. This shift reverses the typical lepidopteran pattern where nuclear rates exceed mitochondrial rates. Interestingly, this mitochondrial acceleration is driven primarily by relaxed purifying selection rather than positive selection. To sustain mitochondrial function, the nuclear genome of Miletinae underwent pervasive, multilayered compensatory evolution. We detected strong signatures of positive selection and accelerated evolution in nuclear genes directly interacting with mitochondrial components across oxidative phosphorylation (OXPHOS) complexes, the mitochondrial translation, and replication and transcription machinery. Furthermore, this nuclear compensatory response extends to systems governing mitochondrial homeostasis, including protein quality control and RNA degradation and stabilization. Our results support a model in which extreme ecological transitions can disrupt ancestral mitonuclear coadaptation and promote the emergence of a new coadapted state through systemic nuclear compensation. This study broadens the conceptual framework of mitonuclear coevolution and highlights its role in facilitating evolutionary persistence after major ecological shifts.},
}
@article {pmid42712903,
year = {2026},
author = {Wang, S and Meng, C and Bian, H and Zhang, X and Cong, M and Ren, J and Sun, J and Zhang, H and Liu, D},
title = {Global Research Landscape of Mitochondrial Dysfunction in Sepsis: A Comprehensive Bibliometric and Visualization Analysis (2000-2025).},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {636359},
pmid = {42712903},
issn = {1178-7031},
abstract = {OBJECTIVE: Sepsis-associated mitochondrial dysfunction represents a central but incompletely understood mechanism underlying organ failure and mortality in critically ill patients. Despite a growing body of literature, no comprehensive bibliometric analysis has systematically mapped the global research landscape, knowledge structure, and emerging frontiers of this field. This study aimed to quantify publication trends, identify key contributors, delineate thematic hotspots, and characterize the evolving knowledge base in sepsis and mitochondria research over the past 25 years.<br><br>METHODS: A systematic search of the Web of Science Core Collection was conducted using a predefined search strategy combining sepsis- and mitochondria-related terms, restricted to publications from January 1, 2000, to December 31, 2025. After sequential exclusion of retracted publications, non-article/review document types, and non-English records, a final dataset of 3545 publications was obtained. Bibliometric analyses were performed using the bibliometrix package in R, VOSviewer (version 1.6.20), and CiteSpace (version 6.2.R4). Analyses included annual publication trends, geographic and institutional distribution, Bradford's Law journal analysis, Lotka's Law author productivity, co-citation and bibliographic coupling network analysis, thematic mapping, and keyword burst detection.<br><br>RESULTS: Annual publication output increased more than nine-fold from 2000 to 2025, with a marked acceleration following the 2016 Sepsis-3 consensus definition. China led in publication volume (n = 1350; 38.1%), while the United States demonstrated the highest citation impact (52,732 total citations; 67.61 average citations per publication). Bradford's Law analysis identified 30 core journals, led by Shock, Frontiers in Immunology, and Critical Care Medicine. Lotka's Law analysis confirmed that 74.94% of contributing authors published a single article. The most cited publication was Zhang Q et al (Nature, 2010; 3080 citations). Thematic map analysis identified mitochondrial dysfunction/acute kidney injury, oxidative stress/reactive oxygen species, and inflammation/mitochondrial DNA as Motor Themes. Keyword burst analysis revealed a temporal evolution from early nitric oxide and cytochrome c research toward current hotspots including NLRP3 inflammasome activation, sepsis-associated encephalopathy, and sepsis-induced cardiomyopathy.<br><br>CONCLUSION: This comprehensive bibliometric analysis provides a systematic overview of 25 years of research at the intersection of sepsis and mitochondrial biology. The field is experiencing sustained growth, with current research frontiers focused on organ-specific mitochondrial injury, innate immune regulation, and neurological complications.},
}
@article {pmid42706326,
year = {2026},
author = {Fang, Y and Ren, Z and Zheng, F and Wang, R and Zhao, S and Zhang, Y and Wang, W and Li, C and Liu-Yang, L and Lin, C and Liu, J and Zou, P},
title = {Directed evolution of Lantern enables rapid RNA and protein proximity labeling.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
pmid = {42706326},
issn = {1552-4469},
support = {2022YFA1304700//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32088101//National Natural Science Foundation of China (National Science Foundation of China)/ ; Bayer Investigator Award//Bayer/ ; },
abstract = {In eukaryotic cells, the precise spatial localization of RNAs and proteins is essential for proper cellular function. Genetically encoded photocatalytic proximity labeling techniques have expanded our ability to map subcellular proteomes and transcriptomes, but their temporal resolution remains limited. Here we introduce Lantern, an engineered flavoprotein optimized via directed evolution, which enables sub‑minute, spatially resolved labeling of cellular biomolecules. Lantern is targetable to diverse subcellular compartments, including the endoplasmic reticulum (ER), mitochondria and stress granules (SGs), to map local transcriptomes (CAP-seq) and proteomes (CAP-MS). Using Lantern, we observed that N[6]-methyladenosine-rich RNAs are recruited to SGs within 10 minutes of stress induction, and ER‑proximal RNAs associate with G3BP1 during early SG assembly. Additionally, Lantern was adapted for cell surface tagging (CAP-CELL), enabling spatially resolved cell typing and identifying cell-cell interactions. Collectively, this study establishes Lantern as a powerful tool that offers unprecedented temporal resolution for investigating the dynamic organization of subcellular molecular networks.},
}
@article {pmid42337626,
year = {2026},
author = {Siriyasatien, P and Intayot, P and Boonserm, R and Ampol, R and Sutthanont, N and Silakom, N and Suwanbamrung, C and Schmidt-Chanasit, J and Phumee, A},
title = {A descriptive assessment of mitochondrial COI genetic diversity and dengue and chikungunya RNA detection in Aedes aegypti across eight provinces in Thailand.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42337626},
issn = {1756-3305},
support = {Grant No. NRCT5-RSA63001-03//National Research Council of Thailand (NRCT)/ ; },
mesh = {Animals ; *Aedes/virology/genetics ; Thailand/epidemiology ; *Genetic Variation ; *Electron Transport Complex IV/genetics ; *Chikungunya virus/genetics/isolation &amp; purification ; *RNA, Viral/genetics/isolation &amp; purification ; *Dengue Virus/genetics/isolation &amp; purification ; Haplotypes ; *Mosquito Vectors/virology/genetics ; Dengue/transmission/virology/epidemiology ; Phylogeny ; Mitochondria/genetics/enzymology ; },
abstract = {BACKGROUND: Aedes aegypti is the principal vector of several medically important arboviruses, including dengue virus (DENV) and chikungunya virus (CHIKV), both of which remain endemic in Thailand. However, studies on arbovirus surveillance and mitochondrial genetic diversity of Ae. aegypti populations across broad geographic scales remain limited. This study aimed to assess the detection of DENV and CHIKV and characterize the mitochondrial genetic diversity of Ae. aegypti across multiple regions of Thailand.<br><br>METHODS: A total of 303 adult Ae. aegypti mosquitoes collected from eight provinces across five geographic regions of Thailand were screened for DENV and CHIKV RNA. Mitochondrial cytochrome c oxidase subunit I (COI) genetic diversity was assessed using haplotype network analysis and analysis of molecular variance (AMOVA).<br><br>RESULTS: CHIKV RNA was detected in 51 mosquitoes (16.8%) from four provinces, with the highest detection rates observed in Prachuap Khiri Khan and Bangkok. DENV RNA was not detected in any sample. COI analysis revealed moderate to high mitochondrial haplotype diversity and geographic variation in haplotype distribution among populations. Both widely shared and province-specific haplotypes were identified. AMOVA indicated that most genetic variation occurred within populations (93.19%), with significant&#xa0;genetic differentiation among populations (&#x3a6;ST&#x2009;=&#x2009;0.068, P&#x2009;<&#x2009;0.001).<br><br>CONCLUSIONS: CHIKV RNA was detected in Ae. aegypti populations from multiple regions of Thailand, whereas DENV RNA was not detected. Mitochondrial COI analysis revealed substantial haplotype diversity and geographic variation among populations. These findings contribute to current knowledge of arbovirus occurrence and mosquito genetic diversity in Thailand and provide a foundation for future vector surveillance studies.},
}
@article {pmid42628870,
year = {2026},
author = {Huang, Y and Du, J and Zeng, X and Zou, P and Zhang, Z and Wang, Y},
title = {Role of the steroid hormone synthesis pathway-related gene StAR-like in gonadal development of mud crab (Scylla paramamosain).},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {320},
number = {},
pages = {112064},
doi = {10.1016/j.cbpa.2026.112064},
pmid = {42628870},
issn = {1531-4332},
mesh = {Animals ; *Brachyura/genetics/growth &amp; development/metabolism ; Male ; Female ; *Phosphoproteins/genetics/metabolism ; Steroidogenic Acute Regulatory Protein ; Amino Acid Sequence ; Gene Expression Regulation, Developmental ; Testis/growth &amp; development/metabolism ; Ovary/growth &amp; development/metabolism ; Phylogeny ; Cholesterol/metabolism ; *Gonads/growth &amp; development/metabolism ; Molecular Sequence Data ; Cloning, Molecular ; *Steroids/biosynthesis ; },
abstract = {In vertebrates, the canonical steroidogenic acute regulatory (StAR) proteins, which lack N-terminal MENTAL domains, transport cholesterol into mitochondria to initiate steroidogenesis. However, whether a vertebrate-like steroidogenic pathway exists in crustaceans remains controversial. In this study, the complete ORF of SpStAR-like was identified from the transcriptome data of the mud crab Scylla paramamosain and subsequently cloned from testicular cDNA. Bioinformatic analysis showed that the SpStAR-like protein, consistent with other crustacean StAR-like homologs, contains an extra N-terminal MENTAL domain and exhibits higher structural homology with StAR-related lipid transfer proteins (StARLTPs) than with canonical vertebrate StAR proteins. qRT-PCR analysis revealed ubiquitous SpStAR-like expression across all mud crab tissues, with transcript levels in testes significantly higher than those in ovaries and other tissues. The gene was expressed throughout gonadal development in both sexes, peaking at testicular stage T2 and ovarian stage O3, respectively. Functional investigations were performed via RNA interference as well as in vitro and in vivo cholesterol supplementation assays. SpStAR-like knockdown significantly repressed the transcription of steroidogenic genes (Hsd3b, Hsd17b, PGMRC1, ERR, GPCR89) and gonadal development-related genes (IAG, vtg, vtgR, CYP3A24, foxl-2). Exogenous cholesterol treatment elevated ovarian pregnenolone concentrations, as determined by ELISA, and up-regulated all aforementioned target genes. In vivo cholesterol injection increased hemolymph pregnenolone levels and promoted ovarian morphological maturation. This study provides preliminary molecular evidence for steroidogenic regulatory cascades in mud crabs and advances our understanding of crustacean reproductive endocrinology.},
}
@article {pmid42704270,
year = {2026},
author = {Boisard, J and Williams, SK and Roger, AJ and Stairs, CW},
title = {CoMR: an integrative scoring pipeline for comprehensive mitochondrial proteome reconstruction across eukaryotes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag474},
pmid = {42704270},
issn = {1477-4054},
support = {2022-06725//Swedish Research Council with access to the UPPMAX and PDC computational infrastructures/ ; 101078476//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/ ; RGPIN-2022-05430//Natural Sciences and Engineering Research Council/ ; FRN-142349/CAPMC/CIHR/Canada ; FRN-142349/CAPMC/CIHR/Canada ; RGPIN-2022-05430//Natural Sciences and Engineering Research Council/ ; 101078476/ERC_/European Research Council/International ; },
mesh = {*Proteome/metabolism ; *Mitochondrial Proteins/metabolism/genetics ; *Mitochondria/metabolism ; Phylogeny ; Saccharomyces cerevisiae/metabolism/genetics ; *Software ; *Computational Biology/methods ; *Proteomics/methods ; *Eukaryota/metabolism/genetics ; },
abstract = {Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting sequences. Accurate reconstruction therefore requires integration of complementary sources of evidence beyond targeting prediction alone. We developed Comprehensive Mitochondrial Reconstructor (CoMR), an integrative workflow that combines targeting prediction, curated homology searches, large-scale similarity searches, and automated phylogenetic analysis within a unified scoring framework. Benchmarking on the model yeast Saccharomyces cerevisiae yielded strong discriminatory performance [receiver operating characteristic (ROC)-area under the curve (AUC) = 0.92], exceeding standalone prediction with TargetP2, a predictor of N-terminal targeting peptides (ROC-AUC = 0.72). In the divergent anaerobic protist Paratrimastix pyriformis, CoMR maintained robust performance (ROC-AUC = 0.86) validated with an experimental proteome despite extreme class imbalance, achieving a precision-recall AUC of 0.183 (~78-fold enrichment over random expectation and ~10-fold improvement over TargetP2). Ablation analyses demonstrate that predictive performance is robust to individual evidence-layer removal, while overlap analyses showed that homology-based searches recovered candidates missed by targeting predictors, particularly in P. pyriformis. Overall, CoMR improves mitochondrial proteome reconstruction over targeting prediction alone and provides a reproducible workflow for predicting mitochondrial and mitochondrion-related organelle protein repertoires across eukaryotes to aid investigations of organelle evolution and proteome reduction.},
}
@article {pmid42697963,
year = {2026},
author = {Cartalemi, AA and Rosano, D and Ferrari, C and Crupi, G and Cassina, L and Gatti, G and Corigliano, F and Punzi, S and Villanti, I and Dupéré-Richer, D and D'Ercole, C and Ruggieri, V and Miluzio, A and Bruno, T and Garcia Manteiga, JM and Giansanti, V and Bennett, RL and Cittaro, D and Madaro, L and Boletta, A and Pievani, T and Biffo, S and Fanciulli, M and Ciboddo, M and Licht, J and Tonon, G},
title = {KDM6A loss enhances oxidative phosphorylation uncovering tissue-level convergent evolution.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {42697963},
issn = {1460-2075},
support = {P0003055//Multiple Myeloma Research Foundation (MMRF)/ ; 2017-0653//Fondazione Cariplo (Cariplo Foundation)/ ; 7037-25//Leukemia and Lymphoma Society (LLS)/ ; IG 28987//Fondazione AIRC per la ricerca sul cancro ETS (AIRC)/ ; 26728-202//Fondazione AIRC per la ricerca sul cancro ETS (AIRC)/ ; R50CA293837//HHS | National Institutes of Health (NIH)/ ; R01CA180475//HHS | NIH | NCI | Center for Cancer Research (CCR)/ ; MSF-005//Myeloma Solutions Fund/ ; },
abstract = {The tumor suppressor KDM6A/UTX, a histone demethylase and a 2-oxoglutarate-dependent dioxygenase, is frequently lost in many cancer types. We show that KDM6A loss pervasively activates oxidative phosphorylation in several solid tumors, generating a pseudo-hyperoxic environment, opposite from the pseudo-hypoxia observed in VHL-mutated renal carcinomas. Mechanistically, KDM6A sustains the expression of the coil-coil domain gene CCDC3, which inhibits CREB1-driven transcription of the mitochondrial regulator PPARGC1A. In the hematological cancer multiple myeloma where KDM6A is frequently deleted, its loss similarly promotes oxidative phosphorylation, but via an alternative mechanism: the increased transfer of mitochondria from stromal to myeloma cells via tunneling nanotubes, triggered by the loss of the mTORC1 inhibitor TRAF3IP3. Beyond cancer, KDM6A regulates oxidative phosphorylation also during development and in adult tissues, engaging either the CCDC3-CREB1 or the TRAF3IP3-mTORC1 pathways. These mutually exclusive associations suggest a tissue-level convergent evolution, positioning KDM6A as a central modulator of mitochondrial activity through context-specific partners.},
}
@article {pmid42690050,
year = {2026},
author = {Kannangara, JR and Connallon, T and Alves, AN and Dowling, DK},
title = {Dissecting contributions of directional and balancing selection to trajectories of mitochondrial haplotype evolution in Drosophila melanogaster.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpag152},
pmid = {42690050},
issn = {1558-5646},
abstract = {Emerging evidence suggests mtDNA haplotypes contribute to fitness variation and local adaptation, with directional thermal selection and negative frequency-dependent selection shaping haplotype diversity. However, their interplay remains unexplored. We conducted experimental evolution using Drosophila melanogaster populations from opposite ends of an Australian latitudinal cline (Melbourne and Townsville), exposing them to contrasting temperatures (17°C versus 27°C) and varying starting frequencies of two mtDNA haplotypes (A1 and B1) that occur at appreciable frequencies in these populations. We paired this with population genetic simulations to estimate selection and its influence on haplotype trajectories. Haplotype frequencies were influenced by interactions involving temperature, starting frequency, and nuclear genomic background (Melbourne, Townsville, or admixed). Although prior work predicted A1 should be favoured at the warmer temperature and B1 at the cooler temperature, A1 was generally favoured across both temperatures. Simulations supported directional selection in populations evolving at 17°C in the Melbourne background; otherwise dynamics were best explained by balancing selection shaped by negative frequency-dependent fitness effects. Patterns also varied across nuclear backgrounds, suggestive of mito-nuclear epistasis. These findings challenge a simple thermal adaptation model of mtDNA dynamics, suggesting that mtDNA evolution is shaped by interacting effects of temperature, frequency-dependence, nuclear background and experimental environment.},
}
@article {pmid42685140,
year = {2026},
author = {Krishnan, N and Zachar, I and Kun, &#xc1; and Gokhale, CS and Garay, J},
title = {Host-initiated microbial association leads to stable ectosymbiosis in an ecological model.},
journal = {PLoS computational biology},
volume = {22},
number = {9},
pages = {e1014699},
doi = {10.1371/journal.pcbi.1014699},
pmid = {42685140},
issn = {1553-7358},
mesh = {*Symbiosis/physiology ; *Models, Biological ; *Host Microbial Interactions/physiology ; Computational Biology ; Ecosystem ; },
abstract = {Microbial symbiosis is widespread among metabolically coupled cells; it presumably gave rise to mitochondria. However, how such symbioses emerge, evolve, and stabilize are unknown, particularly in the prokaryotic domain where endosymbiosis is virtually nonexistent. Yet there is growing evidence suggesting that mitochondria originated from such a metabolically driven prokaryotic partnership rather than phagocytotic predation. While prokaryotes almost ubiquitously engage in metabolic syntrophy, it is unknown whether syntrophy alone can enable stable physical associations that could pave the road toward physical integration. Here, we tested the hypothesis that syntrophy can transition into stable ectosymbiosis, using an ecological mathematical model. Starting from an existing syntrophic partnership between free-living hosts and symbionts, we demonstrate that population-level obligate ectosymbiosis can emerge and stabilize, even in unilateral syntrophy where only the symbiont consumes a host-produced metabolite. A key assumption is that the hosts' by-product inhibits their growth when it accumulates. By consuming the toxic by-product, the symbiont locally reduces hosts' self-inhibition at the contact surface, manifesting as a private benefit providing selective advantage. Our results show that due to the direct and indirect benefits, the ectosymbiotic consortium is stable against free-living forms and the consortial cooperation is ecologically selected for. Furthermore, solid metabolic coupling promotes population-level obligacy, ultimately excluding free-living individuals under stricter conditions. Our results support the hypothesis that cooperative, syntrophic microbes (particularly prokaryotes) are capable of forming stable, physical, and species-specific ectosymbiosis through inhibition reduction, providing a plausible first step toward potential, gradual endosymbiotic integration. Our work bridges the gap between models of microbial cooperation between free-living species and models that assume already-concluded, fully integrated endosymbiosis under multilevel selection.},
}
@article {pmid42637163,
year = {2026},
author = {Cao, Z and Liu, Z and Zhang, J and Chen, Y and Huo, Y and You, L and Meng, L and Wu, Y and Zhang, C and Zhou, Y and Sun, Y},
title = {Functional characterization of Bcl-2-related ovarian killer (Bok) in apoptosis and antibacterial immunity in Trachinotus ovatus.},
journal = {Fish &amp; shellfish immunology},
volume = {178},
number = {},
pages = {111678},
doi = {10.1016/j.fsi.2026.111678},
pmid = {42637163},
issn = {1095-9947},
mesh = {Animals ; *Apoptosis/genetics ; Vibrio/physiology ; Fish Proteins/genetics/immunology/chemistry ; *Fish Diseases/immunology ; *Fishes/immunology/genetics ; *Immunity, Innate/genetics ; Amino Acid Sequence ; Sequence Alignment/veterinary ; *Gene Expression Regulation/immunology ; Vibrio Infections/immunology/veterinary ; Phylogeny ; Gene Expression Profiling/veterinary ; *Proto-Oncogene Proteins c-bcl-2/genetics/immunology/chemistry ; Base Sequence ; },
abstract = {Bok (Bcl-2-related ovarian killer) is a pro-apoptotic member of the Bcl-2 family that plays a critical role in the intrinsic apoptotic pathway in mammals. However, its functional characterization in teleost fish remains largely unexplored. In this study, we identified and characterized TroBok, a Bok ortholog from golden pompano (Trachinotus ovatus), and investigated its role in apoptosis and antibacterial immunity. The full-length coding sequence of TroBok is 642 bp, encoding a protein of 213 amino acids containing four conserved BH domains (BH1-BH4). TroBok was ubiquitously expressed in all tissues examined, with the highest abundance in the head kidney, and was significantly upregulated upon Vibrio harveyi challenge. Subcellular localization revealed that TroBok is predominantly distributed in the cytoplasm. Functional analysis in golden pompano snout (GPS) cells stimulated with rFla B, the flagellin protein of V. harveyi, demonstrated that TroBok overexpression significantly increased apoptosis, promoted mitochondrial membrane potential (MMP) loss, induced DNA fragmentation, and enhanced Caspase-9 and Caspase-3 activities, whereas TroBok knockdown produced opposite effects. Furthermore, TroBok overexpression upregulated pro-apoptotic genes (p53, cytochrome c, Caspase-3, Caspase-7, and Caspase-9) and downregulated the anti-apoptotic Bcl-2, indicating that TroBok activates the intrinsic mitochondrial apoptotic pathway. In vivo, TroBok overexpression significantly reduced V. harveyi burdens in the liver, spleen, and head kidney, whereas TroBok silencing markedly increased bacterial loads. Mechanistically, TroBok promoted apoptosis of head kidney macrophages and elevated Caspase-9 and Caspase-3 activities in head kidney tissues, indicating that the antibacterial effect of TroBok may be associated with its pro-apoptotic function. Our results indicate that TroBok exerts a conserved pro-apoptotic function via the mitochondrial pathway and contributes to antibacterial immunity in golden pompano, providing new insights into the role of BOK family proteins in teleost host defense.},
}
@article {pmid42679361,
year = {2026},
author = {Montoliu-Nerin, M and Strunov, A and Heyworth, E and Schneider, DI and Thoma, J and Hua-Van, A and Courret, C and Klasson, L and Miller, WJ},
title = {Evolutionary persistence of a highly prevalent multicopy mitochondrial-derived nuclear insertion (Mega-NUMT) in Neotropical Drosophila flies.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag227},
pmid = {42679361},
issn = {1537-1719},
abstract = {Although strict maternal transmission of mitochondria is a general feature of animals for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear. Here, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical Drosophila paulistorum using long-read sequencing and in situ hybridization. The copies are organized in one cluster on chromosome 3, which we designated the "Dpau Mega-NUMT". Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the Mega-NUMT copies are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before the D. paulistorum semispecies radiation and speculate based on these findings that it possibly is maintained at relatively high prevalence in nature by balancing selection or due to a yet undetermined function.},
}
@article {pmid42671759,
year = {2026},
author = {Yu, X and Wang, Y and Ju, X and Li, Z and Song, J and Wu, B and Ding, Q and Jiang, Y and Wu, Y},
title = {HOXC9 promotes cell proliferation and suppresses mitochondria-dependent apoptosis through the AKT/mTOR pathway in esophageal squamous cell carcinoma.},
journal = {Molecular and cellular biochemistry},
volume = {},
number = {},
pages = {},
pmid = {42671759},
issn = {1573-4919},
support = {BSQD202237//Bengbu Medical University's Research Start-up Funds for Introduced PhDs/ ; 2022AH040223//Natural Science Research Project of Anhui Educational Committee/ ; HN2026-10//Open Funds of State Key Laboratory of Oncology in South China/ ; },
abstract = {Homeobox C9 (HOXC9) is aberrantly expressed in multiple malignancies; however, its functional role in esophageal squamous cell carcinoma (ESCC) remains elusive. This study investigated the expression, function, and underlying molecular mechanisms of HOXC9 in ESCC. HOXC9 was evaluated via immunohistochemistry in 118 ESCC and paired normal tissues. Stable cell lines with HOXC9 knockout, knockdown, and overexpression were established in KYSE70 and KYSE150 cells. Cell proliferation, apoptosis, mitochondrial membrane potential, and in vivo xenograft growth were assessed. Mechanistic studies were performed using RNA-seq, Western blotting, and PI3K inhibitor LY294002 (30 µM). IHC analysis revealed significantly elevated HOXC9 expression in ESCC versus paired adjacent normal tissues (high expression rate: 57.6% vs. 22.9%, P < 0.0001) and associated with poorer overall survival. Receiver operating characteristic (ROC) curve analysis showed favorable diagnostic value for HOXC9 (area under the curve [AUC] = 0.97). Functional assays showed that HOXC9 promoted ESCC cell proliferation and inhibited mitochondria-dependent apoptosis. Mechanistically, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Western blot analyses indicated that HOXC9 is associated with activation of the protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway. Pharmacological blockade and xenograft experiment further supported the involvement of this pathway in HOXC9-driven oncogenic phenotypes. This study identifies a potential mechanism by which HOXC9 contributes to ESCC progression via AKT/mTOR-mediated inhibition of mitochondria-dependent apoptosis and promotion of cell proliferation. These findings suggest HOXC9 as a candidate prognostic biomarker and preliminary therapeutic target for ESCC, requiring further validation across clinical and molecular subtypes.},
}
@article {pmid42673453,
year = {2026},
author = {Zhang, Z and Zhang, L and An, P and Zhang, X and Xia, Y and Kang, Y and Chen, X and Hua, R and Zhu, Y and Hao, Y and Huang, Y and Luo, Y and Luo, J and Wang, G},
title = {Single-cell profiling of mitochondrial phenotyping-coupled mtDNA genotyping.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {36},
pages = {e2531151123},
doi = {10.1073/pnas.2531151123},
pmid = {42673453},
issn = {1091-6490},
support = {82470442//National Natural Science Foundation of China/ ; No.2022YFF1100100//National Key R&amp;D Program of China/ ; 2024GZkf-05//State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, Chinese Academy of Medical Sciences/ ; 82170429//National Natural Science Foundation of China/ ; 32570908//National Natural Science Foundation of China/ ; 32571359//National Natural Science Foundation of China/ ; B18053//111 project from the Education Ministry of China/ ; 82300345//National Natural Science Foundation of China/ ; No.3332025033//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; No.20250948//Young Elite Scientists Sponsorship Program of the Beijing High Innovation Plan/ ; PC2023B01014//pinduoduo-China Agricultural University Research Fund/ ; 7262078//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Single-Cell Analysis/methods ; *Mitochondria/genetics/metabolism ; Phenotype ; Mutation ; HeLa Cells ; Heteroplasmy ; Genotype ; Reactive Oxygen Species/metabolism ; Membrane Potential, Mitochondrial ; Genome, Mitochondrial ; },
abstract = {Simultaneously profiling mitochondrial DNA (mtDNA) heteroplasmy and phenotypic variability at the single-cell level remains a challenge due to the absence of integrated methods that map mitochondrial genotypes alongside their functional states. We introduce human single-cell mitochondrial phenotype-coupled mtDNA sequencing (scMPCDS), a platform that quantifies mtDNA mutations and heteroplasmy together with mitochondrial membrane potential and reactive oxygen species within individual cells. Unlike bulk sequencing or separate single-omics techniques, scMPCDS directly correlates mitochondrial genomic instability with functional outcomes. Using this approach, we demonstrate that DdCBE-mediated mtDNA editing induces cell-specific off-target mutations in the mitochondrial genome, which coincide with diverse phenotypic changes. Applying scMPCDS to HeLa cells and clear cell renal cell carcinoma tissues, we identify single-cell subpopulations exhibiting distinct mtDNA mutation burdens and altered bioenergetic profiles, implicating potential mitochondrial heterogeneity-driven tumor evolution. Overall, scMPCDS serves as a versatile tool to unravel mitochondrial genotype-phenotype relationships at the single-cell level in both normal and disease states, thereby advancing precise mitochondrial diagnostics and therapeutics.},
}
@article {pmid42667975,
year = {2026},
author = {Li, J and Zhu, C and Chai, G and He, F and Song, Z and Chen, Z and Chen, M and Yi, Z},
title = {Progressive evolutionary trajectories of mitochondrion-related organelles in anaerobic ciliates (Eukaryota, Alveolata) revealed by APM ciliates and a facultatively anaerobic spirotrichean species.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108721},
doi = {10.1016/j.ympev.2026.108721},
pmid = {42667975},
issn = {1095-9513},
abstract = {Ciliates are an excellent model for studying convergent transitions from mitochondria to mitochondrion-related organelles (MROs) in protists. Despite our growing knowledge of adaptive evolution in ciliate MROs, the progressive evolutionary trajectories within anaerobic ciliate lineages and the MRO metabolisms of facultatively anaerobic ciliates remain unexplored. In this study, we predicted MRO metabolisms of eight species within the anaerobic monophyletic APM (Armophorea-Muranotrichea-Parablepharismea) clade and a facultative anaerobe from its sister class Spirotrichea. Our main results are as follows: (1) During their adaptation to anaerobic environments, the MRO electron transfer chain (ETC) components and their associated functions have been progressively lost in the APM clade. (2) The MRO of the last common ancestor of Armophorea likely possesses complexes Ⅰ, Ⅱ, and Ⅴ, but lacks functional complexes Ⅲ and Ⅳ. Subsequently, during their adaptation to anaerobic environments, the armophorean lineage has further lost complex Ⅴ in the order Clevelandellida and Metopida. (3) In the MRO of the facultatively anaerobic ciliate Heterodeviata sinica, complexes Ⅲ and Ⅳ are absent, and alternative oxidases (AOX) play a key role in adaptation to fluctuating dissolved oxygen levels. (4) The fused [FeFe]-hydrogenase appears to have been acquired by the last common ancestor of ciliates through horizontal gene transfer (HGT), followed by multiple independent losses. Our results provide insights into the progressive adaptations of anaerobic ciliates to the low-oxygen environments.},
}
@article {pmid26258511,
year = {2016},
author = {Li, Y and Lu, J and Wang, Z},
title = {Complete mitochondrial genome of Lasiopodomys mandarinus mandarinus (Arvicolinae, Rodentia).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1459-1460},
doi = {10.3109/19401736.2014.953092},
pmid = {26258511},
issn = {2470-1408},
mesh = {Animals ; Arvicolinae/*genetics ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Mandarin voles (Lasiopodomys mandarinus) is a subterranean rodent species that are often used as a model for studying subterranean hypoxic stress in mammals. Its subspecies L. m. mandarinus span in cropland in most area of north China and is regarded as an agricultural pest. In this paper, the complete mitochondrial genome of L. m. mandarinus has been determined. Our results showed that the mitochondrial genome of L. m. mandarinus is a circular molecule of 16,367 bp, which contents 13 protein-coding, 22 tRNAs and 2 rRNAs genes. The overall base composition of the heavy strand is 32.47% A, 27.04% T, 27.01% C, and 13.47% G. with an AT content of 59.51%.},
}
@article {pmid26258516,
year = {2016},
author = {Hu, J and Chen, Y and Zhao, H and Yang, H and Liu, L},
title = {Complete mitochondrial genome of Rhodeus ocellatus (Cypriniformes: Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3489-3490},
doi = {10.3109/19401736.2015.1066362},
pmid = {26258516},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitogenome sequence of Rhodeus ocellatus (Kner) was determined using the next-generation sequencing (NGS). The genome was 16 761 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. The overall nucleotide composition was 30.43% A, 27.50% T, 25.94% C, and 16.13% G, with an A + T bias of 57.93%. The gene composition and the arrangement of the R. ocellatus mitochondrial genome were similar to that of most other vertebrates. The complete mitochondrial genome sequence will help to study the evolutionary relationships and population genetics of Rhodeus fish.},
}
@article {pmid26258518,
year = {2016},
author = {Wu, Z and Li, X},
title = {Complete mitochondrial genome of the Nemipterus virgatus (Perciformes: Nemipteridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3485-3486},
doi = {10.3109/19401736.2015.1066360},
pmid = {26258518},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of the Nemipterus virgatus has been sequenced. The mitochondrial genome is 16 992 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The gene order and composition of N. virgatus mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the light strand is A (27.89%), G (26.61%), C (16.45%), T (29.05%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, N. virgatus, Nemipterus japonicus, and Nemipterus bathybius from the same genus clustered into one branch.},
}
@article {pmid26258519,
year = {2016},
author = {Yu, P and Ding, S and Yang, Q and Li, X and Wan, Q},
title = {The complete mitochondrial genome of Sinibotia robusta (Cypriniformes: Cobitidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3471-3472},
doi = {10.3109/19401736.2015.1066353},
pmid = {26258519},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The Sinibotia robusta mitochondrial genome (GenBank accession no. KP979711) was a circular molecule of 16 575 bp in length, with two rRNA genes, 13 protein-coding genes, 22 tRNA genes, an l-strand replication origin (OL), and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.91% for A, 26.90% for C, 15.56% for G, and 25.63% for T, with an A + T content of 57.54%. And the A + T content of 12S rRNA, 16S rRNA, and D-loop was 51.26%, 56.17%, and 67.73%, respectively.},
}
@article {pmid26260170,
year = {2016},
author = {Luo, X and Kang, X and Zhang, D},
title = {Complete mitochondrial genome of the American flamingo, Phoenicopterus ruber (Phoenicopteriformes, Phoenicopteridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3519-3520},
doi = {10.3109/19401736.2015.1074198},
pmid = {26260170},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Birds/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; United States ; },
abstract = {The American flamingo, Phoenicopterus ruber (P. ruber), is a large species of flamingo closely related to the greater flamingo and Chilean flamingo. In this paper, the complete mitochondrial genome sequence of P. ruber has been assembled for the first time. It was 17 476 bp in length and consisted of 13 typical vertebrate protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 control regions. COI and ND3 genes used GTG and ATC as start codons respectively, but the remaining protein-coding genes were encoded beginning with orthodox ATG codon. Two triplet codons (TAA, AGG) and one single T base were employed as stop codons. The arrangement of the overall genes and noncoding regions was identical to the same genus flamingo Phoenicopterus roseus. The AT content (54.27%) was higher than the GC content. Phylogenetic analysis was performed using 12 protein-coding genes, combined with other 11 species from the same Neognathae, which validated the responsibility and utility of this new mitochondrial genome.},
}
@article {pmid26260172,
year = {2016},
author = {Park, CE and Park, GS and Kim, MC and Kim, KH and Park, HC and Lee, IJ and Shin, JH},
title = {Complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3557-3559},
doi = {10.3109/19401736.2015.1074217},
pmid = {26260172},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Republic of Korea ; Sequence Analysis, DNA/*methods ; },
abstract = {In this study, we sequenced the complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae). The mitogenome, consisted of 16 601 base pairs (bp), encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding regions. The overall base composition of M. yaluensis was G + C: 43.8%, A + T: 56.2%, apparently with a slight AT bias. Phylogenetic analysis showed that M. yaluensis was close to Hemibarbus mylodon.},
}
@article {pmid26260173,
year = {2016},
author = {Yang, X and Xie, GL and Wu, XP and Ouyang, S},
title = {The complete mitochondrial genome of Chinese land snail Aegista aubryana (Gastropoda: Pulmonata: Bradybaenidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3538-3539},
doi = {10.3109/19401736.2015.1074207},
pmid = {26260173},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; China ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Snails/*genetics ; },
abstract = {Aegista aubryana is an endemic land snail in China. The complete mitochondrial genome of A. aubryana was first determined using long PCR reactions and primer walking method (accession number KT192071). The genome has a length of 14 238 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 31.32%, T 37.86%, C 14.46% and G 16.36%. The results of phylogenetic analyses showed that the A. aubryana is most closely related to Mastigeulota kiangsinensis. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analyses in bradybaenid snails and Molluscs at large.},
}
@article {pmid26260175,
year = {2016},
author = {Wilson, JJ and Hefner, M and Walker, CW and Page, ST},
title = {Complete mitochondrial genome of the soft-shell clam Mya arenaria.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3553-3554},
pmid = {26260175},
issn = {2470-1408},
support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Composition ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mya/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We have sequenced and characterized the complete mitochondrial genome of the soft-shell clam, Mya arenaria, an important organism for environmental toxicology and aquaculture. Mya arenaria is located in the taxonomic order Myoida, which lacks any member with a completely annotated mitogenome. The M. arenaria mitochondrial genome is 17 947 bp in length. Like most marine bivalves, the circular mitogenome codes entirely on the heavy strand, with no introns. As with other bivalves, the gene order of the mitochondrion is highly rearranged. The mitogenome contains 12 protein-coding genes but ATP8 is missing, consistent with about half of all bivalve genera. Twenty-three tRNAs were identified. Phylogenetic analysis shows that M. arenaria is related most closely with the bivalves Sinonovacula constricta, and Moerella iridescens, of the infraclass Euheterodonta (unassigned). This, along with the close grouping of the phylogenetic trees, confirms a close tie between Myoida and Euheterodonta (unassigned).},
}
@article {pmid26260177,
year = {2016},
author = {Zhang, G and Wang, R and Mao, J and Yin, S and Tao, P and Chen, J and Yu, X and Tang, Z and Chen, S},
title = {The complete mitochondrial genome and phylogenic analysis of Pseudobagrus vachelli.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3551-3552},
doi = {10.3109/19401736.2015.1074213},
pmid = {26260177},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Catfishes/*genetics ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of Pseudobagrus vachelli has been sequenced. The mitochondrial genome is 16 529 bp in length, with the base composition of 31.61% A, 26.88% T, 26.55% C, and 14.96% G, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The gene order and orientation are similar with some typical fish species. The data will provide useful molecular information for phylogenetic studies concerning P. vachelli and its related species.},
}
@article {pmid26260179,
year = {2016},
author = {Li, Y and Yao, J and Zhao, X and Li, L and Yan, S},
title = {Complete mitochondrial genome sequence of Chestnut-flanked white-eye (Zosterops erythropleurus).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3529-3530},
doi = {10.3109/19401736.2015.1074203},
pmid = {26260179},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The Chestnut-flanked white-eye (Zosterops erythropleurus) is a species of family Zosteropidae, which is distributed widely in the world. In the present study, the complete mitochondrial genome sequence of Chestnut-flanked white-eye was determined. It has a total length of 17 811 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions. The total base composition was 30.2% for A, 31.0% for C, 14.2% for G and 24.6% for T. The phylogenetic tree of Chestnut-flanked white-eye and 13 other species belonging to the order Passeriformes was built. The molecular data presented here will be useful to study the evolutionary relationships and genetic diversity of Chestnut-flanked white-eye.},
}
@article {pmid26260184,
year = {2016},
author = {Das, SP and Bit, A and Patnaik, S and Sahoo, L and Meher, PK and Jayasankar, P and Saha, TM and Patel, AB and Patel, N and Koringa, P and Joshi, CG and Agarwal, S and Pandey, M and Srivastava, S and Kushwaha, B and Kumar, R and Nagpure, NS and Iquebal, MA and Jaiswal, S and Kumar, D and Jena, JK and Das, P},
title = {Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3517-3518},
doi = {10.3109/19401736.2015.1074197},
pmid = {26260184},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time.},
}
@article {pmid26260186,
year = {2016},
author = {Li, W and Liu, Y and Xu, Q},
title = {Complete mitochondrial genome of Schizothorax nukiangensis Tsao (Cyprinidae: Schizothorax).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3549-3550},
doi = {10.3109/19401736.2015.1074212},
pmid = {26260186},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {In this work, we reported the complete mitochondrial genome sequence of the Schizothorax nukiangensis Tsao for the first time. The complete mtDNA genome sequence of S. nukiangensis Tsao was 16 585 bp in length, which contains 22 transfer RNA genes, 2 rRNA genes, 13 protein-coding genes, an origin of light-strand replication (OL) and a control region (D-Loop). The overall base composition of the mitogenome was calculated to be 29.6% for A, 27.0% for C, 17.9% for G and 25.5% for T. The complete mitogenome of the S. nukiangensis Tsao can provide an important data set for further studies on population history, molecular systematics, phylogeography and stock assessment.},
}
@article {pmid26267495,
year = {2015},
author = {Kumar Singh, M and Janardhan Reddy, PV and Sreedhar, AS and Tiwari, PK},
title = {Molecular characterization and expression analysis of hsp60 gene homologue of sheep blowfly, Lucilia cuprina.},
journal = {Journal of thermal biology},
volume = {52},
number = {},
pages = {24-37},
doi = {10.1016/j.jtherbio.2015.05.001},
pmid = {26267495},
issn = {0306-4565},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Cell Nucleus/metabolism/physiology ; Chaperonin 60/biosynthesis/*genetics ; Cloning, Molecular ; Diptera/*physiology ; Gene Expression Regulation/*genetics/*physiology ; Heat-Shock Response/genetics/physiology ; Hot Temperature ; Introns ; Larva/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Temperature ; },
abstract = {The 60kDa heat shock protein (Hsp60) or chaperonin is one among the highly conserved families of heat shock proteins, known to be involved in variety of cellular activities, including protein folding, thermal protection, etc. In this study we sequence characterized hsp60 gene homologue of Lucilia cuprina, isolated and cloned from the genomic library as well as by genomic PCR, followed by RACE- PCR. The L. cuprina hsp60 gene/protein expression pattern was analyzed in various tissues, either at normal temperature (25±1°C) or after exposure to heat stress (42°C). The analysis of nucleotide sequence of Lchsp60 gene revealed absence of intron and the nuclear localizing signal (NLS). The deduced amino acid sequence showed presence of unique conserved sequences, such as those for mitochondrial localization, ATP binding, etc. Unlike Drosophila, Lucilia showed presence of only one isoform, i.e., hsp60A. Phylogenetic analysis of hsp60 gene homologues from different species revealed Lchsp60 to have >88.36% homology with D. melanogaster, 76.86% with L. sericata, 58.31% with mice, 57.99% with rat, and 57.72% with human. Expression analysis using Real Time PCR and fluorescence imaging showed significant enhancement in the expression level of Lchsp60 upon heat stress in a tissue specific manner, indicating its likely role in thermo-tolerance as well as in normal cellular activities.},
}
@article {pmid26273922,
year = {2016},
author = {Jang, YS and Kim, S and Kim, KY and Park, JH},
title = {Complete mitochondrial genome of Sebastes taczanowskii (Scorpaenidae, Scorpaeniformes) from the East Sea, Korea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3531-3533},
doi = {10.3109/19401736.2015.1074204},
pmid = {26273922},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Republic of Korea ; Sequence Analysis, DNA/*methods ; },
abstract = {Sebastes taczanowskii is a subarctic species in the north-western Pacific Ocean. To obtain mitochondrial DNA sequences for phylogeny, the complete mitogenome (16 452 bp in length) of S. taczanowskii was constructed using next-generation sequencing. The circular mitogenome contains 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and the control region, for which gene structure and positions were similar to those of other Scorpaenidae. The complete mitogenome composed of 27.8% A, 26.5% T, 17.3% G and 28.5% C, with a slight AT bias (54.3%). All PCGs use a typical start codon, ATG, except COX1 (GTG). The terminal codon of PCGs was mainly TAR, with the exceptions of ND4 (AGA) and Cytb (incomplete codon, T). Sebastes taczanowskii was clearly divided from other Scorpaenidae in the phylogenetic tree using 2 rRNA and 13 PCGs. The mitogenome of S. taczanowskii can be useful for constructing the molecular phylogenetic tree within Scorpaenidae.},
}
@article {pmid26277108,
year = {2015},
author = {Horáková, E and Changmai, P and Paris, Z and Salmon, D and Lukeš, J},
title = {Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe-S cluster assembly but not heme import into the mitochondrion of Trypanosoma brucei.},
journal = {The FEBS journal},
volume = {282},
number = {21},
pages = {4157-4175},
doi = {10.1111/febs.13411},
pmid = {26277108},
issn = {1742-4658},
mesh = {ATP-Binding Cassette Transporters/antagonists &amp; inhibitors/genetics/*metabolism ; Aconitate Hydratase/metabolism ; Cytosol/metabolism ; Fumarate Hydratase/metabolism ; Gene Knockdown Techniques ; Genes, Protozoan ; Genetic Complementation Test ; Heme/metabolism ; Iron-Sulfur Proteins/metabolism ; Mitochondria/metabolism ; Models, Biological ; ATP-Binding Cassette, Sub-Family C Proteins/antagonists &amp; inhibitors/genetics/metabolism ; Phylogeny ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Trypanosoma brucei brucei/genetics/*metabolism ; },
abstract = {ABC transporter mitochondrial 1 (Atm1) and multidrug resistance-like 1 (Mdl) are mitochondrial ABC transporters. Although Atm1 was recently suggested to transport different forms of glutathione from the mitochondrion, which are used for iron-sulfur (Fe-S) cluster maturation in the cytosol, the function of Mdl remains elusive. In Trypanosoma brucei, we identified one homolog of each of these genes, TbAtm and TbMdl, which were downregulated either separately or simultaneously using RNA interference. Individual depletion of TbAtm and TbMdl led to limited growth defects. In cells downregulated for TbAtm, the enzymatic activities of the Fe-S cluster proteins aconitase and fumarase significantly decreased in the cytosol but not in the mitochondrion. Downregulation of TbMdl did not cause any change in activities of the Fe-S proteins. Unexpectedly, the simultaneous downregulation of TbAtm and TbMdl did not result in any growth defect, nor were the Fe-S cluster protein activities altered in either the cytosolic or mitochondrial compartments. Additionally, TbAtm and TbMdl were able to partially restore the growth of the Saccharomyces cerevisiae Δatm1 and Δmdl2 null mutants, respectively. Because T. brucei completely lost the heme b biosynthesis pathway, this cofactor has to be obtained from the host. Based on our results, TbMdl is a candidate for mitochondrial import of heme b, which was markedly decreased in both TbMdl and TbAtm + TbMdl knockdowns. Moreover, the levels of heme a were strongly decreased in the same knockdowns, suggesting that TbMdl plays a key role in heme a biosynthesis, thus affecting the overall heme homeostasis in T. brucei.},
}
@article {pmid26280086,
year = {2015},
author = {Farhadi, M and Fazaeli, A and Haniloo, A},
title = {Genetic characterization of livestock and human hydatid cyst isolates from northwest Iran, using the mitochondrial cox1 gene sequence.},
journal = {Parasitology research},
volume = {114},
number = {12},
pages = {4363-4370},
pmid = {26280086},
issn = {1432-1955},
mesh = {Animals ; Cattle ; Cattle Diseases/*parasitology ; Cyclooxygenase 1/*genetics ; Echinococcosis/*parasitology/*veterinary ; Echinococcus granulosus/classification/enzymology/genetics/*isolation &amp; purification ; Genotype ; Helminth Proteins/*genetics ; Humans ; Iran ; Livestock ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sheep/parasitology ; Sheep Diseases/*parasitology ; Sheep, Domestic/genetics ; },
abstract = {Cystic echinococcosis (CE), caused by larval stages of the tapeworm Echinococcus granulosus, is one of the most important zoonoses distributed worldwide. Genotype analysis of the parasite isolates from various hosts is required to better understand the host specificity and transmission routes. The aim of this study was to identify the genotypes of E. granulosus isolated from humans and domestic animals from northwest of Iran (Zanjan Province) using the mitochondrial cox1 gene sequence. A total of 86 hydatid cysts including 49 sheep and 28 cattle isolates from the slaughterhouse and nine human isolates from surgical wards of local hospitals were collected. The isolates were subjected to DNA extraction, PCR amplification, and sequence. Eighty-two (95.35 %) isolates, including 47 sheep, 26 cattle, and all nine human isolates, were determined as G1 genotype, and the remaining four (4.65 %), including two sheep and two cattle isolates, were identified as G3 genotype. From the cox1 sequence data, 13 different haplotypes (10 G1s and three G3s) were detected and named as EGH1-EGH13 (GenBank accession numbers, KP859559-KP859571). EGH1 was the major variant among the haplotypes, and it was identified in 46 (53.49 %) isolates (31 sheep, 14 cattle, and one human). Alignment of the partial cox1 sequences showed 12 point mutations including seven (58.3 %) synonymous and five (41.7 %) non-synonymous substitutions. Based on the results, G1 was the major genotype of E. granulosus in northwest of Iran affecting sheep, cattle, and humans. In addition, a minor group of G3 genotype was found to be circulating in this region.},
}
@article {pmid26285652,
year = {2015},
author = {Yu, G and Xiang, H and Tian, J and Yin, J and Pinkert, CA and Li, Q and Zhao, X},
title = {Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {13118},
pmid = {26285652},
issn = {2045-2322},
mesh = {Adenosine Triphosphate/metabolism ; Animals ; Base Sequence ; Cell Line ; Genome, Mitochondrial/genetics ; Haplotypes/*genetics ; Hybrid Cells/*metabolism ; Mitochondria/*genetics ; Mutation, Missense/genetics ; Phylogeny ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; Succinate Dehydrogenase/metabolism ; Sus scrofa/*genetics ; },
abstract = {In farm animals, mitochondrial DNA mutations exist widely across breeds and individuals. In order to identify differences among mtDNA haplotypes, two porcine transmitochondrial cybrids were generated by fusion of a Lantang pig cell line devoid of mitochondrial DNA with enucleated cytoplasm from either a Large White pig or a Xiang pig harboring potentially divergent mitochondrial haplotypes. These cybrid cells were subjected to mitochondrial genome sequencing, copy number detecting and analysis of biochemical traits including succinate dehydrogenase (SDH) activity, ATP content and susceptibility to reactive oxygen species (ROS). The Lantang and Xiang mitochondrial genomes were highly homologous with only 18 polymorphic sites, and differed radically from the Large White with 201 and 198 mutations respectively. The Large White and Xiang cybrids exhibited similar mtDNA copy numbers and different values among biochemical traits, generated greater ROS production (P < 0.05) and less SDH activity (P < 0.05) and a lesser ATP content (P < 0.05). The results show that functional differences exist between cybrid cells which differ in mitochondrial genomic background. In conclusion, transmitochondrial cybrids provide the first direct evidence on pig biochemical traits linking different mitochondrial genome haplotypes.},
}
@article {pmid26287583,
year = {2016},
author = {Li, G and Li, W and Lv, S and Li, C and Qian, Y and Xu, J and Lu, Y and Lin, Y and Yang, P and Lin, Z and Yang, S},
title = {Identification and phylogenetic analysis of the mitogenome of Sarcocheilichthys parvus Nichols (Cypriniformes: Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3542-3543},
doi = {10.3109/19401736.2015.1074209},
pmid = {26287583},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; China ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {In the present study, the complete mitogenome sequence of a Sarcocheilichthys parvus Nichols was sequenced and identified. It contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 non-coding regions. The phylogenetic analysis showed that the mitogenome sequence could be useful data in the field of systematics and conservation biology for S. parvus Nichols and other aquatic species.},
}
@article {pmid26291784,
year = {2016},
author = {Park, JS and Simpson, AG},
title = {Characterization of a Deep-Branching Heterolobosean, Pharyngomonas turkanaensis n. sp., Isolated from a Non-Hypersaline Habitat, and Ultrastructural Comparison of Cysts and Amoebae Among Pharyngomonas Strains.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {1},
pages = {100-111},
doi = {10.1111/jeu.12260},
pmid = {26291784},
issn = {1550-7408},
mesh = {Animals ; Eukaryota/*classification/growth &amp; development/isolation &amp; purification/*ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Phylogeny ; Salinity ; },
abstract = {An unusual heterolobosean amoeba, isolate LO, was isolated recently from a sample with a salinity of ~4‰, from Lake Turkana in East Africa. 18S rDNA phylogenies confirm that isolate LO branches among halophilic amoeboflagellates assigned to Pharyngomonas. We examined the ultrastructure of the amoeba and cyst stages of isolate LO, as well as the amoebae and cysts of Pharyngomonas kirbyi (isolates AS12B and SD1A). The amoebae of all three isolates lacked discrete dictyosomes and had discoidal/flattened mitochondrial cristae, but the mitochondria were not enrobed by rough endoplasmic reticulum. The cysts of all three isolates showed a thick, bipartite cyst wall, and lacked cyst pores. The cysts of isolate LO were distinct in that the ectocyst was very loose-fitting, and could contain "crypts". No flagellate form of isolate LO has been observed to date, and a salinity-for-growth experiment showed that isolate LO can grow at 15-100‰ salinity, indicating that it is halotolerant. By contrast, other studied Pharyngomonas isolates are amoeboflagellates and true halophiles. Therefore, we propose isolate LO as a new species, Pharyngomonas turkanaensis n. sp. It is possible that P. turkanaensis descended from halophilic ancestors, and represents a secondary reestablishment of a physiology adapted for moderate salinity.},
}
@article {pmid26300379,
year = {2016},
author = {Mai, Q and Li, W and Chen, H and Ai, W and Chen, X},
title = {Complete mitochondrial genome and phylogenetic position of the Sicklefin weasel shark Hemigaleus microstoma.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3491-3492},
doi = {10.3109/19401736.2015.1066363},
pmid = {26300379},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Sharks/*genetics ; },
abstract = {The complete mitochondrial genome of the Sicklefin weasel shark Hemigaleus microstoma was first presented in this study. It was 16 701 bp in length with the typical gene arrangement in vertebrates. A total of 25 bp short intergenic spaces and 33 bp overlaps located in 12 and 9 gene junctions, respectively. The overall nucleotide composition was 31.0% A, 26.4% C, 13.5% G and 29.1% T. Two start (ATG and GTG) and three stop (TAG, AGG and TAA/T) codons were found in the protein-coding genes. The size of 22 tRNA genes ranged from 67 to 75 bp. In the phylogenetic tree, H. microstoma (Hemigaleidae) was placed as sister to Galeocerdo cuvier (Carcharhinidae).},
}
@article {pmid26304849,
year = {2015},
author = {Law, YS and Zhang, R and Guan, X and Cheng, S and Sun, F and Duncan, O and Murcha, MW and Whelan, J and Lim, BL},
title = {Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis.},
journal = {Plant physiology},
volume = {169},
number = {2},
pages = {1344-1355},
pmid = {26304849},
issn = {1532-2548},
mesh = {14-3-3 Proteins/metabolism ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Phosphorylation ; Phylogeny ; Plants, Genetically Modified ; Protein Precursors/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Protein Transport ; Transcription Factors/metabolism ; },
abstract = {The nucleus-encoded mitochondria-targeted proteins, multiple organellar RNA editing factors (MORF3, MORF5, and MORF6), interact with Arabidopsis (Arabidopsis thaliana) PURPLE ACID PHOSPHATASE2 (AtPAP2) located on the chloroplast and mitochondrial outer membranes in a presequence-dependent manner. Phosphorylation of the presequence of the precursor MORF3 (pMORF3) by endogenous kinases in wheat germ translation lysate, leaf extracts, or STY kinases, but not in rabbit reticulocyte translation lysate, resulted in the inhibition of protein import into mitochondria. This inhibition of import could be overcome by altering threonine/serine residues to alanine on the presequence, thus preventing phosphorylation. Phosphorylated pMORF3, but not the phosphorylation-deficient pMORF3, can form a complex with 14-3-3 proteins and HEAT SHOCK PROTEIN70. The phosphorylation-deficient mutant of pMORF3 also displayed faster rates of import when translated in wheat germ lysates. Mitochondria isolated from plants with altered amounts of AtPAP2 displayed altered protein import kinetics. The import rate of pMORF3 synthesized in wheat germ translation lysate into pap2 mitochondria was slower than that into wild-type mitochondria, and this rate disparity was not seen for pMORF3 synthesized in rabbit reticulocyte translation lysate, the latter translation lysate largely deficient in kinase activity. Taken together, these results support a role for the phosphorylation and dephosphorylation of pMORF3 during the import into plant mitochondria. These results suggest that kinases, possibly STY kinases, and AtPAP2 are involved in the import of protein into both mitochondria and chloroplasts and provide a mechanism by which the import of proteins into both organelles may be coordinated.},
}
@article {pmid26305230,
year = {2016},
author = {Su, XH and Zhao, S and Wang, K and Xing, LX},
title = {Complete mitochondrial genome of the "floppy-wing" morph reproductive termite, Reticulitermes labralis (Isoptera: Rhinotermitidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3547-3548},
doi = {10.3109/19401736.2015.1074211},
pmid = {26305230},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of Reticulitermes labralis (Isoptera: Rhinotermitidae) was determined for its nucleotide sequence of 16 113 bp. Its gene content and organization were identical with other Reticulitermes species. The 13 protein-coding genes (PCGs) have typical ATN initiation codon. But, the stop codons were TAA, TAG and an incomplete termination codon (T) abutting an adjacent tRNA gene. Twenty-two tRNA genes, in addition to tRNASer(AGN) replaced lacking of the DHU stem with a simple loop, showed the typical clover-leaf secondary structure. The A + T-rich region was 1311 bp in length with 65.98% A + T content. In addition to the A + T-rich region, non-coding sequences of the mtDNA genome harbored 17 intergenic spacers. There were three complete repeats of repeat A in CR, which were not discovered in other termite species. Phylogenetic tree based on the 11 complete mitochondrial genome sequences of closely related termite species accords well with morphological phylogenetic analysis.},
}
@article {pmid26318870,
year = {2015},
author = {Zhong, Z and Norvienyeku, J and Yu, J and Chen, M and Cai, R and Hong, Y and Chen, L and Zhang, D and Wang, B and Zhou, J and Lu, G and Chen, X and Wang, Z},
title = {Two different subcellular-localized Acetoacetyl-CoA acetyltransferases differentiate diverse functions in Magnaporthe oryzae.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {83},
number = {},
pages = {58-67},
doi = {10.1016/j.fgb.2015.08.008},
pmid = {26318870},
issn = {1096-0937},
mesh = {Acetyl-CoA C-Acetyltransferase/genetics/*metabolism ; Amino Acid Sequence ; Cytoplasm/enzymology ; Gene Deletion ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Homologous Recombination ; Hordeum/microbiology ; Magnaporthe/*enzymology/genetics/pathogenicity ; Mevalonic Acid/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Morphogenesis ; Mutagenesis ; Mutation ; Oryza/microbiology ; Phylogeny ; Plant Diseases/microbiology ; Virulence ; },
abstract = {The mevalonate pathway is an efficient biosynthesis pathway that yields isoprenoids for promoting different crucial cellular functions, including ergosterol synthesis and growth regulation. Acetoacetyl-CoA acetyltransferase (EC2.3.1.9) is the first major catalytic enzyme constituting the mevalonate pathway and catalyzes the transformation of Acetoacetyl-CoA from two molecules of acetyl-CoA enroute ergosterol production in fungi. We identified two homologous genes encoding Acetoacetyl-CoA acetyltransferase (MoAcat1 and MoAcat2) in Magnaporthe oryzae, the rice blast fungus. Phylogenetic analysis indicates these two genes have different evolutionary history. We subsequently, conducted targeted gene deletion using homologous recombination technology to ascertain the unique roles of the two MoAcat homologues during the fungal morphogenesis and pathogenesis. The findings from our investigations showed that the activity of MoAcat1 promoted virulence in the rice blast fungus as such, the ΔMoacat1 mutants generated exhibited defect in virulence, whilst ΔMoacat1 mutants did not portray growth defects. ΔMoacat2 mutants on the other hand were characterized by reduction in growth and virulence. Furthermore, MoAcat1 and MoAcat2 showed different expression patterns and subcellular localizations in M. oryzae. From our investigations we came to the conclusion that, different subcellular localization contributes to the diverse functions of MoAcat1 and MoAcat2, which helps the successful establishment of blast disease by promoting efficient development of cell morphology and effective colonization of host tissue.},
}
@article {pmid26321226,
year = {2016},
author = {Ojanguren-Affilastro, AA and Mattoni, CI and Ochoa, JA and Ramírez, MJ and Ceccarelli, FS and Prendini, L},
title = {Phylogeny, species delimitation and convergence in the South American bothriurid scorpion genus Brachistosternus Pocock 1893: Integrating morphology, nuclear and mitochondrial DNA.},
journal = {Molecular phylogenetics and evolution},
volume = {94},
number = {Pt A},
pages = {159-170},
doi = {10.1016/j.ympev.2015.08.007},
pmid = {26321226},
issn = {1095-9513},
mesh = {Acclimatization ; Altitude ; Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Desert Climate ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; Likelihood Functions ; Male ; Mitochondria/genetics ; *Phylogeny ; Scorpions/*anatomy &amp; histology/*genetics ; South America ; },
abstract = {A phylogenetic analysis of the scorpion genus Brachistosternus Pocock, 1893 (Bothriuridae Simon, 1880) is presented, based on a dataset including 41 of the 43 described species and five outgroups, 116 morphological characters and more than 4150 base-pairs of DNA sequence from the nuclear 18S rDNA and 28S rDNA gene loci, and the mitochondrial 12S rDNA, 16S rDNA, and Cytochrome c Oxidase Subunit I gene loci. Analyses conducted using parsimony, Maximum Likelihood and Bayesian Inference were largely congruent with high support for most clades. The results confirmed the monophyly of Brachistosternus, the nominal subgenus, and subgenus Ministernus Francke, 1985, as in previous analyses based only on morphology, but differed in several other respects. Species from the plains of the Atacama Desert diverged basally whereas the high altitude Andean species radiated from a more derived ancestor, presumably as a consequence of Andean uplift and associated changes in climate. Species limits were assessed among species that contain intraspecific variation (e.g., different morphs), are difficult to separate morphologically, and/or exhibit widespread or disjunct distributions. The extent of convergence in morphological adaptation to life on sandy substrata (psammophily) and the complexity of the male genitalia, or hemispermatophores, was investigated. Psammophily evolved on at least four independent occasions. The lobe regions of the hemispermatophore increased in complexity on three independent occasions, and decreased in complexity on another three independent occasions.},
}
@article {pmid26330004,
year = {2016},
author = {Bo, Z and Wenping, S and Kefeng, L and Debin, Z and Chao, M and Guangxia, X},
title = {The complete mitochondrial genome of Cleithenes herzenstein and its phylogenetic analysis.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3663-3665},
doi = {10.3109/19401736.2015.1079845},
pmid = {26330004},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Order ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing ; },
abstract = {The complete mitochondrial genome of Stewartia sinensis was obtained with long PCR approach. Amplification primers were designed according to mitogenome sequences of some other fish species. PCR reactions were according to Kong et al. (2009). The complete mitochondria sequence of Cleithenes herzenstein was deposited in GenBank under the accession number KT223828. Structural and evolutionary analyses were also performed. The length of the complete mitochondrial DNA sequence was 17 175 bp, consisting of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Other than D-loop, another non-coding region named ''OL'' region was found (Table 1). The ''OL'' region (CTTTTTCCCGCCTAGTTTAACCAGTAAAAGGCGGGAA) is 38 bp and has the potential to fold into a stem-loop secondary structure. Most of the genes were encoded on the heavy strand (H strand) except for ND6 and eight tRNA genes (Table 1). The base composition and gene arrangement of C. herzenstein mitogenome was identical to typical vertebrate. For sequence alignment, the mitogenome sequence of C. herzenstein was 96% and 95% similar to that of Platichthys stellatus and Verasper moseri, respectively.},
}
@article {pmid26330185,
year = {2016},
author = {Ren, J and Pu, J and Buchinger, T and Zhu, X and Baker, C and Li, W},
title = {The mitogenomes of the pouched lamprey (Geotria australis) and least brook lamprey (Lampetra aepyptera) with phylogenetic considerations.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3560-3562},
doi = {10.3109/19401736.2015.1074218},
pmid = {26330185},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Dosage ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Lampreys/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We report the mitogenomes of the pouched lamprey (Geotria australis) and least brook lamprey (Lampetra aepyptera) in the families Geotriidae and Petromyzontidae, respectively. Both of the mitogenomes contain the 37 typical vertebrate genes. Their gene order and contents are identical to those of previously described lamprey mitogenomes. The mitogenome of G. australis (17 080 bp) is the largest among the 10 reported lamprey mitogenomes, owed to two long noncoding regions. The mitogenome of L. aepyptera is 77 bp longer (16 236 bp) than that of the congeneric European river lamprey L. fluviatilis, a size difference mostly due to different copy numbers of tandem repeats in the noncoding regions. The phylogenetic analysis supports that the pouched lamprey (Geotriidae) diverged earlier from the common ancestor of lampreys than the Petromyzonids, and the placement of the least brook lamprey in the genus Lampetra.},
}
@article {pmid26334392,
year = {2015},
author = {Zeng, X and Cheng, N and Zheng, X and Diao, Y and Fang, G and Jin, S and Zhou, F and Hu, Z},
title = {Molecular cloning and characterization of two manganese superoxide dismutases from Miscanthus × giganteus.},
journal = {Plant cell reports},
volume = {34},
number = {12},
pages = {2137-2149},
pmid = {26334392},
issn = {1432-203X},
mesh = {Amino Acid Sequence ; Antioxidants/metabolism ; Base Sequence ; Cloning, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Poaceae/*enzymology/genetics ; Sequence Analysis, DNA ; Superoxide Dismutase/*genetics/metabolism ; },
abstract = {Six MnSOD genes were isolated from five Miscanthus species. MgMnSOD1 functions in mitochondria and MgMnSOD1 seems to be the main MnSOD gene involved in stress response of M. × giganteus. Miscanthus × giganteus is a promising biomass energy crop with advantages of vigorous growth, high yield, low fertilizer and pesticide inputs. However, poor overwinter ability limits its widespread cultivation. Moreover, narrow genetic base may increase the risk of susceptibility to diseases and pests. Manganese superoxide dismutase (MnSOD), an important antioxidant enzyme involved in stress tolerance is able to protect plant cells from accumulated reactive oxygen species by converting superoxide to peroxide and oxygen. In many plants, overexpression of MnSOD has shown the ability to enhance the resistance to various stresses. This article describes the studies performed in an attempt to elucidate the molecular and enzymatic properties of MnSODs in M. × giganteus. MnSOD genes from M. × giganteus (MgMnSOD1, MgMnSOD2), M. lutarioriparia (MlMnSOD), M. sacchariflora (MsaMnSOD), M. sinensis (MsiMnSOD), and M. floridulus (MfMnSOD) were cloned and sequenced. The sequence analysis and expression patterns of MgMnSOD1 and MgMnSOD2 suggest that they were orthologous genes which were inherited from the two parents, M. sacchariflora and M. sinensis, respectively. In addition, MgMnSOD1 is predicted to be the main MnSOD gene involved in stress response of M. × giganteus. The activity of purified recombinant MgMnSOD1 was 1854.79 ± 39.98 U mg(-1) (mean ± SD). Further enzymatic assays revealed that the protein exhibited an outstanding thermal stability. MgMnSOD1 is predicted to be targeted to mitochondria and involved in removing the superoxide radical generated by respiration. The presence and sequences of other SOD isozymes transcripts were also investigated in this study.},
}
@article {pmid26336091,
year = {2015},
author = {Bosacchi, M and Gurdon, C and Maliga, P},
title = {Plastid Genotyping Reveals the Uniformity of Cytoplasmic Male Sterile-T Maize Cytoplasms.},
journal = {Plant physiology},
volume = {169},
number = {3},
pages = {2129-2137},
pmid = {26336091},
issn = {1532-2548},
mesh = {Cytoplasm/genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Genome, Plastid/genetics ; Genotype ; Genotyping Techniques ; Mitochondria/genetics ; Phylogeny ; Plant Infertility/*genetics ; Plastids/genetics/metabolism ; Pollen/genetics/physiology ; Sequence Analysis, DNA ; Zea mays/*genetics/physiology ; },
abstract = {Cytoplasmic male-sterile (CMS) lines in maize (Zea mays) have been classified by their response to specific restorer genes into three categories: cms-C, cms-S, and cms-T. A mitochondrial genome representing each of the CMS cytotypes has been sequenced, and male sterility in the cms-S and cms-T cytotypes is linked to chimeric mitochondrial genes. To identify markers for plastid genotyping, we sequenced the plastid genomes of three fertile maize lines (B37, B73, and A188) and the B37 cms-C, cms-S, and cms-T cytoplasmic substitution lines. We found that the plastid genomes of B37 and B73 lines are identical. Furthermore, the fertile and CMS plastid genomes are conserved, differing only by zero to three single-nucleotide polymorphisms (SNPs) in coding regions and by eight to 22 SNPs and 10 to 21 short insertions/deletions in noncoding regions. To gain insight into the origin and transmission of the cms-T trait, we identified three SNPs unique to the cms-T plastids and tested the three diagnostic SNPs in 27 cms-T lines, representing the HA, I, Q, RS, and T male-sterile cytoplasms. We report that each of the tested 27 cms-T group accessions have the same three diagnostic plastid SNPs, indicating a single origin and maternal cotransmission of the cms-T mitochondria and plastids to the seed progeny. Our data exclude exceptional pollen transmission of organelles or multiple horizontal gene transfer events as the source of the mitochondrial urf13-T (unidentified reading frame encoding 13-kD cms-T protein) gene in the cms-T cytoplasms. Plastid genotyping enables a reassessment of the evolutionary relationships of cytoplasms in cultivated maize.},
}
@article {pmid26365128,
year = {2016},
author = {Wei, H and Jia, Q and Chen, G and Chen, S},
title = {The complete mitogenome of lesser striped shrew Sorex bedfordiae (soricidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4290-4291},
doi = {10.3109/19401736.2015.1082100},
pmid = {26365128},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Shrews/*genetics ; },
abstract = {The Sorex genus is type genus in Soricidae. Most of them lack comprehensive biological data. In this study, the complete mitochondrial genome sequence of Sorex bedfordiae was determined. The mitogenome is 17 160 base pairs in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Sorex bedfordiae and other 10 species in Soricidae were used for phylogenetic analyses. Tree constructed using Bayesian phylogenetic methods demonstrated Sorex bedfordiae as a sister to Sorex cylindricauda. Phylogenetic analyses further confirmed that Blarinella diverged prior to Sorex and Anourosorex, but Episoriculus differentiated earlier than Neomys and Nectogale within subfamily Soricinae.},
}
@article {pmid26367084,
year = {2016},
author = {López, K and Angeli, C and Aguilar, C and Loaiza, JR and De León, LF and McMillan, WO and Miller, MJ},
title = {Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3451-3453},
doi = {10.3109/19401736.2015.1066344},
pmid = {26367084},
issn = {2470-1408},
mesh = {Animals ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Panama ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sparrows/classification/*genetics ; Species Specificity ; },
abstract = {We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.},
}
@article {pmid26381927,
year = {2015},
author = {Sheiner, L and Fellows, JD and Ovciarikova, J and Brooks, CF and Agrawal, S and Holmes, ZC and Bietz, I and Flinner, N and Heiny, S and Mirus, O and Przyborski, JM and Striepen, B},
title = {Toxoplasma gondii Toc75 Functions in Import of Stromal but not Peripheral Apicoplast Proteins.},
journal = {Traffic (Copenhagen, Denmark)},
volume = {16},
number = {12},
pages = {1254-1269},
doi = {10.1111/tra.12333},
pmid = {26381927},
issn = {1600-0854},
support = {104111//Wellcome Trust/United Kingdom ; K99 AI103032/AI/NIAID NIH HHS/United States ; R01 AI064671/AI/NIAID NIH HHS/United States ; R01 AI084415/AI/NIAID NIH HHS/United States ; },
mesh = {Apicomplexa/genetics/metabolism ; Apicoplasts/genetics/*metabolism ; Erythrocytes/parasitology ; Fibroblasts/parasitology ; Green Fluorescent Proteins ; Humans ; Intracellular Membranes/*metabolism ; Membrane Proteins/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Mutagenesis, Site-Directed ; Phenylalanine/genetics ; Phylogeny ; Protein Transport ; Protozoan Proteins/genetics/*metabolism ; Toxoplasma/genetics/*metabolism ; },
abstract = {Apicomplexa are unicellular parasites causing important human and animal diseases, including malaria and toxoplasmosis. Most of these pathogens possess a relict but essential plastid, the apicoplast. The apicoplast was acquired by secondary endosymbiosis between a red alga and a flagellated eukaryotic protist. As a result the apicoplast is surrounded by four membranes. This complex structure necessitates a system of transport signals and translocons allowing nuclear encoded proteins to find their way to specific apicoplast sub-compartments. Previous studies identified translocons traversing two of the four apicoplast membranes. Here we provide functional support for the role of an apicomplexan Toc75 homolog in apicoplast protein transport. We identify two apicomplexan genes encoding Toc75 and Sam50, both members of the Omp85 protein family. We localize the respective proteins to the apicoplast and the mitochondrion of Toxoplasma and Plasmodium. We show that the Toxoplasma Toc75 is essential for parasite growth and that its depletion results in a rapid defect in the import of apicoplast stromal proteins while the import of proteins of the outer compartments is affected only as the secondary consequence of organelle loss. These observations along with the homology to Toc75 suggest a potential role in transport through the second innermost membrane.},
}
@article {pmid26384251,
year = {2016},
author = {Jin, JM and Hou, CC and Tan, FQ and Yang, WX},
title = {The potential function of prohibitin during spermatogenesis in Chinese fire-bellied newt Cynops orientalis.},
journal = {Cell and tissue research},
volume = {363},
number = {3},
pages = {805-822},
doi = {10.1007/s00441-015-2280-y},
pmid = {26384251},
issn = {1432-0878},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cloning, Molecular ; DNA, Complementary/genetics ; Fluorescent Antibody Technique ; Gene Expression Regulation ; In Situ Hybridization ; Male ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; Salamandridae/genetics/*physiology ; Sequence Alignment ; Sertoli Cells/cytology/metabolism ; *Spermatogenesis/genetics ; Spermatozoa/cytology/metabolism ; Staining and Labeling ; Time Factors ; },
abstract = {Prohibitin proteins are multifunctional proteins located mainly at the inner membrane of mitochondria expressed in universal species. They play a vital role in mitochondria's function, cell proteolysis, senescence, apoptosis and as a substrate for ubiquitination. In this study, we used PCR cloning, protein and nucleotide acids alignment, protein structure prediction, western blot, in situ hybridization and immunofluorescence to study the characteristics of the prohibitin gene and the potential role of prohibitin in spermatogenesis and spermiogenesis processes in the Chinese fire-bellied newt Cynops orientalis. First, we cloned a 1452-bp full-length cDNA from the testis of Cynops orientalis. Second, we found that the 272 amino acids of prohibitin have a SPFH family domain. Thirdly, the western blots showed high expression of prohibitin in testis while the protein size was approximately 32 kDa. Fourthly, the results of in situ hybridization and immunofluorescence experiments showed that most of the prohibitins travelled with the mitochondria's migration in Cynops orientalis. The quantities of mRNA decreased as spermiogenesis proceeded, although the signals of prohibitins existed during the whole period of spermatogenesis and spermiogenesis. In the mature germ cells, the signals of prohibitins were weak and aggregated at the end of the cell. Finally, we discovered that the Sertoli cells had a large quantity of prohibitins and we made several assumptions of prohibitins' potential roles in those cells. This is the first time that the relationship between mitochondria and prohibitin in different stages of the sperm cells in Cynops orientalis has been examined, which also revealed that Sertoli cells have abundant prohibitins.},
}
@article {pmid26402847,
year = {2015},
author = {Guan, X and Chen, H and Abramson, A and Man, H and Wu, J and Yu, O and Nikolau, BJ},
title = {A phosphopantetheinyl transferase that is essential for mitochondrial fatty acid biosynthesis.},
journal = {The Plant journal : for cell and molecular biology},
volume = {84},
number = {4},
pages = {718-732},
doi = {10.1111/tpj.13034},
pmid = {26402847},
issn = {1365-313X},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Bacterial Proteins/classification/genetics/*metabolism ; Blotting, Western ; Fatty Acids/*biosynthesis ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Glycine/metabolism ; Glycolates/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plants, Genetically Modified ; RNA Interference ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Homology, Amino Acid ; Transferases (Other Substituted Phosphate Groups)/classification/genetics/*metabolism ; },
abstract = {In this study we report the molecular genetic characterization of the Arabidopsis mitochondrial phosphopantetheinyl transferase (mtPPT), which catalyzes the phosphopantetheinylation and thus activation of mitochondrial acyl carrier protein (mtACP) of mitochondrial fatty acid synthase (mtFAS). This catalytic capability of the purified mtPPT protein (encoded by AT3G11470) was directly demonstrated in an in vitro assay that phosphopantetheinylated mature Arabidopsis apo-mtACP isoforms. The mitochondrial localization of the AT3G11470-encoded proteins was validated by the ability of their N-terminal 80-residue leader sequence to guide a chimeric GFP protein to this organelle. A T-DNA-tagged null mutant mtppt-1 allele shows an embryo-lethal phenotype, illustrating a crucial role of mtPPT for embryogenesis. Arabidopsis RNAi transgenic lines with reduced mtPPT expression display typical phenotypes associated with a deficiency in the mtFAS system, namely miniaturized plant morphology, slow growth, reduced lipoylation of mitochondrial proteins, and the hyperaccumulation of photorespiratory intermediates, glycine and glycolate. These morphological and metabolic alterations are reversed when these plants are grown in a non-photorespiratory condition (i.e. 1% CO2 atmosphere), demonstrating that they are a consequence of a deficiency in photorespiration due to the reduced lipoylation of the photorespiratory glycine decarboxylase.},
}
@article {pmid26404517,
year = {2016},
author = {Zhao, M and Ma, H and Ma, C and Zhang, H and Zhang, X and Meng, Y and Wei, H and Chen, F and Ma, L},
title = {The complete mitochondrial genome and gene organization of Cubiceps squamiceps (Perciformes: nomeidae) with phylogenetic consideration.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4296-4297},
doi = {10.3109/19401736.2015.1082103},
pmid = {26404517},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {In this study, we reported the complete mitochondrial DNA sequence of Cubiceps squamiceps, and its phylogenetic relationship. The full length of this mitogenome was 16 510 bp, including 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and a putative control region. The location of genes in mitochondrial genome was similar to other fish species within family Nomeidae. Twenty-eight genes were located on the heavy strand, while nine genes were located on the light strand. The nucleotide composition of this mitogenome was 27.5% for A, 28.5% for C, 17.5% for G, and 26.5% for T. From the NJ phylogenetic tree, we can find that C. squamiceps was genetically closest to C. pauciradiatus among 20 species within suborder Stromateoidei. This study could lay the basis for the future studies in population genetic diversity, taxonomic status, molecular systematics, and conservation genetics in C. squamiceps.},
}
@article {pmid26406120,
year = {2016},
author = {Guan, N and Nie, C and Geng, R and Gao, Z and Zhang, X},
title = {The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4294-4295},
doi = {10.3109/19401736.2015.1082102},
pmid = {26406120},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Chimera/genetics ; Conserved Sequence/genetics ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂) was characterized first in this study. The total length of the genome was identical to the female parent as 16 623 bp, and the overall base composition was 31.23% A, 24.69% T, 27.89% C, and 16.19% G, with a slight A + T bias. It contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication). This study discovered the 99.88% sequence identity between the hybrid and its female parent, which confirmed the maternal inheritance pattern followed by the mitochondrial genome of the hybrid. However, the sequence alignment of mitochondrial genomes between the hybrid and its female parent revealed a total of 20 variable sites in 10 genes or regions, especially 4 sense mutations in 2 PCGs (COX1 and ATPase6). The complete mitochondrial genome sequence of this hybrid bream may provide an important dataset for further study in mitochondrial inheritance mechanism.},
}
@article {pmid26406276,
year = {2016},
author = {Yao, H and Gao, M and Liu, K and Zhao, S},
title = {Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4431-4432},
doi = {10.3109/19401736.2015.1089558},
pmid = {26406276},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Gene Order/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Primates/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Strepsirhini/*genetics ; },
abstract = {The Verreaux's sifaka, Propithecus verreauxi, is a medium-sized lemur that inhabits in tropical dry lowland and montane forest. Here, we reported the complete mitochondrial genome sequence of this species. The mitogenome of P. verreauxi is 17 106 bp in length and composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structure about gene order and composition is identical to that of the other lemur species and related genera. The overall base composition of the heavy strand in descending order is A (32.84%), T (27.13%), C (26.95%), and G (13.08%). Most of the genes are encoded on the heavy strand except for the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes. With the exception of COX3, which terminates with an incomplete stop codon (T-), all the other PCGs initiates with a traditional ATN start codon and ends with the typical mitochondrial stop codon (TAG/TAA/AGA). The phylogenetic tree constructed using the complete mitochondrial genome sequences of P. verreauxi together with 15 other closely related species with Neighbor-Joining (NJ) method shows that P. verreauxi is closer to P. coquereli in the phylogenetic relationship.},
}
@article {pmid26419670,
year = {2015},
author = {Nishimura, K and Apitz, J and Friso, G and Kim, J and Ponnala, L and Grimm, B and van Wijk, KJ},
title = {Discovery of a Unique Clp Component, ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery.},
journal = {The Plant cell},
volume = {27},
number = {10},
pages = {2677-2691},
pmid = {26419670},
issn = {1532-298X},
mesh = {Adaptor Proteins, Signal Transducing/genetics/*metabolism ; Aldehyde Oxidoreductases/genetics/metabolism ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Carrier Proteins/genetics/*metabolism ; Chloroplasts/enzymology ; Endopeptidase Clp/genetics/*metabolism ; *Models, Molecular ; Molecular Chaperones/genetics/metabolism ; Multienzyme Complexes ; Mutation ; Phylogeny ; Protein Interaction Mapping ; *Proteome ; Sequence Analysis, DNA ; Substrate Specificity ; },
abstract = {Clp proteases are found in prokaryotes, mitochondria, and plastids where they play crucial roles in maintaining protein homeostasis (proteostasis). The plant plastid Clp machinery comprises a hetero-oligomeric ClpPRT proteolytic core, ATP-dependent chaperones ClpC and ClpD, and an adaptor protein, ClpS1. ClpS1 selects substrates to the ClpPR protease-ClpC chaperone complex for degradation, but the underlying substrate recognition and delivery mechanisms are currently unclear. Here, we characterize a ClpS1-interacting protein in Arabidopsis thaliana, ClpF, which can interact with the Clp substrate glutamyl-tRNA reductase. ClpF and ClpS1 mutually stimulate their association with ClpC. ClpF, which is only found in photosynthetic eukaryotes, contains bacterial uvrB/C and YccV protein domains and a unique N-terminal domain. We propose a testable model in which ClpS1 and ClpF form a binary adaptor for selective substrate recognition and delivery to ClpC, reflecting an evolutionary adaptation of the Clp system to the plastid proteome.},
}
@article {pmid26435002,
year = {2016},
author = {Manna, S and Harman, A},
title = {Horizontal gene transfer of a Chlamydial tRNA-guanine transglycosylase gene to eukaryotic microbes.},
journal = {Molecular phylogenetics and evolution},
volume = {94},
number = {Pt A},
pages = {392-396},
doi = {10.1016/j.ympev.2015.09.022},
pmid = {26435002},
issn = {1095-9513},
mesh = {Acanthamoeba/*genetics ; Amebiasis/genetics/parasitology ; Chlamydia/enzymology/*genetics ; Deltaproteobacteria/enzymology/genetics ; Dysentery, Bacillary/microbiology ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Pentosyltransferases/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Shigella flexneri/enzymology/genetics ; },
abstract = {tRNA-guanine transglycosylases are found in all domains of life and mediate the base exchange of guanine with queuine in the anticodon loop of tRNAs. They can also regulate virulence in bacteria such as Shigella flexneri, which has prompted the development of drugs that inhibit the function of these enzymes. Here we report a group of tRNA-guanine transglycosylases in eukaryotic microbes (algae and protozoa) which are more similar to their bacterial counterparts than previously characterized eukaryotic tRNA-guanine transglycosylases. We provide evidence demonstrating that the genes encoding these enzymes were acquired by these eukaryotic lineages via horizontal gene transfer from the Chlamydiae group of bacteria. Given that the S. flexneri tRNA-guanine transglycosylase can be targeted by drugs, we propose that the bacterial-like tRNA-guanine transglycosylases could potentially be targeted in a similar fashion in pathogenic amoebae that possess these enzymes such as Acanthamoeba castellanii. This work also presents ancient prokaryote-to-eukaryote horizontal gene transfer events as an untapped resource of potential drug target identification in pathogenic eukaryotes.},
}
@article {pmid26436880,
year = {2015},
author = {Noguchi, F and Shimamura, S and Nakayama, T and Yazaki, E and Yabuki, A and Hashimoto, T and Inagaki, Y and Fujikura, K and Takishita, K},
title = {Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis.},
journal = {Protist},
volume = {166},
number = {5},
pages = {534-550},
doi = {10.1016/j.protis.2015.08.002},
pmid = {26436880},
issn = {1618-0941},
mesh = {Mitochondria/*metabolism ; Phylogeny ; Sequence Analysis, RNA ; Stramenopiles/genetics/*metabolism ; },
abstract = {Functionally and morphologically degenerate mitochondria, so-called mitochondrion-related organelles (MROs), are frequently found in eukaryotes inhabiting hypoxic or anoxic environments. In the last decade, MROs have been discovered from a phylogenetically broad range of eukaryotic lineages and these organelles have been revealed to possess diverse metabolic capacities. In this study, the biochemical characteristics of an MRO in the free-living anaerobic protist Cantina marsupialis, which represents an independent lineage in stramenopiles, were inferred based on RNA-seq data. We found transcripts for proteins known to function in one form of MROs, the hydrogenosome, such as pyruvate:ferredoxin oxidoreductase, iron-hydrogenase, acetate:succinate CoA-transferase, and succinyl-CoA synthase, along with transcripts for acetyl-CoA synthetase (ADP-forming). These proteins possess putative mitochondrial targeting signals at their N-termini, suggesting dual ATP generation systems through anaerobic pyruvate metabolism in Cantina MROs. In addition, MROs in Cantina were also shown to share several features with canonical mitochondria, including amino acid metabolism and an "incomplete" tricarboxylic acid cycle. Transcripts for all four subunits of complex II (CII) of the electron transport chain were detected, while there was no evidence for the presence of complexes I, III, IV, or F1Fo ATPase. Cantina MRO biochemistry challenges the categories of mitochondrial organelles recently proposed.},
}
@article {pmid26436958,
year = {2016},
author = {Wang, FY and Wang, TY and Liao, TY and Liu, MY},
title = {The complete mitochondrial genome sequence of Nemateleotris decora (gobiiformes, gobiidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4274-4275},
doi = {10.3109/19401736.2015.1082091},
pmid = {26436958},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {We determined the mitochondrial genome (mitogenome) sequence of Nemateleotris decora by using a long polymerase chain reaction (PCR) method and next-generation sequence (NGS) technology. The total length of N. decora mitogenome is 16 502 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region. The overall base composition of N. decora is 25.22% for A, 25.90% for T, 30.69% for G, and 18.19% for C. Our results showed the complete mitogenome is a good marker for the phylogenetic study.},
}
@article {pmid26444283,
year = {2015},
author = {Greig, K and Boocock, J and Prost, S and Horsburgh, KA and Jacomb, C and Walter, R and Matisoo-Smith, E},
title = {Complete Mitochondrial Genomes of New Zealand's First Dogs.},
journal = {PloS one},
volume = {10},
number = {10},
pages = {e0138536},
pmid = {26444283},
issn = {1932-6203},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Geography/methods ; Haplotypes/genetics ; Indonesia ; Mitochondria/*genetics ; New Zealand ; Pacific Ocean ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia.},
}
@article {pmid26453092,
year = {2016},
author = {Marangi, M and Hall, MJ and Aitken, A and Ready, PD and Giangaspero, A},
title = {Origins of Wohlfahrtia magnifica in Italy based on the identification of mitochondrial cytochrome b gene haplotypes.},
journal = {Parasitology research},
volume = {115},
number = {2},
pages = {483-487},
pmid = {26453092},
issn = {1432-1955},
mesh = {Animals ; Cytochromes b/*genetics ; Europe ; *Genes, Mitochondrial ; Geography ; Haplotypes ; Italy/epidemiology ; Larva ; Mitochondria ; Myiasis/epidemiology/parasitology/*veterinary ; Phylogeny ; Polymerase Chain Reaction ; Sarcophagidae/*genetics ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; },
abstract = {To identify the geographical origins of larvae of Wohlfahrtia magnifica (Diptera: Sarcophagidae) causing myiasis of sheep in Italy, comparative DNA sequence analysis of the mitochondrial cytochrome b gene was performed, based on gene fragments amplified by PCR from genomic DNA isolated from individual specimens. DNA extractions of 19 larvae from Lazio, Molise, Puglia, and Sicilia generated 17 readable sequences homologous to 2 haplotypes, either CB_magn01 or CB_magn02; DNA extracts from 4 adult flies from Calabria (reared from larvae) produced 4 readable sequences belonging to the haplotype CB_magn01. The two haplotypes found represent both the East and West phylogenetic lineages of W. magnifica, which is consistent with the species' arrival from central/southeast Europe (East lineage) and/or from southwest Europe/northwest Africa (West lineage). This is the first report of the sympatric occurrence of the two lineages, which could have resulted from natural or human-assisted dispersal. Polymorphic nuclear loci will have to be characterized in order to explain the origins and lack of mitochondrial haplotype diversity of this pest in Italy, where it poses increasing veterinary problems.},
}
@article {pmid26457491,
year = {2016},
author = {Liu, F and Bao, X and Fan, Y and Li, J and Yao, X},
title = {Sequencing and analysis of the complete mitochondrial genome of Brown Shrike, Lanius cristatus (Passeriformes, Laniidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3544-3546},
doi = {10.3109/19401736.2015.1074210},
pmid = {26457491},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of the Brown Shrike (Lanius cristatus) was 16 821 bp in length. The accession number was KT004451 and the contents of A, T, C, and G were 31.10%(5237 bp), 25.60%(4309 bp), 28.60%(4814 bp), and 14.60%(2461 bp), respectively. Gene organization and length was similar to other species of birds. It comprises of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. All protein-coding genes use the typical initiation codon ATG, except for COX1 which was initiated with GTG. All the complete stop codon was coincident with the Black-headed Gull (Chroicocephalus ridibundus) and the Grey-backed Shrike (Lanius tephronotus), except for ND2, which was terminated with TAG. In addition, the phylogenetic relationships of Passeriformes based on complete mitochondrial genomes showed that the genetic distance of Laniidae and Corvidae was closer than others.},
}
@article {pmid26462546,
year = {2016},
author = {Sun, Z and Wang, B and Sun, X and Yan, L and Pan, T and Zhang, B},
title = {Phylogenetic studies of Anas clypeata (Anatidae: Anas) based on complete mitochondrial DNA sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4320-4321},
doi = {10.3109/19401736.2015.1089482},
pmid = {26462546},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Ducks/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Northern shoveler (Anas clypeata) is a middle-sized duck living in an extremely geographical range in northern hemisphere. Here, the complete mitochondrial genome of A. clypeata (16 599 bp in length) has been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (29.4%), G (15.7%), C (32.5%) and T (22.4%), the percentage of A and T (51.8%) is slightly higher than G and C (48.2%). All the genes in A. clypeata were distributed on the H-strand, except for the ND6 subunit gene and 9 tRNA genes which were encoded on the L-strand. The phylogenetic relationships of 12 Anatidae species were reconstructed based on the complete mtDNA sequences using the Bayesian inference method.},
}
@article {pmid26463086,
year = {2016},
author = {Hao, RC and Wang, GH and Yang, GZ and Zan, LS},
title = {The complete mitochondrial genome sequence of Zebrias crossolepis (pleuronectiformes: soleidae) and Acrossocheilus monticola (cypriniformes: cyprinidae) and phylogenetic studies.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4326-4327},
doi = {10.3109/19401736.2015.1089485},
pmid = {26463086},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; Cyprinidae/genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/*genetics ; Flatfishes/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing ; },
abstract = {In this study, two complete mitogenome sequences of Zebrias crossolepis and Acrossocheilus monticola were determined and the phylogenetic relationship were constructed based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes. The length of the complete mitogenome sequence are 16 775 bp and 16 605 bp in Z. crossolepis and A. monticola, respectively, both containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.3% A, 26.3% T, 30.0% C, 15.5% G, with a slight AT bias (54.6%) in Z. crossolepis, while 31.4% A, 24.5% T, 28.2% C, 15.9% G, with an slight AT bias (55.9%) in A. monticola. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while ND4 and Cytb in Z. crossolepis and COII, ND4, and Cytb in A. monticola use an incomplete stop codon T. These results are expected to provide useful molecular data for species identification and further phylogenetic studies.},
}
@article {pmid26465068,
year = {2016},
author = {Doña, J and Ruiz-Ruano, FJ and Jovani, R},
title = {DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4475-4478},
doi = {10.3109/19401736.2015.1089573},
pmid = {26465068},
issn = {2470-1408},
mesh = {Africa, Northern ; Animals ; Bayes Theorem ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Gibraltar ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Strigiformes/classification/*genetics ; },
abstract = {Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the PAB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.},
}
@article {pmid26486753,
year = {2016},
author = {Chen, D and Zhang, K and Liu, S and Chen, F},
title = {The complete mitochondrial genome of the Dipodomys ordii (Ord's kangaroo rat).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4322-4323},
doi = {10.3109/19401736.2015.1089483},
pmid = {26486753},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Dipodomys/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Ord's kangaroo rat is a kangaroo rat native to western North America. In this study, we first reported the complete mitochondrial genome of Dipodomys ordii that the first has the complete mitochondrial genome in the genus of Heteromyidae. The mitogenome is a circular molecule of 16 257 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a putative displacement loop region. All protein-coding genes started with a traditional ATN codon and terminated with the mitochondria stop codon (TAA/TAG/AGA) or a single T base. The gene order and composition of mitogenome was similar to that of most other Sciurognathi species and its GC content was 36.73%. Thirteen protein-coding genes of D. ordii together with eight other closely species were used to construct the species phylogenetic tree for verification of the accuracy of new determined mitogenome sequences.},
}
@article {pmid26486988,
year = {2016},
author = {Yang, H and Bao, X and Wang, B and Liu, W},
title = {The complete mitochondrial genome of Chirolophis japonicus (Perciformes: Stichaeidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4419-4420},
doi = {10.3109/19401736.2015.1089552},
pmid = {26486988},
issn = {2470-1408},
mesh = {Amino Acid Sequence/genetics ; Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genome of Chirolophis japonicus was sequenced for the first time in this study. It is a closed-circular molecule of 16 521 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, an origin of light strand replication (OL), and a control region (CR). The overall base composition of the heavy-strand is 25.5% A, 28.6% T, 18.3% G, and 27.6% C, and the lengths of 2 rRNA genes are 946 and 1692 bp, respectively. Maximum likelihood tree based on all the amino acid sequences of 13 mitochondrial PCGs was constructed, in which C. japonicus is close to three species of infraorder Zoarcales. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of genus Chirolophis.},
}
@article {pmid26487090,
year = {2016},
author = {Li, Z and Chen, Z and Gao, J and Wang, L and Chen, X and Zhao, Y},
title = {The complete mitochondrial genome of the Symphysodon aequifasciatus (Pellegrin, 1904).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4425-4426},
doi = {10.3109/19401736.2015.1089555},
pmid = {26487090},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Cichlids/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {In this study, the complete mitogenome sequence of the Symphysodon aequifasciatus has been sequenced by next-generation sequencing method. The mitogenome consists of 16 545 bp, including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of the fish is 28.8% for A, 30.1% for C, 15.0% for G, and 26.1% for T, suggesting a 99% identity to S. discus Heckel and a 98% identity to S. haraldi. It provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Symphysodon phylogeny.},
}
@article {pmid26487483,
year = {2016},
author = {Liu, J and Jin, W and Wu, C},
title = {The first complete mitochondrial genome of Serranidae sp. (Percoidea, Serranidae) and phylogenetic analysis based on Bayesian.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4436-4438},
doi = {10.3109/19401736.2015.1089560},
pmid = {26487483},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Bayes Theorem ; Conserved Sequence/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {In the present study, the complete mitochondrial genome of Serranidae sp. was determined first. The entire mitochondrial genome of Serranidae sp. is 16 512 bp in length, containing 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA) and 2 main non-coding regions (the control region and the origin of the light-strand replication). The gene arrangement, base composition and tRNA structures of Serranidae sp. are similar to most of the bony fishes. The central conserved sequence blocks (CSB-1, CSB-2, and CSB-3) and the core sequence (ACATATATGT) of terminal-associated sequences were recognized in the control region. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light-strand replication of Serranidae sp. Phylogenetic tree, which is constructed based on the complete mitochondrial genome sequences of Serranidae sp., shows that Serranidae sp. is clustered with the fishes of the family Pentacerotidae. We expect that the mitochondrial genome of Serranidae sp. would play a key role in phylogenetic analysis of Serranidae.},
}
@article {pmid26488305,
year = {2016},
author = {Liu, JB and Zeng, YF and Yuan, C and Yue, YJ and Ding, XZ and Guo, TT and Han, JL and Feng, RL and Sun, XP and Niu, CE and Yang, BH and Guo, J},
title = {The complete mitochondrial genome sequence of the dwarf blue sheep, Pseudois schaeferi haltenorth in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4411-4413},
doi = {10.3109/19401736.2015.1089548},
pmid = {26488305},
issn = {2470-1408},
mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Sheep/*genetics ; Whole Genome Sequencing/methods ; },
abstract = {The dwarf blue sheep (Pseudois schaeferi haltenorth) belongs the subfamily Caprinae, which is distributed in Sichuan, Tibet, Yunnan, and Qinghai in China. In this study, the complete mitochondrial genome of Pseudois schaeferi haltenorth was sequenced. The mitogenome was 16 741 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region (D-loop region). As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the Pseudois schaeferi haltenorth is 33.54% A, 26.37% T, 26.91% C, and 13.18% G, A + T (59.91%) was higher than G + C (40.09%). The phylogenetic relationships was analyzed using the complete mitogenome sequence, results show that P. schaeferi haltenorth should be a different species differ from the Genus pseudois hodgson. These information provide useful data for further study on the protection of genetic resources and the taxonomy of Caprinae.},
}
@article {pmid26503662,
year = {2016},
author = {Nuralitha, S and Siregar, JE and Syafruddin, D and Roelands, J and Verhoef, J and Hoepelman, AI and Marzuki, S},
title = {Within-Host Selection of Drug Resistance in a Mouse Model of Repeated Incomplete Malaria Treatment: Comparison between Atovaquone and Pyrimethamine.},
journal = {Antimicrobial agents and chemotherapy},
volume = {60},
number = {1},
pages = {258-263},
pmid = {26503662},
issn = {1098-6596},
mesh = {Amino Acid Substitution ; Animals ; Antimalarials/*pharmacology ; Atovaquone/*pharmacology ; Cell Nucleus/drug effects/enzymology/genetics ; Cytochromes b/*genetics/metabolism ; Drug Resistance/drug effects/*genetics ; Gene Expression ; Host-Parasite Interactions ; Malaria/drug therapy/parasitology ; Mice ; Mice, Inbred BALB C ; Mitochondria/drug effects/enzymology/genetics ; Mutation Rate ; Parasitic Sensitivity Tests ; Plasmodium berghei/*drug effects/enzymology/genetics ; Protozoan Proteins/genetics/metabolism ; Pyrimethamine/*pharmacology ; Selection, Genetic ; Tetrahydrofolate Dehydrogenase/*genetics/metabolism ; Treatment Failure ; },
abstract = {The evolutionary selection of malaria parasites within individual hosts is an important factor in the emergence of drug resistance but is still not well understood. We have examined the selection process for drug resistance in the mouse malaria agent Plasmodium berghei and compared the dynamics of the selection for atovaquone and pyrimethamine. Resistance to these drugs has been shown to be associated with genetic lesions in the dihydrofolate reductase gene in the case of pyrimethamine and in the mitochondrial cytochrome b gene for atovaquone. A mouse malaria model for the selection of drug resistance, based on repeated incomplete treatment (RICT) with a therapeutic dose of antimalarial drugs, was established. The number of treatment cycles for the development of stable resistance to atovaquone (2.47 ± 0.70; n = 19) was found to be significantly lower than for pyrimethamine (5.44 ± 1.46; n = 16; P < 0.0001), even when the parental P. berghei Leiden strain was cloned prior to the resistance selection. Similar results were obtained with P. berghei Edinburgh. Mutational changes underlying the resistance were identified to be S110N in dihydrofolate reductase for pyrimethamine and Y268N, Y268C, Y268S, L271V-K272R, and G280D in cytochrome b for atovaquone. These results are consistent with the rate of mitochondrial DNA mutation being higher than that in the nucleus and suggest that mutation leading to pyrimethamine resistance is not a rare event.},
}
@article {pmid26507459,
year = {2016},
author = {Ogata, T and Senoo, T and Kawano, S and Ikeda, S},
title = {Mitochondrial superoxide dismutase deficiency accelerates chronological aging in the fission yeast Schizosaccharomyces pombe.},
journal = {Cell biology international},
volume = {40},
number = {1},
pages = {100-106},
doi = {10.1002/cbin.10556},
pmid = {26507459},
issn = {1095-8355},
mesh = {Aging/*metabolism ; Antioxidants/metabolism ; DNA, Fungal/genetics ; Mitochondria/metabolism ; Mutation ; Mutation Rate ; Oxidative Stress/physiology ; Reactive Oxygen Species/metabolism ; Schizosaccharomyces/cytology/*enzymology/genetics ; Schizosaccharomyces pombe Proteins/genetics/*metabolism ; Superoxide Dismutase/*deficiency/genetics/metabolism ; Superoxides/metabolism ; Superoxide Dismutase 2 ; },
abstract = {A mitochondrial superoxide dismutase (SOD2) is the first line of antioxidant defense against mitochondrial superoxide. Even though the involvement of SOD2 in lifespan has been studied extensively in several organisms, characterization of the aging process has not been performed for the sod2 mutant (sod2Δ) of a prominent model Schizosaccharomyces pombe. In this study, we measured the chronological lifespan of sod2Δ cells by their ability to survive in long-term culture. SOD2 deficiency drastically decreased cell viability in the stationary phase. The mutation frequency of nuclear DNA in sod2Δ was elevated in the stationary phase, and cellular proteins and nuclear DNA were extensively degraded, concurrent with cell death. The sod2 gene in wild-type cells could be induced by an increase in endogenous oxidative stresses, after which, SOD2 activity was substantially elevated during the stationary phase. Culture in a lower glucose concentration (calorie restriction) prominently extended the sod2Δ lifespan. Therefore, S. pombe SOD2 plays a critical role in longevity through its upregulation in the non-dividing phase.},
}
@article {pmid26510618,
year = {2016},
author = {Yu, P and Yang, QC and Ding, SQ and Zhang, J and Li, XL and Bi, ZH and Wan, Q},
title = {The complete sequence of mitochondrial genome of Sinibotia pulchra (Cypriniformes: Cobitidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4318-4319},
doi = {10.3109/19401736.2015.1089481},
pmid = {26510618},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; Cyprinidae/genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Sinibotia pulchra (Cypriniformes: Cobitidae) is a small cyprinid fish. In this study, the complete mitochondrial genome sequence of S. pulchra is sequenced. The S. pulchra complete mitochondrial genome (GenBank accession no. KT362179) was a circular molecule of 16 568 bp in length, with 13 protein-coding genes (PCGs), 2 ribosome RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.69% for A, 25.63% for T, 26.94% for C and 15.74% for G, with an AT content of 57.32%. The AT content of 12S rRNA, 16S rRNA and D-loop was 50.21%, 56.86% and 66.74%, respectively.},
}
@article {pmid26517908,
year = {2015},
author = {Schaedler, TA and Faust, B and Shintre, CA and Carpenter, EP and Srinivasan, V and van Veen, HW and Balk, J},
title = {Structures and functions of mitochondrial ABC transporters.},
journal = {Biochemical Society transactions},
volume = {43},
number = {5},
pages = {943-951},
doi = {10.1042/BST20150118},
pmid = {26517908},
issn = {1470-8752},
support = {106169/WT_/Wellcome Trust/United Kingdom ; BB/H00288X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {ATP-Binding Cassette Transporters/classification/genetics/*metabolism ; Animals ; Crystallography, X-Ray ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Mutation ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; },
abstract = {A small number of physiologically important ATP-binding cassette (ABC) transporters are found in mitochondria. Most are half transporters of the B group forming homodimers and their topology suggests they function as exporters. The results of mutant studies point towards involvement in iron cofactor biosynthesis. In particular, ABC subfamily B member 7 (ABCB7) and its homologues in yeast and plants are required for iron-sulfur (Fe-S) cluster biosynthesis outside of the mitochondria, whereas ABCB10 is involved in haem biosynthesis. They also play a role in preventing oxidative stress. Mutations in ABCB6 and ABCB7 have been linked to human disease. Recent crystal structures of yeast Atm1 and human ABCB10 have been key to identifying substrate-binding sites and transport mechanisms. Combined with in vitro and in vivo studies, progress is being made to find the physiological substrates of the different mitochondrial ABC transporters.},
}
@article {pmid26530087,
year = {2015},
author = {Wagner, S and Behera, S and De Bortoli, S and Logan, DC and Fuchs, P and Carraretto, L and Teardo, E and Cendron, L and Nietzel, T and Füßl, M and Doccula, FG and Navazio, L and Fricker, MD and Van Aken, O and Finkemeier, I and Meyer, AJ and Szabò, I and Costa, A and Schwarzländer, M},
title = {The EF-Hand Ca2+ Binding Protein MICU Choreographs Mitochondrial Ca2+ Dynamics in Arabidopsis.},
journal = {The Plant cell},
volume = {27},
number = {11},
pages = {3190-3212},
pmid = {26530087},
issn = {1532-298X},
mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/*metabolism ; Calcium ; Calcium Signaling ; Calcium-Binding Proteins/*metabolism ; Cell Respiration ; Cytosol/metabolism ; DNA, Bacterial/genetics ; *EF Hand Motifs ; Mitochondria/*metabolism/ultrastructure ; Mutagenesis, Insertional/genetics ; Phylogeny ; Plant Roots/metabolism/ultrastructure ; Protein Binding ; Protein Transport ; Seedlings/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/metabolism ; },
abstract = {Plant organelle function must constantly adjust to environmental conditions, which requires dynamic coordination. Ca(2+) signaling may play a central role in this process. Free Ca(2+) dynamics are tightly regulated and differ markedly between the cytosol, plastid stroma, and mitochondrial matrix. The mechanistic basis of compartment-specific Ca(2+) dynamics is poorly understood. Here, we studied the function of At-MICU, an EF-hand protein of Arabidopsis thaliana with homology to constituents of the mitochondrial Ca(2+) uniporter machinery in mammals. MICU binds Ca(2+) and localizes to the mitochondria in Arabidopsis. In vivo imaging of roots expressing a genetically encoded Ca(2+) sensor in the mitochondrial matrix revealed that lack of MICU increased resting concentrations of free Ca(2+) in the matrix. Furthermore, Ca(2+) elevations triggered by auxin and extracellular ATP occurred more rapidly and reached higher maximal concentrations in the mitochondria of micu mutants, whereas cytosolic Ca(2+) signatures remained unchanged. These findings support the idea that a conserved uniporter system, with composition and regulation distinct from the mammalian machinery, mediates mitochondrial Ca(2+) uptake in plants under in vivo conditions. They further suggest that MICU acts as a throttle that controls Ca(2+) uptake by moderating influx, thereby shaping Ca(2+) signatures in the matrix and preserving mitochondrial homeostasis. Our results open the door to genetic dissection of mitochondrial Ca(2+) signaling in plants.},
}
@article {pmid26535725,
year = {2015},
author = {Andrade, BS and Góes-Neto, A},
title = {Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {14105-14114},
doi = {10.4238/2015.October.29.30},
pmid = {26535725},
issn = {1676-5680},
mesh = {Agaricales/*enzymology/*genetics ; Cacao/microbiology ; DNA-Directed DNA Polymerase/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; Plasmids/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; },
abstract = {The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.},
}
@article {pmid26544023,
year = {2016},
author = {Shi, X and Zhu, Q and Wu, N and Tu, J and Yang, D and Xu, H and Yao, Y and Yang, M and Li, D},
title = {The complete nucleotide sequence of the mitochondrial genome of Drosophila formosana (Diptera: Drosophilidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4316-4317},
doi = {10.3109/19401736.2015.1089480},
pmid = {26544023},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Nucleotides ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Drosophila formosana (Diptera: Drosophilidae) belongs to the Drosophilidae group of Drosophila. The mitochondrial genome sequence of Drosophila formosana is determined in this study. Mitochondrion of D. formosana is a circular DNA molecule of the 16 100 nucleotide pairs (bp) that contains one encoding region including 37 genes and 1 non-coding A + T-rich region. The similarity and typicality have been showed by the structure and organization analysis. All genes are arranged in the circular DNA molecule. In addition to DN5 that use GTG start codon, all other protein-coding genes (PCGs) start with an ATN start codon. Ten protein-coding genes stop with the termination codon TAN, while other protein-coding genes (PCGs) used incomplete termination codon TA- (cox2, nad5, nad1). The A + T-rich region with a length of 1088 bp is located between rrnS and trnI. The mitochondrial genome of D. formosana has been completely sequenced for the first time in this study.},
}
@article {pmid26596041,
year = {2015},
author = {Titov, VN},
title = {[THE BIOLOGICAL FUNCTION OF NUTRITION, BIOLOGICAL REACTION OF EXOTROPHY, DEPOSITING AND ENDOTROPHY. THE VISCERAL FATTY CELLS AND ADIPOCYTES - PHYLOGENETICALLY, FUNCTIONALLY AND REGULATORY DIFFERENT POOLS OF FATTY TISSUE].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {60},
number = {8},
pages = {14-23},
pmid = {26596041},
issn = {0869-2084},
mesh = {Adipocytes/classification/*metabolism/pathology ; Adiponectin/genetics/metabolism ; Adipose Tissue, Brown/*metabolism/pathology ; Autocrine Communication ; Fatty Acids/metabolism ; Gene Expression Regulation ; Humans ; Intra-Abdominal Fat/*metabolism/pathology ; Leptin/genetics/metabolism ; Lipid Metabolism ; Metabolic Syndrome/genetics/*metabolism/pathology ; Mitochondria/metabolism ; Paracrine Communication ; Phylogeny ; Signal Transduction ; },
abstract = {For billions years, two phylogenetically, functionally and regulatory different pools of fatty cells - visceral fatty acids and adipocytes coexist in vivo. Their becoming occurred at different degrees of phylogenesis. The phylogenetically earlier pool of visceral fatty acids is meant to supply with fatty acids-substrates for gaining energy by those cells which implement biological function of nutrition (trophology), homeostasis, endoecology biological function of adaptation and continuation of species. They have no receptors to phylogenetically later insulin. The adipocytes, later in phylogenesis, implement one biological function - the function of locomotion and they are as insulin-dependent as skeletal myocytes, cardiomyocytes, adipocytes and periportal hepatocytes. The difference in regulation is traced on all levels of "biological perfection " - autocrine (cellular) level, in humoral regulated paracrin cenosises of cells and on the level of organism. In biological function of trophology, paracrin cenosises of visceral fatty acids and adipocytes implement subsequently three biological reactions: exotrophy, deposit of fatty acids and endotrophy. In conditions of humoral regulation of three functionally different biological reactions in paracrin cenosises synthesis of so many humoral mediators is required. The humoral mediators of mechanism of feedback at autocrine level, in paracrin cenosises and at the level of organism are leptin of visceral fatty acids and adiponectin of adipocytes. At the level of organism, phylogenetically earlier paracrin cenosises of fatty cells are regulated by endocrine system. The phylogenetically later paracrin cenosises are regulated by insulin and nuclei of hypothalamus. The metabolic syndrome is a pathology of phylogenetically earlier insulin-independent visceral fatty acids. The obesity is a pathology of phylogenetically later pool of insulin-dependent adipocytes.},
}
@article {pmid26620805,
year = {2016},
author = {Sherrard-Smith, E and Stanton, DW and Cable, J and Orozco-terWengel, P and Simpson, VR and Elmeros, M and van Dijk, J and Simonnet, F and Roos, A and Lemarchand, C and Poledník, L and Heneberg, P and Chadwick, EA},
title = {Distribution and molecular phylogeny of biliary trematodes (Opisthorchiidae) infecting native Lutra lutra and alien Neovison vison across Europe.},
journal = {Parasitology international},
volume = {65},
number = {2},
pages = {163-170},
doi = {10.1016/j.parint.2015.11.007},
pmid = {26620805},
issn = {1873-0329},
mesh = {Animals ; Europe/epidemiology ; France/epidemiology ; Gene Flow ; Germany/epidemiology ; Haplotypes ; Introduced Species ; Mink/*parasitology ; Mitochondria/genetics ; Otters/*parasitology ; Phylogeny ; Poland/epidemiology ; Trematoda/classification/*genetics/*isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; United Kingdom ; },
abstract = {The recent identification of Pseudamphistomum truncatum, (Rudolphi, 1819) (Trematoda: Opisthorchiidae) and Metorchis bilis (Braun, 1790) Odening, 1962 (synonymous with Metorchis albidus (Braun, 1893) Loos, 1899 and Metorchis crassiusculus (Rudolphi, 1809) Looss, 1899 (Trematoda: Opisthorchiidae)) in otters from Britain caused concern because of associated biliary damage, coupled with speculation over their alien status. Here, we investigate the presence, intensity and phylogeny of these trematodes in mustelids (principally otters) across Europe (Czech Republic, Denmark, France, Germany, Norway, Poland and Sweden and Britain). The trematodes were identified to species using the internal transcribed spacer II (ITS2) locus. Both parasites were found across Europe but at unequal frequency. In the German state of Saxony, eight out of eleven (73%) otters examined were infected with P. truncatum whilst this parasite was not found in either mink from Scotland (n=40) or otters from Norway (n=21). Differences in the phylogenies between the two species suggest divergent demographic histories possibly reflecting contrasting host diet or competitive exclusion, with M. bilis exhibiting greater mitochondrial diversity than P. truncatum. Shared haplotypes within the ranges of both parasite species probably reflect relatively unrestricted movements (both natural and anthropogenic) of intermediate and definitive hosts across Europe.},
}
@article {pmid26627655,
year = {2015},
author = {Janardan, N and Harijan, RK and Kiema, TR and Wierenga, RK and Murthy, MR},
title = {Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.},
journal = {Acta crystallographica. Section D, Biological crystallography},
volume = {71},
number = {Pt 12},
pages = {2479-2493},
doi = {10.1107/S1399004715019331},
pmid = {26627655},
issn = {1399-0047},
mesh = {Acetyl-CoA C-Acyltransferase/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Gene Expression ; Kinetics ; Mitochondria/*chemistry/enzymology ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium smegmatis/*chemistry/classification/enzymology ; Phylogeny ; Protein Binding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Substrate Specificity ; },
abstract = {Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1-covering loop-Lα2 region, together with the Nβ2-Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.},
}
@article {pmid26634536,
year = {2015},
author = {Xu, X and Tan, YP and Cheng, G and Liu, XQ and Xia, CJ and Luo, FY and Wang, CT},
title = {Genomic survey and gene expression analysis of the VDAC gene family in rice.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {15683-15696},
doi = {10.4238/2015.December.1.20},
pmid = {26634536},
issn = {1676-5680},
mesh = {Chromosome Mapping ; Cluster Analysis ; Computational Biology/methods ; Gene Duplication ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Order ; Gene Regulatory Networks ; Genetic Loci ; Genome, Plant ; *Genomics ; *Multigene Family ; Oryza/classification/*genetics/metabolism ; Phylogeny ; Voltage-Dependent Anion Channels/*genetics/metabolism ; },
abstract = {The voltage-dependent anion channel (VDAC), also known as a mitochondrial porin, plays an important role in the regulation of metabolic and energetic functions of mitochondria, as well as in mitochondria-mediated apoptosis. Cytoplasmic male sterility (CMS) is of major economic importance for commercial hybrid production and a research model for the interaction be-tween nuclear and cytoplasmic genomes. Recent research has revealed that CMS is associated with programmed cell death. Here, we used the Honglian (HL)-CMS line of rice (Oryza sativa) as material to investigate the association of O. sativa VDAC (OsVDAC) expression to CMS. Eight VDACs were extracted from rice in this study. Bioinformatic analysis of the rice VDACs was conducted at the DNA, cDNA, and protein level. Expression patterns of OsVDACs were analyzed in different organs and during different stages of pollen development using sterile line YuetaiA (YTA), and its maintainer line YuetaiB (YTB). Differential expression of OsVDACs between YTA and YTB was observed, suggesting that VDACs may be involved in the formation of HL-CMS.},
}
@article {pmid26653218,
year = {2015},
author = {Huchon, D and Szitenberg, A and Shefer, S and Ilan, M and Feldstein, T},
title = {Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida.},
journal = {BMC evolutionary biology},
volume = {15},
number = {},
pages = {278},
pmid = {26653218},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; *Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/*classification/*genetics ; RNA Splicing ; },
abstract = {BACKGROUND: Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges.<br><br>RESULTS: We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinella (p) verrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals' mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns.<br><br>CONCLUSIONS: The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.},
}
@article {pmid26678550,
year = {2016},
author = {Huang, R and Zhou, Y and Yao, Y and Zhao, B and Zhang, Y and Xu, HL},
title = {Complete mitochondrial genome and phylogenetic relationship analysis of Garrulax affinis (Passeriformes, Timaliidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3502-3503},
doi = {10.3109/19401736.2015.1066368},
pmid = {26678550},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Garrulax affinis was a medium-sized bird of Timaliidae, and we got its complete mitochondrial genome by the polymerase chain reaction method (PCR). The genome (17 856 in length), it contained 13 protein-coding genes, 2 rRNA (12S and 16S) genes, 2 tRNA genes, 2 control regions (D-loop). All protein-coding, rRNA, and tRNA genes were similar to other Passeriformes in gene arrangement and composition. In 13 PCGs, 12 were initiated with ATG, only COI was GTG, and stopped by five types of stop codons. We constructed a phylogenetic tree based on 13 PCGs of G. affinis and other nine Timaliidae species, found that the species belong to the same Passeriformes all cluster together.},
}
@article {pmid26681479,
year = {2017},
author = {Chen, X and Chen, Y and Yu, M and Sha, Z and Shan, X},
title = {The complete mitochondrial genome of the Azuma emmnion.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {1},
pages = {77-78},
doi = {10.3109/19401736.2015.1110806},
pmid = {26681479},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Genomics ; Perciformes/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genome of the Azuma emmnion has been determined. The total length of a complete nucleotide sequence of the mitochondria is 16 522 bp, which contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and one D-loop region. Its nucleotide sequence and composition of A. emmnion mitochondrion was similar to most other vertebrates. Nucleotide base composition of mitochondrial genome was the following: 25.58% for A, 18.22% for G, 27.67% for C, 28.53% for T. The phylogenetic analysis result, which based on the complete mitogenomes of of A. emmnion and other 11 fish species, indicated that A. emmnion and Pholis crassispina clustered into one branch.},
}
@article {pmid26703096,
year = {2016},
author = {Konovalova, O and Logacheva, M},
title = {Mitochondrial genome of two marine fungal species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4280-4281},
doi = {10.3109/19401736.2015.1082094},
pmid = {26703096},
issn = {2470-1408},
mesh = {Acremonium/*genetics ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome ; Genome, Fungal/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Here is a first record for a mitochondrial genome of marine fungus Acremonium fuci and closely related species Emericellopsis sp. One strain for each species, differentiated by morphological features was studied. Complete mitochondrial sequences are 24 565 and 24 951 bp in length. The circular molecule encodes all genes typical for fungal mitochondrial genomes: 15 protein-coding genes, 28 tRNAs, and large and small subunits of RNA. All structural genes are located on one strand and transcribed in one direction. Mitogenomes of species have 99% identity in protein-coding genes, but differ in some structural features: one of them has additional ORF with a similarity to cox1 gene, and another one has an intron in nad5 gene.},
}
@article {pmid26708415,
year = {2016},
author = {Lütz-Meindl, U and Luckner, M and Andosch, A and Wanner, G},
title = {Structural stress responses and degradation of dictyosomes in algae analysed by TEM and FIB-SEM tomography.},
journal = {Journal of microscopy},
volume = {263},
number = {2},
pages = {129-141},
doi = {10.1111/jmi.12369},
pmid = {26708415},
issn = {1365-2818},
mesh = {Endoplasmic Reticulum/metabolism ; Golgi Apparatus/*metabolism ; Imaging, Three-Dimensional ; Micrasterias/*cytology/metabolism/*ultrastructure ; Microscopy, Electron ; Phylogeny ; Tomography, X-Ray Computed ; },
abstract = {Stress-induced physiological deficiencies in cells are reflected in structural, morphological and functional reactions of organelles. Although numerous investigations have focused on chloroplasts and mitochondria as main targets of different stressors in plant cells, there is insufficient information on the plant Golgi apparatus as stress sensor. By using the advantages of field emission scanning electron microscopy tomography in combination with classical ultrathin sectioning and transmission electron microscopic analyses, we provide structural evidence for common stress responses of the large and highly stable dictyosomes in the algal model system Micrasterias. Stress is induced by different metals such as manganese and lead, by starvation in 9 weeks of darkness or by inhibiting photosynthesis or glycolysis and by disturbing ionic homeostasis via KCl. For the first time a stress-induced degradation pathway of dictyosomes is described that does not follow "classical" autophagy but occurs by disintegration of cisternae into single membrane balls that seem to be finally absorbed by the endoplasmic reticulum (ER). Comparison of the morphological features that accompany dictyosomal degradation in Micrasterias to similar reactions observed during the same stress application in Nitella indicates an ubiquitous degradation process at least in algae. As the algae investigated belong to the closest relatives of higher land plants these results may also be relevant for understanding dictyosomal stress and degradation responses in the latter phylogenetic group. In addition, this study shows that two-dimensional transmission electron microscopy is insufficient for elucidating complex processes such as organelle degradation, and that information from three-dimensional reconstructions as provided by field emission scanning electron microscopy tomography is absolutely required for a comprehensive understanding of the phenomenon.},
}
@article {pmid26709737,
year = {2017},
author = {Guo, C and Zhang, Q and Huang, Y},
title = {The complete mitochondrial genome of the Oedaleus infernalis sauss (Orthoptera: Oedipodidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {1},
pages = {89-90},
doi = {10.3109/19401736.2015.1110812},
pmid = {26709737},
issn = {2470-1408},
mesh = {Animals ; Base Sequence ; China ; Codon ; DNA, Mitochondrial ; Gene Order ; *Genes, Mitochondrial ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Genomics ; Grasshoppers/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The Oedaleus infernalis sauss (Orthoptera: Oedipodidae) is one of the main pests at the rice production area in China, and they mainly feed on leaves and grain of rice. The mitogenome was 15 898 bp long and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Most protein-coding genes started with a traditional ATN codon, and terminated with the mitochondria stop codon (TAA/TAG) or a single T-- base. The average A + T content of the O. infernalis sauss mitochondrial genome protein-coding sequence, rRNA, tRNA gene, and A + T-rich region was corresponding well to the A + T bias generally observed in insect mitochondrial genomes. Using the 12 protein-coding genes of O. infernalis sauss in this study, together with 15 other closely species, a preliminary phylogenetic analysis has been carried out.},
}
@article {pmid26710601,
year = {2015},
author = {Zhang, Y and Guo, L and Zhang, S and Liu, X},
title = {[Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris].},
journal = {Wei sheng wu xue bao = Acta microbiologica Sinica},
volume = {55},
number = {7},
pages = {826-833},
pmid = {26710601},
issn = {0001-6209},
mesh = {Biomarkers/analysis ; Cordyceps/classification/*genetics/isolation &amp; purification ; Fungal Proteins/genetics ; *Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {OBJECTIVE: To screen efficient molecular markers suitable for genetic diversity analysis of Cordyceps militaris from mitochondrial DNA.<br><br>METHODS: We amplified 12 mitochondrial DNA fragments and 3 nuclear DNA fragments from each of 20 C. militaris isolates and analyzed nucleotide variations on these DNA fragments.<br><br>RESULTS: We revealed a greatly higher genetic variation in mitochondrial DNA fragments than in nuclear DNA fragments. Specifically, C. militaris isolates exhibited intron presence/absence diversity in some mitochondrial fragments, and more variable sites were found in mitochondrial fragments than in nuclear fragments. The extent of nucleotide variations also varied by mitochondrial fragment, and intronic proteins seemed to be more vulnerable to amino acid changes than exonic proteins. Genetic diversity increased with the number of molecular markers used.<br><br>CONCLUSION: We recommended using (in order) nad3-cox2. cox2-nad5, cox2, cox3, cob, and cox1 for future genetic diversity and population genetic studies of C. militaris.},
}
@article {pmid26710828,
year = {2017},
author = {Liu, Y and Jiang, L},
title = {The complete mitochondrial genome sequence of the Himalayan goral, Naemorhedus goral (Cetartiodactyla: Caprinae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {2},
pages = {233-235},
doi = {10.3109/19401736.2015.1115856},
pmid = {26710828},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Ruminants/*genetics ; },
abstract = {The Himalayan goral (Naemorhedus goral) belongs to the subfamily Caprinae, which is distributed across the Himalayas including Bhutan, northern India including Sikkim and Arunachal Pradesh, Nepal, southern Tibet, and possibly western Myanmar. In this study, the complete mitochondrial genome of N. goral was sequenced. The mitogenome was 16 533 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the N. goral is 33.7% A, 27.2% T, 26.0% C, and 13.1% G. Phylogenetic analysis based on the mitogenome sequences using the Bayesian inferences method showed that Naemorhedus and Capricornis formed a monophyletic group and the N. goral was closely related to N. griseus. We expect that the present results will facilitate further investigation of the phylogenetic relationships and population genetics of genus Naemorhedus.},
}
@article {pmid26710999,
year = {2017},
author = {Jiang, L and Zhao, L and Liu, Y and Leng, Z and Zhao, L and Ruan, Q},
title = {The complete mitochondrial genome sequence of the Dark-spotted frog Pelophylax nigromaculatus (Amphibia, Anura, Ranidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {2},
pages = {236-237},
doi = {10.3109/19401736.2015.1115857},
pmid = {26710999},
issn = {2470-1408},
mesh = {Amphibian Proteins/genetics ; Animals ; China ; DNA, Mitochondrial/genetics ; Asia, Eastern ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Ranidae/*genetics ; Russia ; },
abstract = {The dark-spotted frog (Pelophylax nigromaculatus) belongs to Ranidae. This species is known from the Russian Far East, central, northern and north-eastern China, the Democratic People's Republic of Korea, the Republic of Korea, and Japan. In this study, the complete mitochondrial genome of P. nigromaculatus was sequenced. The mitogenome was 17 567 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the P. nigromaculatus is 29.2% A, 27.4% T, 28.4% C, and 15.0% G. Phylogenetic analysis showed P. nigromaculatus was closely related to P. plancyi and P. chosenicus. The complete mitogenome of P. nigromaculatus can provide important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.},
}
@article {pmid26713709,
year = {2017},
author = {Wang, P and Chen, S and Ou, Y and Wen, J and Li, J},
title = {Complete mitochondrial genome of Toxabramis houdemeri (Cypriniformes; Cyprinidae) and its phylogenetic analysis.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {2},
pages = {292-293},
doi = {10.3109/19401736.2015.1118085},
pmid = {26713709},
issn = {2470-1408},
mesh = {Animals ; Cyprinidae/*genetics ; Fish Proteins/genetics ; Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Toxabramis houdemeri belongs to the genus Toxabramis in the subfamily of Cultrinae (Cyprinidae). We first determine the complete mitochondrial genome of T. houdemeri in this study. It is 16 618 bp in length, with the base composition on the heavy strand: 30.79% A, 16.61% G, 27.29% C, and 25.31% T. It has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a D-loop region. Phylogenetic analysis showed that T. houdemeri was clustered into one branch of the subfamily of Cultrinae, and closely related to Hemiculter leucisculus. The present study will contribute to genetic resources conservation of T. houdemeri and studying its population genetic structure and phylogenetic relationships.},
}
@article {pmid26713710,
year = {2017},
author = {Urantowka, AD and Mackiewicz, P},
title = {Complete mitochondrial genome of Blue-winged Macaw (Primolius maracana).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {2},
pages = {275-276},
doi = {10.3109/19401736.2015.1118077},
pmid = {26713710},
issn = {2470-1408},
mesh = {Animals ; Body Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Parrots/anatomy &amp; histology/*genetics ; *Phylogeny ; },
abstract = {abtract The presence of bare facial area distinguishes Macaws from other members of the Arini tribe. Genera and species of the Macaw group differ in pattern of this bare skin as well as in body size. Individuals of the genera: Diopsittaca, Orthopsittaca, and Primolius are significantly smaller than the members of the genera: Anodorhynchus, Cyanopsitta, and the most species of the genus Ara. The genus Primolius contains three species: P. auricollis, P. couloni, and P. maracana, which are classified as medium-sized Macaws. So far, mitochondrial genome representative for the genus was sequenced only for Primolius couloni species. Primolius maracana mitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships between Primolius species, as results of molecular researches seems to be inconsistent with Primolius species morphology.},
}
@article {pmid26713722,
year = {2017},
author = {Jebb, D and Foley, NM and Puechmaille, SJ and Teeling, EC},
title = {The complete mitochondrial genome of the Greater Mouse-Eared bat, Myotis myotis (Chiroptera: Vespertilionidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {3},
pages = {347-349},
doi = {10.3109/19401736.2015.1122775},
pmid = {26713722},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Base Sequence ; Chiroptera/*genetics ; DNA, Mitochondrial ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In this study, we report the complete mitochondrial genome of the Greater Mouse-Eared Bat, Myotis myotis. The mitogenome is 17 213 bp with base composition A (34.2%), G (13%), C (22.4%), and T (30.5%). The genome shows conserved synteny with other mammalian mitogenomes, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (D-Loop). The majority of the genes are encoded on the H-Strand, except for ND6 and eight tRNAs. All protein-coding genes start with the ATG start codon, except for ND2, ND3, and ND5 which begin with ATT or ATA. Seven protein-coding genes terminated in a canonical stop codon, TAA or TAG, five contain incomplete stop codons, T or TA. Cytochrome b terminates in the mitochondria specific stop codon AGA. This mitogenome provides a valuable resource for future studies of M. myotis and other bat and mammal species.},
}
@article {pmid26720602,
year = {2015},
author = {Ye, YY and Wu, CW and Li, JJ},
title = {Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage.},
journal = {PloS one},
volume = {10},
number = {12},
pages = {e0146260},
pmid = {26720602},
issn = {1932-6203},
mesh = {Animals ; Bivalvia/*genetics ; China ; DNA, Mitochondrial/genetics ; Demography/methods ; Fisheries ; Genetic Drift ; Genetic Markers/*genetics/*immunology/*physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Geography/methods ; Haplotypes/genetics ; Larva/*genetics ; Mitochondria/*genetics ; Mollusca/*genetics ; Plankton/*genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant FST values were obtained among the different localities on the basis of either COI (FST = 0.100-0.444, p < 0.05) or 12S rRNA (FST = 0.199-0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. FST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation.},
}
@article {pmid26752183,
year = {2016},
author = {Mallela, SK and Almeida, R and Ejsing, CS and Conzelmann, A},
title = {Functions of Ceramide Synthase Paralogs YPR114w and YJR116w of Saccharomyces cerevisiae.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0145831},
pmid = {26752183},
issn = {1932-6203},
mesh = {Acetylcysteine/pharmacology ; Alkaline Ceramidase/genetics/metabolism ; Amidohydrolases/genetics/metabolism ; Antifungal Agents/pharmacology ; Antioxidants/pharmacology ; Cations, Divalent ; Ceramides/*biosynthesis ; Copper/toxicity ; Fatty Acids, Monounsaturated/pharmacology ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Membrane Proteins/genetics/metabolism ; Mitochondria/metabolism ; Oxidoreductases/genetics/metabolism ; Oxygen/pharmacology ; Phylogeny ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/classification/drug effects/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Vacuoles/metabolism ; },
abstract = {Ceramide is synthesized in yeast by two redundant acyl-CoA dependent synthases, Lag1 and Lac1. In lag1∆ lac1∆ cells, free fatty acids and sphingoid bases are elevated, and ceramides are produced through the redundant alkaline ceramidases Ypc1 and Ydc1, working backwards. Even with all four of these genes deleted, cells are surviving and continue to contain small amounts of complex sphingolipids. Here we show that these residual sphingolipids are not synthesized by YPR114w or YJR116w, proteins of unknown function showing a high degree of homology to Lag1 and Lac1. Indeed, the hextuple lag1∆ lac1∆ ypc1∆ ydc1∆ ypr114w∆ yjr116w∆ mutant still contains ceramides and complex sphingolipids. Yjr116w∆ exhibit an oxygen-dependent hypersensitivity to Cu2+ due to an increased mitochondrial production of reactive oxygen species (ROS) and a mitochondrially orchestrated programmed cell death in presence of copper, but also a general copper hypersensitivity that cannot be counteracted by the antioxidant N-acetyl-cysteine (NAC). Myriocin efficiently represses the synthesis of sphingoid bases of ypr114w∆, but not its growth. Both yjr116w∆ and ypr114w∆ have fragmented vacuoles and produce less ROS than wild type, before and after diauxic shift. Ypr114w∆/ypr114w∆ have an increased chronological life span. Thus, Yjr116w and Ypr114w are related, but not functionally redundant.},
}
@article {pmid26776396,
year = {2016},
author = {Patra, AK and Kwon, YM and Kang, SG and Fujiwara, Y and Kim, SJ},
title = {The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.},
journal = {Marine genomics},
volume = {26},
number = {},
pages = {63-71},
doi = {10.1016/j.margen.2015.12.010},
pmid = {26776396},
issn = {1876-7478},
mesh = {Animals ; Base Sequence ; Codon ; DNA/genetics ; Gene Expression Regulation/*physiology ; Genome, Mitochondrial/*genetics ; Phylogeny ; Polychaeta/classification/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.},
}
@article {pmid26782414,
year = {2015},
author = {Yin, SL and Lan, C and Pei, H and Zhu, ZQ},
title = {Mitochondrial transfer RNA mutations and hypertension.},
journal = {Genetics and molecular research : GMR},
volume = {14},
number = {4},
pages = {17692-17698},
doi = {10.4238/2015.December.21.42},
pmid = {26782414},
issn = {1676-5680},
mesh = {DNA, Mitochondrial/*genetics ; Humans ; Hypertension/*genetics/pathology ; Mitochondria/genetics ; Mutation ; *Phylogeny ; Polymorphism, Genetic ; RNA, Transfer/*genetics ; },
abstract = {Mutations in mitochondrial DNA have been found to be associated with hypertension. Of these, mitochondrial transfer RNA (mt-tRNA) is a hot spot for these pathogenic mutations. It is generally believed that these mutations may result in the failure of mt-tRNA metabolism, thereby worsening mitochondrial dysfunction and resulting in hypertension. mt-tRNA is known for its high frequency of polymorphisms and mutations, and the number of reports regarding mt-tRNA mutations and hypertension is increasing significantly. To better understand the molecular basis of maternally inherited hypertension, we reassessed the link between four mt-tRNA mutations (G15927A in tRNA(Thr), C7492T in tRNA(Ser(UCN)), A4386G in tRNA(Gln), and C14686T in tRNA(Glu)) and hypertension. We first used the phylogenetic approach to investigate the deleterious roles of these mutations, then we used RNA Fold Web Server to predict the minimum free energy of these mt-tRNAs with and without mutations. Using the pathogenicity scoring system, we found that the G15927A and C7492T mutations are classified as pathogenic while all other studied mutations are neutral polymorphisms. Our study provides valuable information for the detection of pathogenic mt-tRNA mutations in hypertension.},
}
@article {pmid26787157,
year = {2016},
author = {Teves, SC and Gardim, S and Carbajal de la Fuente, AL and Lopes, CM and Gonçalves, TC and dos Santos Mallet, JR and da Rosa, JA and Almeida, CE},
title = {Mitochondrial Genes Reveal Triatoma jatai as a Sister Species to Triatoma costalimai (Reduviidae: Triatominae).},
journal = {The American journal of tropical medicine and hygiene},
volume = {94},
number = {3},
pages = {686-688},
pmid = {26787157},
issn = {1476-1645},
mesh = {Animals ; Bayes Theorem ; Genetic Speciation ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Triatoma/*genetics ; },
abstract = {Triatoma jatai was described using a set of morphological structures from specimens collected in Paranã municipality of Tocantins State, Brazil. Under a Bayesian framework and using two mitochondrial genes (16S and COI), phylogenetic analysis recovered T. jatai as a sister species to Triatoma costalimai with higher genetic distances than between other well-recognized species. Our results agree with previous suggestions based on morphometric analysis. In the light of the non-monophyly of Matogrossensis subcomplex, the inclusion of T. jatai shall be considered for reevaluating this group.},
}
@article {pmid26794804,
year = {2016},
author = {Nývltová, E and Smutná, T and Tachezy, J and Hrdý, I},
title = {OsmC and incomplete glycine decarboxylase complex mediate reductive detoxification of peroxides in hydrogenosomes of Trichomonas vaginalis.},
journal = {Molecular and biochemical parasitology},
volume = {206},
number = {1-2},
pages = {29-38},
doi = {10.1016/j.molbiopara.2016.01.006},
pmid = {26794804},
issn = {1872-9428},
mesh = {Amino Acid Sequence ; Axenic Culture ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; Glycine Decarboxylase Complex/genetics/*metabolism ; Hydrogen Peroxide/*metabolism ; Kinetics ; Metabolic Detoxication, Phase I/genetics ; Mitochondria/*metabolism/ultrastructure ; Oxidation-Reduction ; Peroxidases/genetics/*metabolism ; Phylogeny ; Protein Binding ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/genetics/*metabolism/ultrastructure ; },
abstract = {Osmotically inducible protein (OsmC) and organic hydroperoxide resistance protein (Ohr) are small, thiol-dependent peroxidases that comprise a family of prokaryotic protective proteins central to the defense against deleterious effects of organic hydroperoxides, which are reactive molecules that are formed during interactions between the host immune system and pathogens. Trichomonas vaginalis, a sexually transmitted parasite of humans, possesses OsmC homologues in its hydrogenosomes, anaerobic mitochondrial organelles that harbor enzymes and pathways that are sensitive to oxidative damage. The glycine decarboxylase complex (GDC), which consists of four proteins (i.e., L, H, P and T), is in eukaryotes exclusively mitochondrial enzymatic system that catalyzes oxidative decarboxylation and deamination of glycine. However, trichomonad hydrogenosomes contain only the L and H proteins, whose physiological functions are unknown. Here, we found that the hydrogenosomal L and H proteins constitute a lipoate-dependent redox system that delivers electrons from reduced nicotinamide adenine dinucleotide (NADH) to OsmC for the reductive detoxification of peroxides. Our searches of genome databases revealed that, in addition to prokaryotes, homologues of OsmC/Ohr family proteins with predicted mitochondrial localization are present in various eukaryotic lineages. Therefore, we propose that the novel OsmC-GDC-based redox system may not be limited to T. vaginalis.},
}
@article {pmid26800039,
year = {2016},
author = {Kersten, B and Faivre Rampant, P and Mader, M and Le Paslier, MC and Bounon, R and Berard, A and Vettori, C and Schroeder, H and Leplé, JC and Fladung, M},
title = {Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.},
journal = {PloS one},
volume = {11},
number = {1},
pages = {e0147209},
pmid = {26800039},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Phylogeny ; *Plant Breeding ; Populus/classification/*genetics ; },
abstract = {Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.},
}
@article {pmid26809915,
year = {2015},
author = {Esmaelizad, M and Zeinedin, H and Razmaraii, N and Mirjalili, A},
title = {Molecular Study of the G1 Haplotypes of Echinococcus granulosus from Iran Based on Cytochrome C Oxidase (Subunit 1) Sequence.},
journal = {Turkiye parazitolojii dergisi},
volume = {39},
number = {4},
pages = {286-290},
doi = {10.5152/tpd.2015.4292},
pmid = {26809915},
issn = {2146-3077},
mesh = {Animals ; Base Sequence ; Cytochromes c1/chemistry/*genetics ; DNA, Helminth/chemistry/isolation &amp; purification ; Echinococcosis, Hepatic/parasitology/*veterinary ; Echinococcus granulosus/*classification/genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Genotype ; Genotyping Techniques ; Goat Diseases/*parasitology ; Goats ; Haplotypes ; Iran ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Alignment ; Sheep ; Sheep Diseases/*parasitology ; },
abstract = {OBJECTIVE: In this study, we attempted to identify new Echinococcus granulosus isolates in the North West provinces of Iran based on the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequence.<br><br>METHODS: Twenty-nine hydatid cysts from sheep and goats were collected. Genomic DNAs were extracted, and a partial sequence of the CO1 gene was amplified. Polymerase chain reaction products were cloned and sequenced with M13 primers in both directions.<br><br>RESULTS: All Iranian isolates were located in G1 and G3 genotypes. For the first time, a new G1 haplotype in two Iranian isolates were identified.<br><br>CONCLUSION: It seems that this new haplotype was transmitted from Jordan to Iran or vice versa.},
}
@article {pmid26810560,
year = {2016},
author = {Ma, L and Dong, WW and Jiang, GF and Wang, X},
title = {The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis.},
journal = {Journal of insect science (Online)},
volume = {16},
number = {1},
pages = {},
pmid = {26810560},
issn = {1536-2442},
mesh = {Animals ; Genome, Insect/*genetics ; Mitochondria/*genetics ; Moths/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; },
abstract = {The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.},
}
@article {pmid26840490,
year = {2016},
author = {Pittis, AA and Gabaldón, T},
title = {Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.},
journal = {Nature},
volume = {531},
number = {7592},
pages = {101-104},
pmid = {26840490},
issn = {1476-4687},
support = {310325/ERC_/European Research Council/International ; },
mesh = {Eukaryotic Cells/*cytology/metabolism ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/*genetics ; Genomics ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; *Phylogeny ; Prokaryotic Cells/*cytology/metabolism ; Symbiosis/*genetics ; },
abstract = {The origin of eukaryotes stands as a major conundrum in biology. Current evidence indicates that the last eukaryotic common ancestor already possessed many eukaryotic hallmarks, including a complex subcellular organization. In addition, the lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Mitochondria are ubiquitous organelles derived from an alphaproteobacterial endosymbiont. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Most competing scenarios can be roughly grouped into either mito-early, which consider the driving force of eukaryogenesis to be mitochondrial endosymbiosis into a simple host, or mito-late, which postulate that a significant complexity predated mitochondrial endosymbiosis. Here we provide evidence for late mitochondrial endosymbiosis. We use phylogenomics to directly test whether proto-mitochondrial proteins were acquired earlier or later than other proteins of the last eukaryotic common ancestor. We find that last eukaryotic common ancestor protein families of alphaproteobacterial ancestry and of mitochondrial localization show the shortest phylogenetic distances to their closest prokaryotic relatives, compared with proteins of different prokaryotic origin or cellular localization. Altogether, our results shed new light on a long-standing question and provide compelling support for the late acquisition of mitochondria into a host that already had a proteome of chimaeric phylogenetic origin. We argue that mitochondrial endosymbiosis was one of the ultimate steps in eukaryogenesis and that it provided the definitive selective advantage to mitochondria-bearing eukaryotes over less complex forms.},
}
@article {pmid26852331,
year = {2016},
author = {Buczek, D and Wojtkowska, M and Suzuki, Y and Sonobe, S and Nishigami, Y and Antoniewicz, M and Kmita, H and Makałowski, W},
title = {Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives.},
journal = {BMC genomics},
volume = {17},
number = {},
pages = {99},
pmid = {26852331},
issn = {1471-2164},
mesh = {Amino Acid Sequence ; Amoebozoa/classification/genetics/*metabolism ; Carrier Proteins/metabolism ; Conserved Sequence ; Exons ; Genetic Variation ; Genome, Protozoan ; Introns ; Mitochondrial Membranes/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Multiprotein Complexes/*metabolism ; Phylogeny ; Protein Subunits ; Protein Transport ; Protozoan Proteins/chemistry/*metabolism ; Transcriptome ; },
abstract = {BACKGROUND: An ancestral trait of eukaryotic cells is the presence of mitochondria as an essential element for function and survival. Proper functioning of mitochondria depends on the import of nearly all proteins that is performed by complexes located in both mitochondrial membranes. The complexes have been proposed to contain subunits formed by proteins common to all eukaryotes and additional subunits regarded as lineage specific. Since Amoebozoa is poorly sampled for the complexes we investigated the outer membrane complexes, namely TOM, TOB/SAM and ERMES complexes, using available genome and transcriptome sequences, including transcriptomes assembled by us.<br><br>RESULTS: The results indicate differences in the organization of the Amoebozoa TOM, TOB/SAM and ERMES complexes, with the TOM complex appearing to be the most diverse. This is reflected by differences in the number of involved subunits and in similarities to the cognate proteins of representatives from different supergroups of eukaryotes.<br><br>CONCLUSIONS: The obtained results clearly demonstrate structural variability/diversity of these complexes in the Amoebozoa lineage and the reduction of their complexity as compared with the same complexes of model organisms.},
}
@article {pmid26876639,
year = {2016},
author = {Kornilios, P and Thanou, E and Kapli, P and Parmakelis, A and Chatzaki, M},
title = {Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae.},
journal = {Molecular phylogenetics and evolution},
volume = {98},
number = {},
pages = {300-313},
doi = {10.1016/j.ympev.2016.01.021},
pmid = {26876639},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Climate ; DNA, Mitochondrial/*genetics ; Greece ; Mitochondria/genetics ; *Mutation Rate ; *Phylogeny ; Phylogeography ; Spiders/*genetics ; Turkey ; },
abstract = {The Aegean region, located in the Eastern Mediterranean, is an area of rich biodiversity and endemism. Its position, geographical configuration and complex geological history have shaped the diversification history of many animal taxa. Mygalomorph spiders have drawn the attention of researchers, as excellent model systems for phylogeographical investigations. However, phylogeographic studies of spiders in the Aegean region are scarce. In this study, we focused on the phylogeography of the endemic ctenizid trap-door spider Cyrtocarenum Ausserer, 1871. The genus includes two morphologically described species: C. grajum (C.L. Koch, 1836) and C. cunicularium (Olivier, 1811). We sampled 60 specimens from the distributions of both species and analyzed four mitochondrial and two nuclear markers. Cyrtocarenum served as an example to demonstrate the importance of natural history traits in the inference of phylogeographic scenarios. The mtDNA substitution rates inferred for the genus are profoundly higher compared to araneomorph spiders and other arthropods, which seems tightly associated with their biology. We evaluate published mtDNA substitution rates followed in the literature for mygalomorph spiders and discuss potential pitfalls. Following gene tree (maximum likelihood, Bayesian inference) and species tree approaches ((*)BEAST), we reconstructed a time-calibrated phylogeny of the genus. These results, combined with a biogeographical ancestral-area analysis, helped build a biogeographic scenario that describes how the major palaeogeographic and palaeoclimatic events of the Aegean may have affected the distribution of Cyrtocarenum lineages. The diversification of the genus seems to have begun in the Middle Miocene in the present west Aegean area, while major phylogenetic events occurred at the Miocene-Pliocene boundary for C. cunicularium, probably related to the Messinian Salinity Crisis. Our results also demonstrate the clear molecular distinction of the two morphologically described species, but possible cryptic lineages may exist within C. cunicularium.},
}
@article {pmid26887409,
year = {2016},
author = {Strassert, JF and Tikhonenkov, DV and Pombert, JF and Kolisko, M and Tai, V and Mylnikov, AP and Keeling, PJ},
title = {Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome.},
journal = {Open biology},
volume = {6},
number = {2},
pages = {150239},
pmid = {26887409},
issn = {2046-2441},
mesh = {Base Sequence ; DNA, Ribosomal/genetics ; *Desert Climate ; Eukaryota/*classification/*genetics/isolation &amp; purification/ultrastructure ; Flagella/ultrastructure ; Gene Order ; *Genome, Mitochondrial ; Nucleotide Motifs ; Phylogeny ; *Soil Microbiology ; },
abstract = {A new jakobid genus has been isolated from Moroccan desert soil. The cyst-forming protist Moramonas marocensis gen. nov., sp. nov. has two anteriorly inserted flagella of which one points to the posterior cell pole accompanying the ventral feeding groove and is equipped with a dorsal vane-a feature typical for the Jakobida. It further shows a flagellar root system consisting of singlet microtubular root, left root (R1), right root (R2) and typical fibres associated with R1 and R2. The affiliation of M. marocensis to the Jakobida was confirmed by molecular phylogenetic analyses of the SSU rRNA gene, five nuclear genes and 66 mitochondrial protein-coding genes. The mitochondrial genome has the high number of genes typical for jakobids, and bacterial features, such as the four-subunit RNA polymerase and Shine-Dalgarno sequences upstream of the coding regions of several genes. The M. marocensis mitochondrial genome encodes a similar number of genes as other jakobids, but is unique in its very large genome size (greater than 264 kbp), which is three to four times higher than that of any other jakobid species investigated yet. This increase seems to be due to a massive expansion in non-coding DNA, creating a bloated genome like those of plant mitochondria.},
}
@article {pmid26914395,
year = {2016},
author = {Kosuda, S and Sasakawa, K and Ikeda, H},
title = {Directional mitochondrial introgression and character displacement due to reproductive interference in two closely related Pterostichus ground beetle species.},
journal = {Journal of evolutionary biology},
volume = {29},
number = {6},
pages = {1121-1130},
doi = {10.1111/jeb.12852},
pmid = {26914395},
issn = {1420-9101},
mesh = {Animals ; *Coleoptera ; Female ; Hybridization, Genetic ; Male ; Mitochondria ; *Phylogeny ; *Reproduction ; Sympatry ; },
abstract = {Reproductive interference due to interspecific hybridization can lead to character displacement among related species with overlapping ranges. However, no studies have examined which reproductive traits are most important in reducing reproductive interference. We conducted molecular analyses of two nuclear genes (28S and Wingless) and a mitochondrial gene (COI) from two closely related ground beetle species, Pterostichus thunbergi and Pterostichus habui (Coleoptera: Carabidae), with overlapping distributions. In addition, we examined four reproductive traits (body size, organ morphologies of intromittent and non-intromittent male genital organs, and female reproductive period) in sympatric and allopatric habitats. We compared male genital morphology using geometric morphometric analysis. The species determined by morphology were classified into separate groups based on the phylogenetic tree constructed by the nuclear gene (Wingless). However, according to the mitochondrial genes examined, P. thunbergi was not monophyletic, whereas at the sympatric sites, these species formed a monophyletic clade. This incongruence suggests that interspecific hybridization and subsequent mitochondrial introgression from P. habui to P. thunbergi have occurred. Concerning genital morphology, both of the intromittent and nonintromittent organs of P. thunbergi differed more from P. habui at the sympatric sites than between allopatric sites, suggesting reproductive character displacement. Pterostichus thunbergi, which likely arrived in P. habui habitat in small numbers, would have experienced stronger selection pressures than P. habui.},
}
@article {pmid26926944,
year = {2016},
author = {Fiorentino, V and Manganelli, G and Giusti, F and Ketmaier, V},
title = {Recent expansion and relic survival: Phylogeography of the land snail genus Helix (Mollusca, Gastropoda) from south to north Europe.},
journal = {Molecular phylogenetics and evolution},
volume = {98},
number = {},
pages = {358-372},
doi = {10.1016/j.ympev.2016.02.017},
pmid = {26926944},
issn = {1095-9513},
mesh = {Animal Shells/anatomy &amp; histology ; Animals ; Cell Nucleus/genetics ; Italy ; Mediterranean Region ; Mitochondria/genetics ; Phenotype ; *Phylogeny ; Phylogeography ; Snails/anatomy &amp; histology/*classification/genetics ; },
abstract = {Little is known about the evolutionary history of Helix, despite the fact that it includes the largest land snails in the western Palaearctic, some of which (e.g. H. pomatia Linnaeus, 1758) are valuable human food. We compared two groups of Helix with apparently contrasting evolutionary histories: the widespread species H. pomatia and the group distributed along the Italian Apennine chain, a relatively unknown set of species with a restricted distribution over a range of altitudes. To reconstruct the evolutionary trajectories of these two groups, we analysed morphological (shell and genitalia) and molecular characters (mitochondrial and nuclear markers) in a total of 59 populations from northern and central Europe (H. pomatia) and along the Apennine chain (various species). We also reconstructed the phylogeny and the evolutionary history of the genus by combining our data with that currently available in the literature. We found that spatial changes did not merely imply fragmentation of populations, but also implied environmental changes (woodlands vs. grasslands) that may have triggered the observed phenotypic diversification. We also found that Anatolia is the ancestral range of Helix and is therefore an important area for the Palaearctic diversity. The results provide insights into the evolutionary history of species richness and more generally into the processes that may have shaped the distribution and diversification of these organisms across Europe and the peri-Mediterranean area.},
}
@article {pmid26930860,
year = {2016},
author = {Banta, G and Jindal, V and Mohindru, B and Sharma, S and Kaur, J and Gupta, VK},
title = {Molecular phylogenetic analysis of mango mealybug, Drosicha mangiferae from Punjab.},
journal = {Journal of environmental biology},
volume = {37},
number = {1},
pages = {49-55},
pmid = {26930860},
issn = {0254-8704},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Hemiptera/*genetics/physiology ; India ; Litchi ; Mangifera ; Mitochondria/enzymology ; Phylogeny ; Psidium ; },
abstract = {Mealybugs (Hemiptera: Pseudococcidae) are major pests of a wide range of crops and ornamental plants worldwide. Their high degree of morphological similarity makes them difficult to identify and limits their study and management. In the present study, four Indian populations of mango mealybug (mango, litchi, guava from Gurdaspur and mango from Jalandhar) were analyzed. The mtCOI region was amplified, cloned, the nucleotide sequences were determined and analysed. All the four species were found to be D. mangiferae. The population from Litchi and Mango from Gurdaspur showed 100% homologus sequence. The population of Guava-Gurdaspur and Mango-Jalandhar showed a single mutation of 'C' instead of 'T' at 18th and 196th position, respectively. Indian populations were compared with populations from Pakistan (21) and Japan (1). The phylogenetic tree resulted in two main clusters. Cluster1 represent all the 4 populations of Punjab, India, 20 of Pakistan (Punjab, Sind, Lahore, Multan, Faisalabad and Karak districts) with homologous sequences. The two population collected from Faisalabad district of Pakistan and Japan made a separate cluster 2 because the gene sequence used in analysis was from the COI-3p region. However, all the other sequence of D. mangiferae samples under study showed a low nucleotide divergence. The homologus mtCO1 sequence of Indian and Pakistan population concluded that the genetic diversity in mealybug population was quite less over a large geographical area.},
}
@article {pmid26946968,
year = {2016},
author = {Chetoui, I and Denis, F and Boussaid, M and Telahigue, K and El Cafsi, M},
title = {Genetic diversity and phylogenetic analysis of two Tunisian bivalves (Mactridae) Mactra corallina (Linnaeus, 1758) and Eastonia rugosa (Helbling, 1799) based on COI gene sequences.},
journal = {Comptes rendus biologies},
volume = {339},
number = {3-4},
pages = {115-122},
doi = {10.1016/j.crvi.2016.02.001},
pmid = {26946968},
issn = {1768-3238},
mesh = {Animals ; Bivalvia/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tunisia ; },
abstract = {A partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) was used as a genetic marker for a genetic diversity and phylogenetic analysis (DNA barcoding) of two Mactridae species, Mactra corallina and Eastonia rugosa, collected from the Tunisian coast. These Mactridae species could be distinguished by DNA barcoding techniques and they will be considered as monophyletic clades with the Neighbor-Joining (NJ) tree. The genetic structure detected that E. rugosa presents three haplotypes with a high frequency of HER1 (0.89). However, M. corralina shared 14 haplotypes. The haplotypic diversity (H) was equal to 0.205 and 0.954, respectively, for E. rugosa and M. corallina. While the nucleotide diversity (π) was higher for M. corallina (π=0.0818), the mismatch distribution showed a unimodal curve for E. rugosa (a recent sudden demographic expansion) and a multimodal distribution for M. corallina (size stability).},
}
@article {pmid26953603,
year = {2016},
author = {de Barsy, M and Frandi, A and Panis, G and Théraulaz, L and Pillonel, T and Greub, G and Viollier, PH},
title = {Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.},
journal = {The ISME journal},
volume = {10},
number = {9},
pages = {2129-2144},
pmid = {26953603},
issn = {1751-7370},
mesh = {Animals ; Bacterial Proteins/genetics ; Chlamydiales/*genetics ; Chlorocebus aethiops ; Chromatin Immunoprecipitation ; Genome, Bacterial/*genetics ; Genomics ; Phylogeny ; Reproducibility of Results ; Transcription Factors/*genetics ; Vero Cells ; Verrucomicrobia/*genetics ; },
abstract = {Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.},
}
@article {pmid26956060,
year = {2016},
author = {Lavikainen, A and Iwaki, T and Haukisalmi, V and Konyaev, SV and Casiraghi, M and Dokuchaev, NE and Galimberti, A and Halajian, A and Henttonen, H and Ichikawa-Seki, M and Itagaki, T and Krivopalov, AV and Meri, S and Morand, S and Näreaho, A and Olsson, GE and Ribas, A and Terefe, Y and Nakao, M},
title = {Reappraisal of Hydatigera taeniaeformis (Batsch, 1786) (Cestoda: Taeniidae) sensu lato with description of Hydatigera kamiyai n. sp.},
journal = {International journal for parasitology},
volume = {46},
number = {5-6},
pages = {361-374},
doi = {10.1016/j.ijpara.2016.01.009},
pmid = {26956060},
issn = {1879-0135},
mesh = {Africa ; Animals ; Arvicolinae ; Asia ; Australia ; Bayes Theorem ; Cat Diseases/*parasitology ; Cats ; Cestoda/anatomy &amp; histology/*classification/genetics ; Cestode Infections/parasitology/*veterinary ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/chemistry ; Electron Transport Complex IV/genetics ; Europe ; Felidae/*parasitology ; Mice ; Mitochondria/enzymology/genetics ; Murinae ; Phylogeny ; Phylogeography ; Rats ; Rodent Diseases/*parasitology ; },
abstract = {The common cat tapeworm Hydatigera taeniaeformis is a complex of three morphologically cryptic entities, which can be differentiated genetically. To clarify the biogeography and the host spectrum of the cryptic lineages, 150 specimens of H. taeniaeformis in various definitive and intermediate hosts from Eurasia, Africa and Australia were identified with DNA barcoding using partial mitochondrial cytochrome c oxidase subunit 1 gene sequences and compared with previously published data. Additional phylogenetic analyses of selected isolates were performed using nuclear DNA and mitochondrial genome sequences. Based on molecular data and morphological analysis, Hydatigera kamiyai n. sp. Iwaki is proposed for a cryptic lineage, which is predominantly northern Eurasian and uses mainly arvicoline rodents (voles) and mice of the genus Apodemus as intermediate hosts. Hydatigera taeniaeformis sensu stricto (s.s.) is restricted to murine rodents (rats and mice) as intermediate hosts. It probably originates from Asia but has spread worldwide. Despite remarkable genetic divergence between H. taeniaeformis s.s. and H. kamiyai, interspecific morphological differences are evident only in dimensions of rostellar hooks. The third cryptic lineage is closely related to H. kamiyai, but its taxonomic status remains unresolved due to limited morphological, molecular, biogeographical and ecological data. This Hydatigera sp. is confined to the Mediterranean and its intermediate hosts are unknown. Further studies are needed to classify Hydatigera sp. either as a distinct species or a variant of H. kamiyai. According to previously published limited data, all three entities occur in the Americas, probably due to human-mediated introductions.},
}
@article {pmid26968366,
year = {2016},
author = {Palmieri, F and Monné, M},
title = {Discoveries, metabolic roles and diseases of mitochondrial carriers: A review.},
journal = {Biochimica et biophysica acta},
volume = {1863},
number = {10},
pages = {2362-2378},
doi = {10.1016/j.bbamcr.2016.03.007},
pmid = {26968366},
issn = {0006-3002},
mesh = {Animals ; Arabidopsis Proteins/metabolism ; Biological Transport ; Gene Expression ; Humans ; Mitochondria/*metabolism ; Mitochondrial Diseases/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/deficiency/genetics/*physiology ; Mitochondrial Membranes/metabolism ; Phylogeny ; Protein Domains ; Recombinant Proteins/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; },
abstract = {Mitochondrial carriers (MCs) are a superfamily of nuclear-encoded proteins that are mostly localized in the inner mitochondrial membrane and transport numerous metabolites, nucleotides, cofactors and inorganic anions. Their unique sequence features, i.e., a tripartite structure, six transmembrane α-helices and a three-fold repeated signature motif, allow MCs to be easily recognized. This review describes how the functions of MCs from Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana (listed in the first table) were discovered after the genome sequence of S. cerevisiae was determined in 1996. In the genomic era, more than 50 previously unknown MCs from these organisms have been identified and characterized biochemically using a method consisting of gene expression, purification of the recombinant proteins, their reconstitution into liposomes and transport assays (EPRA). Information derived from studies with intact mitochondria, genetic and metabolic evidence, sequence similarity, phylogenetic analysis and complementation of knockout phenotypes have guided the choice of substrates that were tested in the transport assays. In addition, the diseases associated to defects of human MCs have been briefly reviewed. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.},
}
@article {pmid26982388,
year = {2016},
author = {Olayemi, A and Obadare, A and Oyeyiola, A and Igbokwe, J and Fasogbon, A and Igbahenah, F and Ortsega, D and Asogun, D and Umeh, P and Vakkai, I and Abejegah, C and Pahlman, M and Becker-Ziaja, B and Günther, S and Fichet-Calvet, E},
title = {Arenavirus Diversity and Phylogeography of Mastomys natalensis Rodents, Nigeria.},
journal = {Emerging infectious diseases},
volume = {22},
number = {4},
pages = {694-697},
pmid = {26982388},
issn = {1080-6059},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Disease Reservoirs ; Genetic Variation ; Host-Pathogen Interactions ; Humans ; Lassa Fever/epidemiology/transmission/*veterinary/virology ; Lassa virus/*classification/genetics/isolation &amp; purification ; Mitochondria/chemistry/genetics ; Murinae/classification/genetics/*virology ; Nigeria/epidemiology ; *Phylogeny ; Phylogeography ; RNA, Viral/*genetics ; Rodent Diseases/epidemiology/virology ; Zoonoses ; },
abstract = {Mastomys natalensis rodents are natural hosts for Lassa virus (LASV). Detection of LASV in 2 mitochondrial phylogroups of the rodent near the Niger and Benue Rivers in Nigeria underlines the potential for LASV emergence in fresh phylogroups of this rodent. A Mobala-like sequence was also detected in eastern Nigeria.},
}
@article {pmid26988412,
year = {2016},
author = {Maldonado-Sánchez, D and Gutiérrez-Rodríguez, C and Ornelas, JF},
title = {Genetic divergence in the common bush-tanager Chlorospingus ophthalmicus (Aves: Emberizidae) throughout Mexican cloud forests: The role of geography, ecology and Pleistocene climatic fluctuations.},
journal = {Molecular phylogenetics and evolution},
volume = {99},
number = {},
pages = {76-88},
doi = {10.1016/j.ympev.2016.03.014},
pmid = {26988412},
issn = {1095-9513},
mesh = {Animal Migration ; Animals ; Bayes Theorem ; *Climate ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Forests ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mexico ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Passeriformes/*genetics ; Phylogeny ; *Phylogeography ; Time Factors ; },
abstract = {By integrating mitochondrial DNA (mtDNA), microsatellites and ecological niche modelling (ENM), we investigated the phylogeography of Mexican populations of the common bush-tanager Chlorospingus ophthalmicus to examine the relative role of geographical and ecological features, as well as Pleistocene climatic oscillations in driving the diversification. We sequenced mtDNA of individuals collected throughout the species range in Mexico and genotyped them at seven microsatellite loci. Phylogeographic, population genetics and coalescent methods were used to assess patterns of genetic structure, gene flow and demographic history. ENM was used to infer contractions and expansions at different time periods as well as differences in climatic conditions among lineages. The retrieved mitochondrial and microsatellite groups correspond with the fragmented cloud forest distribution in mountain ranges and morphotectonic provinces. Differing climatic conditions between mountain ranges were detected, and palaeodistribution modelling as well as demographic history analyses, indicated recent population expansions throughout the Sierra Madre Oriental (SMO). The marked genetic structure of C. ophthalmicus was promoted by the presence of ecological and geographical barriers that restricted the movement of individuals among mountain ranges. The SMO was mainly affected by Pleistocene climatic oscillations, with the moist forests model best fitting the displayed genetic patterns of populations in this mountain range.},
}
@article {pmid27021180,
year = {2016},
author = {Yang, X and Wang, L and Chen, H and Feng, H and Shen, B and Hu, M and Fang, R},
title = {The complete mitochondrial genome of Gastrothylax crumenifer (Gastrothylacidae, Trematoda) and comparative analyses with selected trematodes.},
journal = {Parasitology research},
volume = {115},
number = {6},
pages = {2489-2497},
pmid = {27021180},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Cattle/parasitology ; Cattle Diseases/parasitology ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Paramphistomatidae/*classification/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {In the present study, we sequenced and analyzed the mitochondrial (mt) genome of Gastrothylax crumenifer and compared it with other selected trematodes. The full mt genome of G. crumenifer was amplified, sequenced, assembled, analyzed and then subjected to phylogenetic analysis. The complete mt genome of G. crumenifer is 14,801 bp in length and contains two rRNA genes, two non-coding regions (LNR and SNR), 12 protein-coding genes, and 22 transfer RNA genes. The gene organization of the G. crumenifer mt genome is the same as that of other trematodes, except for Schistosoma haematobium and Schistosoma spindale. All the genes are transcribed in the same direction and rich in "A + T", which is in accordance with other trematodes, such as Fasciola hepatica, Paramphistomum cervi, and Fischoederius elongatus. Phylogenetic analysis using concatenated amino acid sequences of the 12 protein-coding genes showed that G. crumenifer is closely related to F. elongatus. The availability of mt genome sequence of G. crumenifer can provide useful DNA markers for studying the molecular epidemiology and population genetics of this parasite and other paramphistomes.},
}
@article {pmid27032679,
year = {2016},
author = {Sugita, N and Kawakami, K and Nishiumi, I},
title = {Origin of Japanese White-Eyes and Brown-Eared Bulbuls on the Volcano Islands.},
journal = {Zoological science},
volume = {33},
number = {2},
pages = {146-153},
doi = {10.2108/zs150146},
pmid = {27032679},
issn = {0289-0003},
mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; Genetic Variation ; Haplotypes ; Islands ; Japan ; Passeriformes/*genetics/physiology ; Phylogeny ; },
abstract = {The Ogasawara Archipelago comprises two groups of oceanic islands: the Bonin Islands, formed in the Paleogene, and the Volcano Islands, formed in the Quaternary. These groups are located within a moderate distance (ca. 160-270 km) of one another; thus, most land bird species are not distinguished as different subspecies. Two land birds, however, show unusual distribution. The Japanese white-eyes Zosterops japonicus originally inhabited only the Volcano Islands, but has been introduced to the Bonin Islands. The brown-eared bulbuls Hypsipetes amaurotis are distributed as a different subspecies. We investigated their genetic differences and divergences in the Ogasawara Archipelago using mitochondria DNA. The Volcano population of white-eyes had four endemic haplotypes that were divergent from one another, except for the Bonin population, which shared three haplotypes with the Volcano, Izu, and Ryukyu Islands and did not have any endemic haplotype. This is the first genetic suggestion that the Bonin population is a hybrid of introduced populations. With respect to bulbuls, the Volcano and Bonin Islands each had a single endemic haplotype. The Volcano haplotype is closest to a haplotype shared with Izu, the Japanese mainland, Daito and Ryukyu, whereas the Bonin haplotype is closest to one endemic to the south Ryukyu Islands. This indicates that the sources of the two bulbul populations can be geologically and temporally distinguished. The populations of the two species in the Ogasawara Archipelago are irreplaceable, owing to their genetic differences and should be regarded as evolutionarily significant units. In order to prevent introgression between the two populations, we must restrict interisland transfers.},
}
@article {pmid27037593,
year = {2016},
author = {Nakada, T and Tomita, M and Wu, JT and Nozaki, H},
title = {Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.},
journal = {Journal of phycology},
volume = {52},
number = {2},
pages = {283-304},
doi = {10.1111/jpy.12397},
pmid = {27037593},
issn = {1529-8817},
mesh = {Base Sequence ; Bayes Theorem ; Chlamydomonas/*classification/cytology/genetics ; Microscopy, Fluorescence ; Mitochondria/metabolism ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400-600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy-in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria-and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup "Pleiochloris," was included in the genus Ixipapillifera as I. deasonii comb. nov.},
}
@article {pmid27050471,
year = {2016},
author = {Shenkar, N and Koplovitz, G and Dray, L and Gissi, C and Huchon, D},
title = {Back to solitude: Solving the phylogenetic position of the Diazonidae using molecular and developmental characters.},
journal = {Molecular phylogenetics and evolution},
volume = {100},
number = {},
pages = {51-56},
doi = {10.1016/j.ympev.2016.04.001},
pmid = {27050471},
issn = {1095-9513},
mesh = {Animals ; Genome, Mitochondrial ; Mitochondria/genetics ; *Phylogeny ; Regeneration/genetics ; Urochordata/*classification/embryology/*genetics ; },
abstract = {The order Aplousobranchia (Chordata, Ascidiacea) contains approximately 1500 species distributed worldwide. Their phylogeny, however, remains unclear, with unresolved family relationships. While most Aplousobranchia are colonial, debates exist concerning the phylogenetic position of families such as the Diazonidae and Cionidae, which exhibit a solitary lifestyle and share morphological characteristics with both Aplousobranchia and Phlebobranchia orders. To clarify the phylogenetic position of the Diazonidae and Cionidae, we determined the complete mitochondrial sequence of the solitary diazonid Rhopalaea idoneta. The phylogenetic reconstruction based on the 13 mitochondrial protein coding genes strongly supports a positioning of Diazonidae well-nested within the Aplousobranchia rather than a positioning as a sister clade of the Aplousobranchia. In addition, we examined the regenerative ability of R. idoneta. Similar to colonial Aplousobranchia, R. idoneta was found to be able to completely regenerate its thorax. Ciona, also known to possess high regenerative abilities, is the Aplousobranchia sister clade rather than a member of the Phlebobranchia. Our results thus indicate that the colonial lifestyle was acquired in the Aplousobranchia, starting from a Ciona-like solitary ancestor and secondarily lost in Diazonidae representatives such as Rhopalaea. The solitary lifestyle of Rhopalaea is thus a derived characteristic rather than an ancestral trait.},
}
@article {pmid27058122,
year = {2016},
author = {Ji, Y and Sun, Y and Gao, W and Chu, K and Wang, R and Zhao, Q and Sun, H},
title = {Out of the Sichuan Basin: Rapid species diversification of the freshwater crabs in Sinopotamon (Decapoda: Brachyura: Potamidae) endemic to China.},
journal = {Molecular phylogenetics and evolution},
volume = {100},
number = {},
pages = {80-94},
doi = {10.1016/j.ympev.2016.04.003},
pmid = {27058122},
issn = {1095-9513},
mesh = {Animals ; Brachyura/*classification ; Cell Nucleus/genetics ; China ; *Fresh Water ; Genetic Variation ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Time Factors ; },
abstract = {Sinopotamon Bott, 1967 is the most speciose and widely distributed freshwater crab genus in East Asia. Our extensive sampling includes about 76% of the known Sinopotamon taxa, and nearly covers its entire distribution area. Based on mitochondrial cytochrome oxidase I (COI) and 16S rRNA, as well as nuclear 28S rRNA and histone H3, we reconstructed the Sinopotamon phylogeny using maximum likelihood and Bayesian approaches. The divergence time was estimated and multiple methods were used to conduct diversification analyses. The ancestral geographic distribution and character state were reconstructed. Three main clades (Clades I, II and III) that roughly correspond to their main geographic distribution ranges were recovered. Our results challenge the current view of the four major species groups based on the morphological differences in the male first gonopod (G1). The most recent common ancestor of Sinopotamon most likely originated from the Sichuan Basin and surrounding mountains (SBSM) and subsequently dispersed throughout central and eastern China. The exceptionally rapid, recent diversification was detected in Clade II. The high incidence of species-level non-monophyly found in Clade II can be explained by recent rapid radiation. Climatic changes, morphological innovations, range expansion and geographical heterogeneity may all contribute to the diversification in Sinopotamon. This study contributes to our knowledge on diversification of freshwater benthic macro-invertebrates in the East Asian inland ecosystem.},
}
@article {pmid27061962,
year = {2016},
author = {Shiratori, T and Ishida, KI},
title = {Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4).},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {6},
pages = {722-731},
doi = {10.1111/jeu.12319},
pmid = {27061962},
issn = {1550-7408},
mesh = {Amoeba/*classification/genetics/*isolation &amp; purification/ultrastructure ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*parasitology ; Microscopy, Electron, Transmission ; Phylogeny ; },
abstract = {A novel cercozoan filose thecate amoeba, Trachyrhizium urniformis n. g., n. sp., was isolated from a marine sediment sample collected at Agenashiku Island, Okinawa, Japan. We performed light and electron microscopic observations, and a molecular phylogenetic analysis using the small subunit ribosomal RNA gene of the isolate. Cells of T. urniformis are spherical in shape and are covered by a thin theca possessing a wide rounded aperture. Branching and occasionally anastomosing filopodia with small granules emerge from the aperture. The granules are transported in the filopodia bidirectionally. Transmission electron microscopy showed that cells of T. urniformis possess nucleus with permanently condensed chromatin, Golgi apparatuses, microbodies, mitochondria with tubular cristae, and extrusomes. Several morphological and ultrastructural features of T. urniformis (the presence of thecae and nucleus with permanently condensed chromatin) show similarities with those of Thecofilosea. In a phylogenetic analysis, T. urniformis included in Thecofilosea with weak statistical supports and formed a clade with two sequences that constitutes a cercozoan environmental clade, novel clade 4. On the basis of morphological and ultrastructural information and the results of the phylogenetic analysis, we propose T. urniformis as a new member of class Thecofilosea.},
}
@article {pmid27068356,
year = {2016},
author = {Yang, JQ and Hsu, KC and Liu, ZZ and Su, LW and Kuo, PH and Tang, WQ and Zhou, ZC and Liu, D and Bao, BL and Lin, HD},
title = {The population history of Garra orientalis (Teleostei: Cyprinidae) using mitochondrial DNA and microsatellite data with approximate Bayesian computation.},
journal = {BMC evolutionary biology},
volume = {16},
number = {},
pages = {73},
pmid = {27068356},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; China ; Cyprinidae/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetics, Population ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; },
abstract = {BACKGROUND: The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass's phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci.<br><br>RESULTS: In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China.<br><br>CONCLUSION: Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.},
}
@article {pmid27068958,
year = {2016},
author = {Miliara, X and Matthews, S},
title = {Structural comparison of yeast and human intra-mitochondrial lipid transport systems.},
journal = {Biochemical Society transactions},
volume = {44},
number = {2},
pages = {479-485},
doi = {10.1042/BST20150264},
pmid = {27068958},
issn = {1470-8752},
support = {MRC-M019403/WT_/Wellcome Trust/United Kingdom ; 104933/WT_/Wellcome Trust/United Kingdom ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; MR/M019403/1/MRC_/Medical Research Council/United Kingdom ; 100280/WT_/Wellcome Trust/United Kingdom ; WT-100280/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Adaptor Proteins, Signal Transducing/chemistry/metabolism ; Amino Acid Sequence ; Biological Transport ; Crystallography, X-Ray ; Humans ; *Lipids ; Membrane Proteins/chemistry/metabolism ; Mitochondria/*metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Yeasts/*metabolism ; },
abstract = {Mitochondria depend on a tightly regulated supply of phospholipids. The protein of relevant evolutionary and lymphoid interest (PRELI)/Ups1 family together with its mitochondrial chaperones [TP53-regulated inhibitor of apoptosis 1 (TRIAP1)/Mdm35] represents a unique heterodimeric lipid-transfer system that is evolutionary conserved from yeast to man. Recent X-ray crystal structures of the human and yeast systems are compared and discuss here and shed new insight into the mechanism of the PRELI/Ups1 system.},
}
@article {pmid27081924,
year = {2016},
author = {Leung, J and Witt, JD and Norwood, W and Dixon, DG},
title = {Implications of Cu and Ni toxicity in two members of the Hyalella azteca cryptic species complex: Mortality, growth, and bioaccumulation parameters.},
journal = {Environmental toxicology and chemistry},
volume = {35},
number = {11},
pages = {2817-2826},
doi = {10.1002/etc.3457},
pmid = {27081924},
issn = {1552-8618},
mesh = {Amphipoda/*drug effects/genetics/growth &amp; development/metabolism ; Animals ; Copper/metabolism/*toxicity ; Electron Transport Complex IV/genetics ; Fresh Water ; Lethal Dose 50 ; Mitochondria/drug effects/enzymology/genetics ; Nickel/metabolism/*toxicity ; North America ; Phylogeny ; Species Specificity ; Survival Analysis ; Toxicity Tests ; Water Pollutants, Chemical/metabolism/*toxicity ; },
abstract = {Hyalella azteca, an amphipod crustacean, is frequently used in freshwater toxicity tests. Since the mid-1980s, numerous organizations have collected and established cultures of H. azteca originating from localities across North America. However, H. azteca is actually a large cryptic species complex whose members satisfy both the biological and the phylogenetic species concepts. Genetic analysis at the mitochondrial COI gene has revealed that only 2 clades are cultured in 17 North American laboratories; however, there are 85 genetically divergent lineages within this complex in the wild. In the present study, 2 members (clades 1 and 8) of the H. azteca species complex were identified using the mitochondrial COI gene. These 2 clades were exposed to Cu or Ni for 14 d. A saturation-based mortality model and the general growth model were used to determine mortality (lethal concentration, 25% and 50% [LC25 and LC50], lethal body concentration, 25% and 50% [LBC25 and LBC50]) and growth (inhibitory concentration, 25% [IC25, IBC25]) endpoints, respectively. A modified saturation-based model was used to estimate metal bioaccumulation parameters. Clade 8 was significantly more tolerant than clade 1, with differences in LC50s. However, the effects of the metals on growth were not significantly different between clades, even though clade 1 was significantly larger than then clade 8. Differences in Cu or Ni bioaccumulation were not observed between clades 1 and 8. The differences in Cu and Ni LC50s may have implications for risk assessments, and it is recommended that toxicity experiments should only be performed with properly identified members of the H. azteca complex to maintain consistency among laboratories. Environ Toxicol Chem 2016;35:2817-2826. © 2016 SETAC.},
}
@article {pmid27082488,
year = {2016},
author = {Shi, X and Bentolila, S and Hanson, MR},
title = {Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis.},
journal = {Plant signaling &amp; behavior},
volume = {11},
number = {5},
pages = {e1167299},
pmid = {27082488},
issn = {1559-2324},
mesh = {Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Organelles/*metabolism ; Phylogeny ; Plastids/*metabolism ; Protein Binding ; Protein Domains ; *RNA Editing ; RNA Recognition Motif Proteins/chemistry/*metabolism ; },
abstract = {Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome.},
}
@article {pmid27121326,
year = {2016},
author = {Ma, F and Zhang, Y and Wang, Y and Wan, Y and Miao, Y and Ma, T and Yu, Q and Li, M},
title = {Role of Aif1 in regulation of cell death under environmental stress in Candida albicans.},
journal = {Yeast (Chichester, England)},
volume = {33},
number = {9},
pages = {493-506},
doi = {10.1002/yea.3167},
pmid = {27121326},
issn = {1097-0061},
mesh = {Acetic Acid/pharmacology ; Antifungal Agents/pharmacology ; Apoptosis ; Candida albicans/*enzymology/genetics/pathogenicity ; Caspofungin ; Cell Death/*physiology ; Echinocandins/pharmacology ; Fungal Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Enzymologic/physiology ; Gene Expression Regulation, Fungal/physiology ; Hydrogen Peroxide/pharmacology ; Lipopeptides/pharmacology ; Membrane Potential, Mitochondrial/drug effects/physiology ; NADH, NADPH Oxidoreductases/genetics/*metabolism ; Phylogeny ; Reactive Oxygen Species ; *Stress, Physiological ; Virulence ; },
abstract = {Apoptosis-inducing factor (AIF) is a conserved flavoprotein localized in the mitochondria, inducing apoptosis after translocation into the nucleus. However, its role in the important fungal pathogen, Candida albicans, remains to be investigated. In this study, we find that the C. albicans AIF protein Aif1, similar to its homologues in other organisms, is localized at the mitochondria and translocated into the nucleus under apoptosis-inducing conditions. Moreover, deletion of AIF1 causes attenuated apoptosis in this pathogen under apoptosis-inducing conditions, such as the treatment of 2 mm H2 O2 , 10 mm acetic acid or 0.08 mg/l caspofungin, and its overexpression enhances this process. Interestingly, treatment with high levels of these agents leads to reversed sensitivity of aif1Δ/Δ and the overexpression strain AIF1ov. In addition, the virulence of C. albicans is not affected by deletion or overexpression of AIF1. Hence, C. albicans Aif1, as a mitochondria-localized protein, plays a dual role in the regulation of cell death under different concentrations of the stress-caused agents. Copyright © 2016 John Wiley &amp; Sons, Ltd.},
}
@article {pmid27129899,
year = {2016},
author = {Ho, ALFC and Pruett, CL and Lin, J},
title = {Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers.},
journal = {Molecular phylogenetics and evolution},
volume = {101},
number = {},
pages = {32-45},
doi = {10.1016/j.ympev.2016.04.032},
pmid = {27129899},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Central America ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Poecilia/*classification/*genetics ; South America ; Time Factors ; },
abstract = {Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes. A divergence-dating analysis supported the hypothesis of the genus Poecilia dispersing into Central America in the early Pliocene (ancestors of Psychropoecilia+Allopoecilia+Mollienesia: 7.3-2.0Mya) from predominantly South America. Subsequently, one lineage (subgenus Allopoecilia: 5.1-1.3Mya) expanded deeper into South America from Lower-Central America, and one lineage expanded from Nuclear-Central America into South America (subgenus Mollienesia: 0.71-0.14Mya). The subgenus Mollienesia diverged into three monophyletic groups that can be identified by nuptial male dorsal fin morphology and inner jaw dentition. A subclade of the unicuspid short-fins (subgenus Mollienesia) was the lineage that expanded into South America during the middle Pleistocene. Species in this subclade are now distributed across northern South America, where they are partially sympatric with Allopoecilia. However the P. (A.) caucana complex was not monophyletic, with P. (A.) wandae clustering in the Mollienesia subclade that expanded into South America. It is apparent that characters (body size, scale count, pigmentation, and gonopodium morphology) used to define the P. (A.) caucana complex are homoplastic and suggestive of rapid convergence in northern South America. Our improved taxon sampling and divergence-time calibration allowed for insights into the timing and direction of dispersals, and provides an improved understanding of the biogeographic history of an enigmatic group of fishes. Furthermore, we provided strong evidence for the monophyly of the subgenus Mollienesia and further substantiated its species complexes; therefore, we advise a taxonomic re-evaluation for the P. (A.) caucana complex to maintain monophyly of both Mollienesia and Allopoecilia.},
}
@article {pmid27132143,
year = {2016},
author = {Kobori, Y and Mizuta, S},
title = {Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.},
journal = {Genomics, proteomics &amp; bioinformatics},
volume = {14},
number = {2},
pages = {103-112},
pmid = {27132143},
issn = {2210-3244},
mesh = {*Algorithms ; Animals ; Base Sequence ; Genome, Mitochondrial/genetics ; Humans ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Graphical representation of DNA sequences is one of the most popular techniques for alignment-free sequence comparison. Here, we propose a new method for the feature extraction of DNA sequences represented by binary images, by estimating the similarity between DNA sequences using the frequency histograms of local bitmap patterns of images. Our method shows linear time complexity for the length of DNA sequences, which is practical even when long sequences, such as whole genome sequences, are compared. We tested five distance measures for the estimation of sequence similarities, and found that the histogram intersection and Manhattan distance are the most appropriate ones for phylogenetic analyses.},
}
@article {pmid27132943,
year = {2016},
author = {Shibata, H and Chijiwa, T and Hattori, S and Terada, K and Ohno, M and Fukumaki, Y},
title = {The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands.},
journal = {Molecular phylogenetics and evolution},
volume = {101},
number = {},
pages = {91-100},
doi = {10.1016/j.ympev.2016.04.027},
pmid = {27132943},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genome, Mitochondrial ; Geography ; *Islands ; Japan ; Likelihood Functions ; Markov Chains ; Monte Carlo Method ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; Trimeresurus/*classification/*genetics ; *Tropical Climate ; },
abstract = {There are four Habu species currently recognized in Japan: Protobothrops flavoviridis from the Amami Islands and the Okinawa Islands, P. tokarensis from the Tokara Islands, P. elegans from the Yaeyama Islands and Ovophis okinabvensis from the Amami Islands and the Okinawa Islands. To clarify their taxonomic positions, we determined the complete mitochondria genome sequence (approx. 17kb) from two specimens from two different islands each for P. flavoviridis, P. tokarensis and P. elegans as well as one specimen of O. okinavensis and reconstructed the molecular phylogeny of Protobothrops using the published sequences of related species. The maximum likelihood tree showed four major species groups within Protbothrops: Group I consisting of P. cornutus, P. dabieshanensis, P. jerdonii and P. xiangchengensis; Group II consisting of P. flavoviridis and P. tokarensis; Group III consisting of P. maolensis, P. mucrosquamatus and P. elegans; Group IV consisting of P. himalayanus and P. kaubacki. Since we observed an unexpected divergence and the paraphyly of the two samples of P. flavoviridis collected from different islands, Amami-Oshima and Okinawajima within the Group II, we expanded the analysis by increasing the number of P. flavoviridis and P. tokarensis collected from 10 islands: Amami-Oshima (5 specimens), Kakeromajima (4) and Tokunoshima (4) from the Amami Islands, Okinawajima (4), Iheyajima (4), Iejima (4), Tokashikijima (4) and Kumejima (4) from the Okinawa Islands, Kodakarajima (P. tokarensis) (4) and Takarajima (P. tokarensis) (4) from the Tokara Islands. The maximum likelihood tree of the 44 samples replicated the significant divergence of P. flavoviridis between the Amami Clade including Amami-Oshima, Kakeromajima and Tokunoshima and the Okinawa Clade including Okinawajima, Iheyajima, Iejima, Tokashikijima and Kumejima. The Amami Clade also include all specimens from the Tokara Islands currently known as an independent species, P. tokarensis, suggesting the paraphyly of the taxon, P. flavoviridis. In contrast, we observed a distinct lineage of the two specimens from the Yaeyama Islands, supporting the validity of the taxon, P. elegans as an independent species. By MCMC method, we estimated the divergence time between the Amami Clade and the Okinawa Clade to be 6.51MYA, suggesting that the vicariance of the two clades preceded the geological separation of the Amami Islands and the Okinawa Islands (∼1.5MYA). As expected from the limited mobility of terrestrial reptiles including snakes, we observed high genetic divergence in Habu mtDNA among Japanese subtropical island populations.},
}
@article {pmid27150350,
year = {2016},
author = {Ortiz, D and Francke, OF},
title = {Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae).},
journal = {Molecular phylogenetics and evolution},
volume = {101},
number = {},
pages = {176-193},
doi = {10.1016/j.ympev.2016.05.003},
pmid = {27150350},
issn = {1095-9513},
mesh = {Animals ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Female ; Male ; Mexico ; Mitochondria/genetics ; Phylogeny ; Spiders/*classification/genetics ; },
abstract = {Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic diversity and many species redundantly described. Most of these studies have relied only on COI, a mitochondrial marker that has proven its efficacy in animal studies, but which also might lead to an over-estimation of diversity. Here we present an integrative approach to species delimitation in Bonnetina, a poorly known group of tarantulas endemic to Mexico. We employed morphological evidence, as well as different setups with distance-based (Hard-Gap barcoding and ABGD) and tree-based (GMYC, PTP and BPP) molecular barcoding approaches, using one mitochondrial (COI) and one nuclear (ITS1) rapidly evolving loci. BPP is also used as a multi-locus method. We also explored the influence of ambiguous alignment choice and of coding gaps as characters in phylogenetic inference and in species delimitation with that marker. Different delimitation methods with COI gave moderately variable results and this gene exhibited a universal barcode gap. The ITS1 gene tree was well supported and robust to alignment choice; with this locus, coding gaps improved branch support and species delimitation with PTP. No universal barcode gap was found with ITS1, and single locus delimitations returned disparate results. However, this locus helped to highlight cases of under- and overestimations by COI. BPP gave solutions with many lineages, in single locus and combined analyses, especially with the recently implemented unguided methodology. We recognize 12 robustly supported species in our data set, of which seven remain undescribed, and three are morphologically cryptic. For COI Bonnetina species identification, we propose intra- and inter-specific thresholds of 2% and 6% sequence divergence, respectively. We conclude that morphological signal for species delimitation in Bonnetina is higher than for other studied tarantulas, but it fails to recognize several lineages in the genus. COI is a functional barcoding marker, and the most reliable source of evidence that we used, but it may also lead to inaccurate delimitations. ITS1 is a highly informative locus for species delimitation and species-level phylogeny, but it performs poorly as a barcoding marker. Due to variability between delimitation methods, we suggest combining evidence from multiple approaches to get better-supported results.},
}
@article {pmid27158791,
year = {2016},
author = {Cavaleiro, NP and Solé-Cava, AM and Melo, CM and de Almeida, LG and Lazoski, C and Vasconcelos, AT},
title = {The complete mitochondrial genome of Crassostrea gasar (Bivalvia: Ostreidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2939-2940},
doi = {10.3109/19401736.2015.1060450},
pmid = {27158791},
issn = {2470-1408},
mesh = {Animals ; Crassostrea/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {The complete mitochondrial genome of Crassostrea gasar was sequenced using the Ion Proton technology in combination with 454 Roche GS-FLX plataform data. We assembled a 17,686 bp complete circular mitochondrial genome, containing 13 protein-coding genes, a major non-coding region (MNR), two ribosomal RNA genes and 24 transfer RNA genes. Phylogenetic analysis of concatenated amino acid sequences from mitochondria showed monophyletic clades formed with high bootstrap values. This is the first complete mitochondrial sequence of an oyster from South America. Mitogenome sequence was deposited in GenBank under the accession number KR856227.},
}
@article {pmid27158871,
year = {2016},
author = {Sung, CH and Tseng, CT and Wang, LJ and Li, YC and Lu, JK},
title = {The complete mitochondrial genome of Babylonia borneensis (Gastropoda: Neogastropoda: Buccinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3534-3535},
doi = {10.3109/19401736.2015.1074205},
pmid = {27158871},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gastropoda/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome sequence of the Babylonia borneensis is reported for the first time in this study. The length of genome was 15 556 bp, including 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The nucleotide composition of the mitogenome showed AT-rich feature, with the AT content of 68.2%. Comparison of the identity of the B. borneensis mitogenome with B. areolata, B. lani and B. lutosa was 87.5%, 87.4% and 86.9%, respectively. The construction of phylogenetic tree showed high bootstrap support value. Babylonia borneensis grouped together with other Babylons and the lineages of Buccinidae was strongly supported. In this study, our results could provide a further understanding in the phylogenetic relationships of the Neogastropoda.},
}
@article {pmid27158872,
year = {2016},
author = {Froufe, E and Gan, HM and Lee, YP and Carneiro, J and Varandas, S and Teixeira, A and Zieritz, A and Sousa, R and Lopes-Lima, M},
title = {The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3571-3572},
doi = {10.3109/19401736.2015.1074223},
pmid = {27158872},
issn = {2470-1408},
mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/genetics/isolation &amp; purification ; *Endangered Species ; Female ; Fresh Water ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Whole Genome Sequencing ; },
abstract = {Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.},
}
@article {pmid27159687,
year = {2017},
author = {Basheer, VS and Vineesh, N and Bineesh, KK and Kumar, RG and Mohitha, C and Venu, S and Kathirvelpandian, A and Gopalakrishnan, A and Jena, JK},
title = {Mitochondrial signatures for identification of grouper species from Indian waters.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {451-457},
doi = {10.3109/19401736.2015.1137899},
pmid = {27159687},
issn = {2470-1408},
mesh = {Animals ; Bass/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; India ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.},
}
@article {pmid27159697,
year = {2017},
author = {Muangkram, Y and Amano, A and Wajjwalku, W and Pinyopummintr, T and Thongtip, N and Kaolim, N and Sukmak, M and Kamolnorranath, S and Siriaroonrat, B and Tipkantha, W and Maikaew, U and Thomas, W and Polsrila, K and Dongsaard, K and Sanannu, S and Wattananorrasate, A},
title = {Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {4},
pages = {597-601},
doi = {10.3109/24701394.2016.1149828},
pmid = {27159697},
issn = {2470-1408},
mesh = {Animals ; Brazil ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Variation ; Mitochondria/genetics ; Perissodactyla/*classification/genetics ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA/*methods ; Thailand ; },
abstract = {The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.},
}
@article {pmid27159728,
year = {2017},
author = {Ahmed, S and Grobler, P and Madisha, T and Kotze, A},
title = {Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {711-716},
doi = {10.3109/24701394.2016.1174225},
pmid = {27159728},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Egypt ; Genetic Variation ; Goats/*classification/genetics ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA/*methods ; },
abstract = {The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.},
}
@article {pmid27159731,
year = {2017},
author = {Ren, G and Ma, H and Ma, C and Wang, W and Chen, W and Ma, L},
title = {Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {5},
pages = {740-746},
doi = {10.1080/24701394.2016.1177040},
pmid = {27159731},
issn = {2470-1408},
mesh = {Animals ; Brachyura/*classification/genetics ; China ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; },
abstract = {In this paper, population genetic diversity and genetic structure of Portunus sanguinolentus distributed along China coast was investigated based on mitochondrial DNA cytochrome c oxidase subunit I (COI) gene. Sixty-eight haplotypes and 71 polymorphic sites were detected in 110 individuals sampled from four localities. The average haplotype diversity (h) and nucleotide diversity (π) were 0.9576 and 0.0051, respectively. Pairwise FST statistics among different localities were negative or low and insignificant, suggesting a widespread gene flow. The AMOVA analysis also indicated a broad genetic exchange among four localities (FST= -0.0039, p = 0.559). The high dispersal capabilities of larvae of P. sanguinolentus coupled with the limited physical barriers in marine environment may be responsible for the high gene flow among P. sanguinolentus populations along southeastern coast of China. Moreover, neutrality test and mismatch analysis implied that P. sanguinolentus population might have undergone a rapid population expansion event. The time of population expansion was estimated to occur about 229,000-321,000 years ago.},
}
@article {pmid27180575,
year = {2016},
author = {Liu, ZX and Zhang, Y and Liu, YT and Chang, QC and Su, X and Fu, X and Yue, DM and Gao, Y and Wang, CR},
title = {Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae).},
journal = {The Korean journal of parasitology},
volume = {54},
number = {2},
pages = {173-179},
pmid = {27180575},
issn = {1738-0006},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Dogs ; Echinostoma/*genetics ; Genetic Markers ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.},
}
@article {pmid27181928,
year = {2016},
author = {Benz, C and Kovářová, J and Králová-Hromadová, I and Pierik, AJ and Lukeš, J},
title = {Roles of the Nfu Fe-S targeting factors in the trypanosome mitochondrion.},
journal = {International journal for parasitology},
volume = {46},
number = {10},
pages = {641-651},
doi = {10.1016/j.ijpara.2016.04.006},
pmid = {27181928},
issn = {1879-0135},
mesh = {Antibodies, Protozoan/biosynthesis ; Blotting, Western ; Cells, Cultured ; Chemical Fractionation ; Computational Biology ; Down-Regulation ; Electroporation ; HSP70 Heat-Shock Proteins/metabolism ; Iron-Sulfur Proteins/genetics/immunology/*physiology ; Mitochondria/chemistry/*physiology ; Mitochondrial Proteins/*physiology ; Phylogeny ; Plasmids ; Protozoan Proteins/genetics/immunology/*physiology ; RNA Interference ; Trypanosoma brucei brucei/chemistry/classification/genetics/*physiology ; },
abstract = {Iron-sulphur clusters (ISCs) are protein co-factors essential for a wide range of cellular functions. The core iron-sulphur cluster assembly machinery resides in the mitochondrion, yet due to export of an essential precursor from the organelle, it is also needed for cytosolic and nuclear iron-sulphur cluster assembly. In mitochondria all [4Fe-4S] iron-sulphur clusters are synthesised and transferred to specific apoproteins by so-called iron-sulphur cluster targeting factors. One of these factors is the universally present mitochondrial Nfu1, which in humans is required for the proper assembly of a subset of mitochondrial [4Fe-4S] proteins. Although most eukaryotes harbour a single Nfu1, the genomes of Trypanosoma brucei and related flagellates encode three Nfu genes. All three Nfu proteins localise to the mitochondrion in the procyclic form of T. brucei, and TbNfu2 and TbNfu3 are both individually essential for growth in bloodstream and procyclic forms, suggesting highly specific functions for each of these proteins in the trypanosome cell. Moreover, these two proteins are functional in the iron-sulphur cluster assembly in a heterologous system and rescue the growth defect of a yeast deletion mutant.},
}
@article {pmid27194764,
year = {2016},
author = {Marzano, SL and Nelson, BD and Ajayi-Oyetunde, O and Bradley, CA and Hughes, TJ and Hartman, GL and Eastburn, DM and Domier, LL},
title = {Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens.},
journal = {Journal of virology},
volume = {90},
number = {15},
pages = {6846-6863},
pmid = {27194764},
issn = {1098-5514},
mesh = {Ascomycota/*virology ; Fungal Viruses/*classification/*genetics/isolation &amp; purification ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics ; Mycelium/virology ; Phylogeny ; Plant Diseases/*virology ; Plants/*virology ; RNA, Viral/genetics ; *Transcriptome ; },
abstract = {UNLABELLED: Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts.<br><br>IMPORTANCE: Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.},
}
@article {pmid27198783,
year = {2016},
author = {Li, K and Luo, H and Zhang, H and Lan, Y and Han, Z and Shahzad, M and Wang, X and Qiu, G and Huang, S and Jiang, W and Li, J},
title = {First report of Metastrongylus pudendotectus by the genetic characterization of mitochondria genome of cox1 in pigs from Tibet, China.},
journal = {Veterinary parasitology},
volume = {223},
number = {},
pages = {91-95},
doi = {10.1016/j.vetpar.2016.04.036},
pmid = {27198783},
issn = {1873-2550},
mesh = {Animals ; Base Sequence ; DNA, Helminth/genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/*genetics ; Metastrongyloidea/genetics/*isolation &amp; purification ; Phylogeny ; Strongylida Infections/epidemiology/parasitology/*veterinary ; Swine ; Swine Diseases/epidemiology/*parasitology ; Tibet/epidemiology ; },
abstract = {Lungworms, a world wild distributed parasites cause serious respiratory diseases to the pigs. A high infection rate of Metastrongylus lungworms has been found in Tibetan pigs being slaughtered in different slaughter houses of Tibet autonomous region. The main aim of our study was to detect and confirm the lungworm parasite by the genetic characterization of mitochondrial cox1genome isolated from the lungs of Tibetan pig. The adult lungworms were collected from the lungs of slaughtered pigs and identification was done through morphological examinations. Total genomic DNA of the extracted worms was performed and a fragment (∼450bp) of the cox1 of mitochondrial (mt) gene was amplified. Amplicons were cloned into PGEM(®)-T Easy vector and the positive clones were sequenced from a commercial company. Sequence and phylogenetic analysis were performed by software of DNAMAN and MEGA respectively. The results revealed that the lungworms infecting the Tibetan pigs were Metastrongylus pudendotectus (M. pudendotectus). To our knowledge, this is the first report for the isolation and identification for the genetic characterization of mitochondria (mt) genome of cox1 of M. pudendotectus derived from Tibetan pigs in Tibet, China.},
}
@article {pmid27206536,
year = {2016},
author = {Chunnian, L and Wu, X and Ding, X and Wang, H and Guo, X and Chu, M and Bao, P and Yan, P},
title = {Characterization of the complete mitochondrial genome sequence of wild yak (Bos mutus).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4266-4267},
doi = {10.3109/19401736.2015.1060420},
pmid = {27206536},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Cattle/*genetics ; China ; Codon, Initiator/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {Wild yak is a special breed in China and it is regarded as an important genetic resource for sustainably developing the animal husbandry in Tibetan area and enriching region's biodiversity. The complete mitochondrial genome of wild yak (16,322 bp in length) displayed 37 typical animal mitochondrial genes and A + T-rich (61.01%), with an overall G + C content of only 38.99%. It contained a non-coding control region (D-loop), 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Most of the genes have ATG initiation codons, whereas ND2, ND3, and ND5 genes start with ATA and were encoded on H-strand. The gene order of wild yak mitogenome is identical to that observed in most other vertebrates. The complete mitochondrial genome sequence of wild yak reported here could provide valuable information for developing genetic markers and phylogenetic analysis in yak.},
}
@article {pmid27207080,
year = {2016},
author = {Yuan, S and Lu, Z and Wu, X and Fu, H and Bao, D and Malqin, H and Yang, S},
title = {Complete mitochondrial genome of Myospalax aspalax (Rodentia, Spalacidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4250-4251},
doi = {10.3109/19401736.2015.1043532},
pmid = {27207080},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Asia, Eastern ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {False zokor (Myospalax aspalax) is one of the subterranean rodents distributed in East Asia. Molecular data and demography of M. aspalax are unknown, and the population management is difficult, because it is specialized for underground life. In this study, the complete mitochondrial DNA genome of M. aspalax was determined. The results suggested that the mitogenome was 16,436 bp in length, and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one displacement loop. The overall base composition of the heavy strand was A 33.40%, T 29.34%, C 24.90%, and G 12.36%, with A + T > C + G. Myospalax aspalax is a sister to the genus Myospalax, and have a most closely relationship with M. psilurus. The mitogenome data are potentially important for population management of M. aspalax and should contribute to the interspecies comparative analyses of genus Myospalax.},
}
@article {pmid27212703,
year = {2016},
author = {Yamada, M and Emmanuele, V and Sanchez-Quintero, MJ and Sun, B and Lallos, G and Paull, D and Zimmer, M and Pagett, S and Prosser, RW and Sauer, MV and Hirano, M and Egli, D},
title = {Genetic Drift Can Compromise Mitochondrial Replacement by Nuclear Transfer in Human Oocytes.},
journal = {Cell stem cell},
volume = {18},
number = {6},
pages = {749-754},
pmid = {27212703},
issn = {1875-9777},
support = {P01 HD080642/HD/NICHD NIH HHS/United States ; U54 NS078059/NS/NINDS NIH HHS/United States ; },
mesh = {Cell Line ; Cell Nucleus/metabolism ; DNA, Mitochondrial/genetics ; *Genetic Drift ; Genotype ; Humans ; Mitochondria/*genetics ; *Nuclear Transfer Techniques ; Oocytes/*metabolism ; },
abstract = {Replacement of mitochondria through nuclear transfer between oocytes of two different women has emerged recently as a strategy for preventing inheritance of mtDNA diseases. Although experiments in human oocytes have shown effective replacement, the consequences of small amounts of mtDNA carryover have not been studied sufficiently. Using human mitochondrial replacement stem cell lines, we show that, even though the low levels of heteroplasmy introduced into human oocytes by mitochondrial carryover during nuclear transfer often vanish, they can sometimes instead result in mtDNA genotypic drift and reversion to the original genotype. Comparison of cells with identical oocyte-derived nuclear DNA but different mtDNA shows that either mtDNA genotype is compatible with the nucleus and that drift is independent of mitochondrial function. Thus, although functional replacement of the mitochondrial genome is possible, even low levels of heteroplasmy can affect the stability of the mtDNA genotype and compromise the efficacy of mitochondrial replacement.},
}
@article {pmid27233443,
year = {2016},
author = {Carmi, O and Witt, CC and Jaramillo, A and Dumbacher, JP},
title = {Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species.},
journal = {Molecular phylogenetics and evolution},
volume = {102},
number = {},
pages = {152-173},
doi = {10.1016/j.ympev.2016.05.029},
pmid = {27233443},
issn = {1095-9513},
mesh = {Alleles ; Animal Migration/*physiology ; Animals ; Cytochromes b/classification/genetics ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Genetic Variation ; Haplotypes ; Mitochondria/enzymology/metabolism ; NADH Dehydrogenase/classification/genetics ; North America ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Songbirds/*classification/genetics ; South America ; },
abstract = {The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.},
}
@article {pmid27260204,
year = {2016},
author = {Ebrahimi, S and Bordbar, A and Parvizi, P},
title = {Genetic dynamics in the sand fly (Diptera: Psychodidae) nuclear and mitochondrial genotypes: evidence for vector adaptation at the border of Iran with Iraq.},
journal = {Parasites &amp; vectors},
volume = {9},
number = {1},
pages = {319},
pmid = {27260204},
issn = {1756-3305},
mesh = {Adaptation, Biological ; Animals ; Cell Nucleus/genetics ; Cytochromes b/genetics ; Female ; *Genetic Variation ; Genotype ; Geography ; Humans ; Insect Vectors/*genetics/physiology ; Iran/epidemiology ; Iraq/epidemiology ; Leishmaniasis, Cutaneous/epidemiology/*transmission ; Male ; Mitochondria/genetics ; Peptide Elongation Factor 1/genetics ; Phlebotomus/genetics/physiology ; Phylogeny ; Psychodidae/*genetics/physiology ; },
abstract = {BACKGROUND: Our investigation uses nucleotide variations of the genera Phlebotomus and Sergentomyia using the EF-1α and Cyt b genotype regions to describe the sand fly fauna and genetic aspects collected at war-torn sites of the Khuzestan boundary between Iraq and Iran.<br><br>METHODS: All sand fly species were characterized using molecular genetics. The field work was conducted in six districts including 24 locations in remote areas for three&#xa0;years at the peak of sand fly activity during cutaneous leishmaniasis (CL) transmission seasons. The distribution of CL vectors was determined based on the climatic regionalization using the kriging method in ArcGIS model. DNA of sand fly pools were screened via polymerase chain reaction (PCR) using neutrality (Tajima's D) and neutral allele frequency (Fu's F s) tests to measure the effect of randomly evolving DNA sequence on the genetic diversity of sand fly populations in response to habitat fragmentation and landscape modification.<br><br>RESULTS: Among the 1213 specimens, ten species were identified&#xa0;based on morphology. The non-native species Phlebotomus sergenti was unequivocally found for the first time in the studied regions. Nucleotide substitutions of sand fly sequences varied most in the most disrupted districts (Dashte-Azadegan and Abadan; disparity index test: P&#x2009;<&#x2009;0.05). The haplotypes of Cyt b from the subgenus Sergentomyia and P. papatasi revealed more heterogeneity (Tajima's D&#x2009;>&#x2009;+2) than P. alexandri (D&#x2009;>&#x2009;+1), which suggests widespread heteroplasmic mitochondrial DNA mutations in the same mtDNA gene among different sand fly species. Subgenus&#xa0; Sintonius exhibited greater fitness (D&#x2009;=&#x2009;0) and (neutrality test; P&#x2009;>&#x2009;0.05) no evidence of selection. The sequence of the nuclear gene EF-1&#x3b1; indicated similar nucleotide differences, as observed for the Cyt b gene, in all sand fly species, but lower levels of polymorphisms (D&#x2009;>&#x2009;+1) were observed compared with the mitochondrial Cyt b gene (D&#x2009;>&#x2009;+2) in the&#xa0;subgenus&#xa0; Sergentomyia.<br><br>CONCLUSION: Our findings describe random nucleotide diversity in the Phlebotomus and Sergentomyia population gene pools due to recent anthropogenic influence. A phylogenetic analysis showed that the closely related species are positioned in monophyletic clades, except for the&#xa0;subgenus Sergentomyia and P. sergenti, and highlights the importance of haplotype variations for the development of adaptability.},
}
@article {pmid27262428,
year = {2016},
author = {Melo, BF and Sidlauskas, BL and Hoekzema, K and Frable, BW and Vari, RP and Oliveira, C},
title = {Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes).},
journal = {Molecular phylogenetics and evolution},
volume = {102},
number = {},
pages = {189-201},
doi = {10.1016/j.ympev.2016.05.037},
pmid = {27262428},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/genetics ; Characiformes/*classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; South America ; },
abstract = {Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semaprochilodus are resolved. The morphologically similar P. brevis, P. lacustris, P. nigricans and P. rubrotaeniatus are embedded within what is herein designated as the P. nigricans group. Species limits and distributions of these species are problematic and the group clearly merits taxonomic revision.},
}
@article {pmid27289532,
year = {2016},
author = {Hu, JJ and Liu, TT and Liu, Q and Esch, GW and Chen, JQ and Huang, S and Wen, T},
title = {Prevalence, morphology, and molecular characteristics of Sarcocystis spp. in domestic goats (Capra hircus) from Kunming, China.},
journal = {Parasitology research},
volume = {115},
number = {10},
pages = {3973-3981},
pmid = {27289532},
issn = {1432-1955},
mesh = {Animals ; China/epidemiology ; Cyclooxygenase 1/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; Goat Diseases/*epidemiology/parasitology ; Goats ; Mitochondria/enzymology ; Muscles/parasitology ; Phylogeny ; Prevalence ; Protozoan Proteins/genetics ; Sarcocystis/*classification/enzymology/genetics/ultrastructure ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sequence Analysis, DNA/veterinary ; },
abstract = {Despite the importance of worldwide goat production, little is known about the prevalence of Sarcocystis spp. in domestic goats (Capra hircus) in China. The aims of the present study were to determine prevalence of Sarcocystis spp. in domestic goats in Kunming, China, as well as to identify parasite species based on morphological characteristics and DNA sequence analysis. Only microscopic sarcocysts of Sarcocystis spp. were detected in 174 of 225 goats (77.3 %). By light and transmission electron microscopy, two species, i.e., Sarcocystis capracanis and Sarcocystis hircicanis, were identified. Two sarcocysts from each of the two species were randomly selected for DNA extraction; the 18S rRNA gene (18S rRNA), the 28S rRNA gene (28S rRNA), and the mitochondrial cytochrome c oxidase subunit 1 (cox1) were amplified by the polymerase chain reaction (PCR) and subsequently sequenced. The results were compared with other previously sequenced Sarcocystis species retrieved from GenBank. There was little sequence variation between two isolates of the same species. S. capracanis was most closely related with Sarcocystis tenella; 18S rRNA, 28S rRNA, and mitochondrial cox1 sequences shared identities of 95.7-99.1, 95.3, and 92.3-93.2 % with those of S. tenella, respectively. Thus, mitochondrial cox1 sequences seem to perform better than 18S rRNA sequences or 28S rRNA sequences for identification of the two species. S. hircicanis was most closely related to Sarcocystis arieticanis, i.e., 18S rRNA and 28S rRNA sequences of the former species shared 97.2-97.4 and 95.6-96.1 % identities with those of latter, respectively. Phylogenetic analysis inferred from the three genetic markers yielded similar results and indicated the two species were within a group of Sarcocystis species with canines as known, or presumed, definitive hosts.},
}
@article {pmid27297032,
year = {2016},
author = {Safari, R and Salimi, R and Tunca, Z and Ozerdem, A and Ceylan, D and Sakizli, M},
title = {Mutation/SNP analysis in EF-hand calcium binding domain of mitochondrial Ca[Formula: see text] uptake 1 gene in bipolar disorder patients.},
journal = {Journal of integrative neuroscience},
volume = {15},
number = {2},
pages = {163-173},
doi = {10.1142/S0219635216500096},
pmid = {27297032},
issn = {0219-6352},
mesh = {Adult ; Bipolar Disorder/*genetics ; Calcium-Binding Proteins/*genetics ; Cation Transport Proteins/*genetics ; Family ; Female ; Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Male ; Mitochondrial Membrane Transport Proteins/*genetics ; *Mutation ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Homology, Amino Acid ; },
abstract = {Calcium signaling is important for synaptic plasticity, generation of brain rhythms, regulating neuronal excitability, data processing and cognition. Impairment in calcium homeostasis contributed to the development of psychiatric disorders such as bipolar disorder (BP). MCU is the most important calcium transporter in mitochondria inner membrane responsible for influx of Ca[Formula: see text]. MICU1 is linked with MCU and has two canonical EF hands that are vital for its activity and regulates MCU-mediated Ca[Formula: see text] influx. In the current study, we aimed to investigate the role of genetic alteration of EF hand calcium binding motifs of MICU1 on the development of BP. We examined patients with BP, first degree relatives of these patients and healthy volunteers for mutations and polymorphisms in EF hand calcium binding motifs of MICU1. The result showed no SNP/mutation in BP patients, in healthy subjects and in first degree relatives. Additionally, alignment of the EF hand calcium binding regions among species (Gallus-gallus, Canis-lupus-familiaris, Bos-taurus, Mus-musculus, Rattus-norvegicus, Pan-troglodytes, Homosapiens and Danio-rerio) showed exactly the same amino acids (DLNGDGEVDMEE and DCDGNGELSNKE) except in one of the calcium binding domain of Danio-rerio that there was only one difference; leucine instead of Methionine. Our results showed that the SNP on EF-hand Ca[Formula: see text] binding domains of MICU1 gene had no effect in phenotypic characters of BP patients.},
}
@article {pmid27306456,
year = {2016},
author = {Hwang, ST and Choi, D},
title = {A novel rice protein family of OsHIGDs may be involved in early signalling of hypoxia-promoted stem growth in deepwater rice.},
journal = {Plant cell reports},
volume = {35},
number = {10},
pages = {2021-2031},
pmid = {27306456},
issn = {1432-203X},
mesh = {Amino Acid Sequence ; Cell Hypoxia/drug effects/genetics ; Ethylenes/pharmacology ; Gene Expression Regulation, Plant/drug effects ; Gene Regulatory Networks/drug effects ; Green Fluorescent Proteins/metabolism ; *Multigene Family ; Organ Specificity/drug effects/genetics ; Oryza/drug effects/genetics/*growth &amp; development/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Plant Stems/drug effects/*growth &amp; development/*metabolism ; Protein Binding/drug effects ; *Signal Transduction/drug effects/genetics ; Subcellular Fractions/metabolism ; Two-Hybrid System Techniques ; Water ; },
abstract = {OsHIGDs was identified as a novel hypoxia-responsive protein family. Among them, OsHIGD2 is characterized as a mitochondrial protein and is related to hypoxia signalling through interacting with mitochondrial proteins of critical functions in reducing cell damages caused by hypoxia. Recent evidence supports ethylene as a key factor in modulating plant responses to submergence stress. Meanwhile, there has been general consent that ethylene is not the only signal for the submergence-induced stem growth. In this study, we confirmed that hypoxia also promotes stem elongation in deepwater rice even in the absence of ethylene. As components of ethylene-independent hypoxia signalling, five HIGD (hypoxia-induced gene domain) protein genes were identified. Among the genes, OsHIGD2 showed the fastest and strongest induction by hypoxia as well as submergence. Co-expression analysis indicated that OsHIGD2 had a simultaneous expression pattern with fermentation-related genes, such as ADH1 (alcohol dehydrogenase 1) and PDC2 (pyruvate decarboxylase 2). Transient expression of OsHIGD2 in leaf epidermal cells of Nicotiana benthamiana provided evidence that the protein is localized to mitochondria. We further identified OsHIGD2-interacting proteins through the yeast two-hybrid assay using OsHIGD2 as bait. As a result, three mitochondrial proteins were discovered that function in the regulation of redox potential or reduction of protein damages caused by reactive oxygen species. In this report, we propose that OsHIGD2 is a mitochondrial protein which takes part in the early stage of hypoxia signalling by interacting with proteins that are related to oxygen utilization.},
}
@article {pmid27350680,
year = {2016},
author = {Sarswat, M and Dewan, S and Fartyal, RS},
title = {Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India.},
journal = {Journal of genetics},
volume = {95},
number = {2},
pages = {357-367},
pmid = {27350680},
issn = {0973-7731},
mesh = {Altitude ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Drosophilidae/classification/*genetics ; Ecosystem ; Electron Transport Complex IV/*genetics ; Female ; Genetic Speciation ; Genetic Variation ; Haplotypes ; India ; Insect Proteins/*genetics ; Isoenzymes/genetics ; Male ; Mitochondria/enzymology/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2-3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study.},
}
@article {pmid27376282,
year = {2016},
author = {Deng, Y and Zhang, Q and Ming, R and Lin, L and Lin, X and Lin, Y and Li, X and Xie, B and Wen, Z},
title = {Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi.},
journal = {International journal of molecular sciences},
volume = {17},
number = {7},
pages = {},
pmid = {27376282},
issn = {1422-0067},
mesh = {*Genome, Mitochondrial ; Hypocreales/*genetics ; Introns ; Mitochondria/genetics ; Mitochondrial Proteins/classification/metabolism ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Transfer/chemistry/genetics/metabolism ; },
abstract = {Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.},
}
@article {pmid27385510,
year = {2016},
author = {Slocinska, M and Barylski, J and Jarmuszkiewicz, W},
title = {Uncoupling proteins of invertebrates: A review.},
journal = {IUBMB life},
volume = {68},
number = {9},
pages = {691-699},
doi = {10.1002/iub.1535},
pmid = {27385510},
issn = {1521-6551},
mesh = {Amino Acid Sequence/genetics ; Animals ; Invertebrates/*genetics/metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Uncoupling Proteins/*genetics/metabolism ; Oxidative Stress/genetics ; Phylogeny ; },
abstract = {Uncoupling proteins (UCPs) mediate inducible proton conductance in the mitochondrial inner membrane. Herein, we summarize our knowledge regarding UCPs in invertebrates. Since 2001, the presence of UCPs has been demonstrated in nematodes, mollusks, amphioxi, and insects. We discuss the following important issues concerning invertebrate UCPs: their evolutionary relationships, molecular and functional properties, and physiological impact. Evolutionary analysis indicates that the branch of vertebrate and invertebrate UCP4-5 diverged early in the evolutionary process prior to the divergence of the animal groups. Several proposed physiological roles of invertebrate UCPs are energy control, metabolic balance, and preventive action against oxidative stress. © 2016 IUBMB Life, 68(9):691-699, 2016.},
}
@article {pmid27418428,
year = {2016},
author = {Manunza, A and Amills, M and Noce, A and Cabrera, B and Zidi, A and Eghbalsaied, S and de Albornoz, EC and Portell, M and Mercadé, A and Sànchez, A and Balteanu, V},
title = {Romanian wild boars and Mangalitza pigs have a European ancestry and harbour genetic signatures compatible with past population bottlenecks.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {29913},
pmid = {27418428},
issn = {2045-2322},
mesh = {Animals ; Genetic Variation ; *Genetics, Population ; Genome ; Heterozygote ; Homozygote ; Mitochondria/genetics ; *Phylogeny ; Romania ; Sus scrofa/*genetics ; },
abstract = {We aimed to analyse the genetic diversity of Romanian wild boars and to compare it with that from other wild boar and pig populations from Europe and Asia. Partial sequencing of the mitochondrial encoded cytochrome b (MT-CYB) gene from 36 Romanian wild boars and 36 domestic pigs (Mangalitza, Bazna and Vietnamese breeds) showed that the diversity of Romanian wild boars and Mangalitza pigs is fairly reduced, and that most of the members of these two populations share a common MT-CYB haplotype. Besides, in strong contrast with the Bazna animals, Romanian wild boars and Mangalitza swine did not carry Asian variants at the MT-CYB locus. The autosomal genotyping of 18 Romanian wild boars with the Illumina Porcine SNP60 BeadChip revealed that their genetic background is fundamentally European, even though signs of a potential Near Eastern ancestry (~25%) were detectable at K = 4 (the most significant number of clusters), but not at higher K-values. Admixture analysis also showed that two wild boars are of a hybrid origin, which could be explained by the mating of feral animals with domestic pigs. Finally, a number of Romanian wild boars displayed long runs of homozygosity, an observation that is consistent with the occurrence of past population bottlenecks and the raise of inbreeding possibly due to overhunting or to the outbreak of infectious diseases.},
}
@article {pmid27427438,
year = {2016},
author = {Patil, TS and Tamboli, AS and Patil, SM and Bhosale, AR and Govindwar, SP and Muley, DV},
title = {Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).},
journal = {Comptes rendus biologies},
volume = {339},
number = {9-10},
pages = {364-370},
doi = {10.1016/j.crvi.2016.06.001},
pmid = {27427438},
issn = {1768-3238},
mesh = {Alleles ; Animals ; Classification ; Cypriniformes/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Gene Frequency ; Genetic Markers/*genetics ; Genetic Variation ; Heterozygote ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Polymorphism, Restriction Fragment Length ; Species Specificity ; },
abstract = {Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution.},
}
@article {pmid27449222,
year = {2016},
author = {Han, Z and Qin, Y and Kong, F and Deng, Y and Wang, Z and Shen, G and Wang, J and Duan, B and Li, R},
title = {Cloning and Expression Analysis of Eight Upland Cotton Pentatricopeptide Repeat Family Genes.},
journal = {Applied biochemistry and biotechnology},
volume = {180},
number = {6},
pages = {1243-1255},
doi = {10.1007/s12010-016-2164-y},
pmid = {27449222},
issn = {1559-0291},
mesh = {Amino Acid Sequence ; Cloning, Molecular ; *Gene Expression Regulation, Plant/drug effects ; *Genes, Plant ; Gossypium/drug effects/*genetics/physiology ; *Multigene Family ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; *Repetitive Sequences, Amino Acid ; Sodium Chloride/pharmacology ; Stress, Physiological/drug effects/genetics ; Subcellular Fractions/metabolism ; Time Factors ; },
abstract = {The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants. Most PPR genes are localized in mitochondria and chloroplasts functioning in regulation of plant growth and development, fertility restoration for cytoplasmic male sterility (CMS), and stress defense. In this study, using in silico cloning and PCR amplification with degenerate primers based on Arabidopsis PPR genes, we cloned eight new full-length PPR genes encoding protein sequences ranging from 458 to 875 amino acids, with 8 to 16 repetitive PPR elements in upland cotton and all of them lack introns. Expression analysis revealed that eight PPR genes were differently expressed in roots, stems, leaves, and floral buds. As for GhI12, its expression in floral buds at days 3-5 was significantly higher in line 777R (restorer line) than in line 777A (CMS line). Further tests with real-time PCR showed that GhI12 expression peaked at day 3 in 777R, followed by a gradual decline, while its expression fluctuated in 777A, peaking at day 5 and day 13. In addition, Gh155c17 and GhI12 were upregulated under salt stress. This is the first report of upland cotton PPR genes involved in salt stress response.},
}
@article {pmid27463732,
year = {2017},
author = {Kostka, M and Lares-Jiménez, LF and Tyml, T and Dyková, I},
title = {Copromyxa laresi n. sp. (Amoebozoa: Tubulinea) and Transfer of Cashia limacoides (Page, 1967) to Copromyxa Zopf, 1885.},
journal = {The Journal of eukaryotic microbiology},
volume = {64},
number = {2},
pages = {173-182},
doi = {10.1111/jeu.12349},
pmid = {27463732},
issn = {1550-7408},
mesh = {Actins/genetics ; Amoeba ; Amoebozoa/*classification/*genetics/isolation &amp; purification/*ultrastructure ; Animals ; Base Sequence ; Czech Republic ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Elongation Factor 2 Kinase/genetics ; Gills/parasitology ; Lobosea/*classification/*genetics/isolation &amp; purification/*ultrastructure ; Microscopy, Electron ; Mitochondria/parasitology/ultrastructure ; Oligochaeta/parasitology ; Organelles/parasitology/ultrastructure ; *Phylogeny ; Protozoan Proteins/genetics ; Sequence Alignment ; Soil/parasitology ; Spain ; Species Specificity ; Zebrafish/parasitology ; },
abstract = {Five amoeboid organisms of different origin (isolated from fish organs, soil and digestive tract of earthworm) that shared light microscopical and ultrastructural features including type and arrangement of mitochondrial cristae were subjected to phylogenetic analyses based on sequences of SSU rDNA and protein coding genes (actin, cytochrome oxidase I, and eukaryotic elongation factor 2). The reconstruction of multigene phylogeny of the strains studied (i) revealed that they belong to the same single-genus Copromyxa clade; (ii) strongly supported position of Copromyxa cantabrigiensis (syn. Hartmannella cantabrigiensis) within the genus; (iii) together with comparisons of light and electron microscopy data justified reclassification of Cashia limacoides (syn. Vexillifera expectata) to Copromyxa limacoides n. comb., and (iv) justified description of a new species, Copromyxa laresi n. sp.},
}
@article {pmid27463803,
year = {2016},
author = {Fan, X and Chiba, H and Huang, Z and Fei, W and Wang, M and Sáfián, S},
title = {Clarification of the Phylogenetic Framework of the Tribe Baorini (Lepidoptera: Hesperiidae: Hesperiinae) Inferred from Multiple Gene Sequences.},
journal = {PloS one},
volume = {11},
number = {7},
pages = {e0156861},
pmid = {27463803},
issn = {1932-6203},
mesh = {Animals ; Lepidoptera/*classification/genetics ; Mitochondria/genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {Members of the skipper tribe Baorini generally resemble each other and are characterized by dark brown wings with hyaline white spots. These shared characteristics have caused difficulties with revealing the relationships among genera and species in the group, and some conflicting taxonomic views remain unresolved. The present study aims to infer a more comprehensive phylogeny of the tribe using molecular data, to test the monophyly of the tribe as well as the genera it includes in order to clarify their taxonomic status, and finally to revise the current classification of the group. In order to reconstruct a phylogenetic tree, the mitochondrial COI-COII and 16S genes as well as the nuclear EF-1α and 28S genes were analyzed using parsimony, maximum likelihood, and Bayesian inference. The analysis included 67 specimens of 41 species, and we confirmed the monophyly of Baorini, and revealed that 14 genera are well supported. The genus Borbo is separated into three clades: Borbo, Pseudoborbo, and Larsenia gen. nov. We confirmed that Polytremis is polyphyletic and separated into three genera: Polytremis, Zinaida, and Zenonoida gen. nov., and also confirmed that the genus Prusiana is a member of the tribe. Relationships among some genera were strongly supported. For example, Zenonia and Zenonoida were found to be sister taxa, closely related to Zinaida and Iton, while Pelopidas and Baoris were also found to cluster together.},
}
@article {pmid27468745,
year = {2016},
author = {Takahashi, Y and Yoshida, M and Inouye, I and Watanabe, MM},
title = {Fibrophrys columna gen. nov., sp. nov: A member of the family Amphifilidae.},
journal = {European journal of protistology},
volume = {56},
number = {},
pages = {41-50},
doi = {10.1016/j.ejop.2016.06.003},
pmid = {27468745},
issn = {1618-0429},
mesh = {Japan ; Microscopy, Electron, Transmission ; Phylogeny ; Ponds/*parasitology ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Stramenopiles/*classification/cytology/genetics/ultrastructure ; },
abstract = {A novel Diplophrys-like organism, Fibrophrys columna, was isolated from Hiuchigaike Pond in Japan. F. columna showed a nearly orbicular or broadly elliptical cell shape and has fine filamentous, branching ectoplasmic elements emanating from both polar ends of the cell. Cells also contain orange, amber, or colorless lipid bodies. Although its whole cell morphology resembles that of the genus Diplophrys, Fibrophrys is clearly distinct from Diplophrys on the basis of 18S rDNA sequences. Molecular phylogenetic analysis showed a close relationship of F. columna with Amphifila marina, and its sequence is similar to many environmental stramenopile sequences. The cells of F. columna measured 5.0-8.3×5.6-10.3μm and sometimes possessed hernia-like prongs instead of filamentous ectoplasmic elements. An axis-like electron-dense body was observed in the mitochondria. We also studied the ultrastructure of another Fibrophrys strain, Fibrophrys sp. E-1, which is different from the type strain of F. columna. A ladder-like pattern was recognized in the outer part of unidentified cytoplasmic membranes connected with the mitochondria. The unidentified cytoplasmic membranes were connected to the nuclear, lipid body, and mitochondrial outer membranes. We propose a new genus, Fibrophrys, and a new species, F. columna, based on these ultrastructural and molecular features.},
}
@article {pmid27518222,
year = {2016},
author = {Boonrueng, C and Tangpranomkorn, S and Yazhisai, U and Sirikantaramas, S},
title = {Molecular cloning, subcellular localization and characterization of two adenylate kinases from cassava, Manihot esculenta Crantz cv. KU50.},
journal = {Journal of plant physiology},
volume = {204},
number = {},
pages = {66-73},
doi = {10.1016/j.jplph.2016.08.001},
pmid = {27518222},
issn = {1618-1328},
mesh = {Adenylate Kinase/*genetics ; Cloning, Molecular ; Computer Simulation ; Fluorescence ; Gene Expression Regulation, Plant ; Manihot/*enzymology/*genetics ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Recombinant Proteins/isolation &amp; purification ; Subcellular Fractions/enzymology ; },
abstract = {Adenylate kinase (ADK) is a phosphotransferase that plays an important role in cellular energy homeostasis. Many isozymes located in different subcellular compartments have been reported. In this study, we focus on the characterization of cassava (Manihot esculenta) ADKs. We found 15 ADKs that are publicly available in the African cassava genome database. We cloned two ADKs, namely MeADK1 and MeADK2, which are phylogenetically grouped together with the plastidial ADK in potato. Both MeADK1 and MeADK2 showed 66% identity in the amino acid sequences with plastidial ADK in potato. However, we demonstrated that they are localized to mitochondria using GFP fusions of MeADK1 and MeADK2. The Escherichia coli-produced recombinant MeADK1 and MeADK2 preferred forward reactions that produce ATP. They exhibited similar specific activities. The semi-quantitative RT-PCR analysis showed that MeADK1 and MeADK2 in 2-month-old leaves have similar expression patterns under a diurnal light-dark cycle. However, MeADK2 transcripts were expressed at much higher levels than MeADK1 in 5-month-old leaves and roots. Thus, we conclude that MeADK2 might play a vital role in energy homeostasis in cassava mitochondria.},
}
@article {pmid27537861,
year = {2016},
author = {O'Sullivan, NJ and Teasdale, MD and Mattiangeli, V and Maixner, F and Pinhasi, R and Bradley, DG and Zink, A},
title = {A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {31279},
pmid = {27537861},
issn = {2045-2322},
mesh = {Animals ; Animals, Domestic/classification/*genetics ; Animals, Wild/classification/*genetics ; Cattle ; Clothing ; Deer ; Genome, Mitochondrial ; Goats ; Mitochondria/*genetics ; Mummies ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sheep ; Ursidae ; Whole Genome Sequencing/*methods ; },
abstract = {The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today's domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.},
}
@article {pmid27539928,
year = {2017},
author = {Guo, W and Zhu, A and Fan, W and Mower, JP},
title = {Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns.},
journal = {The New phytologist},
volume = {213},
number = {1},
pages = {391-403},
doi = {10.1111/nph.14135},
pmid = {27539928},
issn = {1469-8137},
mesh = {Base Composition/genetics ; DNA, Plant/genetics ; Ferns/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genome, Plant ; Introns/*genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Organelles/*genetics ; Phylogeny ; RNA/genetics ; RNA Editing/genetics ; RNA, Mitochondrial ; Repetitive Sequences, Nucleic Acid/*genetics ; },
abstract = {Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (< 60) of U-to-C edit sites. Overall, the first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.},
}
@article {pmid27567714,
year = {2016},
author = {Hernández-Martínez, F and Briones-Roblero, CI and Nelson, DR and Rivera-Orduña, FN and Zúñiga, G},
title = {Cytochrome P450 complement (CYPome) of Candida oregonensis, a gut-associated yeast of bark beetle, Dendroctonus rhizophagus.},
journal = {Fungal biology},
volume = {120},
number = {9},
pages = {1077-1089},
doi = {10.1016/j.funbio.2016.06.005},
pmid = {27567714},
issn = {1878-6146},
mesh = {Animals ; Candida/*classification/*enzymology/genetics/isolation &amp; purification ; Cell Membrane/enzymology ; Cytochrome P-450 Enzyme System/*genetics ; Gastrointestinal Tract/microbiology ; Intracellular Membranes/enzymology ; *Phylogeny ; Sequence Homology ; Weevils/*microbiology ; },
abstract = {Bark beetles (Curculionidae: Scolytinae) and associated microorganisms must overcome a complex tree's defence system, which includes toxic monoterpenes, to successfully complete their life cycle. A number of studies have suggested these microorganisms could have ecological roles related with the nutrition, detoxification, and semiochemical production. In particular, in filamentous fungi symbionts, cytochrome P450 (CYP) have been involved with terpenoid detoxification and biotransformation processes. Candida oregonensis has been isolated from the gut, ovaries, and frass of different bark beetle species, and it is a dominant species in the Dendroctonus rhizophagus gut. In this study, we identify, characterise, and infer the phylogenetic relationships of C. oregonensis CYP genes. The results indicate that the cytochrome P450 complement (CYPome) is composed of nine genes (CYP51F1, CYP61A1, CYP56D1, CYP52A59, CYP52A60, CYP52A61, CYP52A62, CYP5217A8, and CYP5217B1), which might participate in primary metabolic reactions such as sterol biosynthesis, biodegradation of xenobiotic, and resistance to environmental stress. The prediction of the cellular location suggests that these CYPs to be anchored to the plasma membrane, membranes of the endoplasmic reticulum, mitochondria, and peroxisomes. These findings lay the foundation for future studies about the functional role of P450s, not only for yeasts, but also for the insects with which they interact.},
}
@article {pmid27567984,
year = {2016},
author = {Dos Santos, PF and Moreira, DS and Baba, EH and Volpe, CMO and Ruiz, JC and Romanha, AJ and Murta, SMF},
title = {Molecular characterization of lipoamide dehydrogenase gene in Trypanosoma cruzi populations susceptible and resistant to benznidazole.},
journal = {Experimental parasitology},
volume = {170},
number = {},
pages = {1-9},
doi = {10.1016/j.exppara.2016.08.006},
pmid = {27567984},
issn = {1090-2449},
mesh = {Alleles ; Amino Acid Sequence ; Animals ; Blotting, Northern ; Blotting, Southern ; Cloning, Molecular ; DNA, Protozoan/chemistry/isolation &amp; purification ; Dihydrolipoamide Dehydrogenase/chemistry/*genetics ; *Drug Resistance/genetics ; Gene Dosage ; Gene Expression Regulation, Enzymologic ; Mice ; Mitochondria/enzymology ; Nitroimidazoles/*pharmacology ; Phylogeny ; RNA, Messenger/metabolism ; RNA, Protozoan/chemistry/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Trypanocidal Agents/*pharmacology ; Trypanosoma cruzi/*drug effects/*enzymology/genetics ; },
abstract = {Lipoamide dehydrogenase (LipDH) is a flavin-containing disulfide oxidoreductase from the same group of thioredoxin reductase, glutathione reductase and trypanothione reductase. This enzyme is found in the mitochondria of all aerobic organisms where it takes part in at least three important multienzyme complexes from the citric acid cycle. In this study, we performed a phylogenetic analysis comparing the amino acid sequence of the LipDH from Trypanosoma cruzi (TcLipDH) with the LipDH from other organisms. Subsequently, the copy number of the TcLipDH gene, the mRNA and protein levels, and the enzymatic activity of the LipDH were determined in populations and strains of T. cruzi that were either resistant or susceptible to benznidazole (BZ). In silico analysis showed the presence of two TcLipDH alleles in the T. cruzi genome. It also showed that TcLipDH protein has less than 55% of identity in comparison to the human LipDH, but the active site is conserved in both of them. Southern blot results suggest that the TcLipDH is a single copy gene in the genome of the T. cruzi samples analyzed. Northern blot assays showed one transcript of 2.4 kb in all T. cruzi populations. Northern blot and Real Time RT-PCR data revealed that the TcLipDH mRNA levels were 2-fold more expressed in the BZ-resistant T. cruzi population (17LER) than in its susceptible pair (17WTS). Western blot results revealed that the TcLipDH protein level is 2-fold higher in 17LER sample in comparison to 17WTS sample. In addition, LipDH activity was higher in the 17LER population than in the 17WTS. Sequencing analysis revealed that the amino acid sequences of the TcLipDH from 17WTS and 17LER populations are identical. Our findings show that one of the mechanisms associated with in vitro-induced BZ resistance to T. cruzi correlates with upregulation of LipDH enzyme.},
}
@article {pmid27591172,
year = {2016},
author = {Eyer, PA and Leniaud, L and Tinaut, A and Aron, S},
title = {Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants.},
journal = {Molecular phylogenetics and evolution},
volume = {105},
number = {},
pages = {251-262},
doi = {10.1016/j.ympev.2016.08.020},
pmid = {27591172},
issn = {1095-9513},
mesh = {Animals ; Ants/*genetics ; DNA, Mitochondrial ; Female ; Haplotypes ; *Hybridization, Genetic ; Male ; Mitochondria/genetics ; Parthenogenesis/genetics ; Phylogeny ; Phylogeography ; },
abstract = {Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.},
}
@article {pmid27593700,
year = {2016},
author = {Qin, Y and Man, B and Kosakyan, A and Lara, E and Gu, Y and Wang, H and Mitchell, EA},
title = {Nebela jiuhuensis nov. sp. (Amoebozoa; Arcellinida; Hyalospheniidae): A New Member of the Nebela saccifera - equicalceus - ansata Group Described from Sphagnum Peatlands in South-Central China.},
journal = {The Journal of eukaryotic microbiology},
volume = {63},
number = {5},
pages = {558-566},
doi = {10.1111/jeu.12300},
pmid = {27593700},
issn = {1550-7408},
mesh = {Amoeba/classification ; Amoebozoa/*classification/cytology/genetics/*isolation &amp; purification ; Animals ; Biodiversity ; China ; Classification ; DNA, Protozoan ; Ecology ; Ecosystem ; Electron Transport Complex IV/genetics ; Environmental Pollution ; Lobosea/*classification/cytology/genetics/*isolation &amp; purification ; Microscopy, Electron, Scanning ; Mitochondria/enzymology ; *Phylogeny ; Phylogeography ; Soil/parasitology ; Species Specificity ; Sphagnopsida/*parasitology ; },
abstract = {Hyalospheniids are among the most common and conspicuous testate amoebae in high-latitude peatlands and forest humus. These testate amoebae were widely studied as bioindicators and are increasingly used as models in microbial biogeography. However, data on their diversity and ecology are still very unevenly distributed geographically: notably, data are lacking for low-latitude peatlands. We describe here a new species, Nebela jiuhuensis, from peatlands near the Middle Yangtze River reach of south-central China with characteristic morphology. The test (shell) has hollow horn-like lateral extensions also found in N. saccifera, N. equicalceus (=N. hippocrepis), and N. ansata, three large species restricted mostly to Sphagnum peatlands of Eastern North America. Mitochondrial cytochrome oxidase (COI) data confirm that N. jiuhuensis is closely related to the morphologically very similar North American species N. saccifera and more distantly to N. ansata within the N. penardiana group. These species are all found in wet mosses growing in poor fens. Earlier reports of morphologically similar specimens found in South Korea peatlands suggest that N. jiuhuensis may be distributed in comparable peatlands in Eastern Asia (China and Korea). The discovery of such a conspicuous new species in Chinese peatlands suggests that many new testate amoebae species are yet to be discovered, including potential regional endemics. Furthermore, human activities (e.g., drainage, agriculture, and pollution) have reduced the known habitat of N. jiuhuensis, which can thus be considered as locally endangered. We, therefore, suggest that this very conspicuous micro-organism with a probably limited geographical distribution and specific habitat requirement should be considered as a flagship species for microbial biogeography as well as local environmental conservation and management.},
}
@article {pmid27607916,
year = {2017},
author = {Sarower, MG and Shahriar, SIM and Nakamura, H and Rouf, MA and Okada, S},
title = {Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {28},
number = {6},
pages = {935-940},
doi = {10.1080/24701394.2016.1214726},
pmid = {27607916},
issn = {2470-1408},
mesh = {Animals ; Bangladesh ; Brachyura/classification/*genetics ; Cell Nucleus/genetics ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Taxonomy of mud crabs genus Scylla has been misidentified for several years due to their high morphological plasticity. Several reports concerning mud crab have been published with misleading identification in Bangladesh. In this study, partial fragments of nuclear and mitochondrial DNA of Scylla species obtained from four locations along the Bangladesh coast were used to resolve taxonomical ambiguity of mud crab species. A single PCR product from the nuclear first internal transcribed spacer (ITS-1) marker and phylogenetic trees constructed based on 16S rDNA sequences indicated that all Scylla species obtained in this study were S. olivacea. Both molecular data and morphological characters revealed that S. olivacea is the only major species in Bangladesh coastal waters. Further, the 16S rDNA haplotypes significantly differed with known S. serrata by 33%. From this study it is clear that 'S. serrata' commonly reported from Bangladesh should be S. olivacea.},
}
@article {pmid27609637,
year = {2016},
author = {Torres-Gutierrez, C and Bergo, ES and Emerson, KJ and de Oliveira, TMP and Greni, S and Sallum, MAM},
title = {Mitochondrial COI gene as a tool in the taxonomy of mosquitoes Culex subgenus Melanoconion.},
journal = {Acta tropica},
volume = {164},
number = {},
pages = {137-149},
doi = {10.1016/j.actatropica.2016.09.007},
pmid = {27609637},
issn = {1873-6254},
mesh = {Animals ; Bayes Theorem ; Brazil ; Cluster Analysis ; Culex/classification/*genetics ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; Insect Proteins/*analysis ; Insect Vectors/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.},
}
@article {pmid27613221,
year = {2017},
author = {Pitsch, G and Adamec, L and Dirren, S and Nitsche, F and Šimek, K and Sirová, D and Posch, T},
title = {The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant.},
journal = {The Journal of eukaryotic microbiology},
volume = {64},
number = {3},
pages = {322-335},
doi = {10.1111/jeu.12369},
pmid = {27613221},
issn = {1550-7408},
mesh = {Animals ; Base Sequence ; Chlorophyta/*parasitology ; Ciliophora/*classification/metabolism/physiology ; DNA, Protozoan ; Ecology ; Ecosystem ; Life Cycle Stages ; Mitochondria/genetics ; Oligohymenophorea/*classification ; Oxygen/metabolism ; *Phylogeny ; Plants/*parasitology ; RNA, Ribosomal, 18S/genetics ; Symbiosis/*physiology ; Tetrahymena/*classification/cytology/isolation &amp; purification/metabolism ; Tetrahymena thermophila/classification/genetics ; Tracheophyta/parasitology ; },
abstract = {The genus Tetrahymena (Ciliophora, Oligohymenophorea) probably represents the best studied ciliate genus. At present, more than forty species have been described. All are colorless, i.e. they do not harbor symbiotic algae, and as aerobes they need at least microaerobic habitats. Here, we present the morphological and molecular description of the first green representative, Tetrahymena utriculariae n. sp., living in symbiosis with endosymbiotic algae identified as Micractinium sp. (Chlorophyta). The full life cycle of the ciliate species is documented, including trophonts and theronts, conjugating cells, resting cysts and dividers. This species has been discovered in an exotic habitat, namely in traps of the carnivorous aquatic plant Utricularia reflexa (originating from Okavango Delta, Botswana). Green ciliates live as commensals of the plant in this anoxic habitat. Ciliates are bacterivorous, however, symbiosis with algae is needed to satisfy cell metabolism but also to gain oxygen from symbionts. When ciliates are cultivated outside their natural habitat under aerobic conditions and fed with saturating bacterial food, they gradually become aposymbiotic. Based on phylogenetic analyses of 18S rRNA and mitochondrial cox1 genes T. utriculariae forms a sister group to Tetrahymena thermophila.},
}
@article {pmid27614431,
year = {2016},
author = {Tardu, M and Dikbas, UM and Baris, I and Kavakli, IH},
title = {RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae.},
journal = {Functional &amp; integrative genomics},
volume = {16},
number = {6},
pages = {657-669},
pmid = {27614431},
issn = {1438-7948},
mesh = {Carbon/metabolism ; Chloroplasts/genetics/radiation effects ; Extremophiles/genetics/radiation effects ; Genome, Plant/radiation effects ; High-Throughput Nucleotide Sequencing ; Light ; Mitochondria/genetics ; Photosynthesis/*genetics/radiation effects ; *Phylogeny ; Pigments, Biological/biosynthesis ; Rhodophyta/*genetics/radiation effects ; Transcriptome/*genetics/radiation effects ; },
abstract = {Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red lights were found to regulate 35 % of the total genes in C. merolae. Blue light affected the transcription of genes involved in protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.},
}
@article {pmid27630103,
year = {2016},
author = {Christodoulopoulos, G and Dinkel, A and Romig, T and Ebi, D and Mackenstedt, U and Loos-Frank, B},
title = {Cerebral and non-cerebral coenurosis: on the genotypic and phenotypic diversity of Taenia multiceps.},
journal = {Parasitology research},
volume = {115},
number = {12},
pages = {4543-4558},
pmid = {27630103},
issn = {1432-1955},
mesh = {Africa ; Animals ; *Biodiversity ; Brain/*parasitology ; Dog Diseases/*parasitology ; Dogs ; Europe ; Genotype ; Goat Diseases/*parasitology ; Goats ; Haplotypes ; Mitochondria/*genetics ; Phenotype ; Phylogeny ; Sheep ; Sheep Diseases/*parasitology ; Taenia/classification/genetics/*isolation &amp; purification ; Taeniasis/parasitology/*veterinary ; },
abstract = {We characterised the causative agents of cerebral and non-cerebral coenurosis in livestock by determining the mitochondrial genotypes and morphological phenotypes of 52 Taenia multiceps isolates from a wide geographical range in Europe, Africa, and western Asia. Three studies were conducted: (1) a morphological comparison of the rostellar hooks of cerebral and non-cerebral cysts of sheep and goats, (2) a morphological comparison of adult worms experimentally produced in dogs, and (3) a molecular analysis of three partial mitochondrial genes (nad1, cox1, and 12S rRNA) of the same isolates. No significant morphological or genetic differences were associated with the species of the intermediate host. Adult parasites originating from cerebral and non-cerebral cysts differed morphologically, e.g. the shape of the small hooks and the distribution of the testes in the mature proglottids. The phylogenetic analysis of the mitochondrial haplotypes produced three distinct clusters: one cluster including both cerebral isolates from Greece and non-cerebral isolates from tropical and subtropical countries, and two clusters including cerebral isolates from Greece. The majority of the non-cerebral specimens clustered together but did not form a monophyletic group. No monophyletic groups were observed based on geography, although specimens from the same region tended to cluster. The clustering indicates high intraspecific diversity. The phylogenetic analysis suggests that all variants of T. multiceps can cause cerebral coenurosis in sheep (which may be the ancestral phenotype), and some variants, predominantly from one genetic cluster, acquired the additional capacity to produce non-cerebral forms in goats and more rarely in sheep.},
}
@article {pmid27631278,
year = {2016},
author = {Klimov, VI and Zlatogursky, VV},
title = {Light- and Electron-microscopical Study of Belonocystis marina sp. nov. (Eukaryota: incertae sedis).},
journal = {Protist},
volume = {167},
number = {5},
pages = {479-489},
doi = {10.1016/j.protis.2016.07.003},
pmid = {27631278},
issn = {1618-0941},
mesh = {Eukaryota/classification/*ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Species Specificity ; },
abstract = {BelonocystisRainer, 1968 is an enigmatic protist genus, which currently lacks any supergroup affiliation. The spherical cells of this organism move on the substratum using fine non-branching pseudopodia. The cell surface is surrounded with a spiky covering. Belonocystis marina sp. nov. was studied using light- and electron microscopy. It was clearly shown that the surface structures of Belonocystis were scales, not a capsule. The new species could be distinguished by the morphology of the scales, which had a bulbous base with three "skirts" (circular latticed structures) and a spike consisting of many twisted fibrils. Each scale was associated with a short cytoplasmic outgrowth. The organic nature of these scales was confirmed by energy-dispersive X-ray microanalysis. Large multinucleated stages were discovered in the life-cycle of this organism. A survey of the cell ultrastructure revealed all the common eukaryotic organelles, including mitochondria with tubular cristae. No microtubules were detected in ultrathin sections of pseudopodia. Examination of food vacuole contents confirmed that this organism was bacterivorous. The finding of Belonocystis marina is the first record of the genus in a marine habitat. Many similarities in the scale structure and fine structure of the cell between Belonocystis and Luffisphaera were discussed.},
}
@article {pmid27687288,
year = {2016},
author = {Barasa, JE and Abila, R and Grobler, JP and Agaba, M and Chemoiwa, EJ and Kaunda-Arara, B},
title = {High genetic diversity and population differentiation in Clarias gariepinus of Yala Swamp: evidence from mitochondrial DNA sequences.},
journal = {Journal of fish biology},
volume = {89},
number = {6},
pages = {2557-2570},
doi = {10.1111/jfb.13150},
pmid = {27687288},
issn = {1095-8649},
mesh = {Animals ; Catfishes/*genetics ; DNA, Mitochondrial/*chemistry ; *Genetic Variation ; Haplotypes ; Kenya ; Mitochondria/genetics ; *Phylogeny ; Wetlands ; },
abstract = {In order to improve the conservation and sustainable utilization of the African catfish Clarias gariepinus of the Yala Swamp in Kenya, genetic diversity and population structure of Lakes Kanyaboli and Namboyo populations of the species were studied using DNA sequences of the mitochondrial D-loop control region. Genetic diversity inferred as haplotype and nucleotide diversities and number of singletons and shared haplotypes was higher in the Lake Kanyaboli population (LKG) than the Lake Namboyo population (LNG) of C. gariepinus. Thirty-one haplotypes were inferred, of which 25 (80·6%) were private or singletons, while only six (19·4%) haplotypes were shared between LKG and LNG. Both populations were differentiated, with FST value that was significantly different from zero (P < 0·05). Two clusters were inferred both from the maximum likelihood tree and the spanning networks of phylogenetic relationships of haplotypes. Mismatch distribution for total sample was multi-modal but individually, distributions were uni-modal in LKG, but multimodal in LNG. The mean ± s.d. raggedness index for both populations was 0·085 ± 0·098 and not significantly different from zero (P > 0·05). Individual raggedness indices were 0·015 and 0·154 for LKG and LNG respectively. Fu's Fs was negative for both populations, with LKG recording -14·871, while LNG had -2·565, significantly different from zero for LKG (P < 0·05), but the value for LNG was not significant (P > 0·05). Tajima's D was negative for both populations, with LKG recording -1·734, while LNG had -1·136. Standardized square differences (SSD) were 0·001 for LKG and 0·048 for LNG and non-significant between them (P > 0·05). Values between all populations were also not significantly different (P > 0·05), mean ± s.d. SSD 0·025 ± 0·033.},
}
@article {pmid27701290,
year = {2016},
author = {Hiruta, SF and Kakui, K},
title = {Three new brackish-water thalassocypridine species (Crustacea: Ostracoda: Paracyprididae) from the Ryukyu Islands, southwestern Japan.},
journal = {Zootaxa},
volume = {4169},
number = {3},
pages = {515-539},
doi = {10.11646/zootaxa.4169.3.6},
pmid = {27701290},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Crustacea/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Islands ; Japan ; Male ; Mitochondria/genetics ; Organ Size ; Phylogeny ; },
abstract = {We describe three new species of brackish-water ostracods representing two genera in the ostracod tribe Thalassocypridini from mangrove forests in the Ryukyu Islands, subtropical southwestern Japan, and provide their barcoding sequences for the mitochondrial cytochrome c oxidase subunit I (COI) gene. Mangalocypria ryukyuensis sp. nov. was found on Okinawa Island. We also found a Mangalocypria population on Ishigaki Island that was morphologically identical to M. ryukyuensis on Okinawa, but an individual differed by 4.7% in COI sequence (K2P distance) from an individual from Okinawa. This is the first record for Japan of a species in Mangalocypria. Paracypria longiseta sp. nov., obtained from Okinawa Island, is similar to Pontoparta hartmanni. Paracypria plumosa sp. nov. from Ishigaki Island is similar to Pa. adnata described from Yakushima Island, Japan. The COI genetic distance between individuals of Pa. longiseta and Pa. plumosa was roughly as large as that between either of these species and individuals in the Mangalocypria populations. Our study underscores that genera in Thalassocypridini may not represent natural groups, and that this tribe needs taxonomic revision.},
}
@article {pmid27701310,
year = {2016},
author = {Faille, A and Ribera, I and Fresneda, J},
title = {On the genus Aphaobius Abeille de Perrin, 1878, with description of a new species from the mesovoid shallow substratum (MSS) of Austria (Coleoptera: Leiodidae: Cholevinae: Leptodirini).},
journal = {Zootaxa},
volume = {4169},
number = {1},
pages = {44-56},
doi = {10.11646/zootaxa.4169.1.2},
pmid = {27701310},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Austria ; Body Size ; Coleoptera/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Female ; Male ; Mitochondria/genetics ; Organ Size ; Phylogeny ; },
abstract = {Aphaobius haraldi sp. n. from the mesovoid shallow substratum (MSS) of the Austrian Alps is described, illustrated, and compared with the closest species of the genus. The new species belongs to the A. kraussi species group, formerly including five species. It can be readily separated from other species of the genus by the large parameres, with an enlarged apical part, a unique feature among species of Aphaobius. The phylogenetic position of the new species is clarified using mitochondrial and nuclear data of four related species of Aphaobius, plus some representatives of related genera from the same geographic area. The diversification of the group was estimated to be recent, dating from the Pleistocene. New records and molecular data are provided regarding the enigmatic monospecific genus of the Austrian Alps, Lotharia Mandl, 1944, which was found to be sister to the studied species of Aphaobius.},
}
@article {pmid27706168,
year = {2016},
author = {Chaverri, G and Garin, I and Alberdi, A and Jimenez, L and Castillo-Salazar, C and Aihartza, J},
title = {Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest.},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0162712},
pmid = {27706168},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Central America ; Chiroptera/classification/genetics/*metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/genetics/metabolism ; Forests ; Haplotypes ; Likelihood Functions ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied, particularly for taxa that are difficult to sample such as bats. Aiming to estimate the amount of cryptic diversity among bats of a Neotropical montane cloud forest in Talamanca Range-south-east Central America-, we performed a 15-night sampling campaign, which resulted in 90 captured bats belonging to 8 species. We sequenced their mitochondrial cytochrome c oxidase subunit I (COI) and screened their inter- and intraspecific genetic variation. Phylogenetic relations with conspecifics and closely related species from other geographic regions were established using Maximum Likelihood and Bayesian inference methods, as well as median-joining haplotype networks. Mitochondrial lineages highly divergent from hitherto characterized populations (> 9% COI dissimilarity) were found in Myotis oxyotus and Hylonycteris underwoodi. Sturnira burtonlimi and M. keaysi also showed distinct mitochondrial structure with sibling species and/or populations. These results suggest that mountains in the region hold a high degree of endemicity potential that has previously been ignored in bats. They also warn of the high extinction risk montane bats may be facing due to climatic change, particularly in isolated mountain systems like Talamanca Range.},
}
@article {pmid27706563,
year = {2016},
author = {Ma, CY and Ma, HY and Ren, GJ and Wang, W and Chen, W and Lu, JX and Zou, X and Ma, LB},
title = {Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038719},
pmid = {27706563},
issn = {1676-5680},
mesh = {Animals ; Brachyura/*genetics ; Chromosome Mapping ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA ; },
abstract = {This study determined the mitochondrial genome structure of the blue swimming crab (Portunus pelagicus), and elucidated its phylogenetic relationships among the species within the order Decapoda. The complete mitochondrial genome was 16,155 bp long, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 DNA control region. The gene order of the genome was the same as that found within the family Portunidae. Twenty-three genes were on the heavy strand and 14 were on the light strand. Almost all of the protein-coding genes were initiated by an ATG codon, except for three genes (ATP6, ND1, and ND3) that started with a rare ATT codon. Of the 13 protein-coding genes, 10 ended with complete TAA or TAG stop codons and three ended with an incomplete T codon. Thirteen non-coding regions were identified that ranged from 1 to 30 bp in length. Nine overlaps were found, which ranged 1 to 7 bp in length. Phylogenetic analyses based on 12 concatenated protein-coding genes revealed that P. pelagicus formed a monophyletic group with Portunus trituberculatus, which were in a larger group with Callinectes sapidus, while the genera Charybdis and Thalamita formed another group. These two groups clustered together and grouped with the genus Scylla. The phylogenetic analysis supported the inclusion of Charybdis in subfamily Portuninae of the family Portunidae, and revealed a close relationship between Charybdis and Thalamita. We suggest that Thalamita should also be classified into the subfamily Portuninae. The results can be used in the study of phylogenetic, population genetic and conservation genetics of P. pelagicus.},
}
@article {pmid27706641,
year = {2016},
author = {Cao, YY and Li, ZB},
title = {Genetic diversity and population structure of Fenneropenaeus penicillatus determined by mitochondrial DNA analyses.},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038503},
pmid = {27706641},
issn = {1676-5680},
mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Haplotypes ; *Microsatellite Repeats ; Mitochondria/genetics ; Penaeidae/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Fenneropenaeus penicillatus is a widely distributed economically and ecologically important shrimp species, which is endangered in China. Sequence analysis of 16s rRNA and control region (CR) fragments from mitochondrial DNA was conducted to obtain information on genetic diversity and population structure. Individuals from 12 wild F. penicillatus populations located along the southeast coast of China were used. Polymerase chain reaction (PCR) fragments of the CR gene revealed high genetic diversity among the 12 populations; however, PCR fragments of the 16s rRNA gene revealed very low genetic diversity in the Hainan (HN) and Ningde (ND) populations and high genetic diversity in the DS, BH, PT, XM, and SZ populations. Data obtained from the CR and 16s rRNA genes suggested that high genetic differentiation exists among the 12 populations, which is mainly due to the high genetic differentiation between HN and all other 11 populations. These results may be useful for further sustainable management and utilization of this species.},
}
@article {pmid27706654,
year = {2016},
author = {Ma, HY and Ma, CY and Zhu, JJ and Ren, GJ and Wang, W and Chen, W and Lu, JX and Ma, LB},
title = {Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus).},
journal = {Genetics and molecular research : GMR},
volume = {15},
number = {3},
pages = {},
doi = {10.4238/gmr.15038580},
pmid = {27706654},
issn = {1676-5680},
mesh = {Animals ; Arthropod Proteins/*genetics ; Brachyura/classification/*genetics ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/*genetics ; Genome Size ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; Open Reading Frames ; *Phylogeny ; RNA, Transfer/chemistry/genetics ; },
abstract = {In this study, we determined the whole mitochondrial genome profile of the three-spot swimming crab (Portunus sanguinolentus) and elucidated phylogenetic relationships between representative species in the order Decapoda. The mitochondrial genome was 16,024 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Of the 37 genes, 23 were encoded by the heavy strand while 14 were encoded by the light strand. Four types of start codons were identified; ATG initiated nine genes, ATT initiated two genes, and ATC and GTG each started one gene. Nine protein-coding genes ended with a complete TAA or TAG stop codon, and four genes ended with an incomplete T or TA codon. Fourteen non-coding regions were found, which ranged from 1 to 34 bp in length. Nine overlaps were observed, with lengths between 1 and 7 bp. Phylogenetic analysis suggested that P. sanguinolentus is genetically closest to P. trituberculatus and P. pelagicus. Charybdis feriata, C. japonica, and Thalamita crenata formed a single cluster, and were close to the genera Callinectes and Portunus. Therefore, the genera Charybdis and Thalamita should be classified into the subfamily Portuninae.},
}
@article {pmid27732624,
year = {2016},
author = {Gollner, S and Stuckas, H and Kihara, TC and Laurent, S and Kodami, S and Martinez Arbizu, P},
title = {Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.},
journal = {PloS one},
volume = {11},
number = {10},
pages = {e0163776},
pmid = {27732624},
issn = {1932-6203},
mesh = {Animals ; Copepoda/classification/*genetics ; DNA, Mitochondrial/chemistry/isolation &amp; purification/*metabolism ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Microscopy, Confocal ; Mitochondria/*genetics ; Oceans and Seas ; Phylogeny ; Population Growth ; Sequence Analysis, DNA ; },
abstract = {Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings.},
}
@article {pmid27765655,
year = {2016},
author = {Rajvanshi, S and Choudhary, K and Agrawal, N},
title = {Threading: A novel insilico indagation method for genetic characterization of some diplostomoid metacercariae (Digenea:Diplostomidae Poirier, 1886).},
journal = {Experimental parasitology},
volume = {171},
number = {},
pages = {71-76},
doi = {10.1016/j.exppara.2016.10.013},
pmid = {27765655},
issn = {1090-2449},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/chemistry ; Fish Diseases/parasitology ; Fishes ; Helminth Proteins/*chemistry/genetics ; Imaging, Three-Dimensional ; Metacercariae/chemistry/classification/genetics ; Mitochondria/enzymology ; Models, Biological ; Models, Structural ; Molecular Conformation ; Phylogeny ; Protein Conformation ; Proteomics ; Trematoda/chemistry/classification/*genetics ; Trematode Infections/parasitology/veterinary ; },
abstract = {The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools. Various aspects have been utilized herein for re-validation and infallible discrimination of Trematode diplostomoid metacercariae (Tetracotyle lucknowensis Pandey, 1971; T. xenentodoni Chakrabarti, 1970; T. fausti Rai and Pande, 1969; T. muscularius Chakrabarti, 1970 and Diplostomulum minutum Pandey, 1968), the infective stage in the life cycle, causing severe damage to fish host, whose adults are found mainly in fish eating birds and mammals.},
}
@article {pmid27767210,
year = {2017},
author = {Nakada, T and Tomita, M},
title = {Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae).},
journal = {Journal of phycology},
volume = {53},
number = {1},
pages = {108-117},
doi = {10.1111/jpy.12484},
pmid = {27767210},
issn = {1529-8817},
mesh = {Algal Proteins/genetics ; Amino Acid Sequence ; Japan ; Microscopy, Electron, Transmission ; *Phylogeny ; Sequence Alignment ; Species Specificity ; Volvocida/*classification/cytology/genetics/*ultrastructure ; },
abstract = {New strains of a wall-less unicellular volvocalean flagellate were isolated from a freshwater environment in Japan. Observations of the alga, described here as Hapalochloris nozakii Nakada, gen. et sp. nov., were made using light, fluorescence, and electron microscopy. Each vegetative cell had two flagella, four contractile vacuoles, and a spirally furrowed cup-shaped chloroplast with an axial pyrenoid, and mitochondria located in the furrows. Based on the morphology, H. nozakii was distinguished from other known wall-less volvocalean flagellates. Under electron microscopy, fibrous material, instead of a cell wall and dense cortical microtubules, was observed outside and inside the cell membrane, respectively. Based on the phylogenetic analyses of 18S rRNA gene sequences, H. nozakii was found to be closely related to Asterococcus, Oogamochlamys, Rhysamphichloris, and "Dunaliella" lateralis and was separated from other known wall-less flagellate volvocaleans, indicating independent secondary loss of the cell wall in H. nozakii. In the combined 18S rRNA and chloroplast gene tree, H. nozakii was sister to Lobochlamys.},
}
@article {pmid27812024,
year = {2016},
author = {Jiang, F and Pan, X and Li, X and Yu, Y and Zhang, J and Jiang, H and Dou, L and Zhu, S},
title = {The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe.},
journal = {Scientific reports},
volume = {6},
number = {},
pages = {36426},
pmid = {27812024},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Codon, Terminator ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; Tephritidae/classification/*genetics ; },
abstract = {The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.},
}
@article {pmid27814661,
year = {2017},
author = {Morley, SA and Nielsen, BL},
title = {Plant mitochondrial DNA.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {22},
number = {6},
pages = {1023-1032},
doi = {10.2741/4531},
pmid = {27814661},
issn = {2768-6698},
support = {R15 GM066787/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA Replication ; DNA, Mitochondrial/*genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Genome, Mitochondrial ; Genome, Plant ; Mitochondria/genetics/metabolism ; Phylogeny ; },
abstract = {Plants possess mitochondrial genomes that are large and complex compared to animals. Nearly all animal mitochondrial genomes are about 16.5. kbp in length, whereas plant mitochondrial genomes range between 200-2,000 kbp. This is curious if we assume modern mitochondria originated from a common alpha-proteobacterial ancestor. Despite their size, plant mitochondrial genomes do not contain significantly more genes than their animal counterparts. Most of the additional DNA found in plant mitochondrial genomes consists of large introns, repeats and non-coding regions. Furthermore, plant mtDNA does not exist as large circular DNA molecules but mostly as a collection of linear DNA with combinations of smaller circular and branched molecules. Studies into these highly fragmented genomes heavily imply that recombination is the main mechanism driving replication of plant mtDNA.},
}
@article {pmid27821209,
year = {2017},
author = {Adriano, EA and Okamura, B},
title = {Motility, morphology and phylogeny of the plasmodial worm, Ceratomyxa vermiformis n. sp. (Cnidaria: Myxozoa: Myxosporea).},
journal = {Parasitology},
volume = {144},
number = {2},
pages = {158-168},
doi = {10.1017/S0031182016001852},
pmid = {27821209},
issn = {1469-8161},
mesh = {Animals ; Brazil ; Fish Diseases/epidemiology/parasitology ; Fishes ; Motor Activity/*physiology ; Myxozoa/*genetics/*physiology/ultrastructure ; *Phylogeny ; Rivers ; Species Specificity ; Spores ; },
abstract = {The Myxozoa demonstrate extensive morphological simplification and miniaturization relative to their free-living cnidarian ancestors. This is particularly pronounced in the highly derived myxosporeans, which develop as plasmodia and pseudoplasmodia. To date, motility in these stages has been linked with membrane deformation (e.g. as pseudopodia and mobile folds). Here we illustrate a motile, elongate plasmodium that undergoes coordinated undulatory locomotion, revealing remarkable convergence to a functional worm at the cellular level. Ultrastructural and confocal analyses of these plasmodia identify a highly differentiated external layer containing an actin-rich network, long tubular mitochondria, abundant microtubules, a secreted glycocalyx layer, and an internal region where sporogony occurs and which contains homogeneously distributed granular/fibrillar material. We consider how some of these features may support motility. We also describe the species based on spore morphology and SSU rDNA sequence data, undertake molecular phylogenetic analysis to place it within an early-diverging clade of the ceratomyxids, and evaluate the resultant implications for classification (validity of the genus Meglitschia) and for inferring early host environments (freshwater) of ceratomyxids.},
}
@article {pmid27825872,
year = {2017},
author = {Reem, E and Douek, J and Paz, G and Katzir, G and Rinkevich, B},
title = {Phylogenetics, biogeography and population genetics of the ascidian Botryllus schlosseri in the Mediterranean Sea and beyond.},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {221-231},
doi = {10.1016/j.ympev.2016.10.005},
pmid = {27825872},
issn = {1095-9513},
mesh = {Alleles ; Animals ; Base Sequence ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Principal Component Analysis ; Urochordata/*classification/*genetics ; },
abstract = {The wide distribution of the ascidian Botryllus schlosseri along the Mediterranean coasts has been documented since the eighteenth century. However, despite copious documentation, analyses of dispersal modes and genetic profiles were limited to local populations or restricted regions. In order to get a pan-Mediterranean overview, 288 specimens from 11 populations of B. schlosseri from the western and eastern Mediterranean basins were sampled and analyzed using five microsatellite loci and COI sequences. Both molecular markers revealed high polymorphisms, with 182 microsatellites alleles and 54 COI haplotypes. Overall, Fst, Dest, and COI Фpt values were 0.146, 0.635 and 0.322, respectively, reflecting a high genetic diversity and a significant genetic structure as compared to other B. schlosseri populations worldwide, reflected by substantially higher values for effective number of alleles (Ne) in the Mediterranean. A phylogenetic analysis of the COI sequences resulted in four distinct clades and two molecular operational taxonomic units (OTUs). We recorded a stronger genetic structure among the populations of the eastern basin compared to the western basin (microsatellites Fst=0.217 versus 0.082; COI Фpt=0.416 versus 0.171), suggesting either a restricted connectivity between the basins or a stronger genetic drift in each basin. The occurrence of two OTUs and different ecological conditions may also contribute to this finding. Mean Nei's genetic distance in the eastern Mediterranean populations was more than three times higher compared to the western basin. No correlation was observed between geographic and genetic distances (Mantel test), suggesting that maritime transport is the main dispersal vector of B. schlosseri colonies. The possibility that the Mediterranean is a center of diversity for B. schlosseri, and probably its site of origin, is further discussed.},
}
@article {pmid27833995,
year = {2017},
author = {Thomas, P and Sekhar, AC},
title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.},
journal = {Microbial ecology},
volume = {73},
number = {4},
pages = {885-899},
pmid = {27833995},
issn = {1432-184X},
mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation &amp; purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.},
}
@article {pmid27837088,
year = {2017},
author = {Garibay-Hernández, A and Barkla, BJ and Vera-Estrella, R and Martinez, A and Pantoja, O},
title = {Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga.},
journal = {Plant physiology},
volume = {173},
number = {1},
pages = {390-416},
pmid = {27837088},
issn = {1532-2548},
mesh = {Algal Proteins/*metabolism ; Base Sequence ; Carbon/metabolism ; Cell Membrane/*metabolism ; Electron Transport ; Electrophoresis ; Lipid Metabolism ; Mass Spectrometry ; Membrane Proteins/chemistry/*metabolism ; Microalgae/*classification/metabolism/*physiology ; Mitochondria/metabolism ; Oxidative Phosphorylation ; Photosynthesis ; Phylogeny ; Protein Domains ; Proteome/*metabolism ; Proteomics/*methods ; Subcellular Fractions/metabolism ; },
abstract = {Ettlia oleoabundans is a nonsequenced oleaginous green microalga. Despite the significant biotechnological interest in producing value-added compounds from the acyl lipids of this microalga, a basic understanding of the physiology and biochemistry of oleaginous microalgae is lacking, especially under nitrogen deprivation conditions known to trigger lipid accumulation. Using an RNA sequencing-based proteomics approach together with manual annotation, we are able to provide, to our knowledge, the first membrane proteome of an oleaginous microalga. This approach allowed the identification of novel proteins in E. oleoabundans, including two photoprotection-related proteins, Photosystem II Subunit S and Maintenance of Photosystem II under High Light1, which were considered exclusive to higher photosynthetic organisms, as well as Retinitis Pigmentosa Type 2-Clathrin Light Chain, a membrane protein with a novel domain architecture. Free-flow zonal electrophoresis of microalgal membranes coupled to liquid chromatography-tandem mass spectrometry proved to be a useful technique for determining the intracellular location of proteins of interest. Carbon-flow compartmentalization in E. oleoabundans was modeled using this information. Molecular phylogenetic analyses of protein markers and 18S ribosomal DNA support the reclassification of E. oleoabundans within the trebouxiophycean microalgae, rather than with the Chlorophyceae class, in which it is currently classified, indicating that it may not be closely related to the model green alga Chlamydomonas reinhardtii A detailed survey of biological processes taking place in the membranes of nitrogen-deprived E. oleoabundans, including lipid metabolism, provides insights into the basic biology of this nonmodel organism.},
}
@article {pmid27841052,
year = {2018},
author = {E, GX and Zhao, YJ and Huang, YF},
title = {Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {1},
pages = {91-95},
doi = {10.1080/24701394.2016.1242582},
pmid = {27841052},
issn = {2470-1408},
mesh = {Animals ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Regulatory Sequences, Nucleic Acid ; Sheep/*genetics ; *Tandem Repeat Sequences ; },
abstract = {The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.},
}
@article {pmid27864892,
year = {2017},
author = {Haenel, GJ},
title = {Introgression of mtDNA in Urosaurus lizards: historical and ecological processes.},
journal = {Molecular ecology},
volume = {26},
number = {2},
pages = {606-623},
doi = {10.1111/mec.13930},
pmid = {27864892},
issn = {1365-294X},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Female ; *Genetics, Population ; Genome, Mitochondrial ; *Hybridization, Genetic ; Lizards/*genetics ; Male ; Microsatellite Repeats ; Phylogeny ; },
abstract = {Introgression of mtDNA appears common in animals, but the implications of acquiring a novel mitochondrial genome are not well known. This study investigates mito-genome introgression between the lizard species Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that occupies a wider range of thermal environments. As ectotherms, their metabolic rate is strongly influenced by the thermal environment; with mitochondria being linked to metabolic rates, overall energy budgets could be impacted by introgression. I use mitochondrial gene trees, inferred from Bayesian analyses of Cyt-B and ND1 gene sequences, along with morphology and microsatellites from nineteen populations of these two species to address if the direction and location of mito-nuclear discordance match predictions of introgression resulting from past population expansions. MtDNA is expected to move from resident species into expanding or invading species. Second, does having a heterospecific form of mitochondria impact body size, a trait strongly associated with fitness? Multiple independent introgression events of historic origin were detected. All introgression was unidirectional with U. ornatus-type mtDNA found in U. graciosus parental type individuals. This result was consistent with population expansions detected in U. graciosus but not U. ornatus. Females with heterospecific mtDNA were significantly smaller than homospecific forms, and heterospecific males had a different relationship of body mass to body length than those with homospecific mtDNA. These changes indicate a potential selective disadvantage for individuals with heterospecific mitochondria and are consistent with the theoretical expectation that deleterious alleles are more likely to persist in expanding populations.},
}
@article {pmid27876802,
year = {2016},
author = {Mottawea, W and Chiang, CK and Mühlbauer, M and Starr, AE and Butcher, J and Abujamel, T and Deeke, SA and Brandel, A and Zhou, H and Shokralla, S and Hajibabaei, M and Singleton, R and Benchimol, EI and Jobin, C and Mack, DR and Figeys, D and Stintzi, A},
title = {Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn's disease.},
journal = {Nature communications},
volume = {7},
number = {},
pages = {13419},
pmid = {27876802},
issn = {2041-1723},
support = {R01 DK073338/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; R01 DK047700/DK/NIDDK NIH HHS/United States ; R21 CA195226/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; },
mesh = {Adolescent ; Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; Crohn Disease/*microbiology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Interleukin-10/genetics/metabolism ; Male ; Mice ; Mice, Knockout ; Phylogeny ; },
abstract = {Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. In this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. We report an altered host proteome in CD patients indicative of impaired mitochondrial functions. In particular, mitochondrial proteins implicated in H2S detoxification are downregulated, while the relative abundance of H2S microbial producers is increased. Network correlation analysis reveals that Atopobium parvulum controls the central hub of H2S producers. A. parvulum induces pancolitis in colitis-susceptible interleukin-10-deficient mice and this phenotype requires the presence of the intestinal microbiota. Administrating the H2S scavenger bismuth mitigates A. parvulum-induced colitis in vivo. This study reveals that host-microbiota interactions are disturbed in CD and thus provides mechanistic insights into CD pathogenesis.},
}
@article {pmid27956259,
year = {2017},
author = {Burzyński, A and Soroka, M and Mioduchowska, M and Kaczmarczyk, A and Sell, J},
title = {The complete maternal and paternal mitochondrial genomes of Unio crassus: Mitochondrial molecular clock and the overconfidence of molecular dating.},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {605-608},
doi = {10.1016/j.ympev.2016.12.007},
pmid = {27956259},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Time Factors ; Unio/*genetics ; },
abstract = {The availability of a rapidly growing number of complete mitochondrial genome sequences provokes high confidence dating approaches. However, even if the congruence between mitochondrial and nuclear markers is reasonable, the resulting topologies are frequently questionable. The unique opportunity to study the evolutionary history of two independent mitochondrial genomes in one phylogenetic context exists in the freshwater mussels family Unionidae. The two lineages function under doubly uniparental inheritance since well before the emergence of the family. Despite the relatively high number of available complete sequences of maternally inherited genomes, comparative analyses are limited by the small number of sequences of counterpart paternally inherited genomes. We have sequenced for the first time the representative set of five sequences (two maternal and three paternal) from the species Unio crassus. Comparative analysis of the phylogenies reconstructed using relevant mitogenomic data available in GenBank (13 species in total) reveal that single - genome inferences are congruent only if the relaxed clock is assumed.},
}
@article {pmid27989633,
year = {2017},
author = {Kyei-Poku, G and Sokolova, YY},
title = {The microsporidium Nosema disstriae (Thomson 1959): Fine structure and phylogenetic position within the N. bombycis clade.},
journal = {Journal of invertebrate pathology},
volume = {143},
number = {},
pages = {90-103},
doi = {10.1016/j.jip.2016.12.003},
pmid = {27989633},
issn = {1096-0805},
mesh = {Animals ; Lepidoptera/parasitology ; Microscopy, Electron ; Microsporidiosis/veterinary ; Nosema/*genetics/*ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {A microsporidium Nosema disstriae (Thomson) is a parasite of the forest tent caterpillar Malacasoma disstria (Lepidoptera: Lasiocampidae), a notable defoliator of deciduous trees in North America. The goal of this paper was to demonstrate the ultrastructure of N. disstriae and to determine the position of this microsporidium within the N. bombycis clade (NBC) using comparative morphology and multiple molecular phylogenetic markers: RPB1, LSU-, ITS- and SSU-rDNA. As a part of this goal, the revision of the described members of the NBC has been performed. The ultrastructure of proliferating stages and spores of N. disstriae were similar to previously described Nosema spp. parasitizing lepidopteran species. Meronts produced tubular-like structures on their surfaces and exhibited a tight association with host mitochondria. All stages were diplokaryotic and developed without interfacial envelopes. Disporoblastic sporogony produced typical Nosema-type spores with 9-12 polar filament coils. A vesicle with immature spores was once recognized on sections, concordant with the previous record of octosporous sporogony in the N. disstriae life cycle. Rarely, spores with thinner envelopes and large posterior vacuoles were seen in the midgut. Tracheae were most heavily infected. Midgut, surrounding muscles, haemocytes and fat body also contained microsporidia. SSUrRNA-inferred phylogenies were consistent with previously published articles and did not resolve the relation within the NBC clade. The RPB1-inferred trees and concatenated RPB1 and LSU-ITS-SSUrDNA-based trees demonstrated clustering of N. disstriae with N. antheraeae as early divergent species within the NBC.},
}
@article {pmid27989883,
year = {2017},
author = {Saikia, BB and Dubey, SK and Shanmugam, MK and Sundaresan, P},
title = {Whole mitochondrial genome analysis in South Indian patients with Leber's hereditary optic neuropathy.},
journal = {Mitochondrion},
volume = {36},
number = {},
pages = {21-28},
doi = {10.1016/j.mito.2016.10.006},
pmid = {27989883},
issn = {1872-8278},
mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; Haplotypes ; Humans ; India ; Male ; Mutation Rate ; Optic Atrophy, Hereditary, Leber/*genetics/*pathology ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {Leber's hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) associated neurodegenerative disorder of retinal ganglion cells. In this study, whole mitochondrial genome sequencing of 75 LHON patients and 40 controls was performed to identify the mutation frequency and haplogroup background of South Indian population. Analysis of mtDNA revealed 559 different variants in LHON patients, including 7 pathogenic mutations, 30 private, and 22 other disease associated variants. A significantly higher (p=0.0008) overall variation load per individual was noted among LHON patients versus controls. We reported for the first time, the association of M haplogroup (p=0.028) with LHON in this cohort.},
}
@article {pmid28007567,
year = {2017},
author = {Cornils, A and Wend-Heckmann, B and Held, C},
title = {Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages?.},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {473-485},
doi = {10.1016/j.ympev.2016.12.019},
pmid = {28007567},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Copepoda/*classification ; Electron Transport Complex IV/genetics ; Genetic Variation ; Haplotypes/genetics ; *Internationality ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Plankton/*classification ; Species Specificity ; Time Factors ; },
abstract = {Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.},
}
@article {pmid28017858,
year = {2017},
author = {Podsiadlowski, L and Gamauf, A and Töpfer, T},
title = {Revising the phylogenetic position of the extinct Mascarene Parrot Mascarinus mascarin (Linnaeus 1771) (Aves: Psittaciformes: Psittacidae).},
journal = {Molecular phylogenetics and evolution},
volume = {107},
number = {},
pages = {499-502},
doi = {10.1016/j.ympev.2016.12.022},
pmid = {28017858},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; Genetic Loci ; Mitochondria/genetics ; Parrots/*classification ; *Phylogeny ; Polymorphism, Genetic ; Sequence Alignment ; Species Specificity ; },
abstract = {The phylogenetic position of the extinct Mascarene Parrot Mascarinus mascarin from La Réunion has been unresolved for centuries. A recent molecular study unexpectedly placed M. mascarin within the clade of phenotypically very different Vasa parrots Coracopsis. Based on DNA extracted from the only other preserved Mascarinus specimen, we show that the previously obtained cytb sequence is probably an artificial composite of partial sequences from two other parrot species and that M. mascarin is indeed a part of the Psittacula diversification, placed close to P. eupatria and P. wardi.},
}
@article {pmid28025274,
year = {2017},
author = {Bourguignon, T and Lo, N and Šobotník, J and Ho, SY and Iqbal, N and Coissac, E and Lee, M and Jendryka, MM and Sillam-Dussès, D and Krížková, B and Roisin, Y and Evans, TA},
title = {Mitochondrial Phylogenomics Resolves the Global Spread of Higher Termites, Ecosystem Engineers of the Tropics.},
journal = {Molecular biology and evolution},
volume = {34},
number = {3},
pages = {589-597},
doi = {10.1093/molbev/msw253},
pmid = {28025274},
issn = {1537-1719},
mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; Genome, Mitochondrial ; Introduced Species ; Isoptera/*genetics/growth &amp; development ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Rainforest ; },
abstract = {The higher termites (Termitidae) are keystone species and ecosystem engineers. They have exceptional biomass and play important roles in decomposition of dead plant matter, in soil manipulation, and as the primary food for many animals, especially in the tropics. Higher termites are most diverse in rainforests, with estimated origins in the late Eocene (∼54 Ma), postdating the breakup of Pangaea and Gondwana when most continents became separated. Since termites are poor fliers, their origin and spread across the globe requires alternative explanation. Here, we show that higher termites originated 42-54 Ma in Africa and subsequently underwent at least 24 dispersal events between the continents in two main periods. Using phylogenetic analyses of mitochondrial genomes from 415 species, including all higher termite taxonomic and feeding groups, we inferred 10 dispersal events to South America and Asia 35-23 Ma, coinciding with the sharp decrease in global temperature, sea level, and rainforest cover in the Oligocene. After global temperatures increased, 23-5 Ma, there was only one more dispersal to South America but 11 to Asia and Australia, and one dispersal back to Africa. Most of these dispersal events were transoceanic and might have occurred via floating logs. The spread of higher termites across oceans was helped by the novel ecological opportunities brought about by environmental and ecosystem change, and led termites to become one of the few insect groups with specialized mammal predators. This has parallels with modern invasive species that have been able to thrive in human-impacted ecosystems.},
}
@article {pmid28029387,
year = {2016},
author = {Gracielle, IM and Tidon, R and Báo, SN},
title = {Structure and ultrastructure of spermatozoon in six species of Drosophilidae (Diptera).},
journal = {Tissue &amp; cell},
volume = {48},
number = {6},
pages = {596-604},
doi = {10.1016/j.tice.2016.10.001},
pmid = {28029387},
issn = {1532-3072},
mesh = {Acrosome/ultrastructure ; Animals ; Axoneme/*ultrastructure ; Cell Nucleus/genetics/ultrastructure ; Drosophila/genetics/*ultrastructure ; Male ; Mitochondria/ultrastructure ; *Phylogeny ; Spermatozoa/*ultrastructure ; Testis/ultrastructure ; },
abstract = {The Drosophilidae family is formed by Brachycera Diptera distributed widely across different regions of the planet. It is composed of about 4000 species, 304 of which are found in Brazil. The objective of this work was to characterize morphologically the structure of the male internal reproductive apparatus and the ultrastructure of the spermatozoon in four Neotropical (Drosophila cardini, D. mercatorum, D. nebulosa and D. sturtevanti) and two invasive (D. simulans and Zaprionus indianus) species of drosophilids. The structural aspect of the internal reproductive apparatus corresponds with that described for other drosophilids; however, there are differences in the size and coloration of the structures, such as the testes, in each species analyzed. The spermatozoon of these species was seen to be long and fine, presenting morphological variation. The ultrastructure of the spermatozoon revealed that the morphological pattern is similar to that found in the majority of insects. The head region presents a nucleus with condensed chromatin and the acrosome positioned laterally to the nucleus. In the tail region, the axoneme presents the 9+9+2 pattern commonly described for other species of Diptera. The species presented differences regarding the shape and size of the mitochondrial derivatives. Cytochemical analysis using EPTA also revealed differences in terms of the location of the basic proteins in the mitochondrial derivates. The results obtained contribute to expanding the database for the Drosophilidae family, providing information that may contribute to intra- and inter-specific identification and supplying phylogenetic analyses.},
}
@article {pmid28031475,
year = {2017},
author = {Teardo, E and Carraretto, L and Wagner, S and Formentin, E and Behera, S and De Bortoli, S and Larosa, V and Fuchs, P and Lo Schiavo, F and Raffaello, A and Rizzuto, R and Costa, A and Schwarzländer, M and Szabò, I},
title = {Physiological Characterization of a Plant Mitochondrial Calcium Uniporter in Vitro and in Vivo.},
journal = {Plant physiology},
volume = {173},
number = {2},
pages = {1355-1370},
pmid = {28031475},
issn = {1532-2548},
mesh = {Arabidopsis/cytology/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Calcium/metabolism ; Calcium Channels/genetics/*metabolism ; Calcium-Binding Proteins/metabolism ; Gene Expression Regulation, Plant ; Mitochondria/genetics/metabolism/ultrastructure ; Mutation ; Phylogeny ; Plant Proteins/genetics ; Plant Roots/genetics/metabolism ; },
abstract = {Over the recent years, several proteins that make up the mitochondrial calcium uniporter complex (MCUC) mediating Ca[2+]uptake into the mitochondrial matrix have been identified in mammals, including the channel-forming protein MCU. Although six MCU gene homologs are conserved in the model plant Arabidopsis (Arabidopsis thaliana) in which mitochondria can accumulate Ca[2+], a functional characterization of plant MCU homologs has been lacking. Using electrophysiology, we show that one isoform, AtMCU1, gives rise to a Ca[2+]-permeable channel activity that can be observed even in the absence of accessory proteins implicated in the formation of the active mammalian channel. Furthermore, we provide direct evidence that AtMCU1 activity is sensitive to the mitochondrial calcium uniporter inhibitors Ruthenium Red and Gd[3+], as well as to the Arabidopsis protein MICU, a regulatory MCUC component. AtMCU1 is prevalently expressed in roots, localizes to mitochondria, and its absence causes mild changes in Ca[2+] dynamics as assessed by in vivo measurements in Arabidopsis root tips. Plants either lacking or overexpressing AtMCU1 display root mitochondria with altered ultrastructure and show shorter primary roots under restrictive growth conditions. In summary, our work adds evolutionary depth to the investigation of mitochondrial Ca[2+] transport, indicates that AtMCU1, together with MICU as a regulator, represents a functional configuration of the plant mitochondrial Ca[2+] uptake complex with differences to the mammalian MCUC, and identifies a new player of the intracellular Ca[2+] regulation network in plants.},
}
@article {pmid28034779,
year = {2017},
author = {Huang, HJ and Liu, CW and Zhou, X and Zhang, CX and Bao, YY},
title = {A mitochondrial membrane protein is a target for rice ragged stunt virus in its insect vector.},
journal = {Virus research},
volume = {229},
number = {},
pages = {48-56},
doi = {10.1016/j.virusres.2016.12.016},
pmid = {28034779},
issn = {1872-7492},
mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics/metabolism ; Gene Expression Regulation ; Glutathione Transferase/genetics/metabolism ; Hemiptera/classification/metabolism/ultrastructure/*virology ; Insect Proteins/*genetics/metabolism ; Insect Vectors/metabolism/ultrastructure/virology ; Membrane Proteins/*genetics/metabolism ; Mitochondria/metabolism/ultrastructure/*virology ; Mitochondrial Proton-Translocating ATPases ; Oryza/parasitology/*virology ; Phylogeny ; Plant Diseases/parasitology/virology ; Protein Binding ; RNA, Small Interfering/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reoviridae/*genetics/growth &amp; development/metabolism ; Salivary Glands/metabolism/ultrastructure/virology ; Sequence Alignment ; Two-Hybrid System Techniques ; Viral Load ; Viral Nonstructural Proteins/*genetics/metabolism ; Virion/genetics/growth &amp; development/metabolism ; },
abstract = {Rice ragged stunt virus (RRSV; Reoviridae) is exclusively transmitted by the brown planthopper Nilaparvata lugens in a persistent-propagative manner. It is understood that RNA viral proliferation is associated with the intracellular membranes of the insect host cells. However, the molecular mechanisms of the interaction between the RRSV proliferation and the intracellular membranes remain essentially unknown. It will be of great interest to determine whether RRSV protein(s) directly interact with intracellular membrane components of its host cells. In this study, we identified a RRSV nonstructural protein Pns10 interacting with a host oligomycin-sensitivity conferral protein (OSCP) using yeast two-hybrid system. The interaction between RRSV Pns10 and N. lugens OSCP was verified by a glutathione S-transferase pull-down assay. Confocal miscopy revealed colocalization of these two proteins in the cytoplasm of the salivary gland cells during the viral infection. The virions were further detected in the mitochondria under confocal miscopy and transmission electron microscopy combined with western blotting assay. This is the first observation that RRSV protein has a direct link with mitochondria. Suppressing OSCP gene expression by RNA interference notably decreased the viral loads in RRSV-infected insects. These findings revealed novel aspects of a viral protein in targeting the host mitochondrial membrane and provide insights concerning the mitochondrial membrane protein-based virus proliferation mode in the insect vector.},
}
@article {pmid28052087,
year = {2017},
author = {Grange, LJ and Smith, CR and Lindsay, DJ and Bentlage, B and Youngbluth, MJ},
title = {High Abundance of the Epibenthic Trachymedusa Ptychogastria polaris Allman, 1878 (Hydrozoa, Trachylina) in Subpolar Fjords along the West Antarctic Peninsula.},
journal = {PloS one},
volume = {12},
number = {1},
pages = {e0168648},
pmid = {28052087},
issn = {1932-6203},
mesh = {Animals ; Antarctic Regions ; Bayes Theorem ; Bays ; Body Size ; *Ecosystem ; Electron Transport Complex IV/metabolism ; *Estuaries ; Geography ; Hydrozoa/anatomy &amp; histology/classification/*physiology ; Image Processing, Computer-Assisted ; Mitochondria/enzymology ; Oceans and Seas ; Phylogeny ; },
abstract = {Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P. polaris was recorded in Antarctic Peninsula waters. The trachymedusa, identified from megacore-collected specimens, was a common component of the epifauna in the sediment floored basins at 436-725 m depths in Andvord and Flandres Bays, reaching densities up to 13 m-2, with mean densities in individual basins ranging from 0.06 to 4.19 m-2. These densities are 2 to 400-fold higher than previously reported for P. polaris in either the Arctic or Antarctic. This trachymedusa had an aggregated distribution, occurring frequently in Andvord Bay, but was often solitary in Flandres Bay, with a distribution not significantly different from random. Epibenthic individuals were similar in size, typically measuring 15-25 mm in bell diameter. A morphologically similar trachymedusa, presumably the same species, was also observed in the water column near the bottom in all three fjords. This benthopelagic form attained abundances of up to 7 m-2 of seafloor; however, most P. polaris (~ 80%), were observed on soft sediments. Our findings indicate that fjords provide a prime habitat for the development of dense populations of P. polaris, potentially resulting from high and varied food inputs to the fjord floors. Because P. polaris resides in the water column and at the seafloor, large P. polaris populations may contribute significantly to pelagic-benthic coupling in the WAP fjord ecosystems.},
}
@article {pmid28059116,
year = {2017},
author = {Wang, Q and Zhang, C and Wang, C and Qian, Y and Li, Z and Hong, J and Zhou, X},
title = {Further characterization of Maize chlorotic mottle virus and its synergistic interaction with Sugarcane mosaic virus in maize.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {39960},
pmid = {28059116},
issn = {2045-2322},
mesh = {China ; Chloroplasts/physiology/virology ; Gammaherpesvirinae/classification/genetics/isolation &amp; purification/*pathogenicity ; Mitochondria/virology ; Photosynthesis ; Phylogeny ; Plant Diseases/*virology ; Potyvirus/classification/genetics/isolation &amp; purification/*pathogenicity ; Zea mays/*virology ; },
abstract = {Maize chlorotic mottle virus (MCMV) was first reported in maize in China in 2009. In this study we further analyzed the epidemiology of MCMV and corn lethal necrosis disease (CLND) in China. We determined that CLND observed in China was caused by co-infection of MCMV and sugarcane mosaic virus (SCMV). Phylogenetic analysis using four full-length MCMV cDNA sequences obtained in this study and the available MCMV sequences retrieved from GenBank indicated that Chinese MCMV isolates were derived from the same source. To screen for maize germplasm resistance against MCMV infection, we constructed an infectious clone of MCMV isolate YN2 (pMCMV) and developed an Agrobacterium-mediated injection procedure to allow high throughput inoculations of maize with the MCMV infectious clone. Electron microscopy showed that chloroplast photosynthesis in leaves was significantly impeded by the co-infection of MCMV and SCMV. Mitochondria in the MCMV and SCMV co-infected cells were more severely damaged than in MCMV-infected cells. The results of this study provide further insight into the epidemiology of MCMV in China and shed new light on physiological and cytopathological changes related to CLND in maize.},
}
@article {pmid28081268,
year = {2017},
author = {Li, Z and Ding, B and Zhou, X and Wang, GL},
title = {The Rice Dynamin-Related Protein OsDRP1E Negatively Regulates Programmed Cell Death by Controlling the Release of Cytochrome c from Mitochondria.},
journal = {PLoS pathogens},
volume = {13},
number = {1},
pages = {e1006157},
pmid = {28081268},
issn = {1553-7374},
mesh = {*Apoptosis ; Chromosome Mapping ; Cytochromes c/genetics/*metabolism ; Cytoplasm/metabolism ; Cytosol/metabolism ; Dynamins/genetics/*metabolism ; Gene Expression ; Genes, Reporter ; Mitochondria/enzymology/ultrastructure ; Mutation ; Oryza/genetics/*physiology/ultrastructure ; Phenotype ; Phylogeny ; Plant Leaves/genetics/physiology ; Plant Proteins/genetics/metabolism ; Recombinant Fusion Proteins ; Two-Hybrid System Techniques ; },
abstract = {Programmed cell death (PCD) mediated by mitochondrial processes has emerged as an important mechanism for plant development and responses to abiotic and biotic stresses. However, the role of translocation of cytochrome c from the mitochondria to the cytosol during PCD remains unclear. Here, we demonstrate that the rice dynamin-related protein 1E (OsDRP1E) negatively regulates PCD by controlling mitochondrial structure and cytochrome c release. We used a map-based cloning strategy to isolate OsDRP1E from the lesion mimic mutant dj-lm and confirmed that the E409V mutation in OsDRP1E causes spontaneous cell death in rice. Pathogen inoculation showed that dj-lm significantly enhances resistance to fungal and bacterial pathogens. Functional analysis of the E409V mutation showed that the mutant protein impairs OsDRP1E self-association and formation of a higher-order complex; this in turn reduces the GTPase activity of OsDRP1E. Furthermore, confocal microscopy showed that the E409V mutation impairs localization of OsDRP1E to the mitochondria. The E409V mutation significantly affects the morphogenesis of cristae in mitochondria and causes the abnormal release of cytochrome c from mitochondria into cytoplasm. Taken together, our results demonstrate that the mitochondria-localized protein OsDRP1E functions as a negative regulator of cytochrome c release and PCD in plants.},
}
@article {pmid28102911,
year = {2017},
author = {Attacha, S and Solbach, D and Bela, K and Moseler, A and Wagner, S and Schwarzländer, M and Aller, I and Müller, SJ and Meyer, AJ},
title = {Glutathione peroxidase-like enzymes cover five distinct cell compartments and membrane surfaces in Arabidopsis thaliana.},
journal = {Plant, cell &amp; environment},
volume = {40},
number = {8},
pages = {1281-1295},
doi = {10.1111/pce.12919},
pmid = {28102911},
issn = {1365-3040},
mesh = {Amino Acid Sequence ; Arabidopsis/*cytology/*enzymology ; *Cell Compartmentation ; Cell Membrane/*enzymology ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Glutathione Peroxidase/chemistry/*metabolism ; Green Fluorescent Proteins/metabolism ; Membrane Proteins/chemistry/metabolism ; Mitochondria/metabolism ; Mutation/genetics ; Nuclear Proteins/metabolism ; Phylogeny ; Plastids/metabolism ; Recombinant Fusion Proteins/metabolism ; Secretory Pathway ; Solubility ; Subcellular Fractions/enzymology ; },
abstract = {Glutathione peroxidase-like enzymes (GPXLs) constitute a family of eight peroxidases in Arabidopsis thaliana. In contrast to the eponymous selenocysteine glutathione peroxidases in mammalian cells that use glutathione as electron donor, GPXLs rely on cysteine instead of selenocysteine for activity and depend on the thioredoxin system for reduction. Although plant GPXLs have been implicated in important agronomic traits such as drought tolerance, photooxidative tolerance and immune responses, there remain major ambiguities regarding their subcellular localization. Because their site of action is a prerequisite for an understanding of their function, we investigated the localization of all eight GPXLs in stable Arabidopsis lines expressing N-terminal and C-terminal fusions with redox-sensitive green fluorescent protein 2 (roGFP2) using confocal microscopy. GPXL1 and GPXL7 were found in plastids, while GPXL2 and GPXL8 are cytosolic nuclear. The N-terminal target peptide of GPXL6 is sufficient to direct roGFP2 into mitochondria. Interestingly, GPXL3, GPXL4 and GPXL5 all appear to be membrane bound. GPXL3 was found exclusively in the secretory pathway where it is anchored by a single N-terminal transmembrane domain. GPXL4 and GPXL5 are anchored to the plasma membrane. Presence of an N-terminal myristoylation motif and genetic disruption of membrane association through targeted mutagenesis point to myristoylation as essential for membrane localization.},
}
@article {pmid28104538,
year = {2017},
author = {Davis, A and Abbriano, R and Smith, SR and Hildebrand, M},
title = {Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms.},
journal = {Protist},
volume = {168},
number = {1},
pages = {134-153},
doi = {10.1016/j.protis.2016.10.005},
pmid = {28104538},
issn = {1618-0941},
mesh = {Algal Proteins/genetics ; Diatoms/enzymology/*metabolism ; Malate Dehydrogenase/*metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Photosynthesis ; Phylogeny ; },
abstract = {Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.},
}
@article {pmid28105930,
year = {2016},
author = {Kononov, A and Ustyantsev, K and Wang, B and Mastro, VC and Fet, V and Blinov, A and Baranchikov, Y},
title = {Genetic diversity among eight Dendrolimus species in Eurasia (Lepidoptera: Lasiocampidae) inferred from mitochondrial COI and COII, and nuclear ITS2 markers.},
journal = {BMC genetics},
volume = {17},
number = {Suppl 3},
pages = {157},
pmid = {28105930},
issn = {1471-2156},
mesh = {Animals ; Electron Transport Complex IV/*genetics ; Genetic Markers/*genetics ; Genetic Variation ; Insect Proteins/*genetics ; Mitochondria/*genetics ; Moths/classification/*genetics ; Phylogeny ; },
abstract = {BACKGROUND: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia.<br><br>RESULTS: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five regions of Siberia and the Russian Far East to be able to compare the disparate data from all previous studies. In total, 528 sequences were used in phylogenetic analysis. Two clusters of closely related species in Dendrolimus were found. The first cluster includes D. pini, D. sibiricus, and D. superans; and the second, D. spectabilis, D. punctatus, and D. tabulaeformis. Species D. houi and D. kikuchii appear to be the most basal in the genus.<br><br>CONCLUSION: Genetic difference among the second cluster species is very low in contrast to the first cluster species. Phylogenetic position D. tabulaeformis as a subspecies was supported. It was found that D. sibiricus recently separated from D. superans. Integration of D. sibiricus mitochondrial DNA sequences and the spread of this species to the west of Eurasia have been established as the cause of the unjustified allocation of a new species: D. kilmez. Our study further clarifies taxonomic problems in the genus and gives more complete information on the genetic structure of D. pini, D. sibiricus, and D. superans.},
}
@article {pmid28115024,
year = {2017},
author = {Hornok, S and Sándor, AD and Tomanović, S and Beck, R and D'Amico, G and Kontschán, J and Takács, N and Görföl, T and Bendjeddou, ML and Földvári, G and Farkas, R},
title = {East and west separation of Rhipicephalus sanguineus mitochondrial lineages in the Mediterranean Basin.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {39},
pmid = {28115024},
issn = {1756-3305},
mesh = {Animals ; Arthropod Proteins/genetics ; Dog Diseases/*parasitology ; Dogs ; Female ; Genetic Variation ; Male ; Mediterranean Region ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus sanguineus/*classification/*genetics ; },
abstract = {BACKGROUND: Rhipicephalus sanguineus belongs to a complex of hard tick species with high veterinary-medical significance. Recently, new phylogenetic units have been discovered within R. sanguineus, which therefore needs taxonomic revision. The present study was initiated to provide new information on the phylogeography of relevant haplotypes from less studied regions of Europe and Africa. With this aim, molecular-phylogenetic analyses of two mitochondrial markers were performed on 50 ticks collected in Hungary, the Balkans, countries along the Mediterranean Sea, Kenya and Ivory Coast.<br><br>RESULTS: In the "temperate lineage" of R. sanguineus, based on cytochrome c oxidase subunit 1 (cox1) and 16S rRNA genes, Rhipicephalus sp. I was only found in the eastern part of the Mediterranean Basin (with relatively homogenous haplotypes), whereas Rhipicephalus sp. II occurred in the middle-to-western part of this region (with phylogenetically dichotomous haplotypes). Ticks identified as R. leporis (based on morphology and cox1 gene) were found in Kenya and Ivory Coast. These clustered phylogenetically within R. sanguineus (s.l.) ("tropical lineage").<br><br>CONCLUSIONS: In the Mediterranean Basin two mitochondrial lineages of R. sanguineus, i.e. Rhipicephalus sp. I and Rhipicephalus sp. II exist, which show different geographical distribution. Therefore, data from this study confirm limited gene flow between Rhipicephalus sp. I and Rhipicephalus sp. II, but more evidence (analyses of nuclear markers, extensive morphological and biological comparison etc.) are necessary to infer if they belong to different species or not. The phylogenetic relationships of eastern and western African ticks, which align with R. leporis, need to be studied further within R. sanguineus (s.l.) ("tropical lineage").},
}
@article {pmid28122084,
year = {2017},
author = {Lyon, J},
title = {Sanctioned UK Trial of Mitochondrial Transfer Nears.},
journal = {JAMA},
volume = {317},
number = {5},
pages = {462-464},
doi = {10.1001/jama.2016.18680},
pmid = {28122084},
issn = {1538-3598},
mesh = {Bioethical Issues ; Biomedical Research ; DNA, Mitochondrial/*therapeutic use ; Embryo Research/ethics/*legislation &amp; jurisprudence ; Female ; Genetic Drift ; Genetic Therapy/ethics/*legislation &amp; jurisprudence/methods ; Humans ; In Vitro Techniques/ethics ; Male ; Mitochondria/*transplantation ; Mitochondrial Diseases/genetics/*therapy ; Politics ; Sex Factors ; United Kingdom ; United States ; },
}
@article {pmid28129726,
year = {2018},
author = {Barroso Lima, NC and Prosdocimi, F},
title = {The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {2},
pages = {300-302},
doi = {10.1080/24701394.2016.1275603},
pmid = {28129726},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Mitochondrial/genetics ; DNA, Single-Stranded/*genetics ; Genes, Mitochondrial ; Genome Size ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Vertebrates/*genetics ; },
}
@article {pmid28129729,
year = {2018},
author = {Lin, X and Zheng, HX and Davie, A and Zhou, S and Wen, L and Meng, J and Zhang, Y and Aladaer, Q and Liu, B and Liu, WJ and Yao, XK},
title = {Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {2},
pages = {323-330},
doi = {10.1080/24701394.2016.1278535},
pmid = {28129729},
issn = {2470-1408},
mesh = {Animals ; Australia ; DNA, Mitochondrial/*genetics ; Female ; Genetic Association Studies/*methods ; Haplotypes ; Horses/*classification/genetics/physiology ; Male ; Mutation ; Phylogeny ; Point Mutation ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; RNA, Ribosomal, 16S/chemistry/genetics ; *Running ; Sequence Analysis, DNA/*methods ; },
abstract = {Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.},
}
@article {pmid28129733,
year = {2018},
author = {Li, GL and Xu, YJ and Huang, XM and Xiao, J and Nong, S and Li, CG},
title = {MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {3},
pages = {335-339},
doi = {10.1080/24701394.2016.1278537},
pmid = {28129733},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Brachyura/classification/*genetics ; *DNA Methylation ; Genetic Variation ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.},
}
@article {pmid28172670,
year = {2017},
author = {Sarver, BA and Demboski, JR and Good, JM and Forshee, N and Hunter, SS and Sullivan, J},
title = {Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias).},
journal = {Genome biology and evolution},
volume = {9},
number = {1},
pages = {7-19},
pmid = {28172670},
issn = {1759-6653},
support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; DNA, Mitochondrial ; Gene Flow ; Genome, Mitochondrial ; Hybridization, Genetic ; Mitochondria/*genetics ; Phylogeny ; Sciuridae/*classification/*genetics ; Selection, Genetic ; United States ; },
abstract = {Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.},
}
@article {pmid28173693,
year = {2017},
author = {Lee, JY and Jun, DY and Park, JE and Kwon, GH and Kim, JS and Kim, YH},
title = {Pro-Apoptotic Role of the Human YPEL5 Gene Identified by Functional Complementation of a Yeast moh1Δ Mutation.},
journal = {Journal of microbiology and biotechnology},
volume = {27},
number = {3},
pages = {633-643},
doi = {10.4014/jmb.1610.10045},
pmid = {28173693},
issn = {1738-8872},
mesh = {Amino Acid Sequence ; Apoptosis/*genetics ; Cell Cycle Proteins/chemistry/*genetics ; Fungal Proteins/chemistry/*genetics/metabolism ; Genetic Complementation Test ; Humans ; Multigene Family ; *Mutation ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Yeasts/*genetics/metabolism ; },
abstract = {To examine the pro-apoptotic role of the human ortholog (YPEL5) of the Drosophila Yippee protein, the cell viability of Saccharomyces cerevisiae mutant strain with deleted MOH1, the yeast ortholog, was compared with that of the wild-type (WT)-MOH1 strain after exposure to different apoptogenic stimulants, including UV irradiation, methyl methanesulfonate (MMS), camptothecin (CPT), heat shock, and hyperosmotic shock. The moh1Δ mutant exhibited enhanced cell viability compared with the WT-MOH1 strain when treated with lethal UV irradiation, 1.8 mM MMS, 100 µ CPT, heat shock at 50°C, or 1.2 M KCl. At the same time, the level of Moh1 protein was commonly up-regulated in the WT-MOH1 strain as was that of Ynk1 protein, which is known as a marker for DNA damage. Although the enhanced UV resistance of the moh1Δ mutant largely disappeared following transformation with the yeast MOH1 gene or one of the human YPEL1-YPEL5 genes, the transformant bearing pYES2-YPEL5 was more sensitive to lethal UV irradiation and its UV sensitivity was similar to that of the WT-MOH1 strain. Under these conditions, the UV irradiation-induced apoptotic events, such as FITC-Annexin V stainability, mitochondrial membrane potential (ΔΨm) loss, and metacaspase activation, occurred to a much lesser extent in the moh1Δ mutant compared with the WT-MOH1 strain and the mutant strain bearing pYES2-MOH1 or pYES2-YPEL5. These results demonstrate the functional conservation between yeast Moh1 and human YPEL5, and their involvement in mitochondria-dependent apoptosis induced by DNA damage.},
}
@article {pmid28179510,
year = {2017},
author = {Cong, Q and Shen, J and Borek, D and Robbins, RK and Opler, PA and Otwinowski, Z and Grishin, NV},
title = {When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.},
journal = {Proceedings. Biological sciences},
volume = {284},
number = {1848},
pages = {},
pmid = {28179510},
issn = {1471-2954},
support = {R01 GM094575/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Butterflies/*growth &amp; development ; Central America ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Genome, Insect ; *Genome, Mitochondrial ; Phylogeny ; United States ; },
abstract = {Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.},
}
@article {pmid28191642,
year = {2017},
author = {Satjarak, A and Burns, JA and Kim, E and Graham, LE},
title = {Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis.},
journal = {Journal of phycology},
volume = {53},
number = {3},
pages = {601-615},
doi = {10.1111/jpy.12521},
pmid = {28191642},
issn = {1529-8817},
mesh = {Chlorophyta/classification/*genetics ; DNA, Algal/*genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.},
}
@article {pmid28193450,
year = {2017},
author = {Yuan, K and Yuan, FH and He, HH and Bi, HT and Weng, SP and He, JG and Chen, YH},
title = {Heat shock 70 kDa protein cognate 5 involved in WSSV toleration of Litopenaeus vannamei.},
journal = {Developmental and comparative immunology},
volume = {72},
number = {},
pages = {9-20},
doi = {10.1016/j.dci.2017.02.003},
pmid = {28193450},
issn = {1879-0089},
mesh = {Animals ; Arthropod Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA Virus Infections/*immunology ; HSP70 Heat-Shock Proteins/genetics/*metabolism ; Heat-Shock Response ; Hemocytes/*immunology ; Hot Temperature/adverse effects ; Mitochondria/*metabolism ; Muscles/*virology ; Penaeidae/*immunology ; Phylogeny ; Transcription Factor 4/genetics/metabolism ; Transcriptional Activation ; Unfolded Protein Response ; Up-Regulation ; Viral Load ; White spot syndrome virus 1/*physiology ; },
abstract = {The expression levels of 97 unigenes encoding heat shock proteins of Litopenaeus vannamei was scanned, and ten of them were significantly induced by white spot syndrome virus (WSSV). Among these genes, heat shock 70 kDa protein cognate 5 (LvHSC70-5) was upregulated to the highest extent and subjected to further studies. Subcellular localization assay revealed that LvHSC70-5 was located in the mitochondria. Aside from WSSV infection, unfolded protein response activation and thermal stress could also upregulate LvHSC70-5. Results of reporter gene assay demonstrated that promoter of LvHSC70-5 was activated by L. vannamei heat shock factor protein 1, activating transcription factor 4 and thermal stress. A decrease in the expression of LvHSC70-5 could reduce the aggregation of proteins in hemocytes and the cumulative mortality of WSSV-infected L. vannamei. LvHSC70-5 in L. vannamei hemocytes was upregulated by mild thermal stress. In addition, mild thermal stress, decreased the copy number of WSSV in shrimp muscle and the cumulative mortality of WSSV-infected L. vannamei. Therefore, collecting results suggested that LvHSC70-5 should be involved in WSSV toleration of shrimp L. vannamei.},
}
@article {pmid28202452,
year = {2017},
author = {Spooner, DM and Ruess, H and Iorizzo, M and Senalik, D and Simon, P},
title = {Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.},
journal = {American journal of botany},
volume = {104},
number = {2},
pages = {296-312},
doi = {10.3732/ajb.1600415},
pmid = {28202452},
issn = {1537-2197},
mesh = {Cell Nucleus/*genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/chemistry/classification/genetics ; Daucus carota/classification/*genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Mutagenesis, Insertional ; *Phylogeny ; Plant Proteins/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.<br><br>METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP).<br><br>KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.<br><br>CONCLUSIONS: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.},
}
@article {pmid28212874,
year = {2017},
author = {Leavitt, DH and Marion, AB and Hollingsworth, BD and Reeder, TW},
title = {Multilocus phylogeny of alligator lizards (Elgaria, Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses.},
journal = {Molecular phylogenetics and evolution},
volume = {110},
number = {},
pages = {104-121},
doi = {10.1016/j.ympev.2017.02.010},
pmid = {28212874},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genetic Loci ; Geography ; Lizards/*genetics ; Mitochondria/genetics ; *Models, Genetic ; North America ; *Phylogeny ; Time Factors ; },
abstract = {The increased availability of nuclear DNA sequence data has led to a better appreciation of the role and frequency of introgressive hybridization and subsequent mitochondrial capture in misleading phylogenetic hypotheses based on mtDNA sequence data alone. Relationships among members of the alligator lizard genus Elgaria have been addressed with morphology, allozyme and mtDNA sequence data with discordant results. In this study, we use seven nuclear loci (total of 5.9kb) and ∼3kb of mtDNA to infer the phylogenetic relationships among Elgaria species and test whether the discordance among previous phylogenetic hypotheses is due to introgression and mtDNA capture. While gene tree topologies varied among the different loci, we recovered a well-resolved coalescent-based species tree. Contrary to our expectations, the nDNA-only species tree does not support the sister relationship between E. kingii and E. panamintina inferred from the previous allozyme study. Nevertheless, we found evidence for possible mitochondrial capture in two unexpected situations. The first instance of mtDNA capture involves E. paucicarinata from the Cape Region of Baja California. MtDNA recovered a clade comprising E. paucicarinata and the other two peninsular endemics, while the nDNA-only species tree recovered E. paucicarinata as sister to the continental E. kingii. We hypothesize that this discordance is the result of ancient mitochondrial capture rather than incomplete lineage sorting. Additionally, analyses of nDNA recovered E. panamintina as sister to an E. multicarinata North lineage, whereas the mtDNA gene tree recovers E. panamintina nested within a southern E. multicarinata clade. We hypothesize that this discordance also may be due to mitochondrial capture. Additionally, hybridization between these two lineages may have resulted in geographically limited nuclear introgression. Divergence dating analyses suggest that oviparous Elgaria species diverged within a relatively narrow timeframe from the late Miocene to early Pliocene. We find that accounting for introgressed alleles is important when inferring phylogenetic relationships when using coalescent-based approaches.},
}
@article {pmid28219344,
year = {2017},
author = {Osei-Amponsah, R and Skinner, BM and Adjei, DO and Bauer, J and Larson, G and Affara, NA and Sargent, CA},
title = {Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {193},
pmid = {28219344},
issn = {1471-2164},
support = {BB/N000129/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Genotyping Techniques ; Ghana ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Pigmentation/genetics ; Swine/*genetics ; Y Chromosome/genetics ; },
abstract = {BACKGROUND: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping.<br><br>RESULTS: The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits.<br><br>CONCLUSIONS: The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.},
}
@article {pmid28257510,
year = {2017},
author = {Gao, YS and Jia, XX and Tang, XJ and Fan, YF and Lu, JX and Huang, SH and Tang, MJ},
title = {The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region.},
journal = {PloS one},
volume = {12},
number = {3},
pages = {e0173192},
pmid = {28257510},
issn = {1932-6203},
mesh = {Animals ; Animals, Domestic/genetics ; Avian Proteins/*genetics ; Breeding ; Chickens/genetics ; China ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; beta Carotene/genetics ; beta-Carotene 15,15'-Monooxygenase/*genetics ; },
abstract = {The Jiangxi Province of China has numerous native domestic chicken breeds, including some black skin breeds. The genetic diversity of Jiangxi native chickens is largely unknown, and specifically, the genetic contribution of the grey junglefowl to black skin chickens is not well understood. To address these questions, the complete D-loop region of the mitochondrial DNA (mtDNA) and beta-carotene dioxygenase 2(BCDO2)gene was sequenced in a total of 209 chickens representing seven Jiangxi native breeds. Thirty-one polymorphic sites were identified across the complete mtDNA D-loop region sequence. Twenty-three haplotypes were observed in the seven breeds, which belonged to four distinct mitochondrial clades (A, B, C and E). Clade A and B were dominant in the chickens with a frequency of approximately 67.9%. There were five SNPs that defined two haplotypes, W and Y in BCDO2. Four breeds had one haplotype and three breeds had two. We conclude that Jiangxi native chicken breeds have relatively low genetic diversity and likely share four common maternal lineages from two different maternal ancestors of junglefowl. Furthermore, some Jiangxi chicken populations may have been mixed with chickens with exotic lineage. Further research should be established to protect these domestic chicken resources.},
}
@article {pmid28258572,
year = {2017},
author = {Cerdà, J and Chauvigné, F and Finn, RN},
title = {The Physiological Role and Regulation of Aquaporins in Teleost Germ Cells.},
journal = {Advances in experimental medicine and biology},
volume = {969},
number = {},
pages = {149-171},
doi = {10.1007/978-94-024-1057-0_10},
pmid = {28258572},
issn = {0065-2598},
mesh = {*Adaptation, Physiological ; Animals ; Aquaporins/genetics/*metabolism ; Aquatic Organisms ; Biological Transport ; Cypriniformes/classification/genetics/growth &amp; development/*metabolism ; Female ; Fish Proteins/genetics/*metabolism ; Gene Expression Regulation ; Male ; Oocytes/growth &amp; development/*metabolism ; Osmotic Pressure ; Oxidative Stress ; Perciformes/classification/genetics/growth &amp; development/*metabolism ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Salinity ; Spermatozoa/growth &amp; development/*metabolism ; },
abstract = {The unicellular germ cells and gametes of oviparous teleosts lack the osmoregulatory organs present in juveniles and adults, yet during development and particularly at spawning, they face tremendous osmotic challenges when released into the external aquatic environment. Increasing evidence suggests that transmembrane water channels (aquaporins) evolved to play vital adaptive roles that mitigate the osmotic and oxidative stress problems of the developing oocytes , embryos and spermatozoa. In this chapter, we provide a short overview of the diversity of the aquaporin superfamily in teleosts, and summarize the findings that uncovered a highly specific molecular regulation of aquaporins during oogenesis and spermatogenesis. We further review the multiple functions that these channels play during the establishment of egg buoyancy and the activation and detoxification of spermatozoa in the marine environment.},
}
@article {pmid28274885,
year = {2017},
author = {Brenière, SF and Condori, EW and Buitrago, R and Sosa, LF and Macedo, CL and Barnabé, C},
title = {Molecular identification of wild triatomines of the genus Rhodnius in the Bolivian Amazon: Strategy and current difficulties.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {51},
number = {},
pages = {1-9},
doi = {10.1016/j.meegid.2017.03.002},
pmid = {28274885},
issn = {1567-7257},
mesh = {Animals ; Arecaceae ; Bolivia/epidemiology ; Cell Nucleus/genetics ; Chagas Disease/epidemiology/*transmission ; DNA, Mitochondrial/*genetics ; Female ; Haplotypes ; Humans ; Insect Proteins/*genetics ; Insect Vectors/*classification/genetics/parasitology ; Male ; Mitochondria/genetics ; *Phylogeny ; Rhodnius/*classification/genetics/parasitology ; Trypanosoma cruzi/*genetics/isolation &amp; purification ; },
abstract = {The Amazon region has recently been considered as endemic in Latin America. In Bolivia, the vast Amazon region is undergoing considerable human migrations and substantial anthropization of the environment, potentially renewing the danger of establishing the transmission of Chagas disease. The cases of human oral contamination occurring in 2010 in the town of Guayaramerín provided reasons to intensify research. As a result, the goal of this study was to characterize the species of sylvatic triatomines circulating in the surroundings of Yucumo (Beni, Bolivia), a small Amazonian city at the foot of the Andes between the capital (La Paz) and Trinidad the largest city of Beni. The triatomine captures were performed with mice-baited adhesive traps mostly settled in palm trees in forest fragments and pastures. Species were identified by morphological observation, dissection of genitalia, and sequencing of three mitochondrial gene fragments and one nuclear fragment. Molecular analysis was based on (i) the identity score of the haplotypes with GenBank sequences through the BLAST algorithm and (ii) construction of phylogenetic trees. Thirty-four triatomines, all belonging to the Rhodnius genus, of which two were adult males, were captured in palm trees in forest fragments and pastures (overall infestation rate, 12.3%). The morphology of the phallic structures in the two males confirmed the R. stali species. For the other specimens, after molecular sequencing, only one specimen was identified with confidence as belonging to Rhodnius robustus, the others belonged to one of the species of the Rhodnius pictipes complex, probably Rhodnius stali. The two species, R. robustus and R. stali, had previously been reported in the Alto Beni region (edge of the Amazon region), but not yet in the Beni department situated in the Amazon region. Furthermore, the difficulties of molecular characterization of closely related species within the three complexes of the genus Rhodnius are highlighted and discussed.},
}
@article {pmid28283795,
year = {2017},
author = {Hu, YC and Chu, KF and Yang, WK and Lee, TH},
title = {Na[+], K[+]-ATPase β1 subunit associates with α1 subunit modulating a "higher-NKA-in-hyposmotic media" response in gills of euryhaline milkfish, Chanos chanos.},
journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology},
volume = {187},
number = {7},
pages = {995-1007},
pmid = {28283795},
issn = {1432-136X},
support = {103-2311-B-005-004-MY3//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Animals ; Fish Proteins/chemistry/genetics/*metabolism ; Fishes/genetics/*metabolism ; Fresh Water/*chemistry ; Gene Expression Regulation ; Gills/*enzymology ; Models, Molecular ; Osmoregulation ; Phylogeny ; Protein Conformation ; Protein Subunits ; *Salinity ; *Salt Tolerance ; Seawater/*chemistry ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Sodium-Potassium-Exchanging ATPase/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Tissue Distribution ; },
abstract = {The euryhaline milkfish (Chanos chanos) is a popular aquaculture species that can be cultured in fresh water, brackish water, or seawater in Southeast Asia. In gills of the milkfish, Na[+], K[+]-ATPase (i.e., NKA; sodium pump) responds to salinity challenges including changes in mRNA abundance, protein amount, and activity. The functional pump is composed of a heterodimeric protein complex composed of α- and β-subunits. Among the NKA genes, α1-β1 isozyme comprises the major form of NKA subunits in mammalian osmoregulatory organs; however, most studies on fish gills have focused on the α1 subunit and did not verify the α1-β1 isozyme. Based on the sequenced milkfish transcriptome, an NKA β1 subunit gene was identified that had the highest amino acid homology to β233, a NKA β1 subunit paralog originally identified in the eel. Despite this high level of homology to β233, phylogenetic analysis and the fact that only a single NKA β1 subunit gene exists in the milkfish suggest that the milkfish gene should be referred to as the NKA β1 subunit gene. The results of accurate domain prediction of the β1 subunit, co-localization of α1 and β1 subunits in epithelial ionocytes, and co-immunoprecipitation of α1 and β1 subunits, indicated the formation of a α1-β1 complex in milkfish gills. Moreover, when transferred to hyposmotic media (fresh water) from seawater, parallel increases in branchial mRNA and protein expression of NKA α1 and β1 subunits suggested their roles in hypo-osmoregulation of euryhaline milkfish. This study molecularly characterized the NKA β1 subunit and provided the first evidence for an NKA α1-β1 association in gill ionocytes of euryhaline teleosts.},
}
@article {pmid28288321,
year = {2017},
author = {Hrabáková, L and Koloniuk, I and Petrzik, K},
title = {Phomopsis longicolla RNA virus 1 - Novel virus at the edge of myco- and plant viruses.},
journal = {Virology},
volume = {506},
number = {},
pages = {14-18},
doi = {10.1016/j.virol.2017.03.003},
pmid = {28288321},
issn = {1096-0341},
mesh = {Amino Acid Sequence ; Ascomycota/*virology ; Base Sequence ; Fungal Viruses/classification/genetics/*isolation &amp; purification ; Genome, Viral ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Diseases/virology ; Plant Viruses/classification/genetics/*isolation &amp; purification ; RNA Viruses/classification/genetics/*isolation &amp; purification ; RNA, Viral/genetics ; Viral Proteins/genetics ; },
abstract = {The complete nucleotide sequence of a new RNA mycovirus in the KY isolate of Phomopsis longicolla Hobbs 1985 and its protoplasts subcultures p5, p9, and ME711 was discovered. The virus, provisionally named Phomopsis longicolla RNA virus 1 (PlRV1), was localized in mitochondria and was determined to have a genome 2822 nucleotides long. A single open reading frame could be translated in silico by both standard and mitochondrial genetic codes into a product featuring conservative domains for an RNA-dependent RNA polymerase (RdRp). The RdRp of PlRV1 has no counterpart among mycoviruses, but it is about 30% identical with the RdRp of plant ourmiaviruses. Recently, new mycoviruses related to plant ourmiaviruses and forming one clade with PlRV1 have been discovered. This separate clade could represent the crucial link between plant and fungal viruses.},
}
@article {pmid28314772,
year = {2017},
author = {Kong, P and Ufermann, CM and Zimmermann, DLM and Yin, Q and Suo, X and Helms, JB and Brouwers, JF and Gupta, N},
title = {Two phylogenetically and compartmentally distinct CDP-diacylglycerol synthases cooperate for lipid biogenesis in Toxoplasma gondii.},
journal = {The Journal of biological chemistry},
volume = {292},
number = {17},
pages = {7145-7159},
pmid = {28314772},
issn = {1083-351X},
mesh = {Animals ; Animals, Genetically Modified ; Apicoplasts/enzymology ; Diacylglycerol Cholinephosphotransferase/*genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Fibroblasts/metabolism ; Fluorescent Antibody Technique, Indirect ; Gene Deletion ; Glycerophospholipids/*biosynthesis ; Golgi Apparatus/metabolism ; Humans ; Mice ; Mitochondria/metabolism ; Mutation ; Phosphatidylglycerols/chemistry ; Phosphatidylinositols/chemistry ; Phylogeny ; Protein Domains ; Protozoan Proteins/*genetics/metabolism ; Toxoplasma/*enzymology/genetics ; Virulence ; },
abstract = {Toxoplasma gondii is among the most prevalent protozoan parasites, which infects a wide range of organisms, including one-third of the human population. Its rapid intracellular replication within a vacuole requires efficient synthesis of glycerophospholipids. Cytidine diphosphate-diacylglycerol (CDP-DAG) serves as a major precursor for phospholipid synthesis. Given the peculiarities of lipid biogenesis, understanding the mechanism and physiological importance of CDP-DAG synthesis is particularly relevant in T. gondii Here, we report the occurrence of two phylogenetically divergent CDP-DAG synthase (CDS) enzymes in the parasite. The eukaryotic-type TgCDS1 and the prokaryotic-type TgCDS2 reside in the endoplasmic reticulum and apicoplast, respectively. Conditional knockdown of TgCDS1 severely attenuated the parasite growth and resulted in a nearly complete loss of virulence in a mouse model. Moreover, mice infected with the TgCDS1 mutant became fully resistant to challenge infection with a hyper-virulent strain of T. gondii The residual growth of the TgCDS1 mutant was abolished by consecutive deletion of TgCDS2. Lipidomic analyses of the two mutants revealed significant and specific declines in phosphatidylinositol and phosphatidylglycerol levels upon repression of TgCDS1 and after deletion of TgCDS2, respectively. Our data suggest a "division of labor" model of lipid biogenesis in T. gondii in which two discrete CDP-DAG pools produced in the endoplasmic reticulum and apicoplast are subsequently used for the synthesis of phosphatidylinositol in the Golgi bodies and phosphatidylglycerol in the mitochondria. The essential and divergent nature of CDP-DAG synthesis in the parasite apicoplast offers a potential drug target to inhibit the asexual reproduction of T. gondii.},
}
@article {pmid28323052,
year = {2017},
author = {Schmidt, RC and Bart, HL and Nyingi, WD},
title = {Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).},
journal = {Molecular phylogenetics and evolution},
volume = {111},
number = {},
pages = {35-43},
doi = {10.1016/j.ympev.2017.03.015},
pmid = {28323052},
issn = {1095-9513},
mesh = {Animals ; Cyprinidae/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Genetic Loci ; *Genetic Variation ; Geography ; Growth Hormone/metabolism ; Introns/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa.},
}
@article {pmid28327596,
year = {2017},
author = {Shen, CM and Hu, L and Yang, CH and Yin, CY and Li, ZD and Meng, HT and Guo, YX and Mei, T and Chen, F and Zhu, BF},
title = {Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group.},
journal = {Scientific reports},
volume = {7},
number = {},
pages = {44407},
pmid = {28327596},
issn = {2045-2322},
mesh = {Alleles ; China ; DNA, Mitochondrial/*genetics ; *Ethnicity ; Gene Frequency ; Genetic Loci ; *Genetics, Population ; Haplotypes ; Humans ; Microsatellite Repeats ; Minority Groups ; Mitochondria/*genetics ; *Phylogeny ; *Polymorphism, Single Nucleotide ; },
abstract = {We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.},
}
@article {pmid28329425,
year = {2017},
author = {Morales, HE and Sunnucks, P and Joseph, L and Pavlova, A},
title = {Perpendicular axes of differentiation generated by mitochondrial introgression.},
journal = {Molecular ecology},
volume = {26},
number = {12},
pages = {3241-3255},
doi = {10.1111/mec.14114},
pmid = {28329425},
issn = {1365-294X},
mesh = {Animals ; Australia ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; *Genome, Mitochondrial ; *Hybridization, Genetic ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/*genetics ; },
abstract = {Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north-south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north-south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial-nuclear combinations. This likely generated an axis of coastal-inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north-south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).},
}
@article {pmid28359943,
year = {2017},
author = {Cai, J and Wei, S and Yu, D and Song, R and Lu, Y and Wu, Z and Qin, Q and Jian, J},
title = {BNIP3, a cell pro-apoptotic protein, involved in response to viral infection in orange spotted grouper, Epinephelus coioides.},
journal = {Fish &amp; shellfish immunology},
volume = {64},
number = {},
pages = {407-413},
doi = {10.1016/j.fsi.2017.03.047},
pmid = {28359943},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis Regulatory Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Bass ; Cloning, Molecular ; DNA Virus Infections/genetics/*veterinary/virology ; DNA, Complementary/genetics/metabolism ; Fish Diseases/*genetics/virology ; Fish Proteins/chemistry/*genetics/metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Ranavirus/*physiology ; Sequence Alignment/veterinary ; Tissue Distribution ; },
abstract = {BNIP3 is a kind of BH3-only protein that induces both cell death and autophagy. Here, a BNIP3 gene (EcBNIP3) was identified from orange spotted grouper, Epinephelus coioides. EcBNIP3 possessed 236 amino acids residues, contained a conservative BNIP3 domain and a transmembrane region. Besides, EcBNIP3 expressed at a relative high level in heart and spleen. EcBNIP3 transcript was up-regulated after SGIV infection in vitro. Subcellular localization analysis revealed that EcBNIP3 was predominantly localized in the cytoplasm and co-localized with mitochondria. In addition, overexpression EcBNIP3 accelerated SGIV infection induced cell death but inhibited viral genes transcription. Taken together, these results provided new evidence that fish BNIP3 might involved in response to virus infection.},
}
@article {pmid28380376,
year = {2017},
author = {Anderson, KA and Huynh, FK and Fisher-Wellman, K and Stuart, JD and Peterson, BS and Douros, JD and Wagner, GR and Thompson, JW and Madsen, AS and Green, MF and Sivley, RM and Ilkayeva, OR and Stevens, RD and Backos, DS and Capra, JA and Olsen, CA and Campbell, JE and Muoio, DM and Grimsrud, PA and Hirschey, MD},
title = {SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.},
journal = {Cell metabolism},
volume = {25},
number = {4},
pages = {838-855.e15},
pmid = {28380376},
issn = {1932-7420},
support = {T32 CA059365/CA/NCI NIH HHS/United States ; F32 DK105665/DK/NIDDK NIH HHS/United States ; R56 AG052568/AG/NIA NIH HHS/United States ; T32 DK007012/DK/NIDDK NIH HHS/United States ; T32 EY021453/EY/NEI NIH HHS/United States ; R24 DK085610/DK/NIDDK NIH HHS/United States ; R01 DK089312/DK/NIDDK NIH HHS/United States ; R01 AG045351/AG/NIA NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; P30 AG028716/AG/NIA NIH HHS/United States ; T32 GM007105/GM/NIGMS NIH HHS/United States ; },
mesh = {Amidohydrolases/*metabolism ; Amino Acid Sequence ; Animals ; Carbon-Carbon Ligases/metabolism ; Glucose/metabolism ; HEK293 Cells ; Homeostasis ; Humans ; Insulin/*metabolism ; Insulin Resistance ; Insulin Secretion ; Leucine/*metabolism ; Lysine/*metabolism ; Metabolic Flux Analysis ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Molecular ; Phylogeny ; Sirtuins/chemistry/*metabolism ; },
abstract = {Sirtuins are NAD[+]-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine. The metabolites leading to these post-translational modifications are intermediates in leucine oxidation, and we show a primary role for SIRT4 in controlling this pathway in mice. Furthermore, we find that dysregulated leucine metabolism in SIRT4KO mice leads to elevated basal and stimulated insulin secretion, which progressively develops into glucose intolerance and insulin resistance. These findings identify a robust enzymatic activity for SIRT4, uncover a mechanism controlling branched-chain amino acid flux, and position SIRT4 as a crucial player maintaining insulin secretion and glucose homeostasis during aging.},
}
@article {pmid28407723,
year = {2018},
author = {Huang, Z and Ruan, R},
title = {DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {529-534},
doi = {10.1080/24701394.2017.1315569},
pmid = {28407723},
issn = {2470-1408},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; Mitochondria/*enzymology ; Passeriformes/*classification/*genetics ; *Phylogeny ; },
abstract = {DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.},
}
@article {pmid28410432,
year = {2017},
author = {Antonini, Y and Machado, CB and Galetti, PM and Oliveira, M and Dirzo, R and Fernandes, GW},
title = {Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.},
journal = {PloS one},
volume = {12},
number = {4},
pages = {e0175884},
pmid = {28410432},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Bees/classification/genetics/*physiology ; *Biodiversity ; Brazil ; Genetic Loci ; Male ; Mitochondria/genetics ; Phylogeny ; Rainforest ; Temperature ; },
abstract = {The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.},
}
@article {pmid28416382,
year = {2017},
author = {Luo, X and Fu, X and Liao, G and Chang, O and Huang, Z and Li, N},
title = {Isolation, pathogenicity and characterization of a novel bacterial pathogen Streptococcus uberis from diseased mandarin fish Siniperca chuatsi.},
journal = {Microbial pathogenesis},
volume = {107},
number = {},
pages = {380-389},
doi = {10.1016/j.micpath.2017.03.049},
pmid = {28416382},
issn = {1096-1208},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics ; Apoptosis ; Bacterial Proteins/genetics ; Brain/microbiology/pathology ; Carps/microbiology ; China ; DNA, Bacterial ; Disease Models, Animal ; Fish Diseases/*microbiology ; Fishes/*microbiology ; Genome, Microbial ; Heart/microbiology ; Hydrogen-Ion Concentration ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Streptococcal Infections/*microbiology/mortality/*veterinary ; Streptococcus/genetics/*isolation &amp; purification/*pathogenicity/physiology ; Temperature ; Tilapia/microbiology ; Virulence ; },
abstract = {In recent years, mandarin fish had a high mortality rate associated with abnormal swimming, exophthalmia, corneal opacity and eye hemorrhage on a fish farm located at Foshan city, Guangdong province, China. Three isolates of Gram-positive, chain-forming cocci were recovered from moribund fish, and designated as SS131025-1, SS131025-2, and SS131025-3. These isolates were identified as Streptococcus uberis according to their morphologic and physio-biochemical characteristics as well as phylogenetic analysis based on their 16S rRNA and GapC gene sequences. The pathogenicity of S. uberis to mandarin fish was determined by challenge experiments. Results of artificial challenge showed S. uberis infected healthy mandarin fish and lead to death by eyeball injection or immersion route, and the LD50 of SS131025-1 with eyeball injection was 2.0 × 10[6.42] CFU per fish. Moreover extracellular product (ECP) of the isolated S.uberis induced CPB cell apoptosis and cause death of mandarin fish. In addition, these S. uberis strains could also infect tilapia, but not grass carp and crucian carp, and grew in brain-heart infusion broth with an optimal temperature of 37 °C, pH of 7.0, and salinity of 0%. Antibiotic sensitivity testing indicated that these isolates were susceptible to rifampicin and furazolidone but resistant to 20 kinds of antibiotics. Histopathologically, infection with S. uberis could cause serious pathological changes in brain tissues such as vacuoles in matrix, swollen mitochondria with lysis of cristae and disintegration, and lots of coccus was observed both under electron and light microscope. These results shed some light on the pathogenicity of the isolates and how to prevent and control S. uberis infection in mandarin fish.},
}
@article {pmid28431284,
year = {2017},
author = {Nibert, ML},
title = {Mitovirus UGA(Trp) codon usage parallels that of host mitochondria.},
journal = {Virology},
volume = {507},
number = {},
pages = {96-100},
pmid = {28431284},
issn = {1096-0341},
support = {R01 GM033050/GM/NIGMS NIH HHS/United States ; },
mesh = {Codon/*genetics/metabolism ; Fungi/genetics/metabolism/*virology ; Genome, Viral ; Mitochondria/genetics/metabolism/*virology ; Phylogeny ; RNA Viruses/*genetics/physiology ; *Virus Replication ; },
abstract = {Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes. Thus, the relative exclusion of such codons in a subset of mitoviruses appears to reflect most fundamentally that UGA(Trp) is a rare mitochondrial codon in their particular hosts. The fact that UGA(Trp) is a rare mitochondrial codon in many fungi appears not to have been widely discussed to date.},
}
@article {pmid28456662,
year = {2017},
author = {Kinkar, L and Laurimäe, T and Sharbatkhori, M and Mirhendi, H and Kia, EB and Ponce-Gordo, F and Andresiuk, V and Simsek, S and Lavikainen, A and Irshadullah, M and Umhang, G and Oudni-M'rad, M and Acosta-Jamett, G and Rehbein, S and Saarma, U},
title = {New mitogenome and nuclear evidence on the phylogeny and taxonomy of the highly zoonotic tapeworm Echinococcus granulosus sensu stricto.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {52},
number = {},
pages = {52-58},
doi = {10.1016/j.meegid.2017.04.023},
pmid = {28456662},
issn = {1567-7257},
mesh = {Africa, Northern ; Animals ; Asia ; Cell Nucleus/*genetics ; DNA, Helminth/*genetics ; Echinococcus granulosus/*classification/genetics/isolation &amp; purification/metabolism ; Europe ; Genome, Mitochondrial ; Genotype ; Humans ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; South America ; Zoonoses/parasitology ; },
abstract = {Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1-G8 and G10) of which G1-G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that G1-G3 could be regarded as a distinct species E. granulosus sensu stricto (s. s.), the evidence to support this is inconclusive. Most importantly, data from nuclear DNA that provide means to investigate the exchange of genetic material between G1-G3 is lacking as none of the published nuclear DNA studies have explicitly included G2 or G3. Moreover, the commonly used relatively short mtDNA sequences, including the complete cox1 gene, have not allowed unequivocal differentiation of genotypes G1-G3. Therefore, significantly longer mtDNA sequences are required to distinguish these genotypes with confidence. The main aim of this study was to evaluate the phylogenetic relations and taxonomy of genotypes G1-G3 using sequences of nearly complete mitogenomes (11,443bp) and three nuclear loci (2984bp). A total of 23 G1-G3 samples were analysed, originating from 5 intermediate host species in 10 countries. The mtDNA data demonstrate that genotypes G1 and G3 are distinct mitochondrial genotypes (separated by 37 mutations), whereas G2 is not a separate genotype or even a monophyletic cluster, but belongs to G3. Nuclear data revealed no genetic separation of G1 and G3, suggesting that these genotypes form a single species due to ongoing gene flow. We conclude that: (a) in the taxonomic sense, genotypes G1 and G3 can be treated as a single species E. granulosus s. s.; (b) genotypes G1 and G3 should be regarded as distinct genotypes only in the context of mitochondrial data; (c) we recommend excluding G2 from the genotype list.},
}
@article {pmid28459876,
year = {2017},
author = {Araújo Castro, J and Gomes Ferreira, MD and Santana Silva, RJ and Andrade, BS and Micheli, F},
title = {Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb.},
journal = {PloS one},
volume = {12},
number = {5},
pages = {e0176878},
pmid = {28459876},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Citrus/*enzymology/*genetics ; Conserved Sequence ; Exons ; Gene Expression Regulation, Plant/physiology ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Molecular Docking Simulation ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; Plant Structures/enzymology/genetics ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Species Specificity ; Ubiquinone/metabolism ; Alternative Oxidase ; },
abstract = {The alternative oxidase (AOX) protein is present in plants, fungi, protozoa and some invertebrates. It is involved in the mitochondrial respiratory chain, providing an alternative route for the transport of electrons, leading to the reduction of oxygen to form water. The present study aimed to characterize the family of AOX genes in mandarin (Citrus clementina) and sweet orange (Citrus sinensis) at nucleotide and protein levels, including promoter analysis, phylogenetic analysis and C. sinensis gene expression. This study also aimed to do the homology modeling of one AOX isoform (CcAOXd). Moreover, the molecular docking of the CcAOXd protein with the ubiquinone (UQ) was performed. Four AOX genes were identified in each citrus species. These genes have an open reading frame (ORF) ranging from 852 bp to 1150 bp and a number of exons ranging from 4 to 9. The 1500 bp-upstream region of each AOX gene contained regulatory cis-elements related to internal and external response factors. CsAOX genes showed a differential expression in citrus tissues. All AOX proteins were predicted to be located in mitochondria. They contained the conserved motifs LET, NERMHL, LEEEA and RADE-H as well as several putative post-translational modification sites. The CcAOXd protein was modeled by homology to the AOX of Trypanosona brucei (45% of identity). The 3-D structure of CcAOXd showed the presence of two hydrophobic helices that could be involved in the anchoring of the protein in the inner mitochondrial membrane. The active site of the protein is located in a hydrophobic environment deep inside the AOX structure and contains a diiron center. The molecular docking of CcAOXd with UQ showed that the binding site is a recessed pocket formed by the helices and submerged in the membrane. These data are important for future functional studies of citrus AOX genes and/or proteins, as well as for biotechnological approaches leading to AOX inhibition using UQ homologs.},
}
@article {pmid28478197,
year = {2017},
author = {Copilaş-Ciocianu, D and Rutová, T and Pařil, P and Petrusek, A},
title = {Epigean gammarids survived millions of years of severe climatic fluctuations in high latitude refugia throughout the Western Carpathians.},
journal = {Molecular phylogenetics and evolution},
volume = {112},
number = {},
pages = {218-229},
doi = {10.1016/j.ympev.2017.04.027},
pmid = {28478197},
issn = {1095-9513},
mesh = {Altitude ; Amphipoda/genetics/*physiology ; Animals ; Base Sequence ; Bayes Theorem ; *Climate ; Europe ; Genetic Variation ; Geography ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Refugium ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Isolated glacial refugia have been documented in Central Europe for a number of taxa, but conclusive evidence for epigean aquatic species has remained elusive. Using molecular data (mitochondrial and nuclear markers), we compared the spatial patterns of lineage diversity of the widely distributed Gammarus fossarum species complex between two adjacent biogeographically and geomorphologically distinct Central European regions: the Bohemian Massif and the Western Carpathians. We investigated if the observed patterns of spatial diversity are more likely to stem from historical or present-day factors. Phylogenetic and phylogeographic analyses revealed eight phylogenetically diverse lineages: two exhibiting local signatures of recent demographic expansion inhabit both regions, while the other six display a relict distributional pattern and are found only in the Western Carpathians. Molecular dating indicates that these lineages are old and probably diverged throughout the Miocene (7-18Ma). Furthermore, their distribution does not seem to be constrained by the present boundaries of river catchments or topography. The contrasting spatial patterns of diversity observed between the two regions thus more likely result from historical rather than contemporaneous or recent factors. Our results indicate that despite the high latitude and proximity to the Pleistocene ice sheets, the Western Carpathians functioned as long-term glacial refugia for permanent freshwater fauna, allowing the uninterrupted survival of ancient lineages through millions of years of drastic climatic fluctuations.},
}
@article {pmid28487526,
year = {2017},
author = {Wang, P and Sha, T and Zhang, Y and Cao, Y and Mi, F and Liu, C and Yang, D and Tang, X and He, X and Dong, J and Wu, J and Yoell, S and Yoell, L and Zhang, KQ and Zhang, Y and Xu, J},
title = {Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {1626},
pmid = {28487526},
issn = {2045-2322},
mesh = {Agaricales/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Gene Amplification ; Genetic Loci ; *Genome, Mitochondrial ; Geography ; Heterozygote ; Homozygote ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {In the majority of sexual eukaryotes, the mitochondrial genomes are inherited uniparentally. As a result, individual organisms are homoplasmic, containing mitochondrial DNA (mtDNA) from a single parent. Here we analyzed the mitochondrial genotypes in Clade I of the gourmet mushroom Thelephora ganbajun from its broad geographic distribution range. A total of 299 isolates from 28 geographic locations were sequenced at three mitochondrial loci: the mitochondrial small ribosomal RNA gene, and the cytochrome c oxidase subunits I (COX1) and III (COX3) genes. Quantitative PCR analyses showed that the strains had about 60-160 copies of mitochondrial genomes per cell. Interestingly, while no evidence of heteroplasmy was found at the 12S rRNA gene, 262 of the 299 isolates had clear evidence of heterogeneity at either the COX1 (261 isolates) or COX3 (12 isolates) gene fragments. The COX1 heteroplasmy was characterized by two types of introns residing at different sites of the same region and at different frequencies among the isolates. Allelic association analyses of the observed mitochondrial polymorphic nucleotide sites suggest that mtDNA recombination is common in natural populations of this fungus. Our results contrast the prevailing view that heteroplasmy, if exists, is only transient in basidiomycete fungi.},
}
@article {pmid28493482,
year = {2017},
author = {Dibrova, DV and Shalaeva, DN and Galperin, MY and Mulkidjanian, AY},
title = {Emergence of cytochrome bc complexes in the context of photosynthesis.},
journal = {Physiologia plantarum},
volume = {161},
number = {1},
pages = {150-170},
pmid = {28493482},
issn = {1399-3054},
mesh = {Archaea/metabolism ; Bacteria/metabolism ; Cytochromes b/*metabolism ; Cytochromes c/*metabolism ; *Photosynthesis ; Phylogeny ; },
abstract = {The cytochrome bc (cyt bc) complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four-helical cytochrome b (cyt b) that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b6 f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven- or eight-helical cyt b with only two hemes (cyt bc1 -type complexes). Here we present an updated phylogenomic analysis of the cyt b subunits of cyt bc complexes. This analysis provides further support to our earlier suggestion that (1) the ancestral version of cyt bc complex contained a small four-helical cyt b with three hemes similar to the plant cytochrome b6 and (2) independent fusion events led to the formation of large cyts b in several lineages. In the search for a primordial function for the ancestral cyt bc complex, we address the intimate connection between the cyt bc complexes and photosynthesis. Indeed, the Q-cycle turnover in the cyt bc complexes demands high-potential electron acceptors. Before the Great Oxygenation Event, the biosphere had been highly reduced, so high-potential electron acceptors could only be generated upon light-driven charge separation. It appears that an ancestral cyt bc complex capable of Q-cycling has emerged in conjunction with the (bacterio)chlorophyll-based photosynthetic systems that continuously generated electron vacancies at the oxidized (bacterio)chlorophyll molecules.},
}
@article {pmid28501977,
year = {2017},
author = {Wang, D and Zhao, YQ and Han, YL and Hou, CC and Zhu, JQ},
title = {Characterization of mitochondrial prohibitin from Boleophthalmus pectinirostris and evaluation of its possible role in spermatogenesis.},
journal = {Fish physiology and biochemistry},
volume = {43},
number = {5},
pages = {1299-1313},
pmid = {28501977},
issn = {1573-5168},
support = {Nos. 31272642//National Natural Science Foundation of China/ ; Nos. 2015C110005//Scientific and Technical Project of Ningbo/ ; No.2016A610081//Natural Science Foundation of Ningbo/ ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Fishes/*metabolism ; Male ; Mitochondria/*metabolism ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism ; Spermatogenesis/*physiology ; Testis/metabolism ; },
abstract = {Prohibitin (PHB) is an evolutionarily conserved mitochondrial membrane protein. It plays a vital role in cell proteolysis, senescence, and apoptosis and is associated with spermatogenesis and sperm quality control in mammals. To study the characteristics of the PHB gene and its potential roles during spermatogenesis in Boleophthalmus pectinirostris, we cloned a 1153-bp full-length cDNA from the testis of B. pectinirostris with an open reading frame of 816 bp, which encodes 272 amino acid residues. Real-time quantitative PCR (qPCR) analysis revealed the presence of phb mRNA in all the tissues examined, with higher expression levels found in the testis, kidney, intestine, and muscle tissues. We examined the localization of phb mRNA during spermatogenesis by in situ hybridization (ISH), showing that phb mRNA was distributed in the periphery of the nucleus in primary and secondary spermatocytes. In spermatid and mature sperm, the phb mRNA gradually moved toward one side, where the flagellum is formed. Immunofluorescence (IF) results showed co-localization of the PHB and mitochondria at different stages during spermatogenesis of B. pectinirostris. The signals obtained for PHB decreased as spermatogenesis proceeded; the strongest detection signal was found in secondary spermatocytes, with lower levels of staining in other stages. Additionally, in the mature germ cells, the PHB signals were weak and aggregate in the midpiece of the flagellum.},
}
@article {pmid28539070,
year = {2018},
author = {Emami-Khoyi, A and Paterson, AM and Hartley, DA and Boren, LJ and Cruickshank, RH and Ross, JG and Murphy, EC and Else, TA},
title = {Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {567-580},
doi = {10.1080/24701394.2017.1325478},
pmid = {28539070},
issn = {2470-1408},
mesh = {Animals ; Breeding ; *Feeding Behavior ; Fur Seals/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Population Density ; Recreation ; },
abstract = {The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.},
}
@article {pmid28562139,
year = {2018},
author = {Sun, P and Tang, B and Yin, F},
title = {Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {643-649},
doi = {10.1080/24701394.2017.1334773},
pmid = {28562139},
issn = {2470-1408},
mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; },
abstract = {The Chinese pomfret Pampus chinensis is one of the most economic and ecological important marine fish species in China. In the present study, the population genetic structure and genetic diversity of P. chinensis were evaluated from a total sample size of 180 individuals representing six populations from the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 24 variable sites (including 3 singleton sites and 21 parsimony information sites) were observed, and 18 haplotypes were defined. The haplotype diversity (Hd) of the populations ranged from 0.559 to 0.775, and the nucleotide diversity (π) ranged from 0.330 to 1.090%. Analysis of molecular variance (AMOVA) reveals that the main variation (66.02%) was among individuals within populations. The average pairwise differences and ϕST values indicated significant genetic differentiation between Dongxing population and the other populations. The results of the present study are helpful for the sustainable management and utilization of this species.},
}
@article {pmid28578677,
year = {2017},
author = {Sarvašová, A and Kočišová, A and Candolfi, E and Mathieu, B},
title = {Description of Culicoides (Culicoides) bysta n. sp., a new member of the Pulicaris group (Diptera: Ceratopogonidae) from Slovakia.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {279},
pmid = {28578677},
issn = {1756-3305},
mesh = {Animals ; Arboviruses ; Bluetongue/transmission ; Bluetongue virus ; Ceratopogonidae/anatomy &amp; histology/*classification/genetics/virology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial/genetics ; Insect Vectors/anatomy &amp; histology/*classification/genetics/virology ; Male ; Mitochondria/enzymology/genetics ; *Phylogeny ; Slovakia ; Species Specificity ; },
abstract = {BACKGROUND: Species of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are mainly known as vectors of arboviruses such as bluetongue (BTV) and Schmallenberg (SBV). Among the known vectors, few species within the subgenus Culicoides Latreille, 1809 have been implicated in the transmission of BTV and SBV. Nevertheless, phylogenetic studies had revealed the presence of cryptic and undescribed species in Europe, raising questions about their vectorial role. A previous integrative study, associating morphology and barcode data, raised the hypothesis of the presence of undescribed species in Slovakia. The present study, combining morphological and molecular approaches, is aimed to support the hypothesis and a description of Culicoides bysta n. sp. is provided.<br><br>METHODS: Series of male and female specimens were dissected and several of them were sequenced for the barcode region of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). Bayesian inference phylogenetic analyses based on 72 cox1 sequences of the species belonging to the Pulicaris group of the subgenus Culicoides, were carried out and the frequencies of intra/interspecific variations were analyzed. The morphology of abundant material of the new species (31 females and 12 males) was examined and compared with the paratypes of Culicoides boyi Nielsen, Kristensen &amp; Pape, 2015 and with specimens of Culicoides pulicaris Linnaeus, 1758. For females, suture distances on the eyes were newly evaluated as a diagnostic character and for males we assessed a new measurement on the ninth tergite and on the apicolateral processes.<br><br>RESULTS: Both phylogenetic analysis and barcode distances supported the distinct status of the new species, Culicoides bysta n. sp. described as a member of the Pulicaris group based on the morphology of males and females. The new species is closely related to C. boyi and C. pulicaris but can be distinguished on the basis of the wing pattern and the ratio between the two eye sutures. Both newly evaluated characters, i.e. eyes in females and male genitalia appeared to be diagnostic for distinguishing the new species described herein.<br><br>CONCLUSIONS: The vector potential of the recently described species C. boyi and C. bysta n. sp. to transmit arboviruses, such as BTV and SBV, is unknown. When considering these two species as being close to C. pulicaris, the previous data, such as the vector implication for C. pulicaris in BTV transmission, should be revaluated in future.},
}
@article {pmid28595493,
year = {2018},
author = {Gu, XB and Wang, BJ and Zhao, XB and Li, YF and Yang, GY and Lai, WM and Zhong, ZJ and Peng, GN},
title = {Genetic variation in mitochondrial cox2 of Heterakis gallinarum from poultry in Sichuan, China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {629-634},
doi = {10.1080/24701394.2017.1334771},
pmid = {28595493},
issn = {2470-1408},
mesh = {Animals ; Ascaridida/*genetics/isolation &amp; purification ; Ascaridida Infections/parasitology ; Base Sequence ; Cecum/parasitology ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/enzymology/*genetics ; Phylogeny ; Poultry ; },
abstract = {Heterakis gallinarum is one of the common parasitic nematodes found in the caecum of poultry. To investigate the genetic diversity and genetic structure of the H. gallinarum population in Sichuan, we amplified and sequenced the complete mitochondrial (mt) cytochrome c oxidase subunit II (cox2) gene of 59 H. gallinarum isolates from seven different geographical regions, then analyzed their genetic polymorphisms. All cox2 genes of the 59 H. gallinarum isolates were 696 bp in length, with an average A + T content of 67.1%. Fifty-nine sequences contained 34 variable sites, and were classified into 23 haplotypes (HS1-HS23). The values of haplotype diversity (Hd) and nucleotide diversity (π) were 0.688 and 0.00288, respectively. Based on values of FST and Nm (FST = 0.01929, Nm = 12.71), there was a frequent gene flow but no significant genetic differentiation observed among the populations. The network map showed that the most prominent haplotype was HS1, and the other haplotypes (HS2-HS23) were centered on HS1 with a star-like topology, indicating that H. gallinarum had previously experienced a population expansion. To our knowledge, this is the first research on the population genetics of H. gallinarum based on mitochondrial cox2.},
}
@article {pmid28599069,
year = {2017},
author = {Wang, L and Feng, C and Zheng, X and Guo, Y and Zhou, F and Shan, D and Liu, X and Kong, J},
title = {Plant mitochondria synthesize melatonin and enhance the tolerance of plants to drought stress.},
journal = {Journal of pineal research},
volume = {63},
number = {3},
pages = {},
doi = {10.1111/jpi.12429},
pmid = {28599069},
issn = {1600-079X},
mesh = {Amino Acid Sequence ; Arabidopsis ; Arylalkylamine N-Acetyltransferase/genetics/*metabolism ; Gene Expression Regulation, Plant ; Malus/*enzymology/genetics ; Melatonin/*biosynthesis ; Mitochondria/*enzymology ; *Oxidative Stress ; Phylogeny ; Plants, Genetically Modified ; Sequence Homology, Amino Acid ; },
abstract = {Synthesis of melatonin in mitochondria was reported in animals. However, there is no report on whether plant mitochondria also produce melatonin. Herein, we show that plant mitochondria are a major site for melatonin synthesis. In an in vitro study, isolated apple mitochondria had the capacity to generate melatonin. Subcellular localization analysis documented that an apple SNAT isoform, MzSNAT5, was localized in the mitochondria of both Arabidopsis protoplasts and apple callus cells. The kinetic analysis revealed that the recombinant MzSNAT5 protein exhibited high enzymatic activity to catalyze serotonin to N-acetylserotonin with the Km and Vmax of 55 μmol/L and 0.909 pmol/min/mg protein at 35°C, respectively; this pathway functioned over a wide range of temperatures from 5 to 75°C. In an in vivo study, MzSNAT5 was drought inducible. The transgenic Arabidopsis ectopically expressing MzSNAT5 elevated the melatonin level and, hence, enhanced drought tolerance. The mechanistic study indicated that the ectopically expressing MzSNAT5 allows plant mitochondria to increase melatonin synthesis. As a potent free radical scavenger, melatonin reduces the oxidative stress caused by the elevated reactive oxygen species which are generated under drought stress in plants. Our findings provide evidence that engineered melatonin-enriched plants exhibit enhanced oxidative tolerance.},
}
@article {pmid28602831,
year = {2017},
author = {Turissini, DA and Gomez, OM and Teixeira, MM and McEwen, JG and Matute, DR},
title = {Species boundaries in the human pathogen Paracoccidioides.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {106},
number = {},
pages = {9-25},
pmid = {28602831},
issn = {1096-0937},
support = {R01 GM121750/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Loci ; *Genetic Speciation ; Genome, Fungal ; Humans ; Microsatellite Repeats ; Mitochondria/genetics ; Paracoccidioides/*classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; Statistics, Nonparametric ; },
abstract = {The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.},
}
@article {pmid28607415,
year = {2017},
author = {Hofmann, S and Stöck, M and Zheng, Y and Ficetola, FG and Li, JT and Scheidt, U and Schmidt, J},
title = {Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger).},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {3308},
pmid = {28607415},
issn = {2045-2322},
mesh = {Animals ; Anura/*classification ; Calibration ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Tibet ; Time Factors ; },
abstract = {The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the "Tibetan-origin hypothesis" suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a "Tibetan-origin hypothesis", current sampling (10/22 species; 1 revalidated : S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.},
}
@article {pmid28622748,
year = {2018},
author = {Iswarya Deepti, V and Kandula, S and Khedkar, GD},
title = {DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {659-663},
doi = {10.1080/24701394.2017.1339188},
pmid = {28622748},
issn = {2470-1408},
mesh = {Animals ; Bass/*genetics ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; },
abstract = {Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters. Mean interspecific genetic distance is in the range 0.079-0.164.The phylogeny tree revealed distinct clades for species that are in concurrence with previous taxonomic and allozyme electrophoretic studies carried out from central eastern coast of India. Barcode sequences generated for the first time for species E. heniochus from Indian waters for E. magniscuttis so far there are no reference sequences in GenBank.},
}
@article {pmid28646188,
year = {2017},
author = {Wang, J and Xiang, H and Liu, L and Kong, M and Yin, T and Zhao, X},
title = {Mitochondrial haplotypes influence metabolic traits across bovine inter- and intra-species cybrids.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4179},
pmid = {28646188},
issn = {2045-2322},
mesh = {Acids/metabolism ; Animals ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; Female ; Gene Dosage ; Gene Expression Regulation ; Genome, Mitochondrial ; Haplotypes/*genetics ; Hybrid Cells/metabolism ; *Hybridization, Genetic ; Lipids/biosynthesis ; Mitochondria/*genetics/*metabolism ; Organelle Biogenesis ; Oxygen Consumption ; Phylogeny ; *Quantitative Trait, Heritable ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens). Yak primary cells illustrated a stronger metabolic capacity than that of Luxi. However, all yak cybrid parameters illustrated a drop in relative yak mtDNA compared to Luxi mtDNA, in line with a mitonuclear imbalance in yak interspecies cybrid. Luxi has 250 divergent variations relative to the mitogenome of Holsteins. In cybrids there were generally higher rates of oxygen consumption (OCR) and extracellular acidification (ECAR), and lower mRNA expression levels of nuclear-encoded mitochondrial genes, potentially reflecting active energy metabolism and cellular stress resistance. The results demonstrate that functional differences exist between bovine cybrid cells. While cybrid viability was similar between Holstein and Luxi breeds, the mitonuclear mismatch caused a marked metabolic dysfunction in cattle:yak cybrid species.},
}
@article {pmid28651540,
year = {2017},
author = {Srirattana, K and McCosker, K and Schatz, T and St John, JC},
title = {Cattle phenotypes can disguise their maternal ancestry.},
journal = {BMC genetics},
volume = {18},
number = {1},
pages = {59},
pmid = {28651540},
issn = {1471-2156},
mesh = {Animals ; Cattle/classification/*genetics/physiology ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Embryo, Mammalian/cytology/metabolism ; Female ; Genetic Speciation ; *Maternal Inheritance ; Mitochondria/genetics ; Oocytes/cytology/metabolism ; *Phenotype ; Phylogeny ; },
abstract = {BACKGROUND: Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments.<br><br>RESULTS: A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P&#xa0;<&#xa0;0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype.<br><br>CONCLUSIONS: The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.},
}
@article {pmid28651548,
year = {2017},
author = {Thai, QK and Chung, DA and Tran, HD},
title = {Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.},
journal = {BMC genetics},
volume = {18},
number = {1},
pages = {60},
pmid = {28651548},
issn = {1471-2156},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Genetic Variation ; *Haplotypes ; *Internet ; Mitochondria/genetics ; Phylogeny ; Wolves/*genetics ; },
abstract = {BACKGROUND: Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes.<br><br>DESCRIPTION: The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download.<br><br>CONCLUSIONS: The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582&#xa0;bp sequences.},
}
@article {pmid28655342,
year = {2017},
author = {Li, WX and Zhang, D and Boyce, K and Xi, BW and Zou, H and Wu, SG and Li, M and Wang, GT},
title = {The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes.},
journal = {Parasites &amp; vectors},
volume = {10},
number = {1},
pages = {314},
pmid = {28655342},
issn = {1756-3305},
mesh = {Animals ; Cestoda/*genetics ; Cestode Infections/parasitology/*veterinary ; DNA, Mitochondrial/genetics ; Fish Diseases/*parasitology ; Fishes ; *Gene Order ; Gene Rearrangement ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {BACKGROUND: External segmentation and internal proglottization are important evolutionary characters of the Eucestoda. The monozoic caryophyllideans are considered the earliest diverging eucestodes based on partial mitochondrial genes and nuclear rDNA sequences, yet, there are currently no complete mitogenomes available. We have therefore sequenced the complete mitogenomes of three caryophyllideans, as well as the polyzoic Schyzocotyle acheilognathi, explored the phylogenetic relationships of eucestodes and compared the gene arrangements between unsegmented and segmented cestodes.<br><br>RESULTS: The circular mitogenome of Atractolytocestus huronensis was 15,130&#xa0;bp, the longest sequence of all the available cestodes, 14,620&#xa0;bp for Khawia sinensis, 14,011&#xa0;bp for Breviscolex orientalis and 14,046&#xa0;bp for Schyzocotyle acheilognathi. The A-T content of the three caryophyllideans was found to be lower than any other published mitogenome. Highly repetitive regions were detected among the non-coding regions (NCRs) of the four cestode species. The evolutionary relationship determined between the five orders (Caryophyllidea, Diphyllobothriidea, Bothriocephalidea, Proteocephalidea and Cyclophyllidea) is consistent with that expected from morphology and the large fragments of mtDNA when reconstructed using all 36 genes. Examination of the 54 mitogenomes from these five orders, revealed a unique arrangement for each order except for the Cyclophyllidea which had two types that were identical to that of the Diphyllobothriidea and the Proteocephalidea. When comparing gene order between the unsegmented and segmented cestodes, the segmented cestodes were found to have the lower similarities due to a long distance transposition event. All rearrangement events between the four arrangement categories took place at the junction of rrnS-tRNA [Arg] (P1) where NCRs are common.<br><br>CONCLUSIONS: Highly repetitive regions are detected among NCRs of the four cestode species. A long distance transposition event is inferred between the unsegmented and segmented cestodes. Gene arrangements of Taeniidae and the rest of the families in the Cyclophyllidea are found be identical to those of the sister order Proteocephalidea and the relatively basal order Diphyllobothriidea, respectively.},
}
@article {pmid28655915,
year = {2017},
author = {Bernardino, AF and Li, Y and Smith, CR and Halanych, KM},
title = {Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {4295},
pmid = {28655915},
issn = {2045-2322},
mesh = {Animals ; Annelida/classification/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.},
}
@article {pmid28657486,
year = {2018},
author = {Suk, HY and Lee, MY and Bae, HG and Lee, SJ and Poyarkov, N and Lee, H and Min, MS},
title = {Phylogenetic structure and ancestry of Korean clawed salamander, Onychodactylus koreanus (Caudata: Hynobiidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {4},
pages = {650-658},
doi = {10.1080/24701394.2017.1339187},
pmid = {28657486},
issn = {2470-1408},
mesh = {Animals ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genetic Speciation ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Republic of Korea ; Species Specificity ; Caudata/*genetics ; },
abstract = {Onychodactylus koreanus, a hynobiid salamander species endemic to the Korean Peninsula, can be regarded as a strict ecological specialist, probably vulnerable to anthropogenic environmental modifications and climate change. We used mitochondrial cytochrome b gene to analyze the genetic diversity and phylogenetic structure of O. koreanus from 19 populations collected in an attempt to cover its major distribution within South Korea. A total of 76 haplotypes of O. koreanus obtained in our analyses could be subdivided into three phylogenetic clades, KR, NE and SE. Clade KR haplotypes occur in most of the regions throughout the Korean Peninsula with four distinct subclades (KR I-IV). Clade NE and SE haplotypes were only observed in two populations YY and YS, respectively. Haplotype sharing was scarce even among populations in geographical proximity, and most of the populations were represented by a single clade or subclade, indicating the low level of gene flow among populations. O. koreanus likely originated from the historical southward dispersal of its ancestral lineages following divergence from Chinese O. zhaoermii that was recovered as the sister of O. koreanus in our phylogenetic analysis. Our results have critical implications for the taxonomic status of O. koreanus and its long-term management plan.},
}
@article {pmid28665258,
year = {2017},
author = {Hu, JJ and Huang, S and Wen, T and Esch, GW and Liang, Y and Li, HL},
title = {Morphology, Molecular Characteristics, and Demonstration of a Definitive Host for Sarcocystis rommeli from Cattle (Bos taurus) in China.},
journal = {The Journal of parasitology},
volume = {103},
number = {5},
pages = {471-476},
doi = {10.1645/16-187},
pmid = {28665258},
issn = {1937-2345},
mesh = {Animals ; Cat Diseases/parasitology ; Cats ; Cattle ; Cattle Diseases/*parasitology ; China ; Cloning, Molecular ; DNA, Protozoan/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Feces/parasitology ; Intestine, Small/parasitology ; Life Cycle Stages ; Microscopy, Electron, Transmission/veterinary ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 18S/genetics ; Sarcocystis/classification/*genetics/growth &amp; development/*ultrastructure ; Sarcocystosis/parasitology/*veterinary ; Sequence Alignment/veterinary ; Sequence Analysis, DNA ; },
abstract = {Sarcocysts of Sarcocystis rommeli were found for the first time in 6 of 34 (17.6%) cattle (Bos taurus) in China. With light microscopy, sarcocysts of S. rommeli were up to 1,130 μm long, with a striated, 4-8-μm-thick cyst wall. Using transmission electron microscopy, the villar protrusions (vp) were 4.7-5.2 × 0.2-0.3 μm, and 0.3-0.5 μm apart from each other. The vp contained microtubules extending from the top of the vp to the middle of the ground substance layer (gsl). A BLAST search of the near full-length 18S rRNA and partial mitochondrial cox1 sequences of S. rommeli revealed 98.7% identity and 99.2% identity with sequences of Sarcocystis bovini in GenBank, respectively. Two domestic cats (Felis catus) fed sarcocysts of S. rommeli shed oocysts/sporocysts in their feces with a prepatent period of 14 to 15 days; the partial mitochondrial cox1 sequences of these oocysts/sporocysts shared the high identities, that is, 99.4% and 99.5%, with cox1 sequences of S. rommeli sarcocysts and S. bovini sarcocysts, respectively. This is the first demonstration of a definitive host for S. rommeli.},
}
@article {pmid28673190,
year = {2018},
author = {Koç, H and Bülbül, U and Kurnaz, M and İhsan Eroğlu, A and Kutrup, B},
title = {Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {664-673},
doi = {10.1080/24701394.2017.1342245},
pmid = {28673190},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Turkey ; },
abstract = {The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.},
}
@article {pmid28689636,
year = {2017},
author = {Zhao, YQ and Yang, HY and Zhang, DD and Han, YL and Hou, CC and Zhu, JQ},
title = {Dynamic transcription and expression patterns of KIF3A and KIF3B genes during spermiogenesis in the shrimp, Palaemon carincauda.},
journal = {Animal reproduction science},
volume = {184},
number = {},
pages = {59-77},
doi = {10.1016/j.anireprosci.2017.06.017},
pmid = {28689636},
issn = {1873-2232},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Gene Expression Regulation/*physiology ; Kinesins/genetics/*metabolism ; Male ; Models, Molecular ; Palaemonidae/*metabolism ; Phylogeny ; Protein Conformation ; RNA, Messenger/genetics/metabolism ; Spermatogenesis/*physiology ; },
abstract = {Spermiogenesis is a highly ordered and complex process in the male germ cell differentiation. The microtubule-based motor proteins KIF3A and KIF3B are required for the progression of the stages of spermiogenesis. In this study, the main goal was to determine whether KIF3A and KIF3B have a key role in spermiogenesis in Palaemon carincauda. The complete cDNA of KIF3A/3B from the testis of P. carincauda was cloned by using PCR and rapid amplification of cDNA ends (RACE). The predicted secondary and tertiary structures of KIF3A/3B contained three domains which were the: a) head region, b) stalk region, and c) tail region. Real-time quantitative PCR (qPCR) results revealed that KIF3A and KIF3B mRNAs were obtained for all the tissues examined, with the greatest gene expression in the testis. In situ hybridization indicated the KIF3A and KIF3B mRNAs were distributed in the periphery of the nuclear in the early spermatid of spermiogenesis. In the middle and late spermatid stages, KIF3A and KIF3B mRNAs were gradually upregulated and assembled to one side where acrosome biogenesis begins. In the mature sperm, KIF3A and KIF3B mRNAs were distributed in the acrosome cap and spike. Immunofluorescence studies indicated that KIF3A, tubulin, mitochondria, and Golgi were co-localized in different stages during spermiogenesis in P. carincauda. The temporal and spatial gene expression dynamics of KIF3A/3B indicate that KIF3A and KIF3B proteins may be involved in acrosome formation and nucleus shaping. Moreover, these proteins can transport the mitochondria and Golgi that facilitate acrosome formation in P. carincauda.},
}
@article {pmid28690127,
year = {2017},
author = {Nacer, DF and Raposo do Amaral, F},
title = {Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons.},
journal = {Molecular phylogenetics and evolution},
volume = {115},
number = {},
pages = {1-6},
doi = {10.1016/j.ympev.2017.07.002},
pmid = {28690127},
issn = {1095-9513},
mesh = {Animals ; Cytochromes b/classification/genetics ; Electron Transport Complex IV/classification/genetics ; Falconiformes/*classification ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; },
abstract = {Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.},
}
@article {pmid28712317,
year = {2018},
author = {Han, CC and Fang, LS and Chang, IM and Lin, HD},
title = {Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {687-694},
doi = {10.1080/24701394.2017.1350948},
pmid = {28712317},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Decapoda/*genetics ; Electron Transport Complex IV/*genetics ; Fresh Water ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; Rivers ; Sequence Analysis, DNA/methods ; Shellfish ; Taiwan ; },
abstract = {Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.},
}
@article {pmid28712321,
year = {2018},
author = {Wang, ZL and Yang, XQ and Wang, TZ and Yu, X},
title = {Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {695-702},
doi = {10.1080/24701394.2017.1350949},
pmid = {28712321},
issn = {2470-1408},
mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/*genetics ; Farms ; Genetic Speciation ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Spiders/*genetics ; },
abstract = {DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.},
}
@article {pmid28745537,
year = {2018},
author = {Nakazawa, T and Liu, SV and Sakai, Y and Araki, KS and Tsai, CH and Okuda, N},
title = {Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {756-764},
doi = {10.1080/24701394.2017.1357708},
pmid = {28745537},
issn = {2470-1408},
mesh = {Animals ; Body Size/*genetics ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Japan ; Lakes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Phylogeny ; },
abstract = {Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.},
}
@article {pmid28745560,
year = {2018},
author = {Bhatti, S and Abbas, S and Aslamkhan, M and Attimonelli, M and Trinidad, MS and Aydin, HH and de Souza, EMS and Gonzalez, GR},
title = {Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {714-726},
doi = {10.1080/24701394.2017.1350951},
pmid = {28745560},
issn = {2470-1408},
mesh = {Adult ; Asian People/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Pakistan ; Phylogeny ; Phylogeography ; Social Class ; White People/genetics ; },
abstract = {To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.},
}
@article {pmid28749584,
year = {2017},
author = {Kopečná, M and Vigouroux, A and Vilím, J and Končitíková, R and Briozzo, P and Hájková, E and Jašková, L and von Schwartzenberg, K and Šebela, M and Moréra, S and Kopečný, D},
title = {The ALDH21 gene found in lower plants and some vascular plants codes for a NADP[+] -dependent succinic semialdehyde dehydrogenase.},
journal = {The Plant journal : for cell and molecular biology},
volume = {92},
number = {2},
pages = {229-243},
doi = {10.1111/tpj.13648},
pmid = {28749584},
issn = {1365-313X},
mesh = {Bryophyta/enzymology/*genetics ; Ferns/enzymology/*genetics ; Genes, Plant/*genetics/physiology ; Phylogeny ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity ; Succinate-Semialdehyde Dehydrogenase/*genetics/metabolism ; Succinic Acid/metabolism ; gamma-Aminobutyric Acid/analogs &amp; derivatives/metabolism ; },
abstract = {Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP[+] -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD[+] is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP[+] binding induces a conformational change of the loop carrying Arg-228, which seals the NADP[+] in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.},
}
@article {pmid28752773,
year = {2018},
author = {Koroiva, R and Kvist, S},
title = {Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {765-771},
doi = {10.1080/24701394.2017.1357709},
pmid = {28752773},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.},
}
@article {pmid28758818,
year = {2018},
author = {Manger, A and Behere, GT and Firake, DM and Sharma, B and Deshmukh, NA and Firake, PD and Azad Thakur, NS and Ngachan, SV},
title = {Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {29},
number = {5},
pages = {792-799},
doi = {10.1080/24701394.2017.1357713},
pmid = {28758818},
issn = {2470-1408},
mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genome, Mitochondrial/genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/*genetics ; },
abstract = {The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.},
}
@article {pmid28763510,
year = {2017},
author = {Oliveira Da Silva, W and Pieczarka, JC and Ferguson-Smith, MA and O'Brien, PCM and Mendes-Oliveira, AC and Sampaio, I and Carneiro, J and Nagamachi, CY},
title = {Chromosomal diversity and molecular divergence among three undescribed species of Neacomys (Rodentia, Sigmodontinae) separated by Amazonian rivers.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0182218},
pmid = {28763510},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Brazil ; *Chromosome Mapping ; Chromosome Painting ; Chromosomes/*ultrastructure ; Cytochromes b/metabolism ; Electron Transport Complex IV/metabolism ; Female ; Genetic Variation ; Geography ; Haplotypes ; In Situ Hybridization, Fluorescence ; Karyotyping ; Likelihood Functions ; Male ; Mitochondria/genetics ; Phylogeny ; Rodentia/classification/*genetics ; },
abstract = {The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68) and Neacomys sp. B (NSP-B, 2n = 54/FN = 66) differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70) shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17]) and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25) and Sigmodontinae subfamily (HME 15 and 24), which can be used as taxonomic markers for these groups.},
}
@article {pmid28766501,
year = {2017},
author = {Hu, JJ and Huang, S and Wen, T and Esch, GW and Liang, Y and Li, HL},
title = {Sarcocystis spp. in domestic sheep in Kunming City, China: prevalence, morphology, and molecular characteristics.},
journal = {Parasite (Paris, France)},
volume = {24},
number = {},
pages = {30},
pmid = {28766501},
issn = {1776-1042},
mesh = {Animals ; China/epidemiology ; DNA, Protozoan/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Microscopy, Electron, Transmission/veterinary ; Mitochondria/enzymology ; Muscles/parasitology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sarcocystis/classification/genetics/*isolation &amp; purification/ultrastructure ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; },
abstract = {Sheep (Ovis aries) are intermediate hosts for at least six named species of Sarcocystis: S. tenella, S. arieticanis, S. gigantea, S. medusiformis, S. mihoensis, and S. microps. Here, only two species, S. tenella and S. arieticanis, were found in 79 of 86 sheep (91.9%) in Kunming, China, based on their morphological characteristics. Four genetic markers, i.e., 18S rRNA gene, 28S rRNA gene, mitochondrial cox1 gene, and ITS-1 region, were sequenced and characterized for the two species of Sarcocystis. Sequences of the three former markers for S. tenella shared high identities with those of S. capracanis in goats, i.e., 99.0%, 98.3%, and 93.6%, respectively; the same three marker sequences of S. arieticanis shared high identities with those of S. hircicanis in goats, i.e., 98.5%, 96.5%, and 92.5%, respectively. No sequences in GenBank were found to significantly resemble the ITS-1 regions of S. tenella and S. arieticanis. Identities of the four genetic markers for S. tenella and S. arieticanis were 96.3%, 95.4%, 82.5%, and 66.2%, respectively.},
}
@article {pmid28779732,
year = {2016},
author = {Aziz, NMA and Esa, Y and Arshad, A},
title = {DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene.},
journal = {Journal of environmental biology},
volume = {37},
number = {4 Spec No},
pages = {725-733},
pmid = {28779732},
issn = {0254-8704},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Haplotypes ; Mitochondria/*enzymology ; *Phylogeny ; Species Specificity ; },
abstract = {The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?},
}
@article {pmid28780151,
year = {2017},
author = {Addy, F and Wassermann, M and Kagendo, D and Ebi, D and Zeyhle, E and Elmahdi, IE and Umhang, G and Casulli, A and Harandi, MF and Aschenborn, O and Kern, P and Mackenstedt, U and Romig, T},
title = {Genetic differentiation of the G6/7 cluster of Echinococcus canadensis based on mitochondrial marker genes.},
journal = {International journal for parasitology},
volume = {47},
number = {14},
pages = {923-931},
doi = {10.1016/j.ijpara.2017.06.003},
pmid = {28780151},
issn = {1879-0135},
mesh = {Africa ; Animals ; Camelus ; Cattle ; DNA, Mitochondrial/chemistry ; Deer ; Dogs ; Echinococcus/classification/*genetics ; Europe ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Goats ; Haplotypes/genetics ; Humans ; Middle East ; Mitochondria/*genetics ; Multigene Family/*genetics ; Phylogeny ; Polymorphism, Genetic ; Swine ; Wolves ; },
abstract = {Among the genotype/species causing cystic echinococcosis, the taxonomic status of Echinococcus canadensis is only partially resolved. Within E. canadensis, four genotypes (G6, G7, G8 and G10) have been described based on short mitochondrial sequences, of which G6 and G7 (the 'camel' and the 'pig' strain, respectively) are closely related and variously regarded as microvariants of a single strain G6/7. Globally, this G6/7 cluster is the second most important agent of human cystic echinococcosis and is the predominant Echinococcus taxon in large parts of sub-Saharan Africa. To add data on the internal structure and the geographical distribution of this cluster, we analysed diversity and population structure of 296 isolates of E. canadensis from sub-Saharan Africa, the Middle East and Europe using the complete mitochondrial cytochrome c oxidase subunit 1 (cox1) (1,608bp) and NADH dehydrogenase subunit 1 (nad1) (894bp) gene sequences. Polymorphism of the mtDNA loci gave 51 (cox1), 33 (nad1) and 73 (cox1-nad1 concatenated) haplotypes. African and Middle Eastern isolates mainly grouped in a star-like structure around a predominant haplotype, while the European isolates produced more diversified networks. Although the cox1 diagnostic sequence for G6 is frequent in the African/Middle Eastern sub-cluster, and that for G7 is common in the European isolates, numerous intermediate variants prevent a clear distinction into 'G6' or 'G7', and the entire taxon is best treated as a common haplotype cluster G6/7. Meanwhile, the G6/7 cluster is clearly distinct from sequences of wildlife isolates of G8 and G10 from the northern hemisphere, and sequences of the latter genotypes were remarkably distant from each other. It is clear from the present study that, based on mitochondrial data, G6/7 is a coherent genotypic entity within E. canadensis that retains substantial intraspecific variance, and sub-populations share common ancestral polymorphisms and haplotypes. This study provides the basis for wider biogeographic comparison and population genetics studies of this taxon.},
}
@article {pmid28811531,
year = {2017},
author = {Moghaddam, MB and Gross, T and Becker, A and Vilcinskas, A and Rahnamaeian, M},
title = {The selective antifungal activity of Drosophila melanogaster metchnikowin reflects the species-dependent inhibition of succinate-coenzyme Q reductase.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {8192},
pmid = {28811531},
issn = {2045-2322},
mesh = {Animals ; Antifungal Agents/*pharmacology ; Antimicrobial Cationic Peptides/genetics/*pharmacology ; Cell Line ; Drosophila Proteins/genetics/*pharmacology ; Drosophila melanogaster/genetics/*metabolism ; Electron Transport Complex II/*antagonists &amp; inhibitors/genetics ; Enzyme Inhibitors/*pharmacology ; Mitochondria/enzymology/genetics ; Phylogeny ; Recombinant Proteins/pharmacology ; },
abstract = {Insect-derived antifungal peptides have a significant economic potential, particularly for the engineering of pathogen-resistant crops. However, the nonspecific antifungal activity of such peptides could result in detrimental effects against beneficial fungi, whose interactions with plants promote growth or increase resistance against biotic and abiotic stress. The antifungal peptide metchnikowin (Mtk) from Drosophila melanogaster acts selectively against pathogenic Ascomycota, including Fusarium graminearum, without affecting Basidiomycota such as the beneficial symbiont Piriformospora indica. Here we investigated the mechanism responsible for the selective antifungal activity of Mtk by using the peptide to probe a yeast two-hybrid library of F. graminearum cDNAs. We found that Mtk specifically targets the iron-sulfur subunit (SdhB) of succinate-coenzyme Q reductase (SQR). A functional assay based on the succinate dehydrogenase (SDH) activity of mitochondrial complex II clearly demonstrated that Mtk inhibited the SDH activity of F. graminearum mitochondrial SQR by up to 52%, but that the equivalent enzyme in P. indica was unaffected. A phylogenetic analysis of the SdhB family revealed a significant divergence between the Ascomycota and Basidiomycota. SQR is one of the key targets of antifungal agents and we therefore propose Mtk as an environmentally sustainable and more selective alternative to chemical fungicides.},
}
@article {pmid28848044,
year = {2017},
author = {Srivastava, S and Savanur, MA and Sinha, D and Birje, A and R, V and Saha, PP and D'Silva, P},
title = {Regulation of mitochondrial protein import by the nucleotide exchange factors GrpEL1 and GrpEL2 in human cells.},
journal = {The Journal of biological chemistry},
volume = {292},
number = {44},
pages = {18075-18090},
pmid = {28848044},
issn = {1083-351X},
mesh = {Biomarkers/metabolism ; Genetic Complementation Test ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Intracellular Signaling Peptides and Proteins/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Ligands ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; *Models, Molecular ; Molecular Chaperones/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Oxidative Stress ; Phylogeny ; Protein Isoforms/metabolism ; Protein Multimerization ; Protein Stability ; Protein Transport ; RNA Interference ; Recombinant Fusion Proteins/chemistry/metabolism ; },
abstract = {Mitochondria are organelles indispensable for maintenance of cellular energy homeostasis. Most mitochondrial proteins are nuclearly encoded and are imported into the matrix compartment where they are properly folded. This process is facilitated by the mitochondrial heat shock protein 70 (mtHsp70), a chaperone contributing to mitochondrial protein quality control. The affinity of mtHsp70 for its protein clients and its chaperone function are regulated by binding of ATP/ADP to mtHsp70's nucleotide-binding domain. Nucleotide exchange factors (NEFs) play a crucial role in exchanging ADP for ATP at mtHsp70's nucleotide-binding domain, thereby modulating mtHsp70's chaperone activity. A single NEF, Mge1, regulates mtHsp70's chaperone activity in lower eukaryotes, but the mammalian orthologs are unknown. Here, we report that two putative NEF orthologs, GrpE-like 1 (GrpEL1) and GrpEL2, modulate mtHsp70's function in human cells. We found that both GrpEL1 and GrpEL2 associate with mtHsp70 as a hetero-oligomeric subcomplex and regulate mtHsp70 function. The formation of this subcomplex was critical for conferring stability to the NEFs, helped fine-tune mitochondrial protein quality control, and regulated crucial mtHsp70 functions, such as import of preproteins and biogenesis of Fe-S clusters. Our results also suggested that GrpEL2 has evolved as a possible stress resistance protein in higher vertebrates to maintain chaperone activity under stress conditions. In conclusion, our findings support the idea that GrpEL1 has a role as a stress modulator in mammalian cells and highlight that multiple NEFs are involved in controlling protein quality in mammalian mitochondria.},
}
@article {pmid28859174,
year = {2017},
author = {Hudson, W},
title = {Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines.},
journal = {PloS one},
volume = {12},
number = {8},
pages = {e0184309},
pmid = {28859174},
issn = {1932-6203},
mesh = {Agriculture ; Animals ; DNA, Mitochondrial/*genetics ; Egypt ; Haplotypes/genetics ; Horses/*genetics ; Mitochondria/genetics ; Pedigree ; *Phylogeny ; },
abstract = {BACKGROUND: Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program.<br><br>FINDINGS: Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel.<br><br>CONCLUSIONS: Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses.},
}
@article {pmid28863891,
year = {2017},
author = {Lu, L and Wang, X and Wu, S and Song, X and Zou, Z and Xie, X and Xiao, J and Chen, S and Feng, H},
title = {Black carp STING functions importantly in innate immune defense against RNA virus.},
journal = {Fish &amp; shellfish immunology},
volume = {70},
number = {},
pages = {13-24},
doi = {10.1016/j.fsi.2017.08.037},
pmid = {28863891},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Carps/*genetics/*immunology ; Fish Diseases/*immunology ; Fish Proteins/chemistry/genetics/immunology ; Gene Expression Profiling ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Membrane Proteins/chemistry/*genetics/*immunology ; Phylogeny ; Reoviridae/physiology ; Reoviridae Infections/immunology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology ; },
abstract = {Stimulator of interferon genes (STING) is a central and multifaceted mediator in the innate immune response of higher vertebrates. To explore its role in teleost fish, the STING homolog of black carp (Mylopharyngodon piceus) (bcSTING) has been cloned and characterized in this paper. bcSTING transcription in Mylopharyngodon piceus fin (MPF) cells increased remarkably in response to GCRV and SVCV infection, or poly (I:C) stimulation. bcSTING migrated around 42 KDa in immunoblot assay and was identified as a cytosolic protein locating on ER majorly through immunofluorescence staining. Under condition of SVCV/GCRV infection or poly (I:C) stimulation, the subcellular distribution of bcSTING majorly displayed on mitochondria, which overlapped with that of bcMAVS. HA-bcSTING instead of bcSTING-HA presented strong IFN-inducing activity in reporter assay and antiviral ability against both SVCV and GCRV in plaque assay. Site mutation of serine (S) on C-terminus of bcSTING demonstrated that both S371 and S379 were crucial for its mediated signaling. Taken together, our study support the conclusion that bcSTING plays an important role in host innate immune defense against RNA virus such as SVCV and GCRV, in which its C-terminus functions crucially.},
}
@article {pmid28882896,
year = {2017},
author = {Sultana, S and Solotchi, M and Ramachandran, A and Patel, SS},
title = {Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.},
journal = {The Journal of biological chemistry},
volume = {292},
number = {44},
pages = {18145-18160},
pmid = {28882896},
issn = {1083-351X},
support = {R35 GM118086/GM/NIGMS NIH HHS/United States ; },
mesh = {8-Hydroxy-2'-Deoxyguanosine ; Bacteriophage T7/enzymology ; Base Pair Mismatch ; DNA Damage ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Deoxyguanosine/analogs &amp; derivatives/metabolism ; Fluorescence Polarization ; Humans ; Mitochondrial Proteins/genetics/*metabolism ; *Mutation ; Mutation Rate ; Oxidation-Reduction ; Recombinant Fusion Proteins/metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Substrate Specificity ; *Transcription Elongation, Genetic ; Transcription Factors/metabolism ; Viral Proteins/genetics/*metabolism ; },
abstract = {Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10[-6]), yeast mitochondrial Rpo41 (6 × 10[-6]), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10[-5]) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10[-4] The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10[-5]-10[-6]), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10[-7]-10[-10]). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10[-4]). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of in vitro transcribed RNAs.},
}
@article {pmid28883650,
year = {2017},
author = {Liu, M and Guo, X},
title = {A novel and stress adaptive alternative oxidase derived from alternative splicing of duplicated exon in oyster Crassostrea virginica.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {10785},
pmid = {28883650},
issn = {2045-2322},
mesh = {*Alternative Splicing ; Animals ; Crassostrea/genetics/*physiology ; *Exons ; Gene Expression Regulation ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Models, Biological ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; *Stress, Physiological ; Alternative Oxidase ; },
abstract = {Alternative oxidase (AOX) is a mitochondrial inner-membrane oxidase that accepts electrons directly from ubiquinol and reduces oxygen to water without involving cytochrome-linked electron transport chain. It is highly conserved in many non-vertebrate taxa and may protect cells against hypoxia and oxidative stress. We identified two AOX mRNAs in eastern oyster Crassostrea virginica, CvAOXA and CvAOXB, which differ by 170 bp but encode AOXs of the same size. Sequence analyses indicate that CvAOX has 10 exons with a tandem duplication of exon 10, and 3' alternative splicing using either the first or second exon 10 produces the two variants CvAOXB or CvAOXA, respectively. The second exon 10 in CvAOXA is more conserved across taxa, while the first exon 10 in CvAOXB contains novel mutations surrounding key functional sites. Both variants are expressed in all organs with the expression of CvAOXA higher than that of CvAOXB under normal condition. Under stress by air exposure, CvAOXB showed significantly higher expression than CvAOXA and became the dominant variant. This is the first case of alternative splicing of duplicated exon in a mollusc that produces a novel variant adaptive to stress, highlighting genome's versatility in generating diversity and phenotypic plasticity.},
}
@article {pmid28904365,
year = {2017},
author = {Ma, X and Yao, L and Yang, B and Lee, YK and Chen, F and Liu, J},
title = {RNAi-mediated silencing of a pyruvate dehydrogenase kinase enhances triacylglycerol biosynthesis in the oleaginous marine alga Nannochloropsis salina.},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {11485},
pmid = {28904365},
issn = {2045-2322},
mesh = {Biomarkers ; Carbohydrate Metabolism ; Gene Expression Regulation ; Gene Knockdown Techniques ; *Gene Silencing ; Genotype ; Lipid Metabolism ; Microalgae/classification/*genetics/*metabolism ; Photosynthesis ; Phylogeny ; Protein Serine-Threonine Kinases/chemistry/*genetics ; Protein Transport ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; *RNA Interference ; Sequence Analysis, DNA ; Triglycerides/*biosynthesis ; },
abstract = {Oleaginous microalgae have been emerging as the third-generation feedstocks for biofuel production. Genetic manipulation for improving triacylglycerol (TAG) accumulation represents a promising approach towards the economics of microalgal biofuels. Acetyl-CoA, the essential carbon precursor for de novo fatty acid biosynthesis, can be derived from pyruvate catalyzed by pyruvate dehydrogenase, which is negatively regulated by pyruvate dehydrogenase kinase (PDK). In the present study, we characterized a PDK gene (NsPDK) from Nannochloropsis salina. Subcellular localization assay assisted by green fluorescence protein (GFP) fusion indicated the localization of NsPDK in mitochondria of N. salina cells. NsPDK knockdown via RNA interference strategy attenuated NsPDK expression at the mRNA level and its enzymatic activity in vivo, leading to faster TAG accumulation without compromising cell growth under high light stress conditions. Interestingly, the TAG increase was accompanied by a decline in membrane polar lipids. NsPDK knockdown also altered fatty acid profile in N. salina. Furthermore, transcriptional analysis suggested that the carbon metabolic pathways might be influenced by NsPDK knockdown leading to diverted carbon flux towards TAG synthesis. Taken together, our results demonstrate the role of NsPDK in regulating TAG accumulation and provide valuable insights into future manipulation of oleaginous microalgae for improving biofuel production.},
}
@article {pmid28910691,
year = {2017},
author = {Tyml, T and Dyková, I},
title = {Phylogeny and taxonomy of new and re-examined strains of Tubulinea (Amoebozoa).},
journal = {European journal of protistology},
volume = {61},
number = {Pt A},
pages = {41-47},
doi = {10.1016/j.ejop.2017.08.002},
pmid = {28910691},
issn = {1618-0429},
mesh = {Lobosea/*classification/cytology ; Norway ; *Phylogeny ; Species Specificity ; },
abstract = {Morphological and molecular characterizations of three newly isolated tubulinean strains and re-examination of five strains formerly considered representatives of Saccamoeba and one strain formerly considered as Trichamoeba resulted in (a) the determination of strain BA02, isolated from a dripping rock ledge in Skansbukta (Billefjorden, Svalbard), as a new representative of Ptolemeba bulliensis Brown et al., 2014; (b) identification of strain ATCC[®] 50249™, deposited in the American Type Culture Collection as Trichamoeba, as the same species (P. bulliensis); (c) characterization of the new strain POHL into the Saccamoeba clade as a member closely related to S. lacustris; and (d) changing the generic residence of three strains formerly considered as representatives of Saccamoeba (strain PV67 to the P. bulliensis clade, and W187G and DP7 into the sister group of Ptolemeba noxubium Brown et al., 2014) whereas two other strains (MSED6, NTSHR) retain their original Saccamoeba clade position. Within the individual clades, the ultrastructure (especially the inner architecture of mitochondria) is congruent and thus of superior taxonomic value to that of light microscopic (morphometric) features.},
}
@article {pmid28911184,
year = {2017},
author = {Xia, L and Liang, H and Xu, L and Chen, J and Bekaert, M and Zhang, H and Lu, Y},
title = {Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae.},
journal = {FEMS microbiology letters},
volume = {364},
number = {17},
pages = {},
doi = {10.1093/femsle/fnx143},
pmid = {28911184},
issn = {1574-6968},
mesh = {Animals ; Apoptosis ; Cell Line ; Cloning, Molecular ; Cyprinidae/*microbiology ; Cytoplasm/*enzymology ; Epithelial Cells/cytology/microbiology/ultrastructure ; Escherichia coli/genetics ; Gene Expression ; Green Fluorescent Proteins/genetics ; Host-Pathogen Interactions ; Microscopy, Fluorescence ; Mitochondria/enzymology/ultrastructure ; Nocardia/cytology/*enzymology/genetics ; Phylogeny ; Recombinant Fusion Proteins/metabolism ; Transfection ; Type C Phospholipases/*chemistry/genetics/*metabolism ; Virulence Factors/chemistry/*metabolism ; },
abstract = {Fish nocardiosis is a chronic systemic granulomatous disease, and Nocardia seriolae is the main pathogen that causes it. The pathogenesis and virulence factors of N. seriolae are not fully understood. A phospholipase C (PLC), which is likely to be a secreted protein targeting host cell mitochondria, was found by a bioinformatics analysis of the whole genome sequence of N. seriolae. In order to determine the subcellular localization and study the preliminary function of PLC from N. seriolae (NsPLC), in this study gene cloning, secreted protein identification, subcellular localization in host cells and apoptosis detection of NsPLC were carried out. Mass spectrometry analysis of extracellular products from N. seriolae showed that NsPLC was a secreted protein. Subcellular localization of NsPLC-GFP fusion protein in fathead minnow (FHM) cells revealed that the green fluorescence exhibited a punctate distribution near the nucleus and did not co-localize with mitochondria. In addition, an apoptosis assay suggested that apoptosis was induced in FHM cells by the overexpression of NsPLC. This study may lay the foundations for further studies on the function of NsPLC and promote the understanding of the virulence factors and pathogenic mechanism of N. seriolae.},
}
@article {pmid28918565,
year = {2017},
author = {Scala, A and Mirabella, R and Goedhart, J and de Vries, M and Haring, MA and Schuurink, RC},
title = {Forward genetic screens identify a role for the mitochondrial HER2 in E-2-hexenal responsiveness.},
journal = {Plant molecular biology},
volume = {95},
number = {4-5},
pages = {399-409},
pmid = {28918565},
issn = {1573-5028},
support = {818.02.017//NWO/ ; },
mesh = {Aldehydes/*pharmacology ; Arabidopsis/cytology/drug effects/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Mitochondria/drug effects/metabolism ; Mutation ; Oxidation-Reduction/drug effects ; Phylogeny ; Plant Leaves/cytology/drug effects/genetics/physiology ; Plant Roots/cytology/drug effects/genetics/physiology ; Erb-b2 Receptor Tyrosine Kinases/genetics/*metabolism ; Seedlings/cytology/drug effects/genetics/physiology ; Signal Transduction/drug effects ; },
abstract = {This work adds a new player, HER2, downstream of the perception of E-2-hexenal, a green leaf volatile, and shows that E-2-hexenal specifically changes the redox status of the mitochondria. It is widely accepted that plants produce and respond to green leaf volatiles (GLVs), but the molecular components involved in transducing their perception are largely unknown. The GLV E-2-hexenal inhibits root elongation in seedlings and, using this phenotype, we isolated E-2-hexenal response (her) Arabidopsis thaliana mutants. Using map-based cloning we positioned the her2 mutation to the At5g63620 locus, resulting in a phenylalanine instead of serine on position 223. Knockdown and overexpression lines of HER2 confirmed the role of HER2, which encodes an oxidoreductase, in the responsiveness to E-2-hexenal. Since E-2-hexenal is a reactive electrophile species, which are known to influence the redox status of cells, we utilized redox sensitive GFP2 (roGFP2) to determine the redox status of E-2-hexenal-treated root cells. Since the signal peptide of HER2 directed mCherry to the mitochondria, we targeted the expression of roGFP2 to this organelle besides the cytosol. E-2-hexenal specifically induced a change in the redox status in the mitochondria. We did not see a difference in the redox status in her2 compared to wild-type Arabidopsis. Still, the mitochondrial redox status did not change with Z-3-hexenol, another abundant GLV. These results indicate that HER2 is involved in transducing the perception of E-2-hexenal, which changes the redox status of the mitochondria.},
}
@article {pmid28938742,
year = {2017},
author = {Wells, D and Ravichandran, K and McCaffrey, C and Grifo, J and Morales, A and Perloe, M and Munne, S and Fragouli, E},
title = {Reply: Mitochondrial DNA Quantification-the devil in the detail.},
journal = {Human reproduction (Oxford, England)},
volume = {32},
number = {10},
pages = {2150-2151},
doi = {10.1093/humrep/dex279},
pmid = {28938742},
issn = {1460-2350},
mesh = {*DNA, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria ; Phylogeny ; },
}
@article {pmid28947489,
year = {2017},
author = {Majsec, K and Bhuiyan, NH and Sun, Q and Kumari, S and Kumar, V and Ware, D and van Wijk, KJ},
title = {The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.},
journal = {The Plant cell},
volume = {29},
number = {11},
pages = {2687-2710},
pmid = {28947489},
issn = {1532-298X},
mesh = {Arabidopsis Proteins/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Mitochondria/*enzymology/genetics ; Peptide Hydrolases/classification/genetics/*metabolism ; Phylogeny ; Plastids/*enzymology/genetics ; Proteome/genetics/metabolism ; Proteostasis/genetics ; },
abstract = {Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.},
}
@article {pmid28963083,
year = {2018},
author = {Eldridge, RA and Achmadi, AS and Giarla, TC and Rowe, KC and Esselstyn, JA},
title = {Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi.},
journal = {Molecular phylogenetics and evolution},
volume = {118},
number = {},
pages = {306-317},
doi = {10.1016/j.ympev.2017.09.018},
pmid = {28963083},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; DNA/chemistry/isolation &amp; purification/metabolism ; Gene Flow ; Genetic Variation ; Genetics, Population ; Indonesia ; Islands ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; Shrews/*classification ; },
abstract = {Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C. elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata, like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs.},
}
@article {pmid28969942,
year = {2018},
author = {Chen, S and Wu, Z and Zhang, J and Wang, M and Jia, R and Zhu, D and Liu, M and Sun, K and Yang, Q and Wu, Y and Zhao, X and Cheng, A},
title = {Duck stimulator of interferon genes plays an important role in host anti-duck plague virus infection through an IFN-dependent signalling pathway.},
journal = {Cytokine},
volume = {102},
number = {},
pages = {191-199},
doi = {10.1016/j.cyto.2017.09.008},
pmid = {28969942},
issn = {1096-0023},
mesh = {Amino Acid Sequence ; Animals ; Avian Proteins/genetics/immunology ; Bird Diseases/*genetics/*immunology/virology ; Ducks/*genetics/*immunology/virology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Innate/genetics ; Interferon-beta/genetics ; Mardivirus/*immunology/*pathogenicity/physiology ; Marek Disease/*genetics/*immunology/virology ; NF-kappa B/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Signal Transduction ; Virus Replication ; },
abstract = {The human stimulator of interferon gene (STING) is an important molecule in innate immunity that stimulates type I interferon (IFN) production. However, the role of duck STING (duSTING) in innate immunity has yet to be explained. In this study, the full length of the duSTING cDNA sequence (1149bp), which encodes 382 amino acid (aa) residues, was reported and showed the highest sequence similarity with chicken STINGs. The phylogenetic analysis based on STING aa showed that duSTING was grouped onto the birds clade. According to the tissue distribution spectrum analysis, duSTING was highly present in the bursa of Fabricius, glandular stomach, liver, pancreas, and small intestine of ducklings, as well as in the blood and pancreas of the adult duck. DuSTING mainly colocalized with the endoplasmic reticulum (ER) and mitochondria in transfected Baby Hamster Syrian Kidney (BHK21) and duck embryo fibroblasts (DEF) cells by an indirect immunofluorescence assay. The transfection of the DEFs with duSTING activated NF-κB, which induced the transcription of IFN-β, and the activated IFN induced the interferon-stimulated response element (ISRE). Furthermore, the overexpression of duSTING significantly upregulated the mRNA level of duck IFN-β and IFN-stimulated genes (ISGs), such as duMx and duOASL and inhibited the replication of the double-stranded DNA duck plague virus (DPV) in vitro. In addition, the knockdown of endogenous duSTING by shRNA significantly reduced the poly (I:C) (pIC), poly (dA:dT), and Tembusu virus (TMUV), induced IFN-β production and significantly promoted DPV replication in vitro. In general, these data demonstrate that duSTING is vital for duck type I interferon induction and plays an important role in the host defence of DPV infection.},
}
@article {pmid28986237,
year = {2018},
author = {Liu, Y and Song, F and Jiang, P and Wilson, JJ and Cai, W and Li, H},
title = {Compositional heterogeneity in true bug mitochondrial phylogenomics.},
journal = {Molecular phylogenetics and evolution},
volume = {118},
number = {},
pages = {135-144},
doi = {10.1016/j.ympev.2017.09.025},
pmid = {28986237},
issn = {1095-9513},
mesh = {Animals ; Base Composition ; Base Sequence ; Bayes Theorem ; Genetic Variation ; *Genome, Mitochondrial ; Heteroptera/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; },
abstract = {Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.},
}
@article {pmid28989067,
year = {2018},
author = {Ogedengbe, ME and El-Sherry, S and Ogedengbe, JD and Chapman, HD and Barta, JR},
title = {Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa).},
journal = {International journal for parasitology},
volume = {48},
number = {1},
pages = {59-69},
doi = {10.1016/j.ijpara.2017.07.008},
pmid = {28989067},
issn = {1879-0135},
mesh = {Animals ; Cell Nucleus/*genetics/metabolism ; DNA, Protozoan/*genetics/metabolism ; DNA, Ribosomal/*genetics/metabolism ; Eimeria/classification/*genetics/growth &amp; development/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/*genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither 'Eimeria-type' nor 'Isospora-type' oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.},
}
@article {pmid29024751,
year = {2018},
author = {Mokodongan, DF and Montenegro, J and Mochida, K and Fujimoto, S and Ishikawa, A and Kakioka, R and Yong, L and Mulis, and Hadiaty, RK and Mandagi, IF and Masengi, KWA and Wachi, N and Hashiguchi, Y and Kitano, J and Yamahira, K},
title = {Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae).},
journal = {Molecular phylogenetics and evolution},
volume = {118},
number = {},
pages = {194-203},
doi = {10.1016/j.ympev.2017.10.005},
pmid = {29024751},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Female ; *Genomics ; Geography ; Indonesia ; Male ; Mitochondria/genetics ; Oryzias/*anatomy &amp; histology/*genetics ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; },
abstract = {The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations. Second, their phylogenetic relationships did not support the presence of three species; phylogenies using mitochondrial DNA and genomic data obtained from RNA-Seq revealed that the eight populations could not be sorted into three different clades representing three described species. Third, phylogenetic corrections of body shape variations and ancestral state reconstruction of body shapes demonstrated that body shape divergence between riverine and lacustrine populations persisted even if the phylogenies were considered and that body shape evolved rapidly irrespective of phylogeny. Sexual dimorphism in body shape was also evident, but the degree of dimorphism did not significantly differ between riverine and lacustrine populations after phylogenetic corrections, suggesting that sexual selection may not substantially contribute to geographical variations in body shape. Overall, these results indicate that the deep-elongated body shape divergence of the O. woworae species group evolved locally in response to habitat environments, such as water currents, and that a thorough taxonomic reexamination of the O. woworae species group may be necessary.},
}
@article {pmid29032499,
year = {2017},
author = {Hu, L and Yang, Y and Zhao, Y and Niu, D and Yang, R and Wang, R and Lu, Z and Li, X},
title = {DNA barcoding for molecular identification of Demodex based on mitochondrial genes.},
journal = {Parasitology research},
volume = {116},
number = {12},
pages = {3285-3290},
pmid = {29032499},
issn = {1432-1955},
support = {81471972//National Natural Science Foundation of China/ ; 81271856//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Dog Diseases ; Dogs ; *Genes, Mitochondrial ; Mite Infestations/parasitology/veterinary ; Mites/*classification ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.},
}
@article {pmid29061908,
year = {2017},
author = {Yang, Y and Zhu, G and Li, R and Yan, S and Fu, D and Zhu, B and Tian, H and Luo, Y and Zhu, H},
title = {The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato.},
journal = {Plant physiology},
volume = {175},
number = {4},
pages = {1690-1702},
pmid = {29061908},
issn = {1532-2548},
mesh = {CRISPR-Cas Systems ; Fruit/*physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/*physiology ; Gene Silencing ; Solanum lycopersicum/genetics/*physiology ; Mitochondria ; Mutation ; Phylogeny ; Plant Development/genetics/physiology ; Plant Proteins/genetics/*metabolism ; RNA Editing/genetics/*physiology ; },
abstract = {RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.},
}
@article {pmid29074460,
year = {2018},
author = {Smith, CH and Johnson, NA and Pfeiffer, JM and Gangloff, MM},
title = {Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {50-62},
doi = {10.1016/j.ympev.2017.10.018},
pmid = {29074460},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Bivalvia/*anatomy &amp; histology/*genetics ; Florida ; *Fresh Water ; *Genetic Speciation ; Geography ; Haplotypes/genetics ; Louisiana ; Mitochondria/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.},
}
@article {pmid29100916,
year = {2018},
author = {Krishnan, R and Girish Babu, P and Jeena, K and Tripathi, G and Pani Prasad, K},
title = {Molecular characterization, ontogeny and expression profiling of mitochondrial antiviral signaling adapter, MAVS from Asian seabass Lates calcarifer, Bloch (1790).},
journal = {Developmental and comparative immunology},
volume = {79},
number = {},
pages = {175-185},
doi = {10.1016/j.dci.2017.10.019},
pmid = {29100916},
issn = {1879-0089},
mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Animals ; Bass/*immunology ; Cloning, Molecular ; Fish Diseases/*immunology ; Fish Proteins ; Gene Expression Profiling ; Immunity, Innate ; Mitochondria/*metabolism ; Nodaviridae/*physiology ; Phylogeny ; RNA Virus Infections/*immunology ; Signal Transduction ; Spleen/*metabolism ; Zebrafish Proteins/genetics ; },
abstract = {Mitochondrial antiviral signaling protein (MAVS), an innate immune signaling adapter coordinates the signals received from two independent cytosolic pathogen recognition receptors (RIG-1 and MDA5) to induce antiviral genes. In the present study the MAVS gene of Lates calcarifer (LcMAVS) was cloned and characterized. The complete cDNA sequence of LcMAVS was 3160 bp and encodes a poly peptide of 577 amino acids. Structural analysis of LcMAVS revealed an N-terminal CARD-like domain, central proline-rich domain and a C-terminal transmembrane domain. Phylogenetic analysis indicated that LcMAVS exhibited the closest relationship to P. olivaceous MAVS. LcMAVS was ubiquitously expressed in all tested tissues of healthy fish viz., brain, gill, heart, liver, spleen, kidney and intestine, with highest transcript level in spleen. The mRNA transcript level of LcMAVS in different developmental stages showed constitutive expression in all the stages tested suggesting the maternal transfer of the gene. Significant up regulation in MAVS expression was observed post nervous necrosis virus (NNV) challenge in vivo in all the selected tissues. Further, time course analysis showed that LcMAVS transcripts significantly increased in the brain and spleen tissues after NNV infection. These findings provide useful information for further elucidating the function of LcMAVS in antiviral innate immune response against NNV in Asian seabass.},
}
@article {pmid29104141,
year = {2018},
author = {Lüddecke, T and Krehenwinkel, H and Canning, G and Glaw, F and Longhorn, SJ and Tänzler, R and Wendt, I and Vences, M},
title = {Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {63-70},
doi = {10.1016/j.ympev.2017.10.015},
pmid = {29104141},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Silk/*genetics ; Spiders/*classification/*genetics ; },
abstract = {The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.},
}
@article {pmid29107618,
year = {2018},
author = {da Cruz, MOR and Weksler, M},
title = {Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {1-12},
doi = {10.1016/j.ympev.2017.10.021},
pmid = {29107618},
issn = {1095-9513},
mesh = {Animals ; Arvicolinae/*classification ; Bayes Theorem ; Mitochondria/metabolism ; *Phylogeny ; Probability ; Species Specificity ; Time Factors ; },
abstract = {The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled.},
}
@article {pmid29117562,
year = {2017},
author = {Redrejo-Rodríguez, M and Ordóñez, CD and Berjón-Otero, M and Moreno-González, J and Aparicio-Maldonado, C and Forterre, P and Salas, M and Krupovic, M},
title = {Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements.},
journal = {Cell reports},
volume = {21},
number = {6},
pages = {1574-1587},
pmid = {29117562},
issn = {2211-1247},
support = {340440/ERC_/European Research Council/International ; },
mesh = {Amino Acid Sequence ; Bacteriophage M13/genetics ; DNA/*biosynthesis ; DNA Primers/*metabolism ; DNA, Single-Stranded/biosynthesis ; DNA-Directed DNA Polymerase/chemistry/classification/genetics/*metabolism ; Databases, Genetic ; Escherichia coli/enzymology ; Phylogeny ; Plasmids/genetics/metabolism ; Recombinant Proteins/biosynthesis/isolation &amp; purification ; Sequence Alignment ; Transcription, Genetic ; },
abstract = {Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities. Remarkably, the protein is also capable of template-dependent de novo DNA synthesis, i.e., DNA-priming activity, thereby breaking the long-standing dogma that replicative DNA polymerases require a pre-existing primer for DNA synthesis. We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance.},
}
@article {pmid29137957,
year = {2018},
author = {Saunders, GW and Jackson, C and Salomaki, ED},
title = {Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae).},
journal = {Molecular phylogenetics and evolution},
volume = {119},
number = {},
pages = {151-159},
doi = {10.1016/j.ympev.2017.11.002},
pmid = {29137957},
issn = {1095-9513},
mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Transcriptome/*genetics ; },
abstract = {Phylogenetic analyses of transcriptome data for representatives of the red algal Acrochaetiales-Palmariales Complex provided robust support for the assignment of genera to the constituent families. In the Acrochaetiales, the genera Acrochaetium, Grania, and an unnamed genus-level lineage (Acrochaetiac sp._1Aus) were assigned to the Acrochaetiaceae, while Audouinella is placed in a resurrected Audouinellaceae and Rhodochorton and Rhododrewia constitute the resurrected Rhodochortonaceae. For the Palmariales, transcriptome data solidly support the inclusion of Camontagnea and Rhodothamniella in the Rhodothamniellaceae, Meiodiscus and Rubrointrusa in the Meiodiscaceae, Rhodonematella and Rhodophysema in the Rhodophysemataceae, while Devaleraea and Palmaria remained in the Palmariaceae. These analyses, however, questioned the monophyly of Palmaria, which prompted a second round of analyses using eight common red algal phylogenetic markers and including a broader sampling of red algal genera in our analyses. These results supported transfer of Palmaria callophylloides and P. mollis to the genus Devaleraea necessitating new combinations, and further added the genus Halosaccion to the Palmariaceae and the genera Kallymenicola and Rhodophysemopsis to the Meiodiscaceae. Finally, DNA barcode (mitochondrial COI-5P) and ITS data were explored and supported the continued recognition of Palmaria palmata as a single species in the North Atlantic.},
}
@article {pmid29138502,
year = {2017},
author = {Pannek, M and Simic, Z and Fuszard, M and Meleshin, M and Rotili, D and Mai, A and Schutkowski, M and Steegborn, C},
title = {Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.},
journal = {Nature communications},
volume = {8},
number = {1},
pages = {1513},
pmid = {29138502},
issn = {2041-1723},
mesh = {Acylation ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Lysine/*chemistry/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Sirtuins/*chemistry/genetics/metabolism ; Xenopus ; Xenopus Proteins/*chemistry/genetics/metabolism ; },
abstract = {Sirtuins are evolutionary conserved NAD[+]-dependent protein lysine deacylases. The seven human isoforms, Sirt1-7, regulate metabolism and stress responses and are considered therapeutic targets for aging-related diseases. Sirt4 locates to mitochondria and regulates fatty acid metabolism and apoptosis. In contrast to the mitochondrial deacetylase Sirt3 and desuccinylase Sirt5, no prominent deacylase activity and structural information are available for Sirt4. Here we describe acyl substrates and crystal structures for Sirt4. The enzyme shows isoform-specific acyl selectivity, with significant activity against hydroxymethylglutarylation. Crystal structures of Sirt4 from Xenopus tropicalis reveal a particular acyl binding site with an additional access channel, rationalizing its activities. The structures further identify a conserved, isoform-specific Sirt4 loop that folds into the active site to potentially regulate catalysis. Using these results, we further establish efficient Sirt4 activity assays, an unusual Sirt4 regulation by NADH, and Sirt4 effects of pharmacological modulators.},
}
@article {pmid29161481,
year = {2017},
author = {Arrivillaga-Henríquez, J and Enríquez, S and Romero, V and Echeverría, G and Pérez-Barrera, J and Poveda, A and Navarro, JC and Warburg, A and Benítez, W},
title = {[Eco-epidemiological aspects, natural detection and molecular identification of Leishmania spp. in Lutzomyia reburra, Lutzomyia barrettoi majuscula and Lutzomyia trapidoi].},
journal = {Biomedica : revista del Instituto Nacional de Salud},
volume = {37},
number = {0},
pages = {83-97},
doi = {10.7705/biomedica.v37i0.3536},
pmid = {29161481},
issn = {2590-7379},
mesh = {Animals ; Cell Nucleus/enzymology ; DNA Topoisomerases, Type II/genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; Ecuador ; Feeding Behavior ; Female ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation &amp; purification/physiology ; Leishmaniasis, Cutaneous/parasitology/*transmission ; Mitochondria/enzymology ; Phylogeny ; Phylogeography ; Protozoan Proteins/genetics ; Psychodidae/*parasitology ; Species Specificity ; },
abstract = {INTRODUCTION: The province of Pichincha in Ecuador is an endemic area of cutaneous leishmaniasis, where anthropophilic sand flies with natural infection by Leishmania, have been reported as vectors. However, the role in transmission of zoophilic species has not been evaluated.<br><br>OBJECTIVE: To evaluate natural infection by Leishmania in two zoophilic phlebotomine sand fly species, Lutzomyia reburra and Lu. barrettoi majuscula, and one anthropophilic species, Lu. trapidoi, as well as the endophagy and synanthropism of these species in the northwest of Pichincha.<br><br>MATERIALS AND METHODS: Phlebotomines were collected using CDC light traps in different habitats and altitudes with presence of cutaneous leishmaniasis. Leishmania infection was detected using genomic DNA from females of the collected sand flies. We amplified the internal transcribed spacer gene of ribosomal RNA I (ITS1), the mitochondrial topoisomerase II gene (mtTOPOII), and the nuclear topoisomerase II gene (TopoII). Percentages of positivity for Leishmania, at spatio-temporal scale, proportion of endophagy and synanthropism index were calculated.<br><br>RESULTS: Natural infection was determined for Le. amazonensis in Lu. reburra (9.5%) and Lu. b. majuscula (23.8%), while in Lu. trapidoi we detected Le. amazonensis, Le. brazilienis and Le. naiffi-lainsoni. Phlebotomines were asynanthropic and with low endophagy.<br><br>CONCLUSION: Natural infection with Le. amazonensis was recorded for the first time in Lu. reburra and Lu. b. majuscula, demonstrating the importance of zoophilic phlebotomines in the maintenance of the Leishmania transmission cycle in endemic foci.},
}
@article {pmid29171872,
year = {2017},
author = {Luévano-Martínez, LA and Kowaltowski, AJ},
title = {Topological characterization of the mitochondrial phospholipid scramblase 3.},
journal = {FEBS letters},
volume = {591},
number = {24},
pages = {4056-4066},
doi = {10.1002/1873-3468.12917},
pmid = {29171872},
issn = {1873-3468},
mesh = {Animals ; Cardiolipins/chemistry/metabolism ; Crystallography, X-Ray ; Intracellular Membranes/metabolism ; Male ; Mitochondria/*enzymology ; Models, Molecular ; Phospholipid Transfer Proteins/*chemistry/genetics/metabolism ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; Saccharomyces cerevisiae ; },
abstract = {Scramblases redistribute phospholipids in biological membranes. Phospholipid scramblase 3 (PLSCR3), which is located in mitochondria, has been reported to be involved in cardiolipin distribution from the inner to the outer membrane, thus regulating cellular processes such as apoptosis or mitophagy. However, the localization and topology of this protein has not been convincingly addressed to support a role in intermembrane phospholipid transfer. Here, we studied PLSCR3 topology within mitochondria. We show that PLSCR3 inserts in the inner membrane (IM) via its C-terminal transmembrane helix, whereas its N-terminal portion is oriented toward the intermembrane space where it is activated by calcium. Our results suggest that PLSCR3, via its C-terminal transmembrane domain, participates in the bidirectional movement of phospholipids within the IM.},
}
@article {pmid29176839,
year = {2017},
author = {Peçanha, WT and Althoff, SL and Galiano, D and Quintela, FM and Maestri, R and Gonçalves, GL and Freitas, TRO},
title = {Pleistocene climatic oscillations in Neotropical open areas: Refuge isolation in the rodent Oxymycterus nasutus endemic to grasslands.},
journal = {PloS one},
volume = {12},
number = {11},
pages = {e0187329},
pmid = {29176839},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; Genetic Variation ; Geography ; *Grassland ; Haplotypes/genetics ; Mitochondria/genetics ; Models, Theoretical ; *Paleontology ; Phylogeny ; Rodentia/genetics/*physiology ; Skull/anatomy &amp; histology ; Species Specificity ; Time Factors ; *Tropical Climate ; Uruguay ; },
abstract = {Pleistocene climatic oscillations favoured the expansion of grassland ecosystems and open vegetation landscapes throughout the Neotropics, and influenced the evolutionary history of species adapted to such environments. In this study, we sampled populations of the rodent Oxymycterus nasutus endemic to open areas in the Pampas and Atlantic Forest biomes to assess the tempo and mode of population divergence using an integrative approach, including coalescence theory, ecological niche models, and morphometry. Our results indicated that these O. nasutus populations exhibited high levels of genetic structure. Six major mtDNA clades were found, structuring these biomes into distinct groups. Estimates of their divergence times was indicated to be 0.571 myr. The high degree of genetic structure is reflected in the analyses of geometric morphometric; skull differences between lineages in the two ecoregions were detected. During the last glacial maximum, there was a strong increase in suitable abiotic conditions for O. nasutus. Distinct molecular markers revealed a population expansion over time, with a possible demographic retraction during the post-glacial period. Considering that all clades coalesce with the last interglacial maximum, our results indicated that reduction in suitable conditions during this period may have resulted in a possible vicariance associated with refuge isolation.},
}
@article {pmid29179728,
year = {2017},
author = {Li, D and Du, X and Guo, X and Zhan, L and Li, X and Yin, C and Chen, C and Li, M and Li, B and Yang, H and Xing, J},
title = {Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations.},
journal = {Journal of experimental &amp; clinical cancer research : CR},
volume = {36},
number = {1},
pages = {168},
pmid = {29179728},
issn = {1756-9966},
mesh = {Amino Acids/genetics ; Codon/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Databases, Genetic ; Humans ; Mitochondria/chemistry/*genetics ; Mutation Rate ; Neoplasms/*genetics ; *Point Mutation ; Selection, Genetic ; },
abstract = {BACKGROUND: Previous studies have indicated that tumor mitochondrial DNA (mtDNA) mutations are primarily shaped by relaxed negative selection, which is contradictory to the critical roles of mtDNA mutations in tumorigenesis. Therefore, we hypothesized that site-specific selection may influence tumor mtDNA mutations.<br><br>METHODS: To test our hypothesis, we developed the largest collection of tumor mtDNA mutations to date and evaluated how natural selection shaped mtDNA mutation patterns.<br><br>RESULTS: Our data demonstrated that both positive and negative selections acted on specific positions or functional units of tumor mtDNAs, although the landscape of these mutations was consistent with the relaxation of negative selection. In particular, mutation rate (mutation number in a region/region bp length) in complex V and tRNA coding regions, especially in ATP8 within complex V and in loop and variable regions within tRNA, were significantly lower than those in other regions. While the mutation rate of most codons and amino acids were consistent with the expectation under neutrality, several codons and amino acids had significantly different rates. Moreover, the mutations under selection were enriched for changes that are predicted to be deleterious, further supporting the evolutionary constraints on these regions.<br><br>CONCLUSION: These results indicate the existence of site-specific selection and imply the important role of the mtDNA mutations at some specific sites in tumor development.},
}
@article {pmid29193148,
year = {2018},
author = {Damerau, M and Freese, M and Hanel, R},
title = {Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos.},
journal = {Journal of fish biology},
volume = {92},
number = {1},
pages = {190-202},
doi = {10.1111/jfb.13509},
pmid = {29193148},
issn = {1095-8649},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus ; DNA, Mitochondrial ; Fishes/*genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.},
}
@article {pmid29196205,
year = {2018},
author = {Medina, CD and Avila, LJ and Sites, JW and Santos, J and Morando, M},
title = {Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers.},
journal = {Molecular phylogenetics and evolution},
volume = {120},
number = {},
pages = {158-169},
doi = {10.1016/j.ympev.2017.11.017},
pmid = {29196205},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Lizards/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods.},
}
@article {pmid29199107,
year = {2018},
author = {Solano-Zavaleta, I and Nieto-Montes de Oca, A},
title = {Species limits in the Morelet's Alligator lizard (Anguidae: Gerrhonotinae).},
journal = {Molecular phylogenetics and evolution},
volume = {120},
number = {},
pages = {16-27},
doi = {10.1016/j.ympev.2017.11.011},
pmid = {29199107},
issn = {1095-9513},
mesh = {Alligators and Crocodiles/*physiology ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; DNA, Mitochondrial/genetics ; Lizards/genetics/*physiology ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; Time Factors ; },
abstract = {The widely distributed, Central American anguid lizard Mesaspis moreletii is currently recognized as a polytypic species with five subspecies (M. m. fulvus, M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis). We reevaluated the species limits within Mesaspis moreletii using DNA sequences of one mitochondrial and three nuclear genes. The multi-locus data set included samples of all of the subspecies of M. moreletii, the other species of Mesaspis in Central America (M. cuchumatanus and M. monticola), and some populations assignable to M. moreletii but of uncertain subspecific identity from Honduras and Nicaragua. We first used a tree-based method for delimiting species based on mtDNA data to identify potential evolutionary independent lineages, and then analized the multilocus dataset with two species delimitation methods that use the multispecies coalescent model to evaluate different competing species delimitation models: the Bayes factors species delimitation method (BFD) implemented in [∗]BEAST, and the Bayesian Phylogenetics and Phylogeography (BP&amp;P) method. Our results suggest that M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis represent distinct evolutionary independent lineages, and that the populations of uncertain status from Honduras and Nicaragua may represent additional undescribed species. Our results also suggest that M. m. fulvus is a synonym of M. m. moreletii. The biogeography of the Central American lineages of Mesaspis is discussed.},
}
@article {pmid29244187,
year = {2017},
author = {Salinas-Giegé, T and Cavaiuolo, M and Cognat, V and Ubrig, E and Remacle, C and Duchêne, AM and Vallon, O and Maréchal-Drouard, L},
title = {Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii.},
journal = {Nucleic acids research},
volume = {45},
number = {22},
pages = {12963-12973},
pmid = {29244187},
issn = {1362-4962},
mesh = {Base Sequence ; Chlamydomonas reinhardtii/*genetics/metabolism ; Chlorophyta/classification/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Poly C/metabolism ; RNA, Messenger/*genetics/metabolism ; RNA, Mitochondrial ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; },
abstract = {The unicellular photosynthetic organism, Chlamydomonas reinhardtii, represents a powerful model to study mitochondrial gene expression. Here, we show that the 5'- and 3'-extremities of the eight Chlamydomonas mitochondrial mRNAs present two unusual characteristics. First, all mRNAs start primarily at the AUG initiation codon of the coding sequence which is often marked by a cluster of small RNAs. Second, unusual tails are added post-transcriptionally at the 3'-extremity of all mRNAs. The nucleotide composition of the tails is distinct from that described in any other systems and can be partitioned between A/U-rich tails, predominantly composed of Adenosine and Uridine, and C-rich tails composed mostly of Cytidine. Based on 3' RACE experiments, 22% of mRNAs present C-rich tails, some of them composed of up to 20 consecutive Cs. Polycytidylation is specific to mitochondria and occurs primarily on mRNAs. This unprecedented post-transcriptional modification seems to be a specific feature of the Chlorophyceae class of green algae and points out the existence of novel strategies in mitochondrial gene expression.},
}
@article {pmid29245571,
year = {2017},
author = {Pickersgill, M and Zimkus, BM and Raw, LRG},
title = {A new species of Phrynobatrachus (Anura: Phrynobatrachidae) from the Eastern Arc Mountians of Tanzania.},
journal = {Zootaxa},
volume = {4350},
number = {1},
pages = {151-163},
doi = {10.11646/zootaxa.4350.1.9},
pmid = {29245571},
issn = {1175-5334},
mesh = {Animals ; *Anura ; Male ; Mitochondria ; Phylogeny ; RNA, Ribosomal, 16S ; Tanzania ; },
abstract = {Phrynobatrachus discogularis sp. nov. (Anura, Phrynobatrachidae) is described from the Eastern Arc Mountains in Tanzania. It occupies upland grasslands and while it morphologically most resembles West and Central African P. gutturosus (Chabanaud, 1921), P. rungwensis (Loveridge, 1932), and P. anotis Schmidt and Inger, 1959, preliminary analysis of mitochondrial 16S rRNA indicates that the new species differs from all other species with published sequence data by a minimum distance of 4.1% and has affinities with P. rungwensis, P. uzungwensis Grandison and Howell, 1983 and P. keniensis Barbour and Loveridge, 1928-all diminutive upland eastern African taxa. The shape and colour of the male's external gular apparatus distinguish this species from all other described Phrynobatrachus species. Although geographically either sympatric or closely allopatric with P. uzungwensis, the lack of overlapping morphological characters indicates the two forms are distinct species. The new taxon is compared with other species from the region.},
}
@article {pmid29247559,
year = {2018},
author = {Lee, K and Lee, HY and Back, K},
title = {Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants.},
journal = {Journal of pineal research},
volume = {64},
number = {2},
pages = {},
doi = {10.1111/jpi.12460},
pmid = {29247559},
issn = {1600-079X},
mesh = {Arabidopsis/*metabolism ; Arylalkylamine N-Acetyltransferase/metabolism ; Histone Deacetylases/*metabolism ; Melatonin/*biosynthesis ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Serotonin/analogs &amp; derivatives/metabolism ; },
abstract = {In plants, melatonin production is strictly regulated, unlike the production of its precursor, serotonin, which is highly inducible in response to stimuli, such as senescence and pathogen exposure. Exogenous serotonin treatment does not greatly induce the production of N-acetylserotonin (NAS) and melatonin in plants, which suggests the possible existence of one or more regulatory genes in the pathway for the biosynthesis of melatonin from serotonin. In this report, we found that NAS was rapidly and abundantly converted into serotonin in rice seedlings, indicating the presence of an N-acetylserotonin deacetylase (ASDAC). To clone the putative ASDAC gene, we screened 4 genes that were known as histone deacetylase (HDAC) genes, but encoded proteins targeted into chloroplasts or mitochondria rather than nuclei. Of 4 recombinant Escherichia coli strains expressing these genes, one E. coli strain expressing the rice HDAC10 gene was found to be capable of producing serotonin in response to treatment with NAS. The recombinant purified rice HDAC10 (OsHDAC10) protein exhibited ASDAC enzyme activity toward NAS, N-acetyltyramine (NAT), N-acetyltryptamine, and melatonin, with the highest ASDAC activity for NAT. In addition, its Arabidopsis ortholog, AtHDAC14, showed similar ASDAC activity to that of OsHDAC10. Both OsHDAC10 and AtHDAC14 were found to be expressed in chloroplasts. Phylogenetic analysis indicated that ASDAC homologs were present in archaea, but not in cyanobacteria, which differs from the distribution of serotonin N-acetyltransferase (SNAT). This suggests that SNAT and ASDAC may have evolved differently from ancestral eukaryotic cells.},
}
@article {pmid29249204,
year = {2018},
author = {Stentiford, GD and Ross, S and Minardi, D and Feist, SW and Bateman, KS and Gainey, PA and Troman, C and Bass, D},
title = {Evidence for trophic transfer of Inodosporus octospora and Ovipleistophora arlo n. sp. (Microsporidia) between crustacean and fish hosts.},
journal = {Parasitology},
volume = {145},
number = {8},
pages = {1105-1117},
doi = {10.1017/S0031182017002256},
pmid = {29249204},
issn = {1469-8161},
mesh = {Animals ; DNA, Ribosomal ; Fishes/*microbiology ; Microscopy, Electron, Transmission ; Microsporidia/genetics/*isolation &amp; purification/ultrastructure ; Microsporidiosis/transmission/*veterinary ; Muscles/*microbiology ; Oocytes/microbiology ; Palaemonidae/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Viral Tropism ; },
abstract = {Within aquatic habitats, the hyper-abundant Order Crustacea appear to be the predominant host group for members of the Phylum Microsporidia. The musculature, a common site of infection, provides access to biochemical (carbohydrate-rich) and physiological (mitochondria-rich) conditions conducive to prolific parasite replication and maturation. The significant proportion of body plan devoted to skeletal musculature in Crustacea provides the location for a highly efficient intracellular parasite factory. In this study, we utilize histological, ultrastructural and phylogenetic evidence to describe a previously known (Inodosporus octospora) and novel (Ovipleistophora arlo n. sp.) microsporidian parasites infecting the musculature of the common prawn (Palaemon serratus) from the same site, at the same time of year. Despite similar clinical signs of infection, both parasites are otherwise distinct in terms of pathogenesis, morphology and phylogeny. Based upon partial subunit ribosomal RNA (SSU rDNA) sequence, we show that that I. octospora may be identical to a Kabatana sp. previously described infecting two-spot goby (Gobiusculus flavescens) in Europe, or at least that Inodosporus and Kabatana genera are synonyms. In addition, SSU rDNA sequence for O. arlo places it within a distinct clade containing Ovipleistophora mirandellae and Ovipleistophora ovariae, both infecting the oocytes of freshwater fish in Europe. Taken together, our data provide strong evidence for trophic-transfer between crustacean and fish hosts for two different microsporidians within clade 5 of the phylum. Furthermore, it demonstrates that morphologically and phylogenetically distinct microsporidians can infect the same tissues of the same host species to impart clinical signs which mimic infection with the other.},
}
@article {pmid29253894,
year = {2017},
author = {Wei, W and Gomez-Duran, A and Hudson, G and Chinnery, PF},
title = {Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations.},
journal = {PLoS genetics},
volume = {13},
number = {12},
pages = {e1007126},
pmid = {29253894},
issn = {1553-7404},
support = {/WT_/Wellcome Trust/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Alleles ; Base Sequence ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Founder Effect ; Gene Frequency ; Genetic Variation ; Haplotypes ; Humans ; Mitochondria/genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber/*genetics ; Phylogeny ; },
abstract = {Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups.},
}
@article {pmid29284403,
year = {2017},
author = {Wojtkowska, M and Buczek, D and Suzuki, Y and Shabardina, V and Makałowski, W and Kmita, H},
title = {The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.},
journal = {BMC genomics},
volume = {18},
number = {1},
pages = {997},
pmid = {29284403},
issn = {1471-2164},
support = {MPD/2010/3//Fundacja na rzecz Nauki Polskiej/International ; 01/KNOW2/2014//Polish Ministry of Science and Higher Education/International ; },
mesh = {Acanthamoeba castellanii/genetics ; Amoebozoa/classification/*genetics ; Cells, Cultured ; Dictyostelium/genetics ; Gene Expression Profiling ; Genomics ; Mitochondrial Membrane Transport Proteins/classification/*genetics ; Phylogeny ; Protein Subunits/genetics ; },
abstract = {BACKGROUND: The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences.<br><br>RESULTS: When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones.<br><br>CONCLUSION: The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.},
}
@article {pmid29293597,
year = {2018},
author = {Silva, SR and Michael, TP and Meer, EJ and Pinheiro, DG and Varani, AM and Miranda, VFO},
title = {Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0190321},
pmid = {29293597},
issn = {1932-6203},
mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; Magnoliopsida/classification/*genetics ; NADPH Dehydrogenase/*genetics ; Phylogeny ; },
abstract = {In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.},
}
@article {pmid29294404,
year = {2018},
author = {Qu, M and Tang, W and Liu, Q and Wang, D and Ding, S},
title = {Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker.},
journal = {Molecular phylogenetics and evolution},
volume = {121},
number = {},
pages = {46-51},
doi = {10.1016/j.ympev.2017.12.031},
pmid = {29294404},
issn = {1095-9513},
mesh = {Animals ; Biomarkers/*metabolism ; Cell Nucleus/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Ryanodine Receptor Calcium Release Channel/*genetics ; Species Specificity ; },
abstract = {Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.},
}
@article {pmid29301905,
year = {2018},
author = {Dai, D and Luan, S and Chen, X and Wang, Q and Feng, Y and Zhu, C and Qi, W and Song, R},
title = {Maize Dek37 Encodes a P-type PPR Protein That Affects cis-Splicing of Mitochondrial nad2 Intron 1 and Seed Development.},
journal = {Genetics},
volume = {208},
number = {3},
pages = {1069-1082},
pmid = {29301905},
issn = {1943-2631},
mesh = {Cloning, Molecular ; *Gene Expression Regulation, Plant ; *Introns ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Mutation ; NADH Dehydrogenase/metabolism ; Phenotype ; Phylogeny ; Plant Proteins/*genetics ; Protein Transport ; *RNA Splicing ; Seeds/*genetics ; Zea mays/*genetics ; },
abstract = {Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds. Mitochondrial transcripts analysis indicated that dek37 mutation decreases splicing efficiency of mitochondrial nad2 intron 1, leading to reduced assembly and NADH dehydrogenase activity of complex I. Transmission Electron Microscopy (TEM) revealed severe morphological defects of mitochondria in dek37 Transcriptome analysis of dek37 endosperm indicated enhanced expression in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function. These results indicated that Dek37 is involved in cis-splicing of mitochondrial nad2 intron 1 and is required for complex I assembly, mitochondrial function, and seed development in maize.},
}
@article {pmid29318727,
year = {2018},
author = {Kaur, B and Valach, M and Peña-Diaz, P and Moreira, S and Keeling, PJ and Burger, G and Lukeš, J and Faktorová, D},
title = {Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine microeukaryotes Diplonemida (Euglenozoa).},
journal = {Environmental microbiology},
volume = {20},
number = {3},
pages = {1030-1040},
doi = {10.1111/1462-2920.14041},
pmid = {29318727},
issn = {1462-2920},
support = {MOP 70309//CIHR/Canada ; },
mesh = {Aquatic Organisms ; Drug Resistance ; Euglenozoa/genetics/*physiology ; Eukaryota/genetics ; Gene Expression Regulation ; Mitochondria ; Phylogeny ; Puromycin/pharmacology ; RNA, Messenger/genetics/metabolism ; *Transformation, Genetic ; },
abstract = {Diplonema papillatum is the type species of diplonemids, which are among the most abundant and diverse heterotrophic microeukaryotes in the world's oceans. Diplonemids are also known for a unique form of post-transcriptional processing in mitochondria. However, the lack of reverse genetics methodologies in these protists has hampered elucidation of their cellular and molecular biology. Here we report a protocol for D. papillatum transformation. We have identified several antibiotics to which D. papillatum is sensitive and thus are suitable selectable markers, and focus in particular on puromycin. Constructs were designed encoding antibiotic resistance markers, fluorescent tags, and additional genomic sequences from D. papillatum to facilitate vector integration into chromosomes. We established conditions for effective electroporation, and demonstrate that electroporated constructs can be stably integrated in the D. papillatum nuclear genome. In D. papillatum transformants, the heterologous puromycin resistance gene is transcribed into mRNA and translated into protein, as determined by Southern hybridization, reverse transcription, and Western blot analyses. This is the first documented case of transformation in a euglenozoan protist outside the well-studied kinetoplastids, making D. papillatum a genetically tractable organism and potentially a model system for marine microeukaryotes.},
}
@article {pmid29330875,
year = {2018},
author = {Wai, KT and Barash, M and Gunn, P},
title = {Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform.},
journal = {Electrophoresis},
volume = {39},
number = {21},
pages = {2776-2784},
doi = {10.1002/elps.201700371},
pmid = {29330875},
issn = {1522-2683},
mesh = {DNA, Mitochondrial/*genetics ; Female ; Forensic Genetics/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Mitochondria/genetics ; Nucleic Acid Denaturation ; Phylogeny ; Hot Temperature ; },
abstract = {The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120, and 240 min; total n = 25). The quality of DNA was assessed via a real-time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all samples and had an amplicon coverage averaging between 66X to 2803X. Most amplicons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five amplicons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all samples and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240-min heat-treated samples (n = 10) were Sanger-sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA samples.},
}
@article {pmid29337274,
year = {2018},
author = {Ballesteros, JA and Hormiga, G},
title = {Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae).},
journal = {Molecular phylogenetics and evolution},
volume = {121},
number = {},
pages = {183-197},
doi = {10.1016/j.ympev.2018.01.002},
pmid = {29337274},
issn = {1095-9513},
mesh = {Animals ; Brazil ; Calibration ; Canada ; Ecosystem ; Florida ; Geography ; Male ; Mexico ; Mitochondria/genetics ; North America ; *Phylogeny ; Probability ; Species Specificity ; Spiders/classification/*genetics ; Time Factors ; United States ; },
abstract = {The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.},
}
@article {pmid29339819,
year = {2018},
author = {Sharma, I and Sharma, V and Khan, A and Kumar, P and Rai, E and Bamezai, RNK and Vilar, M and Sharma, S},
title = {Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {851},
pmid = {29339819},
issn = {2045-2322},
mesh = {DNA, Mitochondrial/chemistry/classification/metabolism ; Female ; Genetic Variation ; Haplotypes ; *Human Migration ; Humans ; India ; Male ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Jammu and Kashmir (J&amp;K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.},
}
@article {pmid29359358,
year = {2018},
author = {Zhang, MY and Wei, D and Li, R and Jia, HT and Liu, YW and Taning, CNT and Wang, JJ and Smagghe, G},
title = {Cytoplasmic glutamine synthetase gene expression regulates larval development in Bactrocera dorsalis (Hendel).},
journal = {Archives of insect biochemistry and physiology},
volume = {97},
number = {4},
pages = {},
doi = {10.1002/arch.21447},
pmid = {29359358},
issn = {1520-6327},
mesh = {Amino Acid Sequence ; Animals ; Female ; Glutamate-Ammonia Ligase/genetics/*metabolism ; Insect Proteins/metabolism ; Larva/enzymology/growth &amp; development ; Methionine Sulfoximine ; Phylogeny ; RNA Interference ; Tephritidae/*enzymology/genetics/*growth &amp; development ; },
abstract = {In insects, glutamine synthetase (GS), a key enzyme in the synthesis of glutamine, has been reported to be associated with embryonic development, heat shock response, and fecundity regulation. However, little is known about the influence of GS on postembryonic development. In this study, we demonstrate that blocking the activity of GS in the oriental fruit fly (Bactrocera dorsalis) with use of a GS-specific inhibitor (L-methionine S-sulfoximine), led to a significant delay in larval development, pupal weight loss, and inhibition of pupation. We further identify cloned and characterized two GS genes (BdGS-c and BdGS-m) from B. dorsalis. The two GS genes identified in B. dorsalis were predicted to be located in the cytosol (BdGS-c) and mitochondria (BdGS-m), and homology analysis indicated that both genes were similar to homologs from other Dipterans, such as Drosophila melanogaster and Aedes aegypti. BdGS-c was highly expressed in the larval stages, suggesting that cytosolic GS plays a predominant role in larval development. Furthermore, RNA interference experiments against BdGS-c, to specifically decrease the expression of cytosolic GS, resulted in delay in larval development as well as pupal weight loss. This study presents the prominent role played by BdGS-c in regulating larval development and suggests that the observed effect could have been modulated through ecdysteroid synthesis, agreeing with the reduced expression of the halloween gene spook. Also, the direct effects of BdGS-c silencing on B. dorsalis, such as larval lethality, delayed pupation, and late emergence, can be further exploited as novel insecticide target in the context of pest management.},
}
@article {pmid29360606,
year = {2018},
author = {Hou, CC and Gao, XM and Ni, J and Mu, DL and Yang, HY and Liu, C and Zhu, JQ},
title = {The expression pattern and potential functions of PHB in the spermiogenesis of Phascolosoma esculenta.},
journal = {Gene},
volume = {652},
number = {},
pages = {25-38},
doi = {10.1016/j.gene.2018.01.056},
pmid = {29360606},
issn = {1879-0038},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Male ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/classification/*genetics/growth &amp; development/metabolism ; Polyubiquitin/genetics/metabolism ; Prohibitins ; Protein Domains ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/genetics/metabolism ; Repressor Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spermatogenesis/*genetics ; Spermatozoa/growth &amp; development/*metabolism ; },
abstract = {Prohibitin (PHB) is a ubiquitous, evolutionarily conserved protein that is mainly localized in the inner mitochondrial membrane and exerts various mitochondrial functions. Here, we first cloned the phb gene from P. esculenta. The Pe-PHB protein has high homology and a similar protein structure to that of other animals, and it can be divided into the N-terminal hydrophobic/transmembrane domain, SPFH domain, and C-terminal coiled-coil domain. The Pe-phb gene is widely expressed, and the gene expression of phb is highest in coelomic fluid where spermiogenesis occurs, indicating a specific function in the coelom. We further observed continuous expression of the phb gene and localization of PHB proteins in mitochondria during spermiogenesis, indicating that PHB, as a mitochondrial component, may play a role during this process via its mitochondrial function. In addition, ubiquitination of mitochondria was detected, and the PHB signal was co-localized with the poly-ubiquitin signal during spermiogenesis. Mature sperm also showed ubiquitination of mitochondria and PHB. Therefore, PHB may be a substrate of poly-ubiquitin to regulate the ubiquitination of mitochondria and even subsequent elimination during P. esculenta spermiogenesis, and it has a potential role in guaranteeing the maternal inheritance of mitochondria. Taken together, these results support the hypothesis that PHB participates in the spermiogenesis of P. esculenta by maintaining the normal function of mitochondria and regulating the degradation of mitochondria.},
}
@article {pmid29374514,
year = {2018},
author = {Godahewa, GI and Perera, NCN and Nam, BH and Lee, J},
title = {Antioxidative properties and structural features of atypical 2-Cys peroxiredoxin from Sebastes schlegelii.},
journal = {Developmental and comparative immunology},
volume = {82},
number = {},
pages = {152-164},
doi = {10.1016/j.dci.2018.01.015},
pmid = {29374514},
issn = {1879-0089},
mesh = {Animals ; Antioxidants ; Cloning, Molecular ; Cysteine/genetics ; Fish Proteins/*genetics/metabolism ; Fishes/*metabolism ; Gills/*metabolism ; Insulin/metabolism ; Liver/*metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Peroxiredoxins/*genetics/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; Streptococcal Infections/*immunology ; Streptococcus iniae/*immunology ; Structure-Activity Relationship ; Transcriptome ; Vertebrates ; },
abstract = {Atypical 2-Cys peroxiredoxin (Prx5) is an antioxidant protein that exerts its antioxidant function by detoxifying different reactive oxygen species (ROS). Here, we identified mitochondrial Prx5 from rockfish (SsPrx5) and described its specific structural and functional characteristics. The open reading frame (ORF) of SsPrx5 (570 bp) was translated into a 190-amino acid polypeptide that contained a mitochondrial targeting sequence (MTS), thioredoxin 2 domain, two Prx-specific signature motifs, and three conserved cysteine residues. Sequence comparison indicated that the SsPrx5 protein sequence shared greatest identity with teleost orthologs, where the phylogenetic results showed an evolutionary position within the fish Prx5. The coding sequence of SsPrx5 was scattered in six exons as found in other vertebrates. Additionally, the potent antioxidant functions of recombinantly expressed SsPrx5 protein was demonstrated by insulin reduction and extracellular H2O2 scavenging both in vitro and in vivo. Quantitative real time PCR (qPCR) detected ubiquitous mRNA expression of SsPrx5 in healthy rockfish tissues, with remarkable expression observed in gill, liver, and reproductive tissues. Prompt transcription of SsPrx5 was shown in the immune-stimulated gill and liver tissues against Streptococcus iniae and lipopolysaccharide injection. Taken together, present results suggest the indispensable role of SsPrx5 in the rockfish antioxidant defense system against oxidative stresses and its role in maintaining redox balance upon pathogen invasion.},
}
@article {pmid29381758,
year = {2018},
author = {Song, N and Lin, A and Zhao, X},
title = {Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data.},
journal = {PloS one},
volume = {13},
number = {1},
pages = {e0191826},
pmid = {29381758},
issn = {1932-6203},
mesh = {Animals ; Genes, Insect ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Neoptera/*classification/genetics ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).},
}
@article {pmid29410353,
year = {2018},
author = {Rose, JP and Kleist, TJ and Löfstrand, SD and Drew, BT and Schönenberger, J and Sytsma, KJ},
title = {Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections.},
journal = {Molecular phylogenetics and evolution},
volume = {122},
number = {},
pages = {59-79},
doi = {10.1016/j.ympev.2018.01.014},
pmid = {29410353},
issn = {1095-9513},
mesh = {Animals ; *Biodiversity ; Chloroplasts/genetics ; Asia, Eastern ; Fossils/history ; Genetic Speciation ; History, Ancient ; Magnoliopsida/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Phylogeography/history ; Ribosomes/genetics ; },
abstract = {Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.},
}
@article {pmid29427777,
year = {2019},
author = {Prager, M},
title = {Unweaving a taxon tangle: Comments on De Silva et al. (2017).},
journal = {Molecular phylogenetics and evolution},
volume = {131},
number = {},
pages = {229-232},
doi = {10.1016/j.ympev.2018.02.005},
pmid = {29427777},
issn = {1095-9513},
mesh = {Animals ; Biomarkers ; *Birds ; Cell Nucleus ; *Mitochondria ; Phylogeny ; },
}
@article {pmid29433421,
year = {2018},
author = {Li, Q and Dong, K and Xu, L and Jia, X and Wu, J and Sun, W and Zhang, X and Fu, S},
title = {The distribution of three candidate cold-resistant SNPs in six minorities in North China.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {134},
pmid = {29433421},
issn = {1471-2164},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Adaptation, Physiological/*genetics ; Asian People/genetics ; Carnitine O-Palmitoyltransferase/genetics ; China ; *Cold Temperature ; Ethnicity/classification/*genetics ; Fatty Acid Desaturases/genetics ; Gene Frequency ; Genotype ; Humans ; Linkage Disequilibrium ; Phylogeny ; *Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A encodes a protein that imports long-chain fatty acids into the mitochondria for fatty-acid oxidation. FADS is an essential enzyme for the synthesis of long-chain polyunsaturated fatty acids.<br><br>RESULTS: In the present study, we investigated the distributions of three cold resistance-related SNPs (rs80356779 G&#x2009;>&#x2009;A in CPT1A, rs7115739 T&#x2009;>&#x2009;G in FADS3 and rs174570 C&#x2009;>&#x2009;T in FADS2) from six populations that included 1093 individuals who have lived in Heilongjiang Province for at least three generations. The frequencies of rs174570 and rs7115739 were different in our six north minorities compared to the Chinese Dai in Xishuangbanna (CDX) in southern China. All the SNPs in Hezhen were significantly different from other five studied populations. In addition, the genetic distribution of rs174570 in Daur was significantly different from Manchu and Korea, and the frequency of rs7115739 in Ewenki was significantly different from the other populations. The results also showed that the frequencies of the three SNPs in the six minorities were different from those of Greenlandic Inuit and Siberian population.<br><br>CONCLUSIONS: Our results showed the distributions of the three cold resistance-related SNPs from six populations that included 1093 individuals in northern China. Distributions of the allele frequencies for the cold resistance-related SNPs in northern China were statistically different from those in southern China. These data help to establish the DNA genome database for the six populations and fully preserve existing minority genetic information.},
}
@article {pmid29451846,
year = {2018},
author = {Briosio-Aguilar, R and Pinto, HA and Rodríguez-Santiago, MA and López-García, K and García-Varela, M and de León, GP},
title = {Link Between the Adult and the Metacercaria of Clinostomum heluans Braun, 1899 (Trematoda: Clinostomidae) Through DNA Sequences, and its Phylogenetic Position Within the Genus Clinostomum Leidy, 1856.},
journal = {The Journal of parasitology},
volume = {104},
number = {3},
pages = {292-296},
doi = {10.1645/17-183},
pmid = {29451846},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Bird Diseases/*parasitology ; Birds ; Brazil ; Cichlids/parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/*chemistry/genetics ; Electron Transport Complex IV/chemistry/genetics ; Fish Diseases/*parasitology ; Metacercariae/classification/genetics ; Mexico ; Mitochondria/enzymology/genetics ; *Phylogeny ; Trematoda/*classification/genetics/growth &amp; development ; Trematode Infections/parasitology/*veterinary ; },
abstract = {The phylogenetic position of Clinostomum heluans Braun, 1899 within the genus Clinostomum Leidy, 1856 is reported in this study based on sequences of the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). Additionally, molecular data are used to link the adult and the metacercariae of the species. The metacercariae of C. heluans were found encysted infecting the cichlid fish Australoheros sp. in Minas Gerais, Brazil, whereas the adults were obtained from the mouth cavity of the Great White Egret, Ardea alba, in Campeche, Mexico. The COX1 sequences obtained for the Mexican clinostomes and the Brazilian metacercaria were almost identical (0.2% molecular divergence), indicating conspecificity. Similar molecular divergence (0.2-0.4%) was found between sequences of C. heluans reported here and Clinostomum sp. 6 previously obtained from a metacercaria recovered from the cichlid Cichlasoma boliviense in Santa Cruz, Bolivia. Both maximum likelihood and Bayesian inference analyses unequivocally showed the conspecificity between C. heluans and Clinostomum sp. 6, which form a monophyletic clade with high nodal support and very low genetic divergence. Moreover, tree topology reveals that C. heluans occupies a basal position with respect to New World species of Clinostomum, although a denser taxon sampling of species within the genus is further required. The metacercaria of C. heluans seems to be specific to cichlid fish because both samples from South America were recovered from species of this fish family, although not closely related.},
}
@article {pmid29466431,
year = {2018},
author = {Ravago-Gotanco, R and de la Cruz, TL and Pante, MJ and Borsa, P},
title = {Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.},
journal = {PloS one},
volume = {13},
number = {2},
pages = {e0193220},
pmid = {29466431},
issn = {1932-6203},
mesh = {Animals ; Fishes/classification/*genetics ; *Genetic Loci ; *Genotype ; *Microsatellite Repeats ; Mitochondria/*genetics ; Oceans and Seas ; *Phylogeny ; },
abstract = {The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.},
}
@article {pmid29476907,
year = {2018},
author = {Layton, KKS and Gosliner, TM and Wilson, NG},
title = {Flexible colour patterns obscure identification and mimicry in Indo-Pacific Chromodoris nudibranchs (Gastropoda: Chromodorididae).},
journal = {Molecular phylogenetics and evolution},
volume = {124},
number = {},
pages = {27-36},
doi = {10.1016/j.ympev.2018.02.008},
pmid = {29476907},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/genetics/*physiology ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Molecular Mimicry/*genetics ; Phylogeny ; Pigmentation/*genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris. This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus.},
}
@article {pmid29509408,
year = {2018},
author = {Wisnovsky, S and Sack, T and Pagliarini, DJ and Laposa, RR and Kelley, SO},
title = {DNA Polymerase θ Increases Mutational Rates in Mitochondrial DNA.},
journal = {ACS chemical biology},
volume = {13},
number = {4},
pages = {900-908},
pmid = {29509408},
issn = {1554-8937},
support = {R01 GM115591/GM/NIGMS NIH HHS/United States ; R01 GM116886/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cell Line, Tumor ; DNA Replication ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*physiology ; Humans ; *Mutation Rate ; Neoplasms/genetics ; Oxidative Stress ; DNA Polymerase theta ; },
abstract = {Replication and maintenance of mitochondrial DNA (mtDNA) is essential for cellular function, yet few DNA polymerases are known to function in mitochondria. Here, we conclusively demonstrate that DNA polymerase θ (Polθ) localizes to mitochondria and explore whether this protein is overexpressed in patient-derived cells and tumors. Polθ appears to play an important role in facilitating mtDNA replication under conditions of oxidative stress, and this error-prone polymerase was found to introduce mutations into mtDNA. In patient-derived cells bearing a pathogenic mtDNA mutation, Polθ expression levels were increased, indicating that the oxidative conditions in these cells promote higher expression levels for Polθ. Heightened Polθ expression levels were also associated with elevated mtDNA mutation rates in a selected panel of human tumor tissues, suggesting that this protein can influence mutational frequencies in tumors. The results reported indicate that the mitochondrial function of Polθ may have relevance to human disease.},
}
@article {pmid29511984,
year = {2018},
author = {Zhao, YQ and Mu, DL and Wang, D and Han, YL and Hou, CC and Zhu, JQ},
title = {Analysis of the function of KIF3A and KIF3B in the spermatogenesis in Boleophthalmus pectinirostris.},
journal = {Fish physiology and biochemistry},
volume = {44},
number = {3},
pages = {769-788},
pmid = {29511984},
issn = {1573-5168},
support = {No. 31272642//National Natural Science Foundation of China (CN)/ ; No. 2015C110005//Scientific and Technical Project of Ningbo/ ; No.2016A610081//Ningbo Natural Science Foundation/ ; },
mesh = {Animals ; *Fish Proteins/chemistry/genetics/metabolism ; Gills/metabolism ; Kidney/metabolism ; *Kinesins/chemistry/genetics/metabolism ; Liver/metabolism ; Male ; Microscopy, Electron, Transmission ; Muscles/metabolism ; Myocardium/metabolism ; *Perciformes ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Analysis, DNA ; Spermatogenesis/genetics/*physiology ; Spermatozoa/metabolism/ultrastructure ; Spleen/metabolism ; Testis/metabolism ; },
abstract = {Spermatogenesis represents one of the most complicated morphological transformation procedures. During this process, the assembly and maintenance of the flagella and intracellular transport of membrane-bound organelles required KIF3A and KIF3B. Our main goal was to test KIF3A and KIF3B location during spermatogenesis of Boleophthalmus pectinirostris. We cloned complete cDNA of KIF3A/3B from the testis of B. pectinirostris by PCR and rapid amplification of cDNA ends (RACE). The predicted secondary and tertiary structures of B. pectinirostris KIF3A/3B contained three domains: (a) the head region, (b) the stalk region, and (c) the tail region. Real-time quantitative PCR (qPCR) results revealed that KIF3A and KIF3B mRNA were presented in all the tissues examined, with the highest expression seen in the testis. In situ hybridization (ISH) showed that KIF3A and KIF3B were distributed in the periphery of the nuclear in the spermatocyte and the early spermatid. In the late spermatid and mature sperm, the KIF3A and KIF3B mRNA were gradually gathered to one side where the flagella formed. Immunofluorescence (IF) showed that KIF3A, tubulin, and mitochondria were co-localized in different stages during spermiogenesis in B. pectinirostris. The temporal and spatial expression dynamics of KIF3A/3B indicate that KIF3A and KIF3B might be involved in flagellar assembly and maintenance at the mRNA and protein levels. Moreover, these proteins may transport the mitochondria resulting in flagellum formation in B. pectinirostris.},
}
@article {pmid29524652,
year = {2018},
author = {Berriman, JS and Ellingson, RA and Awbrey, JD and Rico, DM and Valdés, &#xc1;A and Wilson, NG and Aguilar, A and Herbert, DG and Hirano, YM and Trowbridge, CD and Krug, PJ},
title = {A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae".},
journal = {Molecular phylogenetics and evolution},
volume = {126},
number = {},
pages = {356-370},
pmid = {29524652},
issn = {1095-9513},
support = {R25 GM061331/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/*physiology ; Gastropoda/*physiology ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; Tooth/*physiology ; },
abstract = {Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.},
}
@article {pmid29529094,
year = {2018},
author = {Bourret, TB and Choudhury, RA and Mehl, HK and Blomquist, CL and McRoberts, N and Rizzo, DM},
title = {Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0192502},
pmid = {29529094},
issn = {1932-6203},
mesh = {Cell Nucleus/genetics ; Likelihood Functions ; Mitochondria/genetics ; Peronospora/*genetics ; *Phylogeny ; Phytophthora/*genetics ; Plant Diseases/parasitology ; },
abstract = {Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.},
}
@article {pmid29533769,
year = {2018},
author = {Marsit, S and Dion-Côté, AM and Barbash, DA},
title = {Did Mitochondria Kill the Frog?.},
journal = {Developmental cell},
volume = {44},
number = {5},
pages = {539-541},
doi = {10.1016/j.devcel.2018.02.020},
pmid = {29533769},
issn = {1878-1551},
mesh = {*Genome ; Genomics ; Hybridization, Genetic ; Mitochondria ; *Reproductive Isolation ; },
abstract = {Genomic divergence can cause reproductive isolation between species. The molecular mechanisms underlying reproductive isolation can thus reveal which genomic features evolve rapidly and become unstable or incompatible in hybrids. In a recent paper in Nature, Gibeaux et al. (2018) report paternal genome instability and metabolic imbalance in hybrids between frog species.},
}
@article {pmid29543917,
year = {2018},
author = {Visser, JH and Bennett, NC and Jansen van Vuuren, B},
title = {Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment.},
journal = {PloS one},
volume = {13},
number = {3},
pages = {e0194165},
pmid = {29543917},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Cytochromes b/genetics ; Ecosystem ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Mole Rats/*genetics ; Phylogeny ; Phylogeography ; South Africa ; },
abstract = {The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.},
}
@article {pmid29567505,
year = {2018},
author = {O'Connell, KA and Smith, EN},
title = {The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis).},
journal = {Molecular phylogenetics and evolution},
volume = {127},
number = {},
pages = {356-366},
doi = {10.1016/j.ympev.2018.03.018},
pmid = {29567505},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; Colubridae/*classification ; Cytochromes c/genetics ; Geography ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; },
abstract = {A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use genome-wide SNP data and coalescent species delimitation to explore lineage relationships within several North American whipsnake species, test the species status of several lineages, and test the effect of missing data on species delimitation. We find support for the elevation of several previously recognized subspecies to full species status, and formally elevate two species. This study demonstrates the power of molecular data and model-based delimitation methods to identify evolutionary relationships, and finds that missing data have little impact on the outcome of delimitation analyses.},
}
@article {pmid29575366,
year = {2018},
author = {Ivanov, V and Lee, KM and Mutanen, M},
title = {Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression.},
journal = {Molecular ecology},
volume = {27},
number = {7},
pages = {1681-1695},
doi = {10.1111/mec.14564},
pmid = {29575366},
issn = {1365-294X},
mesh = {Animals ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Spiders/*genetics ; },
abstract = {Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.},
}
@article {pmid29579296,
year = {2018},
author = {Caspermeyer, J},
title = {Cockroach Ancient Geographic and Genomic History Traced Back to Last Supercontinent.},
journal = {Molecular biology and evolution},
volume = {35},
number = {4},
pages = {1035},
doi = {10.1093/molbev/msy039},
pmid = {29579296},
issn = {1537-1719},
mesh = {Animals ; *Cockroaches ; Genomics ; Mitochondria ; *Phylogeny ; },
}
@article {pmid29587633,
year = {2018},
author = {Chase, EE and Robicheau, BM and Veinot, S and Breton, S and Stewart, DT},
title = {The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {221},
pmid = {29587633},
issn = {1471-2164},
support = {217175//Natural Sciences and Engineering Research Council of Canada/International ; },
mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/genetics ; Disorders of Sex Development/*genetics ; Female ; Fresh Water ; *Genome, Mitochondrial ; Male ; Mitochondrial Proteins/genetics ; *Open Reading Frames ; Phylogeny ; Sex Factors ; Unionidae/classification/*genetics ; },
abstract = {BACKGROUND: Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages.<br><br>RESULTS: In silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA.<br><br>CONCLUSION: In silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.},
}
@article {pmid29609620,
year = {2018},
author = {Hornok, S and Beck, R and Farkas, R and Grima, A and Otranto, D and Kontschán, J and Takács, N and Horváth, G and Szőke, K and Szekeres, S and Majoros, G and Juhász, A and Salant, H and Hofmann-Lehmann, R and Stanko, M and Baneth, G},
title = {High mitochondrial sequence divergence in synanthropic flea species (Insecta: Siphonaptera) from Europe and the Mediterranean.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {221},
pmid = {29609620},
issn = {1756-3305},
support = {115854//OTKA/International ; },
mesh = {Animals ; *Base Sequence ; Ctenocephalides/classification/genetics ; Europe ; Flea Infestations/parasitology ; *Genetic Variation ; Haplotypes ; Humans ; Insect Vectors/classification/genetics ; Mediterranean Region ; Mitochondria/*genetics ; Phylogeny ; Siphonaptera/*classification/*genetics ; },
abstract = {BACKGROUND: Adult fleas are haematophagous ectoparasites of warm-blooded vertebrates, particularly mammals. Among them, the cat flea (Ctenocephalides felis) and the human flea (Pulex irritans) have high veterinary-medical significance, owing to their cosmopolitan distribution and role in the transmission of important vector-borne pathogens. While the taxonomy of Ct. felis has been investigated on a morphological basis during the past decades, its molecular-phylogenetic analyses have been only recently conducted. This study expands the knowledge on Ct. felis from hitherto less studied geographical regions, and includes representatives from additional flea families, less investigated with molecular approaches.<br><br>METHODS: Fleas were collected in four countries of the Mediterranean Basin (Croatia, Italy, Malta and Israel), as well as in Hungary, from domestic and wild carnivores, rodents and humans. The DNA extracts of representative fleas (n = 148), belonging to ten species of eight genera, were used for PCR amplification of part of their cytochrome c oxidase subunits 1, 2 (cox1, cox2) and 18S rRNA genes, followed by sequencing and phylogenetic analyses.<br><br>RESULTS: The majority (65.6%) of Ct. felis felis cox2 sequences showed 99.4-100% similarity to each other (haplogroup A), whereas those from Malta and Israel had 98.1-98.7% sequence similarity (haplogroup B), and a third sequence from Israel (haplotype C) had as low as 96.3% sequence similarity in comparison with a reference sequence from group "A". Except for the shape of the head, no consistent morphological differences (e.g. in chaetotaxy) were found between haplogroups "A" and "C". Haplotypes of Ct. canis were genetically more homogenous, with 99.6-100% sequence similarity to each other. However, when P. irritans collected from humans was compared to those from three species of wild carnivores, these only had 96.6% cox2 similarity. The mouse flea, Leptopsylla segnis and the northern rat flea, Nosopsyllus fasciatus were both shown to have haplotypes with low intraspecific cox2 similarities (96.2 and 94.4%, respectively). Taken together, differences between mitochondrial lineages within four flea species exceeded that observed between two Chaetopsylla spp. (which had 97.3% cox2 similarity). The topologies of cox1 and cox2 phylogenetic trees were in line with relevant sequence comparisons. Conversely, 18S rRNA gene analyses only resolved differences above the species level.<br><br>CONCLUSIONS: Ctenocephalides felis felis, P. irritans, L. segnis and N. fasciatus were shown to have such a high level of mitochondrial gene heterogeneity, that the uniformity of these flea taxa should be reconsidered. Although the present results are limited (especially in the case of L. segnis and N. fasciatus), there appears to be no geographical or host restriction, which could explain the divergence of these genetic lineages.},
}
@article {pmid29618317,
year = {2018},
author = {Doyle, JM and Bell, DA and Bloom, PH and Emmons, G and Fesnock, A and Katzner, TE and LaPré, L and Leonard, K and SanMiguel, P and Westerman, R and Andrew DeWoody, J},
title = {New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus).},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {233},
pmid = {29618317},
issn = {1471-2164},
support = {L12AC20102, L11PX02237, L12AC2010//U.S. Bureau of Land Management/ ; University Faculty Scholar program//Provost's Office at Purdue University/ ; PINN645-21//National Park Service/ ; BIO170038//XSEDE/ ; },
mesh = {Animals ; Avian Proteins/*genetics ; California ; Falconiformes/*classification/genetics ; Female ; Genetics, Population ; Idaho ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*veterinary ; },
abstract = {BACKGROUND: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.<br><br>RESULTS: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated >&#x2009;16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring >&#x2009;140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~&#x2009;100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.<br><br>CONCLUSIONS: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California's prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.},
}
@article {pmid29653091,
year = {2018},
author = {Islam, W and Lin, W and Qasim, M and Islam, SU and Ali, H and Adnan, M and Arif, M and Du, Z and Wu, Z},
title = {A nation-wide genetic survey revealed a complex population structure of Bemisia tabaci in Pakistan.},
journal = {Acta tropica},
volume = {183},
number = {},
pages = {119-125},
doi = {10.1016/j.actatropica.2018.04.015},
pmid = {29653091},
issn = {1873-6254},
mesh = {Agriculture ; Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genetic Variation ; Hemiptera/*genetics ; Insect Proteins/genetics ; Mitochondria/genetics ; *Molecular Epidemiology ; Pakistan ; *Phylogeny ; },
abstract = {The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex distributed worldwide. In Pakistan, B. tabaci poses a serious threat to agriculture production. To understand its diversity in Pakistan, a large-scale sampling was conducted from various locations of all four provinces of the country and Mitochondrial cytochrome oxidase I (mtCOI) gene sequencing was used to determine the whiteflies genetically. The study revealed the presence of five different cryptic species in Pakistan namely Asia II-1, Asia II-5, Asia II-7, Asia II-8 and MEAM-1, respectively. Among them, Asia II-1, which was previously reported from a few areas in the country, had been found now to be prevalent all over the country covering 88.7% of all the sequenced samples. Based on the mtCOI sequences and genetic distance analyses, the diversity of Asia II-1 was much greater than all other cryptic species, which exist only in small patches.},
}
@article {pmid29656105,
year = {2018},
author = {Dias, C and Lima, KA and Araripe, J and Aleixo, A and Vallinoto, M and Sampaio, I and Schneider, H and Rêgo, PSD},
title = {Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae).},
journal = {Molecular phylogenetics and evolution},
volume = {126},
number = {},
pages = {314-320},
doi = {10.1016/j.ympev.2018.04.017},
pmid = {29656105},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Passeriformes/*classification/*genetics ; *Phylogeny ; },
abstract = {Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 and COI) and nuclear (MYO, G3PDh and I5BF) markers in a multilocus analysis, to evaluate relationships and inter-specific limits among L. iris, L. nattereri, and L. vilasboasi, which are known to hybridize in eastern Amazonia. The results revealed a complex pattern, whereby events of secondary contact and gene flow after isolation and genetic and phenotypic differentiation prevented the recuperation of reciprocal monophyly among the studied taxa. The mitochondrial data indicate that L. nattereri is divided into two non-sister groups, one monophyletic, and the other, paraphyletic, with L. iris iris being more closely related to one of the two L. nattereri groups, while L. iris eucephala forms an undifferentiated clade with L. vilasboasi, probably resulting from an extensive process of mitochondrial introgression. In agreement with a previous study based on Single Nucleotide Polymorphism (SNP) data, mitochondrial haplotype networks also support that L. vilasboasi does not represent a recent "hybrid swarm" between L. iris and L. nattereri, but instead a genetically divergent lineage with a separate species status. Finally, the sister relationship recovered herein between L. iris iris and some western populations of L. nattereri currently in allopatry is also apparently explained by mitochondrial introgression, as also supported for nuclear genes by SNP data, indicating a complex scenario of past contact and gene flow between currently geographically distant Lepidothrix lineages.},
}
@article {pmid29675902,
year = {2018},
author = {Morin, PA and Foote, AD and Baker, CS and Hancock-Hanser, BL and Kaschner, K and Mate, BR and Mesnick, SL and Pease, VL and Rosel, PE and Alexander, A},
title = {Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses.},
journal = {Molecular ecology},
volume = {27},
number = {11},
pages = {2604-2619},
doi = {10.1111/mec.14698},
pmid = {29675902},
issn = {1365-294X},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Demography ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; Population Density ; Sperm Whale/*genetics ; },
abstract = {Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally-transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion vs. a selective sweep due to cultural hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean-specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species.},
}
@article {pmid29689791,
year = {2018},
author = {Sadasivan, K and Ramesh, MB and Palot, MJ and Ambekar, M and Mirza, ZA},
title = {A new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala, southern India.},
journal = {Zootaxa},
volume = {4374},
number = {4},
pages = {545-564},
doi = {10.11646/zootaxa.4374.4.5},
pmid = {29689791},
issn = {1175-5334},
mesh = {Animals ; India ; *Lizards ; Mitochondria ; Phylogeny ; },
abstract = {We here describe Sitana attenboroughii sp. nov., a new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala in southern India. The new species morphologically is closer to Sitana visiri Deepak, 2016 (in Deepak et al. 2016a), however, differs in having higher numbers of ventral scales and a comparatively short but richly colored dewlap. Genetically the new species shows affinity to Sitana marudhamneydhal Deepak, Khandekar, Varma Chaitanya, 2016 from which it differs in an uncorrected pairwise sequence divergence of 2.2% for a fragment of mitochondrial Nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 2 gene.},
}
@article {pmid29698456,
year = {2018},
author = {Peña-Diaz, P and Mach, J and Kriegová, E and Poliak, P and Tachezy, J and Lukeš, J},
title = {Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase.},
journal = {PloS one},
volume = {13},
number = {4},
pages = {e0196474},
pmid = {29698456},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Down-Regulation ; Electron Transport Complex IV/metabolism ; Metalloendopeptidases/antagonists &amp; inhibitors/classification/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Phylogeny ; Protein Subunits/antagonists &amp; inhibitors/genetics/metabolism ; RNA Interference ; RNA, Small Interfering/metabolism ; Substrate Specificity ; Trypanosoma brucei brucei/*metabolism ; Mitochondrial Processing Peptidase ; },
abstract = {Upon their translocation into the mitochondrial matrix, the N-terminal pre-sequence of nuclear-encoded proteins undergoes cleavage by mitochondrial processing peptidases. Some proteins require more than a single processing step, which involves several peptidases. Down-regulation of the putative Trypanosoma brucei mitochondrial intermediate peptidase (MIP) homolog by RNAi renders the cells unable to grow after 48 hours of induction. Ablation of MIP results in the accumulation of the precursor of the trypanosomatid-specific trCOIV protein, the largest nuclear-encoded subunit of the cytochrome c oxidase complex in this flagellate. However, the trCOIV precursor of the same size accumulates also in trypanosomes in which either alpha or beta subunits of the mitochondrial processing peptidase (MPP) have been depleted. Using a chimeric protein that consists of the N-terminal sequence of a putative subunit of respiratory complex I fused to a yellow fluorescent protein, we assessed the accumulation of the precursor protein in trypanosomes, in which RNAi was induced against the alpha or beta subunits of MPP or MIP. The observed accumulation of precursors indicates MIP depletion affects the activity of the cannonical MPP, or at least one of its subunits.},
}
@article {pmid29718949,
year = {2018},
author = {Lv, C and Li, Q and Kong, L},
title = {Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.},
journal = {PloS one},
volume = {13},
number = {5},
pages = {e0196466},
pmid = {29718949},
issn = {1932-6203},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Bayes Theorem ; Bivalvia/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.},
}
@article {pmid29728774,
year = {2018},
author = {Gong, S and Vamberger, M and Auer, M and Praschag, P and Fritz, U},
title = {Millennium-old farm breeding of Chinese softshell turtles (Pelodiscus spp.) results in massive erosion of biodiversity.},
journal = {Die Naturwissenschaften},
volume = {105},
number = {5-6},
pages = {34},
pmid = {29728774},
issn = {1432-1904},
support = {31471966//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Biodiversity ; *Breeding ; China ; DNA, Mitochondrial/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Turtles/*classification/*genetics ; },
abstract = {Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.},
}
@article {pmid29754387,
year = {2018},
author = {Zhu, C and Chen, P and Han, Y and Ruan, L},
title = {Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China.},
journal = {Biochemical genetics},
volume = {56},
number = {6},
pages = {586-617},
doi = {10.1007/s10528-018-9862-9},
pmid = {29754387},
issn = {1573-4927},
support = {NSFC no. 30960052//National Science Foundation of China/ ; no. 31260510//National Science Foundation of China/ ; no. KT201537//Water - resource Department of Jiangxi Province Science and Technological Project/ ; },
mesh = {Animals ; Birds/*genetics ; DNA, Mitochondrial ; *Gene Flow ; *Genetic Structures ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.},
}
@article {pmid29770661,
year = {2018},
author = {Cang-Lin, Z and Jia, P and Zhen, R and Jin-Rong, Z and Ya-Ming, Y},
title = {[Genotyping and polymorphism analysis of cytochrome c oxidase subunit Ⅰ gene of Pomacea canaliculata from Lincang City in Yunnan Province].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {30},
number = {2},
pages = {179-183},
doi = {10.16250/j.32.1374.2017163},
pmid = {29770661},
issn = {1005-6661},
mesh = {Angiostrongylus cantonensis ; Animals ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gastropoda/enzymology/*genetics ; Genotype ; Haplotypes ; Phylogeny ; },
abstract = {OBJECTIVE: To analyze the genetic diversity of Pomacea canaliculata based on the mitochondria DNA cytochrome c oxidase subunit Ⅰ (mtDNA COⅠ) gene as a molecular marker in Lincang City of Yunnan Province, so as to provide the scientific data for monitoring Angiostrongylus cantonensis in local areas.<br><br>METHODS: The genotypes and polymorphisms of 38 specimens of P. canaliculata collected from Mengding Town of Lincang City were analyzed by sequencing CO&#x2160; gene. The phylogenetic tree and genetic distances were produced based on the haplotypes from GenBank and the present study by using the neighbourjoining method with the software MEGA version 6.06.<br><br>RESULTS: Totally 31 sequences were acquired in the present study and they produced 3 unique haplotypes. Haplotype 1 showed a higher frequency compared to the others and it accounted for 83.9 % (26/31). The data showed that the least genetic distances ranged from 0 to 0.052 between P. canaliculata and 3 haplotypes, as well as the largest genetic distances ranged from 0.021 to 0.239 between Pila conica and 3 haplotypes. Otherwise, the analysis of the phylogenetic trees based on CO&#x2160; gene sequences of P. canaliculata indicated that all of 3 haplotypes clustered into one big clade with that from Japan (GenBank accession number: AB433769), China (GenBank accession number: KT313034) and USA (GenBank accession number: EU523129), which owned the closet relationship amongst them. Their genetic relationships were distantly related to the GenBank's reference sequences of P. insularum (GenBank accession number: EF514942), P. camena (GenBank accession number: EF515059) and so on.<br><br>CONCLUSIONS: There is a P. canaliculata species in Lincang City of Yunnan Province as well as a high genetic diversity amongst the acquired 3 haplotypes in this study.},
}
@article {pmid29787733,
year = {2018},
author = {Younas, F and Soltanmohammadi, N and Knapp, O and Benz, R},
title = {The major outer membrane protein of Legionella pneumophila Lpg1974 shows pore-forming characteristics similar to the human mitochondrial outer membrane pore, hVDAC1.},
journal = {Biochimica et biophysica acta. Biomembranes},
volume = {1860},
number = {8},
pages = {1544-1553},
doi = {10.1016/j.bbamem.2018.05.008},
pmid = {29787733},
issn = {0005-2736},
mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/classification/genetics/*metabolism ; Escherichia coli/metabolism ; Humans ; Legionella pneumophila/*metabolism ; Lipid Bilayers/chemistry/metabolism ; Phylogeny ; Protein Structure, Secondary ; Recombinant Proteins/biosynthesis/chemistry/isolation &amp; purification ; Sequence Alignment ; Voltage-Dependent Anion Channel 1/chemistry/*metabolism ; },
abstract = {Legionella pneumophila is an aerobic and nonspore-forming pathogenic Gram-negative bacterium of the genus Legionella. It is the causative agent of Legionnaires' disease, also known as Legionellosis. The hosts of this organism are diverse, ranging from simple water borne protozoans such as amoebae to more complex hosts such as macrophages in humans. Genome analyses have shown the presence of genes coding for eukaryotic like proteins in several Legionella species. The presence of these proteins may assist L. pneumophila in its adaptation to the eukaryotic host. We studied the characteristics of a protein (Lpg1974) of L. pneumophila that shows remarkable homologies in length of the primary sequence and for the identity/homology of many amino acids to the voltage dependent anion channel (human VDAC1, Porin 31HL) of human mitochondria. Two different forms of Lpg1974 were overexpressed in Escherichia coli and purified to homogeneity: the one containing a putative N-terminal signal sequence and one without it. Reconstituted protein containing the signal sequence formed ion-permeable pores in lipid bilayer membranes with a conductance of approximately 5.4 nS in 1 M KCl. When the predicted N-terminal signal peptide of Lpg1974 comprising an α-helical structure similar to that at the N-terminus of hVDAC1 was removed, the channels formed in reconstitution experiments had a conductance of 7.6 nS in 1 M KCl. Both Lpg1974 proteins formed pores that were voltage-dependent and anion-selective similar to the pores formed by hVDAC1. These results suggest that Lpg1974 of L. pneumophila is indeed a structural and functional homologue to hVDAC1.},
}
@article {pmid29794164,
year = {2018},
author = {Ries, LNA and José de Assis, L and Rodrigues, FJS and Caldana, C and Rocha, MC and Malavazi, I and Bayram, &#xd6; and Goldman, GH},
title = {The Aspergillus nidulans Pyruvate Dehydrogenase Kinases Are Essential To Integrate Carbon Source Metabolism.},
journal = {G3 (Bethesda, Md.)},
volume = {8},
number = {7},
pages = {2445-2463},
pmid = {29794164},
issn = {2160-1836},
mesh = {Aspergillus nidulans/classification/genetics/*metabolism ; Carbon/*metabolism ; Catabolite Repression ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Glucose/metabolism ; Hydrolysis ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Multigene Family ; Phylogeny ; Protein Interaction Mapping ; Protein Interaction Maps ; Protein Serine-Threonine Kinases/genetics/*metabolism ; Protein Transport ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; },
abstract = {The pyruvate dehydrogenase complex (PDH), that converts pyruvate to acetyl-coA, is regulated by pyruvate dehydrogenase kinases (PDHK) and phosphatases (PDHP) that have been shown to be important for morphology, pathogenicity and carbon source utilization in different fungal species. The aim of this study was to investigate the role played by the three PDHKs PkpA, PkpB and PkpC in carbon source utilization in the reference filamentous fungus Aspergillus nidulans, in order to unravel regulatory mechanisms which could prove useful for fungal biotechnological and biomedical applications. PkpA and PkpB were shown to be mitochondrial whereas PkpC localized to the mitochondria in a carbon source-dependent manner. Only PkpA was shown to regulate PDH activity. In the presence of glucose, deletion of pkpA and pkpC resulted in reduced glucose utilization, which affected carbon catabolite repression (CCR) and hydrolytic enzyme secretion, due to de-regulated glycolysis and TCA cycle enzyme activities. Furthermore, PkpC was shown to be required for the correct metabolic utilization of cellulose and acetate. PkpC negatively regulated the activity of the glyoxylate cycle enzyme isocitrate lyase (ICL), required for acetate metabolism. In summary, this study identified PDHKs important for the regulation of central carbon metabolism in the presence of different carbon sources, with effects on the secretion of biotechnologically important enzymes and carbon source-related growth. This work demonstrates how central carbon metabolism can affect a variety of fungal traits and lays a basis for further investigation into these characteristics with potential interest for different applications.},
}
@article {pmid29842994,
year = {2018},
author = {Weerts, MJA and Timmermans, EC and van de Stolpe, A and Vossen, RHAM and Anvar, SY and Foekens, JA and Sleijfer, S and Martens, JWM},
title = {Tumor-Specific Mitochondrial DNA Variants Are Rarely Detected in Cell-Free DNA.},
journal = {Neoplasia (New York, N.Y.)},
volume = {20},
number = {7},
pages = {687-696},
pmid = {29842994},
issn = {1476-5586},
mesh = {Aged ; Aged, 80 and over ; Alleles ; *Biomarkers, Tumor ; *Circulating Tumor DNA ; Computational Biology/methods ; *DNA, Mitochondrial ; *DNA, Neoplasm ; Female ; Gene Frequency ; Genetic Heterogeneity ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Neoplasm Staging ; Neoplasms/*genetics/pathology ; Phylogeny ; },
abstract = {The use of blood-circulating cell-free DNA (cfDNA) as a "liquid biopsy" in oncology is being explored for its potential as a cancer biomarker. Mitochondria contain their own circular genomic entity (mitochondrial DNA, mtDNA), up to even thousands of copies per cell. The mutation rate of mtDNA is several orders of magnitude higher than that of the nuclear DNA. Tumor-specific variants have been identified in tumors along the entire mtDNA, and their number varies among and within tumors. The high mtDNA copy number per cell and the high mtDNA mutation rate make it worthwhile to explore the potential of tumor-specific cf-mtDNA variants as cancer marker in the blood of cancer patients. We used single-molecule real-time (SMRT) sequencing to profile the entire mtDNA of 19 tissue specimens (primary tumor and/or metastatic sites, and tumor-adjacent normal tissue) and 9 cfDNA samples, originating from 8 cancer patients (5 breast, 3 colon). For each patient, tumor-specific mtDNA variants were detected and traced in cfDNA by SMRT sequencing and/or digital PCR to explore their feasibility as cancer biomarker. As a reference, we measured other blood-circulating biomarkers for these patients, including driver mutations in nuclear-encoded cfDNA and cancer-antigen levels or circulating tumor cells. Four of the 24 (17%) tumor-specific mtDNA variants were detected in cfDNA, however at much lower allele frequencies compared to mutations in nuclear-encoded driver genes in the same samples. Also, extensive heterogeneity was observed among the heteroplasmic mtDNA variants present in an individual. We conclude that there is limited value in tracing tumor-specific mtDNA variants in blood-circulating cfDNA with the current methods available.},
}
@article {pmid29843598,
year = {2018},
author = {Perry, KD and Baker, GJ and Powis, KJ and Kent, JK and Ward, CM and Baxter, SW},
title = {Cryptic Plutella species show deep divergence despite the capacity to hybridize.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {77},
pmid = {29843598},
issn = {1471-2148},
support = {UA00146//University of Adelaide/International ; DAS00094//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DP120100047//Australian Research Council/International ; FT140101303//Australian Research Council/International ; },
mesh = {Animals ; Australia ; Biological Assay ; Crosses, Genetic ; DNA, Mitochondrial/genetics ; Female ; Fertility ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Heterozygote ; *Hybridization, Genetic/drug effects ; Insecticide Resistance/drug effects/genetics ; Insecticides/toxicity ; Likelihood Functions ; Male ; Mitochondria/genetics ; Moths/*genetics/microbiology ; Phylogeny ; Species Specificity ; Sympatry ; Wolbachia/drug effects/physiology ; },
abstract = {BACKGROUND: Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry &amp; Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays.<br><br>RESULTS: The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of P. xylostella.<br><br>CONCLUSIONS: Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.},
}
@article {pmid29848319,
year = {2018},
author = {Bronstein, O and Kroh, A and Haring, E},
title = {Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {80},
pmid = {29848319},
issn = {1471-2148},
support = {P 29508/FWF_/Austrian Science Fund FWF/Austria ; P 29508-B25//Austrian Science Fund/International ; },
mesh = {Algorithms ; Animals ; Base Sequence ; DNA Primers/metabolism ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Genetic Markers ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Sea Urchins/*genetics ; },
abstract = {BACKGROUND: In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.<br><br>RESULTS: Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.<br><br>CONCLUSIONS: Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.},
}
@article {pmid29852093,
year = {2018},
author = {Li, Z and You, XL and Wang, LL and Yan, ZT and Zhou, ZY},
title = {Spore morphology and ultrastructure of an Ascosphaera apis strain from the honeybees (Apis mellifera) in southwest China.},
journal = {Mycologia},
volume = {110},
number = {2},
pages = {325-338},
doi = {10.1080/00275514.2018.1442084},
pmid = {29852093},
issn = {1557-2536},
mesh = {Animals ; Bees/*microbiology ; Cell Wall/chemistry ; China ; Chitin/analysis ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Onygenales/classification/*cytology/isolation &amp; purification/*ultrastructure ; Organelles/ultrastructure ; Phylogeny ; RNA, Ribosomal, 5.8S ; Sequence Analysis, DNA ; Spores, Fungal/*cytology/*ultrastructure ; },
abstract = {Ascosphaera apis is an intestinally infective, spore-forming, filamentous fungus that infects honeybees and causes deadly chalkbrood disease. Although A. apis has been known for 60 y, little is known about the ultrastructure of the spores. In this study, the fine morphology and ultrastructure of an isolate, A. apis CQ1 from southwest China, was comprehensively identified by transmission electron microscopy, confocal laser scanning microscopy, scanning electron microscopy, and optical microscopy. The high sequence similarity and phylogenetic data based on nuc rDNA ITS1-5.8S-ITS2 (ITS) supported the hypothesis that the CQ1 strain is a new member of the A. apis species. Morphological observation indicated that the mature spores are long ovals with an average size of 2 × 1.2 µm and are tightly packed inside spherical spore balls. More than 10 spore balls that were 8-16 µm in diameter were wrapped and formed a spherical, nearly hyaline spore cyst of 50-60 µm in diameter. Ultrastructural analysis showed that mature spores have two nuclei with distinctly different sizes. A large nucleus with double nuclear membranes was found in the center of the spore, whereas the small nucleus was only one-fifth of the large nucleus volume and was located near the end of the spore. Numerous ribosomes filled the cytoplasm, and many mitochondria with well-defined structures were arranged along the inner spore wall. The spore wall consists of an electron-dense outer surface layer, an electron-lucent layer, and an inner plasma membrane. Chitin is the major component of the spore wall. The germinated spore was observed as an empty spore coat, whereas the protoplasts, including the nuclei, mitochondria, and ribosomes, had been discharged. In addition to these typical fungal spore organelles, an unknown electron-dense regular structure might be the growing mycelium, which was arranged close to the inner spore wall and almost covered the entire wall area.},
}
@article {pmid29855375,
year = {2018},
author = {Amzati, GS and Pelle, R and Muhigwa, JB and Kanduma, EG and Djikeng, A and Madder, M and Kirschvink, N and Marcotty, T},
title = {Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.},
journal = {Parasites &amp; vectors},
volume = {11},
number = {1},
pages = {329},
pmid = {29855375},
issn = {1756-3305},
support = {ABC089//Africa Biosciences Challenge Fund (ABCF) program, BecA-ILRI Hub/ ; S0020***10402//Agence Universitaire de la Francophonie/ ; IFS-92890CA3//International Foundation for Science/ ; Bourses institutionnelles-Ceruna//Universit&#xe9; de Namur/ ; 006/014//Communaut&#xe9; &#xe9;conomique des pays des Grands Lacs (CEPGL)/ ; },
mesh = {Africa/epidemiology ; Animals ; Arachnid Vectors/*genetics/parasitology ; Cattle ; Genetic Structures ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; Rhipicephalus/*genetics/parasitology ; Theileria parva/*physiology ; Theileriasis/epidemiology/*parasitology ; },
abstract = {BACKGROUND: The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa.<br><br>METHODS: Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution.<br><br>RESULTS: Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa.<br><br>CONCLUSIONS: Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.},
}
@article {pmid29864497,
year = {2018},
author = {Banerjee, B and Koner, D and Bhuyan, G and Saha, N},
title = {Differential expression of multiple glutamine synthetase genes in air-breathing magur catfish, Clarias magur and their induction under hyper-ammonia stress.},
journal = {Gene},
volume = {671},
number = {},
pages = {85-95},
doi = {10.1016/j.gene.2018.05.111},
pmid = {29864497},
issn = {1879-0038},
mesh = {Ammonia/*pharmacology ; Animals ; Brain/metabolism ; Catfishes/*genetics/metabolism ; Cytosol/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation/drug effects ; Gills/metabolism ; Glutamate-Ammonia Ligase/*genetics ; Kidney/metabolism ; Liver/metabolism ; Mitochondria/metabolism ; Muscle Cells/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Stress, Physiological ; Tissue Distribution ; *Up-Regulation ; },
abstract = {The present study demonstrates the unique presence of three different gs genes (cmgs01, cmgs02, and cmgs03) in air-breathing ureogenic magur catfish (Clarias magur), which is otherwise reported to be encoded by a single gene in higher vertebrates. Of these three genes, two (cmgs01and cmgs03) were identified as 'liver' form, predominantly expressed in liver cells, and the third one as 'brain' form (cmgs02), expressed chiefly in brain cells. Molecular characterization studies have revealed conservation of homologous active site residues in all the three gs genes. In silico analysis, accompanied by GS enzyme assay and Western blot analysis of different GS isoforms in different subcellular fractions indicated the mitochondrial localization of cmGS01 and cmGS03 in liver and kidney cells and cytosolic localization of cmGS02 in brain cells. Further, exposure of magur catfish to high external ammonia (HEA; 25 mM NH4Cl) led to a significant induction of multiple gs genes as evidenced by higher expression of different gs mRNAs at variable levels in different tissues. The cmgs01 and cmgs03 mRNA levels elevated significantly in liver, kidney, muscle, and gills, whereas the cmgs02 mRNA level increased considerably in the brain after 14 days of exposure to HEA. These increases in mRNA levels were associated with a significant rise in cmGS01 and cmGS03 proteins in liver, kidney, muscle, and gills, and the cmGS02 protein in the brain after 14 days of exposure to HEA. Therefore, it can be concluded that the unique differential expression of three gs genes and their induction under high ammonia level probably helps in detoxification of ammonia to glutamine and further to urea via the ornithine-urea cycle in ureogenic as well as non-ureogenic tissues of these magur catfish.},
}
@article {pmid29870859,
year = {2018},
author = {Bolstad, KSR and Braid, HE and Strugnell, JM and Lindgren, AR and Lischka, A and Kubodera, T and Laptikhovsky, VL and Roura Labiaga, A},
title = {A mitochondrial phylogeny of the family Onychoteuthidae (Cephalopoda: Oegopsida).},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {88-97},
doi = {10.1016/j.ympev.2018.05.032},
pmid = {29870859},
issn = {1095-9513},
mesh = {Animals ; Cephalopoda/*classification/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; },
abstract = {The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 individuals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia); 29 genetically distinct species were recovered, with the BIN (Barcode Index Number) analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family diversity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the diversity and evolutionary relationships for the Onychoteuthidae can be achieved.},
}
@article {pmid29880721,
year = {2018},
author = {Zhang, H and Burr, SP and Chinnery, PF},
title = {The mitochondrial DNA genetic bottleneck: inheritance and beyond.},
journal = {Essays in biochemistry},
volume = {62},
number = {3},
pages = {225-234},
doi = {10.1042/EBC20170096},
pmid = {29880721},
issn = {1744-1358},
support = {101876/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UP_1501/2//Medical Research Council/United Kingdom ; G0601943//Medical Research Council/United Kingdom ; },
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Predisposition to Disease ; Humans ; Mitochondria/physiology ; Organelle Biogenesis ; Selection, Genetic ; },
abstract = {mtDNA is a multicopy genome. When mutations exist, they can affect a varying proportion of the mtDNA present within every cell (heteroplasmy). Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency seen during transmission from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be revealed. Several questions remain, including the role of selection for and against specific alleles, whether all bottlenecks are the same, and precisely how the bottleneck is controlled during development. Although originally thought to be limited to the germline, there is evidence that bottlenecks exist in other cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. Moreover, tissue-specific bottlenecks may occur throughout life in response to environmental influences, adding further complexity to the situation. Here we review key recent findings, and suggest ways forward that will hopefully advance our understanding of the role of mtDNA in human disease.},
}
@article {pmid29883862,
year = {2018},
author = {Tyagi, A and Pramanik, R and Vishnubhatla, S and Ali, S and Bakhshi, R and Chopra, A and Singh, A and Bakhshi, S},
title = {Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia.},
journal = {Mutation research},
volume = {810},
number = {},
pages = {13-18},
doi = {10.1016/j.mrfmmm.2018.05.002},
pmid = {29883862},
issn = {1873-135X},
mesh = {Adolescent ; Base Sequence ; Child ; Child, Preschool ; Cyclooxygenase 1/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I/*genetics ; Humans ; Infant ; Leukemia, Myeloid, Acute/*genetics ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Mutation Rate ; Prospective Studies ; Sequence Analysis, DNA ; },
abstract = {Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.},
}
@article {pmid29885222,
year = {2017},
author = {Rydin, C and Wikström, N and Bremer, B},
title = {Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny.},
journal = {American journal of botany},
volume = {104},
number = {10},
pages = {1522-1532},
doi = {10.3732/ajb.1700255},
pmid = {29885222},
issn = {1537-2197},
mesh = {Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Rubiaceae/*genetics ; Sequence Analysis, DNA ; },
abstract = {PREMISE OF THE STUDY: Reconstruction of plant phylogeny has heavily relied on single-gene or multigene plastid data. New sequencing methods have led to an increasing number of studies based on data from the entire plastid, but the mitochondrion has rarely been used to infer plant phylogeny because of an assumed information poverty and demonstrated lateral transfer of mitochondrial gene regions between distantly related species.<br><br>METHODS: We explored phylogenetic information from the plant mitochondrion using 57 representatives of the species-rich coffee family as study system and assessed consistency with previous results based (mostly) on plastid data.<br><br>KEY RESULTS: We showed that the mitochondrial genome can provide structured and statistically significant information on plant phylogeny. While most of our results are consistent with those based on plastid data, some surprising and statistically significant conflicts emerge, and our study demonstrates with striking clarity that the phylogeny of Rubiaceae is far from resolved.<br><br>CONCLUSIONS: It appears unlikely that conflicts between results retrieved from the different genomic compartments would be restricted to Rubiaceae. Rather, they are probably a general phenomenon and an important factor behind longstanding "difficult" phylogenetic questions. The biological processes responsible for the conflicting results detected here are unclear, but some conflicts are likely caused by hybridization events that occurred tens of millions of years ago. Whether such ancient events can be reconstructed based on molecular data from extant plants remains to be seen, but future studies of the nuclear genome may provide a way forward.},
}
@article {pmid29893915,
year = {2018},
author = {Chen, N and Wang, P and Li, C and Wang, Q and Pan, J and Xiao, F and Wang, Y and Zhang, K and Li, C and Yang, B and Sun, C and Deng, X},
title = {A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice.},
journal = {Plant &amp; cell physiology},
volume = {59},
number = {9},
pages = {1905-1917},
doi = {10.1093/pcp/pcy108},
pmid = {29893915},
issn = {1471-9053},
mesh = {Base Sequence ; Chloroplasts/*metabolism ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/metabolism ; Oryza/*genetics ; Photosynthesis/genetics/physiology ; Phylogeny ; Plant Leaves/*metabolism ; Plant Proteins/metabolism ; *Polymorphism, Single Nucleotide ; Terpenes/*metabolism ; },
abstract = {Plant isoprenoids are dependent on two independent pathways, the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. IspE is one of seven known enzymes in the MEP pathway. Currently, no IspE gene has been identified in rice. In addition, no virescent mutants have been reported to result from a gene mutation affecting the MEP pathway. In this study, we isolated a green-revertible yellow leaf mutant gry340 in rice. The mutant exhibited a reduced level of photosynthetic pigments, and an arrested development of chloroplasts and mitochondria in its yellow leaves. Map-based cloning revealed a missense mutation in OsIspE (LOC_Os01g58790) in gry340 mutant plants. OsIspE is constitutively expressed in all tissues, and its encoded protein is targeted to the chloroplast. Further, the mutant phenotype of gry340 was rescued by introduction of the wild-type gene. Therefore, we have successfully identified an IspE gene in monocotyledons via map-based cloning, and confirmed that the green-revertible yellow leaf phenotype of gry340 does result from a single nucleotide mutation in the IspE gene. In addition, the ispE ispF double mutant displayed an etiolation lethal phenotype, indicating that the isoprenoid precursors from the cytosol cannot efficiently compensate for the deficiency of the MEP pathway in rice chloroplasts. Furthermore, real-time quantitative reverse transcription-PCR suggested that this functional defect in OsIspE affected the expression of not only other MEP pathway genes but also that of MVA pathway genes, photosynthetic genes and mitochondrial genes.},
}
@article {pmid29897900,
year = {2018},
author = {Chadha, S and Vijayan, R and Gupta, S and Munde, M and Gourinath, S and Madhubala, R},
title = {Genetic manipulation of Leishmania donovani threonyl tRNA synthetase facilitates its exploration as a potential therapeutic target.},
journal = {PLoS neglected tropical diseases},
volume = {12},
number = {6},
pages = {e0006575},
pmid = {29897900},
issn = {1935-2735},
mesh = {Drug Delivery Systems ; Escherichia coli/enzymology/genetics ; Fatty Alcohols/pharmacology ; Gene Expression ; Humans ; Leishmania donovani/drug effects/*enzymology/genetics/pathogenicity ; Leishmaniasis, Visceral/*parasitology ; Organisms, Genetically Modified ; Phylogeny ; Protein Domains ; Protein Transport ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/isolation &amp; purification/metabolism ; Recombinant Proteins ; Sequence Deletion ; Threonine-tRNA Ligase/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/metabolism ; },
abstract = {BACKGROUND: Aminoacyl tRNA synthetases are central enzymes required for protein synthesis. These enzymes are the known drug targets in bacteria and fungi. Here, we for the first time report the functional characterization of threonyl tRNA synthetase (LdThrRS) of Leishmania donovani, a protozoan parasite, the primary causative agent of visceral leishmaniasis.<br><br>METHODOLOGY: Recombinant LdThrRS (rLdThrRS) was expressed in E. coli and purified. The kinetic parameters for rLdThrRS were determined. The subcellular localization of LdThrRS was done by immunofluorescence analysis. Heterozygous mutants of LdThrRS were generated in Leishmania promastigotes. These genetically manipulated parasites were checked for their proliferation, virulence, aminoacylation activity and sensitivity to the known ThrRS inhibitor, borrelidin. An in silico generated structural model of L. donovani ThrRS was compared to that of human.<br><br>CONCLUSIONS: Recombinant LdThrRS displayed aminoacylation activity, and the protein is possibly localized to both the cytosol and mitochondria. The comparison of the 3D-model of LdThrRS to human ThrRS displayed considerable similarity. Heterozygous parasites showed restrictive growth phenotype and had attenuated infectivity. These heterozygous parasites were more susceptible to inhibition by borrelidin. Several attempts to obtain ThrRS homozygous null mutants were not successful, indicating its essentiality for the Leishmania parasite. Borrelidin showed a strong affinity for LdThrRS (KD: 0.04 &#x3bc;M) and was effective in inhibiting the aminoacylation activity of the rLdThrRS (IC50: 0.06 &#x3bc;M). Borrelidin inhibited the promastigotes (IC50: 21 &#x3bc;M) stage of parasites. Our data shows that LdThrRS is essential for L. donovani survival and is likely to bind with small drug-like molecules with strong affinity, thus making it a potential target for drug discovery efforts.},
}
@article {pmid29902241,
year = {2018},
author = {Yoshino, H and Yamaji, F and Ohsawa, TA},
title = {Genetic structure and dispersal patterns in Limnoria nagatai (Limnoriidae, Isopoda) dwelling in non-buoyant kelps, Eisenia bicyclis and E. arborea, in Japan.},
journal = {PloS one},
volume = {13},
number = {6},
pages = {e0198451},
pmid = {29902241},
issn = {1932-6203},
mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Isopoda/*classification/physiology ; Japan ; Kelp/*classification/physiology ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; },
abstract = {The marine isopod genus Limnoria contains algae-eating species. Previous phylogeographic studies have suggested that Limnoria species feeding on buoyant kelp underwent low genetic differentiation on a large spatial scale because rafting on floating host kelps promotes high levels of gene flow. In this paper, we survey the genetic structure of Limnoria nagatai, which bores into the non-buoyant kelps Eisenia bicyclis and E. arborea. We analyze the mitochondrial DNA (cytochrome oxidase subunit I [COI] gene) and morphological traits of L. nagatai, and the host kelps E. bicyclis and E. arborea from 14 populations along the Japanese archipelago of the Pacific Ocean and the Sea of Japan. Four major lineages are recognized within L. nagatai: three lineages in the Pacific Ocean, and one lineage in the Sea of Japan which might be a cryptic species. For L. nagatai, we show high genetic differentiation between geographically separated habitats in the Pacific Ocean, while low differentiation is found among continuous host kelps habitats in the Pacific Ocean as well as the Sea of Japan. L. nagatai in E. bicyclis in the Pacific Ocean has experienced large population expansion after the Last Glacial Maximum (LGM), whereas the lineage in E. bicyclis in the Sea of Japan has not. We suggest that Limnoria feeding on non-buoyant kelps, may attain low genetic differentiation because they might be able to disperse long distance if the habitat of host kelps is continuous. The historical events affecting Limnoria after the LGM may differ between the coasts of the Pacific Ocean and the Sea of Japan.},
}
@article {pmid29909242,
year = {2018},
author = {Pinheiro, GMS and Ramos, CHI},
title = {Initial characterization of newly identified mitochondrial and chloroplast small HSPs from sugarcane shows that these chaperones have different oligomerization states and substrate specificities.},
journal = {Plant physiology and biochemistry : PPB},
volume = {129},
number = {},
pages = {285-294},
doi = {10.1016/j.plaphy.2018.06.002},
pmid = {29909242},
issn = {1873-2690},
mesh = {Chloroplasts/*metabolism ; Chromatography, Gel ; Cloning, Molecular ; Heat-Shock Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Saccharum/genetics/*metabolism ; Sequence Alignment ; Spectrometry, Fluorescence ; Substrate Specificity ; },
abstract = {Chaperones belonging to the small heat shock protein (sHSP) family are ubiquitous and exhibit elevated expression under stresses conditions to protect proteins against aggregation, thereby contributing to the stress tolerance of the organism. Tropical plants are constantly exposed to high temperatures, and the mechanisms by which these plants tolerate heat stress are of foremost importance to basic science as well as applied agrobiotechnology. Therefore, this study aims to characterize sHSPs from different organelles from sugarcane, an important crop that is associated with sugar and bioenergy production. An expression sequence tag database of sugarcane was searched, and sHsp genes of mitochondrial and chloroplast organelles were selected and cloned. The proteins were expressed in Escherichia coli and isolated and purified by two chromatographic steps with high purity as single species. Circular dichroism and fluorescence spectroscopy showed that both proteins were purified in their folded states with a predominant β-sheet secondary structure. Determination of the molecular weight, diffusion coefficient and Stokes radius parameters showed that both chaperones form large spherical-like oligomers in solution. The two sHSPs had different oligomeric states and substrate specificities. The mitochondrial sHSP was a 20-mer with ability to protect model substrates that differ from that of the 16-meric sHSP from chloroplasts. These results indicate that both sHSPs are key agents to protect against stress confirming the importance of the great diversity of sHSP chaperones in plants for homeostasis maintenance. Moreover, to our knowledge, this is the first report about small HSPs from sugarcane organelles.},
}
@article {pmid29916730,
year = {2018},
author = {Chang, CH and Dai, WY and Chen, TY and Lee, AH and Hou, HY and Liu, SH and Jang-Liaw, NH},
title = {DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens.},
journal = {Genome},
volume = {61},
number = {8},
pages = {615-624},
doi = {10.1139/gen-2017-0264},
pmid = {29916730},
issn = {1480-3321},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Government ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Taiwan ; Turtles/classification/*genetics ; },
abstract = {Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.},
}
@article {pmid29938587,
year = {2019},
author = {Gvozdanović, K and Margeta, V and Margeta, P and Djurkin Kušec, I and Galović, D and Dovč, P and Kušec, G},
title = {Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.},
journal = {Animal biotechnology},
volume = {30},
number = {3},
pages = {242-251},
doi = {10.1080/10495398.2018.1478847},
pmid = {29938587},
issn = {1532-2378},
mesh = {Animals ; Breeding ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency ; *Genetic Variation ; Haplotypes ; Male ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Sus scrofa ; Swine/*genetics ; },
abstract = {The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.},
}
@article {pmid29942045,
year = {2018},
author = {Li, D and Waite, DW and Fan, QH and George, S and Semeraro, L and Blacket, MJ},
title = {Molecular detection of small hive beetle Aethina tumida Murray (Coleoptera: Nitidulidae): DNA barcoding and development of a real-time PCR assay.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {9623},
pmid = {29942045},
issn = {2045-2322},
mesh = {Animals ; *Bees ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; *Real-Time Polymerase Chain Reaction ; },
abstract = {Small hive beetle (SHB), Aethina tumida can feed on honey, pollen and brood in honey bee colonies. It was endemic to Africa, but since 1996 has been detected in a number of countries worldwide, including Australia, Brazil, Canada, Italy, Mexico, South Korea, Philippines and the USA where it has had economic effects on local apiculture. To improve SHB identification, we obtained the first reference sequences from the DNA barcoding 5' COI gene region for SHB and some species of the family Nitidulidae associated with beehives. Phylogenetic analysis of SHB COI sequences (3' COI) revealed two divergent lineages, with those from Australia and USA being genetically different from the recent detection in Italy. Many countries, including New Zealand, are currently free from SHB, and require a rapid detection method for biosecurity. Here we present the development and validation of a real-time PCR assay for detection of SHB. The assay showed high specificity and sensitivity for detecting SHB, with no cross-reaction observed with closely related species, such as A. concolor. The real-time PCR is sensitive, detecting the target sequences up to 100 copies/µL. This assay should prove a useful biosecurity tool for rapid detection of SHB worldwide.},
}
@article {pmid29945242,
year = {2018},
author = {Buchanan, JL and Meiklejohn, CD and Montooth, KL},
title = {Mitochondrial Dysfunction and Infection Generate Immunity-Fecundity Tradeoffs in Drosophila.},
journal = {Integrative and comparative biology},
volume = {58},
number = {3},
pages = {591-603},
pmid = {29945242},
issn = {1557-7023},
support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Drosophila melanogaster/genetics/*physiology ; Drosophila simulans/genetics/*physiology ; Female ; Fertility ; *Genotype ; Hybridization, Genetic ; Immunity, Innate ; *Life History Traits ; Male ; Mitochondria/*physiology ; Nutritional Status ; Oxidative Phosphorylation ; Stress, Physiological ; },
abstract = {Physiological responses to short-term environmental stressors, such as infection, can have long-term consequences for fitness, particularly if the responses are inappropriate or nutrient resources are limited. Genetic variation affecting energy acquisition, storage, and usage can limit cellular energy availability and may influence resource-allocation tradeoffs even when environmental nutrients are plentiful. Here, we utilized Drosophila mitochondrial-nuclear genotypes to test whether disrupted mitochondrial function interferes with nutrient-sensing pathways, and whether this disruption has consequences for tradeoffs between immunity and fecundity. We found that an energetically-compromised genotype was relatively resistant to rapamycin-a drug that targets nutrient-sensing pathways and mimics resource limitation. Dietary resource limitation decreased survival of energetically-compromised flies. Furthermore, survival of infection with a natural pathogen was decreased in this genotype, and females of this genotype experienced immunity-fecundity tradeoffs that were not evident in genotypic controls with normal energy metabolism. Together, these results suggest that this genotype may have little excess energetic capacity and fewer cellular nutrients, even when environmental nutrients are not limiting. Genetic variation in energy metabolism may therefore act to limit the resources available for allocation to life-history traits in ways that generate tradeoffs even when environmental resources are not limiting.},
}
@article {pmid29948332,
year = {2018},
author = {van der Sluis, R},
title = {Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B.},
journal = {Molecular genetics and genomics : MGG},
volume = {293},
number = {5},
pages = {1279-1292},
pmid = {29948332},
issn = {1617-4623},
support = {Self-Initiated research grant//South African Medical Research Council/ ; 99323//National Research Foundation/ ; },
mesh = {Coenzyme A Ligases/*genetics/metabolism ; *Genetic Variation ; Glycine/metabolism ; *Haplotypes ; Humans ; Mitochondria, Liver/*enzymology ; Phylogeny ; Substrate Specificity ; Xenobiotics/*metabolism ; },
abstract = {Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.},
}
@article {pmid29949074,
year = {2018},
author = {Zhang, R and Wang, X},
title = {Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae).},
journal = {Genes &amp; genomics},
volume = {40},
number = {10},
pages = {1033-1040},
pmid = {29949074},
issn = {2092-9293},
mesh = {Animals ; Base Composition ; Contig Mapping ; Cyprinidae/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.},
}
@article {pmid29955026,
year = {2018},
author = {Liu, SY and He, K and Chen, SD and Jin, W and Murphy, RW and Tang, MK and Liao, R and Li, FJ},
title = {How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.},
journal = {Zoological research},
volume = {39},
number = {5},
pages = {309-320},
pmid = {29955026},
issn = {2095-8137},
mesh = {Animals ; China ; Cytochromes b/*genetics ; Mitochondria/*genetics ; Murinae/anatomy &amp; histology/*genetics ; Phylogeny ; Rats/anatomy &amp; histology/*genetics ; Skull/anatomy &amp; histology ; Surveys and Questionnaires ; Tooth/anatomy &amp; histology ; },
abstract = {Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.},
}
@article {pmid29967381,
year = {2018},
author = {Pietras, Z and Wojcik, MA and Borowski, LS and Szewczyk, M and Kulinski, TM and Cysewski, D and Stepien, PP and Dziembowski, A and Szczesny, RJ},
title = {Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {2558},
pmid = {29967381},
issn = {2041-1723},
support = {UMO-2014/12/W/NZ1/00463 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2014/13/D/NZ2/01114 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2013/11/13/NZ1/00089 to PPS//Narodowe Centrum Nauki (National Science Centre)/International ; 309419 PAPs &amp; PUPs to AD//EC | European Research Council (ERC)/International ; },
mesh = {Animals ; DEAD-box RNA Helicases/metabolism ; Endoribonucleases/metabolism ; Exoribonucleases/genetics/metabolism ; *G-Quadruplexes ; Genome, Mitochondrial/*genetics ; HEK293 Cells ; HeLa Cells ; Humans ; Mitochondria/genetics/*metabolism ; Multienzyme Complexes/metabolism ; Phylogeny ; Poly(A)-Binding Proteins/genetics/*metabolism ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA Helicases/metabolism ; RNA, Small Interfering/metabolism ; RNA, Untranslated/genetics/*metabolism ; Mitochondrial Proteins ; },
abstract = {The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.},
}
@article {pmid29986214,
year = {2018},
author = {Angers, B and Chapdelaine, V and Deremiens, L and Vergilino, R and Leung, C and Doucet, SL and Glémet, H and Angers, A},
title = {Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {27},
number = {},
pages = {77-84},
doi = {10.1016/j.cbd.2018.06.007},
pmid = {29986214},
issn = {1878-0407},
mesh = {Animals ; Cell Nucleus/genetics ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Epigenesis, Genetic ; Female ; *Gene Flow ; Genetic Speciation ; Male ; Mitochondria/genetics ; Sympatry ; },
abstract = {Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.},
}
@article {pmid30005062,
year = {2018},
author = {Salunke, R and Mourier, T and Banerjee, M and Pain, A and Shanmugam, D},
title = {Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii.},
journal = {PLoS biology},
volume = {16},
number = {7},
pages = {e2006128},
pmid = {30005062},
issn = {1545-7885},
mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Gene Expression Regulation ; Genetic Variation ; Hemagglutinins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proton-Translocating ATPases/*metabolism ; Parasites/metabolism ; Phylogeny ; Plasmodium falciparum/metabolism ; Protein Multimerization ; Protein Subunits/*metabolism ; Proteome/metabolism ; Proteomics ; Protozoan Proteins/chemistry/isolation &amp; purification/metabolism ; Recombinant Fusion Proteins/metabolism ; Toxoplasma/*enzymology ; },
abstract = {The mitochondrial F-type ATP synthase, a multisubunit nanomotor, is critical for maintaining cellular ATP levels. In T. gondii and other apicomplexan parasites, many subunit components necessary for proper assembly and functioning of this enzyme appear to be missing. Here, we report the identification of 20 novel subunits of T. gondii F-type ATP synthase from mass spectrometry analysis of partially purified monomeric (approximately 600 kDa) and dimeric (>1 MDa) forms of the enzyme. Despite extreme sequence diversification, key FO subunits a, b, and d can be identified from conserved structural features. Orthologs for these proteins are restricted to apicomplexan, chromerid, and dinoflagellate species. Interestingly, their absence in ciliates indicates a major diversion, with respect to subunit composition of this enzyme, within the alveolate clade. Discovery of these highly diversified novel components of the apicomplexan F-type ATP synthase complex could facilitate the development of novel antiparasitic agents. Structural and functional characterization of this unusual enzyme complex will advance our fundamental understanding of energy metabolism in apicomplexan species.},
}
@article {pmid30017823,
year = {2018},
author = {Chesser, RT and Vaseghi, H and Hosner, PA and Bergner, LM and Cortes-Rodriguez, MN and Welch, AJ and Collins, CT},
title = {Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae).},
journal = {Molecular phylogenetics and evolution},
volume = {128},
number = {},
pages = {162-171},
doi = {10.1016/j.ympev.2018.07.006},
pmid = {30017823},
issn = {1095-9513},
mesh = {Animals ; Birds/*classification ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; North America ; Panama ; Phylogeny ; Seasons ; South America ; Species Specificity ; },
abstract = {Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura. Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura. We recommend that C. viridipennis, currently generally treated as specifically distinct from C. chapmani, be returned to its former status as C. chapmani viridipennis, and that C. andrei, now generally regarded as synonymous with C. vauxi aphanes, again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa, C. egregia, and C. martinica. Geographically structured genetic variation within some other species of Chaetura, especially notable in C. cinereiventris, suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.},
}
@article {pmid30021129,
year = {2018},
author = {Sun, S and Sha, Z and Wang, Y},
title = {Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea.},
journal = {Gene},
volume = {676},
number = {},
pages = {123-138},
doi = {10.1016/j.gene.2018.07.026},
pmid = {30021129},
issn = {1879-0038},
mesh = {Animals ; Base Composition ; Decapoda/*genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry ; RNA, Mitochondrial ; Sequence Analysis, DNA/*methods ; },
abstract = {Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78-144 Mya).},
}
@article {pmid30032461,
year = {2018},
author = {Sylvester, C and Krishna, MS and Rao, JS and Chandrasekar, A},
title = {Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India.},
journal = {Genetica},
volume = {146},
number = {4-5},
pages = {383-389},
pmid = {30032461},
issn = {1573-6857},
mesh = {Asian People/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; India/ethnology ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.},
}
@article {pmid30063873,
year = {2019},
author = {Kumar Jadav, K and Pratap Singh, A and Srivastav, AB and Sarkhel, BC},
title = {Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus).},
journal = {Animal biotechnology},
volume = {30},
number = {2},
pages = {186-191},
doi = {10.1080/10495398.2018.1469506},
pmid = {30063873},
issn = {1532-2378},
mesh = {Animals ; Breeding ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Sus scrofa/*genetics ; },
abstract = {The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251 bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European-American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.},
}
@article {pmid30071011,
year = {2018},
author = {Grinter, R and Hay, ID and Song, J and Wang, J and Teng, D and Dhanesakaran, V and Wilksch, JJ and Davies, MR and Littler, D and Beckham, SA and Henderson, IR and Strugnell, RA and Dougan, G and Lithgow, T},
title = {FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.},
journal = {PLoS biology},
volume = {16},
number = {8},
pages = {e2006026},
pmid = {30071011},
issn = {1545-7885},
support = {106077/Z/14/Z//Wellcome Trust/United Kingdom ; },
mesh = {Bacteria/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/metabolism ; Ferredoxins/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/*metabolism ; Metalloendopeptidases/metabolism ; Pectobacterium/*metabolism ; Phylogeny ; Plant Proteins/metabolism ; Plants/metabolism ; Protein Transport/physiology ; Mitochondrial Processing Peptidase ; },
abstract = {Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Reports of iron-bearing proteins being used as a source of iron indicate specific protein import reactions across the bacterial outer membrane. The molecular mechanism by which a folded protein can be imported in this way had remained mysterious, as did the evolutionary process that could lead to such a protein import pathway. How does the bacterium evolve the specificity factors that would be required to select and import a protein encoded on another organism's genome? We describe here a model whereby the plant iron-bearing protein ferredoxin can be imported across the outer membrane of the plant pathogen Pectobacterium by means of a Brownian ratchet mechanism, thereby liberating iron into the bacterium to enable its growth in plant tissues. This import pathway is facilitated by FusC, a member of the same protein family as the mitochondrial processing peptidase (MPP). The Brownian ratchet depends on binding sites discovered in crystal structures of FusC that engage a linear segment of the plant protein ferredoxin. Sequence relationships suggest that the bacterial gene encoding FusC has previously unappreciated homologues in plants and that the protein import mechanism employed by the bacterium is an evolutionary echo of the protein import pathway in plant mitochondria and plastids.},
}
@article {pmid30071112,
year = {2018},
author = {Caza, M and Hu, G and Nielson, ED and Cho, M and Jung, WH and Kronstad, JW},
title = {The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungus Cryptococcus neoformans.},
journal = {PLoS pathogens},
volume = {14},
number = {8},
pages = {e1007220},
pmid = {30071112},
issn = {1553-7374},
support = {R01 AI053721/AI/NIAID NIH HHS/United States ; MOP13234/CAPMC/CIHR/Canada ; },
mesh = {Animals ; Biological Transport ; Cryptococcosis/metabolism/microbiology/pathology ; *Cryptococcus neoformans/genetics/metabolism/pathogenicity ; Female ; Fungal Proteins/*physiology ; Iron/*metabolism ; Mice ; Mice, Inbred BALB C ; Mitochondria/*physiology ; Organisms, Genetically Modified ; Phylogeny ; Virulence/*genetics ; Virulence Factors/genetics/*physiology ; },
abstract = {The battle for iron between invading microorganisms and mammalian hosts is a pivotal determinant of the outcome of infection. The pathogenic fungus, Cryptococcus neoformans, employs multiple mechanisms to compete for iron during cryptococcosis, a disease primarily of immunocompromised hosts. In this study, we examined the role of endocytic trafficking in iron uptake by characterizing a mutant defective in the Sec1/Munc18 (SM) protein Vps45. This protein is known to regulate the machinery for vesicle trafficking and fusion via interactions with SNARE proteins. As expected, a vps45 deletion mutant was impaired in endocytosis and showed sensitivity to trafficking inhibitors. The mutant also showed poor growth on iron-limited media and a defect in transporting the Cfo1 ferroxidase of the high-affinity iron uptake system from the plasma membrane to the vacuole. Remarkably, we made the novel observation that Vps45 also contributes to mitochondrial function in that a Vps45-Gfp fusion protein associated with mitotracker, and a vps45 mutant showed enhanced sensitivity to inhibitors of electron transport complexes as well as changes in mitochondrial membrane potential. Consistent with mitochondrial function, the vps45 mutant was impaired in calcium homeostasis. To assess the relevance of these defects for virulence, we examined cell surface properties of the vps45 mutant and found increased sensitivity to agents that challenge cell wall integrity and to antifungal drugs. A change in cell wall properties was consistent with our observation of altered capsule polysaccharide attachment, and with attenuated virulence in a mouse model of cryptococcosis. Overall, our studies reveal a novel role for Vps45-mediated trafficking for iron uptake, mitochondrial function and virulence.},
}
@article {pmid30074999,
year = {2018},
author = {Brew-Appiah, RAT and York, ZB and Krishnan, V and Roalson, EH and Sanguinet, KA},
title = {Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat.},
journal = {PloS one},
volume = {13},
number = {8},
pages = {e0201439},
pmid = {30074999},
issn = {1932-6203},
mesh = {Aegilops/*genetics ; Diploidy ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/physiology ; Genes, Plant/*genetics ; Genome, Plant/genetics ; Herbicide Resistance/genetics ; Mitochondrial Proteins/*genetics ; Multigene Family/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Polyploidy ; Stress, Physiological/physiology ; Triticum/genetics/*physiology ; Whole Genome Sequencing ; Alternative Oxidase ; },
abstract = {A comprehensive understanding of wheat responses to environmental stress will contribute to the long-term goal of feeding the planet. ALERNATIVE OXIDASE (AOX) genes encode proteins involved in a bypass of the electron transport chain and are also known to be involved in stress tolerance in multiple species. Here, we report the identification and characterization of the AOX gene family in diploid and hexaploid wheat. Four genes each were found in the diploid ancestors Triticum urartu, and Aegilops tauschii, and three in Aegilops speltoides. In hexaploid wheat (Triticum aestivum), 20 genes were identified, some with multiple splice variants, corresponding to a total of 24 proteins for those with observed transcription and translation. These proteins were classified as AOX1a, AOX1c, AOX1e or AOX1d via phylogenetic analysis. Proteins lacking most or all signature AOX motifs were assigned to putative regulatory roles. Analysis of protein-targeting sequences suggests mixed localization to the mitochondria and other organelles. In comparison to the most studied AOX from Trypanosoma brucei, there were amino acid substitutions at critical functional domains indicating possible role divergence in wheat or grasses in general. In hexaploid wheat, AOX genes were expressed at specific developmental stages as well as in response to both biotic and abiotic stresses such as fungal pathogens, heat and drought. These AOX expression patterns suggest a highly regulated and diverse transcription and expression system. The insights gained provide a framework for the continued and expanded study of AOX genes in wheat for stress tolerance through breeding new varieties, as well as resistance to AOX-targeted herbicides, all of which can ultimately be used synergistically to improve crop yield.},
}
@article {pmid30075756,
year = {2018},
author = {Burke, SV and Ungerer, MC and Duvall, MR},
title = {Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae).},
journal = {BMC plant biology},
volume = {18},
number = {1},
pages = {152},
pmid = {30075756},
issn = {1471-2229},
support = {DEB-1120856//National Science Foundation/ ; DEB-1120761//National Science Foundation/ ; },
mesh = {DNA, Intergenic/genetics ; DNA, Plant/genetics ; Mitochondria/*genetics ; Paspalum/*genetics ; Phylogeny ; Plastids/*genetics ; Poaceae/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {BACKGROUND: The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae.<br><br>RESULTS: Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6&#xa0;Ma, with the insert arising at 8.7&#xa0;Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA.<br><br>CONCLUSIONS: A hypothetical ancestral insert, 17,685&#xa0;bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808&#xa0;bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.},
}
@article {pmid30076323,
year = {2018},
author = {Duong, NT and Macholdt, E and Ton, ND and Arias, L and Schröder, R and Van Phong, N and Thi Bich Thuy, V and Ha, NH and Thi Thu Hue, H and Thi Xuan, N and Thi Phuong Oanh, K and Hien, LTT and Hoang, NH and Pakendorf, B and Stoneking, M and Van Hai, N},
title = {Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {11651},
pmid = {30076323},
issn = {2045-2322},
mesh = {Asia, Southeastern ; Asian People/genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; *Genetics, Population ; Haplotypes ; Humans ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Taiwan ; Whole Genome Sequencing ; },
abstract = {Vietnam is an important crossroads within Mainland Southeast Asia (MSEA) and a gateway to Island Southeast Asia, and as such exhibits high levels of ethnolinguistic diversity. However, comparatively few studies have been undertaken of the genetic diversity of Vietnamese populations. In order to gain comprehensive insights into MSEA mtDNA phylogeography, we sequenced 609 complete mtDNA genomes from individuals belonging to five language families (Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian) and analyzed them in comparison with sequences from other MSEA countries and Taiwan. Within Vietnam, we identified 399 haplotypes belonging to 135 haplogroups; among the five language families, the sequences from Austronesian groups differ the most from the other groups. Phylogenetic analysis revealed 111 novel Vietnamese mtDNA lineages. Bayesian estimates of coalescence times and associated 95% HPD for these show a peak of mtDNA diversification around 2.5-3 kya, which coincides with the Dong Son culture, and thus may be associated with the agriculturally-driven expansion of this culture. Networks of major MSEA haplogroups emphasize the overall distinctiveness of sequences from Taiwan, in keeping with previous studies that suggested at most a minor impact of the Austronesian expansion from Taiwan on MSEA. We also see evidence for population expansions across MSEA geographic regions and language families.},
}
@article {pmid30097722,
year = {2018},
author = {Ding, CQ and Ng, S and Wang, L and Wang, YC and Li, NN and Hao, XY and Zeng, JM and Wang, XC and Yang, YJ},
title = {Genome-wide identification and characterization of ALTERNATIVE OXIDASE genes and their response under abiotic stresses in Camellia sinensis (L.) O. Kuntze.},
journal = {Planta},
volume = {248},
number = {5},
pages = {1231-1247},
pmid = {30097722},
issn = {1432-2048},
support = {1610212017003//Central Public-interest Scientific Institution Basal Research Fund/ ; CARS-19//Earmarked Fund for China Agriculture Research System/ ; 2016C02053-4//The Major Project of Agricultural Science and Technology in Breeding of Tea Plant Variety in Zhejiang Province/ ; ALTF1239-2015//European Molecular Biology Organization/ ; LTFCOFUND2013//FP PEOPLE: Marie cutie actions/ ; GA-2013-609409//FP PEOPLE: Marie cutie actions/ ; },
mesh = {Camellia sinensis/enzymology/*genetics/physiology ; Cloning, Molecular ; Conserved Sequence/genetics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Mitochondrial Proteins/*genetics/physiology ; Oxidoreductases/*genetics/physiology ; Phylogeny ; Plant Proteins/*genetics/physiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Physiological ; Transcriptome ; Alternative Oxidase ; },
abstract = {Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L.) O. Kuntze cv. Longjing43). Our results showed that tea plant possesses four AOX genes, i.e., CsAOX1a, CsAOX1d, CsAOX2a and CsAOX2b. Gene structure and protein sequence analyses revealed that all CsAOXs share a four-exon/three-intron structure with highly conserved regions and amino acid residues, which are necessary for AOX secondary structures, catalytic activities and post-translational regulations. All CsAOX were shown to localize in mitochondria using the green fluorescent protein (GFP)-targeting assay. Both CsAOX1a and CsAOX1d were induced by cold, salt and drought stresses, and with different expression patterns in young and mature leaves. Reactive oxygen species (ROS) accumulated strongly after 72 and 96 h cold treatments in both young and mature leaves, while the polyphenol and total catechin decreased significantly only in mature leaves. In comparison to AtAOX1a in Arabidopsis thaliana, CsAOX1a lost almost all of the stress-responsive cis-acting regulatory elements in its promoter region (1500 bp upstream), but possesses a flavonoid biosynthesis-related MBSII cis-acting regulatory element. These results suggest a link between CsAOX1a function and the metabolism of some secondary metabolites in tea plant. Our studies provide a basis for the further elucidation of the biological function and regulation of the AOX pathway in tea plants.},
}
@article {pmid30102371,
year = {2018},
author = {Hillebrand, A and Matz, JM and Almendinger, M and Müller, K and Matuschewski, K and Schmitz-Linneweber, C},
title = {Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite.},
journal = {Nucleic acids research},
volume = {46},
number = {19},
pages = {10417-10431},
pmid = {30102371},
issn = {1362-4962},
mesh = {Chloroplasts/genetics ; Genome/genetics ; Malaria, Falciparum/*genetics/parasitology ; Mitochondria/chemistry/genetics ; Organelles/*genetics ; Peptides/chemistry/genetics ; Phylogeny ; Plasmodium falciparum/*genetics/pathogenicity ; RNA, Ribosomal/chemistry/genetics ; RNA-Binding Proteins/chemistry/*genetics ; Ribosomes/chemistry/genetics ; },
abstract = {Gene expression in mitochondria of Plasmodium falciparum is essential for parasite survival. The molecular mechanisms of Plasmodium organellar gene expression remain poorly understood. This includes the enigmatic assembly of the mitochondrial ribosome from highly fragmented rRNAs. Here, we present the identification of clustered organellar short RNA fragments (cosRNAs) that are possible footprints of RNA-binding proteins (RBPs) in Plasmodium organelles. In plants, RBPs of the pentatricopeptide repeat (PPR) class produce footprints as a consequence of their function in processing organellar RNAs. Intriguingly, many of the Plasmodium cosRNAs overlap with 5'-ends of rRNA fragments. We hypothesize that these are footprints of RBPs involved in assembling the rRNA fragments into a functioning ribosome. A bioinformatics search of the Plasmodium nuclear genome identified a hitherto unrecognized organellar helical-hairpin-repeat protein family that we term heptatricopeptide repeat (HPR) proteins. We demonstrate that selected HPR proteins are targeted to mitochondria in P. berghei and that one of them, PbHPR1, associates with RNA, but not DNA in vitro. A phylogenetic search identified HPR proteins in a wide variety of eukaryotes. We hypothesize that HPR proteins are required for processing and stabilizing RNAs in Apicomplexa and other taxa.},
}
@article {pmid30102976,
year = {2018},
author = {Baron, S and van der Merwe, NA and Maritz-Olivier, C},
title = {The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure.},
journal = {Molecular phylogenetics and evolution},
volume = {129},
number = {},
pages = {60-69},
doi = {10.1016/j.ympev.2018.08.003},
pmid = {30102976},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cattle ; Cell Nucleus/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Geography ; Likelihood Functions ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Rhipicephalus/classification/*genetics ; South Africa ; },
abstract = {Rhipicephalus microplus and R. decoloratus are one-host ticks that preferentially feed on cattle. They are capable of transmitting various tick-borne pathogens which may be detrimental to the agricultural and livestock industry in South Africa. Previous studies have shown that R. microplus forms five lineages in the R. microplus complex, segregating into different geographical areas based on mitochondrial markers. This study examined the phylogenetic relationship within and between R. microplus and R. decoloratus using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The results showed that the nuclear ITS2 marker is informative for interspecific variation but lacks the resolution for intraspecific variation. Analysis of the mitochondrial COI gene revealed that R. microplus ticks from South Africa grouped into a clade comprised of ticks from Asia and South America. The population structure of these two tick species was also investigated using novel microsatellite markers. Population structure analyses revealed that both the R. microplus and R. decoloratus populations presented with two genetic clusters. Rhipicephalus microplus ticks from the Kwa-Zulu Natal (KZN) province belonged to cluster 1, and those from the Eastern Cape (EC) province predominantly grouped into cluster 2. No observable population structure was noted for R. decoloratus. The overlap of genetic clusters in both species could be attributed to inbreeding between the regions by unrestricted movement of cattle across provinces. Such movement promotes tick mobility, gene flow and the homogenisation of tick populations.},
}
@article {pmid30107223,
year = {2018},
author = {Reyes-Ramos, CA and Peregrino-Uriarte, AB and Cota-Ruiz, K and Valenzuela-Soto, EM and Leyva-Carrillo, L and Yepiz-Plascencia, G},
title = {Phosphoenolpyruvate carboxykinase cytosolic and mitochondrial isoforms are expressed and active during hypoxia in the white shrimp Litopenaeus vannamei.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {226},
number = {},
pages = {1-9},
doi = {10.1016/j.cbpb.2018.08.001},
pmid = {30107223},
issn = {1879-1107},
mesh = {Amino Acid Sequence ; Animals ; Aquaculture ; Conserved Sequence ; Cytosol/*enzymology/metabolism ; Databases, Protein ; *Gene Expression Regulation, Developmental ; Gills/enzymology/growth &amp; development/metabolism ; Hepatopancreas/enzymology/growth &amp; development/metabolism ; Hypoxia/*enzymology/metabolism ; Isoenzymes/genetics/metabolism ; Mitochondria/*enzymology/metabolism ; Muscle, Skeletal/enzymology/growth &amp; development/metabolism ; Organ Specificity ; Penaeidae/growth &amp; development/*physiology ; Phosphoenolpyruvate Carboxykinase (GTP)/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {Hypoxic zones in marine environments are spreading around the world affecting the survival of many organisms. Marine animals have several strategies to respond to hypoxia, including the regulation of gluconeogenesis. Phosphoenolpyruvate carboxykinase (PEPCK) is a key regulatory enzyme of gluconeogenesis. The objective of this work was to study two isoforms of PEPCK, one mitochondrial (PEPKC-M) and one cytosolic (PEPCK-C), from the white shrimp Litopenaeus vannamei and the response to hypoxia. Both PEPCK isoforms are 72 kDa proteins and have 92% identity at the amino acid level. The mitochondrial isoform has a N-terminal signal peptide for mitochondrial import. Gene expression and enzymatic activity in subcellular fractions were detected in gills, hepatopancreas and muscle in normoxic and hypoxic conditions. Expression of PEPCK-C was higher than PEPCK-M in all the tissues and induced in response to hypoxia at 48 h in hepatopancreas, while the enzymatic activity of PEPCK-M was higher than PEPCK-C in gills and hepatopancreas, but not in muscle and also increased in response to hypoxia in hepatopancreas but decreased in gills and muscle. During limiting oxygen conditions, shrimp tissues obtain energy by inducing anaerobic glycolysis, and although gluconeogenesis implies energy investment, due to the need to maintain glucose homeostasis, these gluconeogenic enzymes are active with contrasting behaviors in the cytosol and mitochondrial cell compartments and appear to be up-regulated in hepatopancreas indicating this tissue pivotal role in gluconeogenesis during the response to hypoxia.},
}
@article {pmid30138782,
year = {2018},
author = {Treitli, SC and Kotyk, M and Yubuki, N and Jirounková, E and Vlasáková, J and Smejkalová, P and Šípek, P and Čepička, I and Hampl, V},
title = {Molecular and Morphological Diversity of the Oxymonad Genera Monocercomonoides and Blattamonas gen. nov.},
journal = {Protist},
volume = {169},
number = {5},
pages = {744-783},
doi = {10.1016/j.protis.2018.06.005},
pmid = {30138782},
issn = {1618-0941},
mesh = {Genetic Variation ; Microscopy, Electron ; Oxymonadida/*genetics/*growth &amp; development/ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Oxymonads are a group of flagellates living as gut symbionts of insects or vertebrates. They have several unique features, one of them being the absence of mitochondria. Diversity of this group is seriously understudied, which is particularly true for small species from the family Polymastigidae. We isolated 34 strains of oxymonads with Polymastigidae-like morphology from 24 host species and unused cesspits and sequenced the SSU rRNA gene. Our strains formed two clades in the phylogenetic tree with Streblomastix strix branching between them. This topology was also supported by a three-gene phylogenetic analysis. Despite considerable genetic differences between the clades, light and electron microscopy revealed only subtle differences. The larger clade is considered genus Monocercomonoides and the isolates belonging here were classified into three new species (including the first potentially free-living species), two previously described species, and three unclassified lineages. The smaller clade, here described as Blattamonas gen. nov., consists of three newly described species. Concomitantly with the description of Blattamonas, we elevate the Monocercomonoides subgenus Brachymonas to the genus level. Our study shows that, despite their conserved morphology, the molecular diversity of Polymastigidae-like oxymonads is broad and represents a substantial part of the diversity of oxymonads.},
}
@article {pmid30158483,
year = {2018},
author = {Kozieł, E and Otulak-Kozieł, K and Bujarski, JJ},
title = {Ultrastructural Analysis of Prune DwarfVirus Intercellular Transport and Pathogenesis.},
journal = {International journal of molecular sciences},
volume = {19},
number = {9},
pages = {},
pmid = {30158483},
issn = {1422-0067},
support = {505-10-011100-Q00190-99//Warsaw Univeristy of Life Sciences WULS-SGGW/ ; },
mesh = {Alfalfa mosaic virus/genetics/*pathogenicity/*ultrastructure ; Biological Transport/genetics/physiology ; Phylogeny ; RNA, Viral ; Viral Proteins/metabolism/ultrastructure ; },
abstract = {Prune dwarf virus (PDV) is an important viral pathogen of plum, sweet cherry, peach, and many herbaceous test plants. Although PDV has been intensively investigated, mainly in the context of phylogenetic relationship of its genes and proteins, many gaps exist in our knowledge about the mechanism of intercellular transport of this virus. The aim of this work was to investigate alterations in cellular organelles and the cell-to-cell transport of PDV in Cucumis sativus cv. Polan at ultrastructural level. To analyze the role of viral proteins in local transport, double-immunogold assays were applied to localize PDV coat protein (CP) and movement protein (MP). We observe structural changes in chloroplasts, mitochondria, and cellular membranes. We prove that PDV is transported as viral particles via MP-generated tubular structures through plasmodesmata. Moreover, the computer-run 3D modeling reveals structural resemblances between MPs of PDV and of Alfalfa mosaic virus (AMV), implying similarities of transport mechanisms for both viruses.},
}
@article {pmid30160146,
year = {2018},
author = {Goh, CJ and Park, D and Kim, H and Sebastiani, F and Hahn, Y},
title = {Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum).},
journal = {Acta virologica},
volume = {62},
number = {3},
pages = {304-309},
doi = {10.4149/av_2018_224},
pmid = {30160146},
issn = {0001-723X},
mesh = {Flexiviridae/classification/genetics/*isolation &amp; purification/physiology ; Genome, Viral ; Ocimum basilicum/*virology ; Phylogeny ; Plant Diseases/*virology ; RNA-Dependent RNA Polymerase/genetics ; Viral Proteins/genetics ; },
abstract = {Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.},
}
@article {pmid30165810,
year = {2018},
author = {Galen, SC and Nunes, R and Sweet, PR and Perkins, SL},
title = {Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {128},
pmid = {30165810},
issn = {1471-2148},
support = {1358465//National Science Foundation/International ; },
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Loci ; *Genetic Variation ; Haemosporida/*genetics ; Haplotypes/genetics ; *Host Specificity ; Malaria/*parasitology ; Mitochondria/*genetics ; Parasites/*genetics ; Phylogeny ; Songbirds/parasitology ; Species Specificity ; },
abstract = {BACKGROUND: Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska.<br><br>RESULTS: We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~&#x2009;0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization.<br><br>CONCLUSION: Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.},
}
@article {pmid30166340,
year = {2018},
author = {Valach, M and Léveillé-Kunst, A and Gray, MW and Burger, G},
title = {Respiratory chain Complex I of unparalleled divergence in diplonemids.},
journal = {The Journal of biological chemistry},
volume = {293},
number = {41},
pages = {16043-16056},
pmid = {30166340},
issn = {1083-351X},
support = {MOP-79309//CIHR/Canada ; },
mesh = {DNA, Mitochondrial/*metabolism ; Electron Transport ; Electron Transport Complex I/*metabolism ; Euglenozoa/*genetics/*metabolism ; Mass Spectrometry ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; NADH Dehydrogenase/metabolism ; Phenylalanine/chemistry ; Phylogeny ; Protons ; RNA Editing ; RNA Splicing ; Ubiquinone/chemistry ; },
abstract = {Mitochondrial genes of Euglenozoa (Kinetoplastida, Diplonemea, and Euglenida) are notorious for being barely recognizable, raising the question of whether such divergent genes actually code for functional proteins. Here we demonstrate the translation and identify the function of five previously unassigned y genes encoded by mitochondrial DNA (mtDNA) of diplonemids. As is the rule in diplonemid mitochondria, y genes are fragmented, with gene pieces transcribed separately and then trans-spliced to form contiguous mRNAs. Further, y transcripts undergo massive RNA editing, including uridine insertions that generate up to 16-residue-long phenylalanine tracts, a feature otherwise absent from conserved mitochondrial proteins. By protein sequence analyses, MS, and enzymatic assays in Diplonema papillatum, we show that these y genes encode the subunits Nad2, -3, -4L, -6, and -9 of the respiratory chain Complex I (CI; NADH:ubiquinone oxidoreductase). The few conserved residues of these proteins are essentially those involved in proton pumping across the inner mitochondrial membrane and in coupling ubiquinone reduction to proton pumping (Nad2, -3, -4L, and -6) and in interactions with subunits containing electron-transporting Fe-S clusters (Nad9). Thus, in diplonemids, 10 CI subunits are mtDNA-encoded. Further, MS of D. papillatum CI allowed identification of 26 conventional and 15 putative diplonemid-specific nucleus-encoded components. Most conventional accessory subunits are well-conserved but unusually long, possibly compensating for the streamlined mtDNA-encoded components and for missing, otherwise widely distributed, conventional subunits. Finally, D. papillatum CI predominantly exists as a supercomplex I:III:IV that is exceptionally stable, making this protist an organism of choice for structural studies.},
}
@article {pmid30172009,
year = {2018},
author = {Pavón-Vázquez, CJ and García-Vázquez, UO and Bryson, RW and Feria-Ortiz, M and Manríquez-Morán, NL and de Oca, AN},
title = {Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae).},
journal = {Molecular phylogenetics and evolution},
volume = {129},
number = {},
pages = {242-257},
doi = {10.1016/j.ympev.2018.08.020},
pmid = {30172009},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Loci ; Geography ; Lizards/*classification/genetics ; Mexico ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Species Specificity ; Time Factors ; },
abstract = {Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.},
}
@article {pmid30176793,
year = {2018},
author = {Yin, M and Wang, X and Ma, X and Gießler, S and Petrusek, A and Griebel, J and Hu, W and Wolinska, J},
title = {Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres.},
journal = {BMC evolutionary biology},
volume = {18},
number = {1},
pages = {130},
pmid = {30176793},
issn = {1471-2148},
support = {31670380//National Natural Science Foundation of China/International ; 16ZR1402900//Natural Science Foundation of Shanghai/International ; WO 1587/6-1//German Science Foundation/International ; },
mesh = {Alleles ; Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; China ; DNA/genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Europe ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/*genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Zooplankton/genetics ; },
abstract = {BACKGROUND: The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci.<br><br>RESULTS: Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe.<br><br>CONCLUSIONS: Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.},
}
@article {pmid30194707,
year = {2018},
author = {Grandi, G and Astolfi, G and Chicca, M and Pezzi, M},
title = {Ultrastructural investigations on spermatogenesis and spermatozoan morphology in the endangered Adriatic sturgeon, Acipenser naccarii (Chondrostei, Acipenseriformes).},
journal = {Journal of morphology},
volume = {279},
number = {10},
pages = {1376-1396},
doi = {10.1002/jmor.20847},
pmid = {30194707},
issn = {1097-4687},
support = {16-01-14404//Italian Ministry of University and Research (MIUR)/International ; },
mesh = {Acrosome/ultrastructure ; Animals ; *Endangered Species ; Fishes/*anatomy &amp; histology ; Male ; Phylogeny ; Principal Component Analysis ; Spermatids/cytology/ultrastructure ; *Spermatogenesis ; Spermatogonia/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; Testis/ultrastructure ; },
abstract = {Spermatogenesis was investigated in the Adriatic sturgeon, Acipenser naccarii, by light and electron microscopy. The testis of the unrestricted type had a germinal compartment composed of lobules containing germ cells and Sertoli cells, and separated by a basal lamina from the interstitial compartment, in which Leydig and myoid cells were detected for the first time in Acipenseridae. Spermatogenesis occurred in spermatocysts produced when Sertoli cells became associated with type A spermatogonia of subsequent generations, which produced a clone of synchronized aligned spermatogonia. In primary spermatocytes at zygo-pachytene stage, the large spherical nucleus contained synaptonemal complexes. The smaller secondary spermatocytes were ovoid with a central round nucleus and scarce cytoplasm. Spermatids were interconnected by cytoplasmic bridges until early spermiogenesis. Chromatin initially condensed as long, twisted, and nonhomogeneous fibers and finally as a compact structure made of thick filaments. Early spermatids showed the flagellum, the primordia of centriole complex and of "implantation fossa," followed by the acrosomal vesicle formed by Golgi complexes and a fibrous body associated to centriole complex. The spermatozoan head had 10 postero-lateral projections and a trapezoidal nucleus, a cylindrical midpiece with six to eight mitochondria, the centriole complex, and a "9 + 2" flagellum with a pair of lateral fins. Three helical endonuclear canals crossed the nucleus from the acrosome base to the implantation fossa; their spiralization and that of chromatin fibers suggest a spiral twisting of the nucleus during spermiogenesis. The Sertoli cells performed phagocytosis of degenerating spermatids and spermatozoa. Significant interindividual differences were detected in most morphological parameters of spermatozoa. Data on spermatogenesis in A. naccarii and morphometric measurements on mature spermatozoa provide information about the reproductive biology of the species useful not only for phylogenetic studies but also for evaluation of sperm quality for artificial reproduction projects and restocking of this and other critically endangered sturgeon species.},
}
@article {pmid30196672,
year = {2018},
author = {Eom, KS and Park, H and Lee, D and Choe, S and Kang, Y and Bia, MM and Lee, SH and Keyyu, J and Fyumagwa, R and Jeon, HK},
title = {Molecular and Morphologic Identification of Spirometra ranarum Found in the Stool of African Lion, Panthera leo in the Serengeti Plain of Tanzania.},
journal = {The Korean journal of parasitology},
volume = {56},
number = {4},
pages = {379-383},
pmid = {30196672},
issn = {1738-0006},
support = {2017R1D1A3B03035976//National Research Foundation of Korea/ ; PRB000720//Parasite Resource Bank of Korea/ ; },
mesh = {Animals ; Cyclooxygenase 1/genetics ; Feces/*parasitology ; Host-Parasite Interactions ; Lions/*parasitology ; Male ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Spirometra/anatomy &amp; histology/*genetics/*isolation &amp; purification ; Tanzania ; },
abstract = {The present study was performed with morphological and molecular analysis (cox1 and nad1 mitochondrial genes) to identify the proglottids of spirometrid tapeworm found in the stool of an African lion, Panthera leo, in the Serengeti plain of Tanzania. A strand of tapeworm strobila, about 75 cm in length, was obtained in the stool of a male African lion in the Serengeti National Park (34˚ 50' E, 02˚ 30' S), Tanzania, in February 2012. The morphological features of the adult worm examined exhibited 3 uterine coils with a bow tie appearance and adopted a diagonal direction in the second turn. The posterior uterine coils are larger than terminal uterine ball and the feature of uteri are swirling rather than spirally coiling. The sequence difference between the Spirometra species (Tanzania origin) and S. erinaceieuropaei (GenBank no. KJ599680) was 9.4% while those of S. decipiens (GenBank no. KJ599679) differed by 2.1% in the cox1 and nad1 genes. Phylogenetic tree topologies generated using the 2 analytic methods were identical and presented high level of confidence values for the 3 major branches of the 3 Spirometra species in the cox1 gene. The morphological and molecular findings obtained in this study were nearly coincided with those of S. ranarum. Therefore, we can know for the first time that the African lion, Panthera leo, is to the definitive host of this tapeworm.},
}
@article {pmid30204084,
year = {2018},
author = {Seidi, A and Muellner-Wong, LS and Rajendran, E and Tjhin, ET and Dagley, LF and Aw, VY and Faou, P and Webb, AI and Tonkin, CJ and van Dooren, GG},
title = {Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
pmid = {30204084},
issn = {2050-084X},
support = {DP110103144//Australian Research Council/International ; },
mesh = {Animals ; Biotinylation ; Computational Biology ; Electron Transport Complex IV/*metabolism ; Gene Knockdown Techniques ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Oxygen Consumption ; Parasites/growth &amp; development/metabolism ; Phenotype ; Phylogeny ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/metabolism ; Toxoplasma/growth &amp; development/*metabolism ; },
abstract = {The mitochondrion of apicomplexan parasites is critical for parasite survival, although the full complement of proteins that localize to this organelle has not been defined. Here we undertake two independent approaches to elucidate the mitochondrial proteome of the apicomplexan Toxoplasma gondii. We identify approximately 400 mitochondrial proteins, many of which lack homologs in the animals that these parasites infect, and most of which are important for parasite growth. We demonstrate that one such protein, termed TgApiCox25, is an important component of the parasite cytochrome c oxidase (COX) complex. We identify numerous other apicomplexan-specific components of COX, and conclude that apicomplexan COX, and apicomplexan mitochondria more generally, differ substantially in their protein composition from the hosts they infect. Our study highlights the diversity that exists in mitochondrial proteomes across the eukaryotic domain of life, and provides a foundation for defining unique aspects of mitochondrial biology in an important phylum of parasites.},
}
@article {pmid30208106,
year = {2018},
author = {Viret, A and Tsaparis, D and Tsigenopoulos, CS and Berrebi, P and Sabatini, A and Arculeo, M and Fassatoui, C and Magoulas, A and Marengo, M and Morales-Nin, B and Caill-Milly, N and Durieux, EDH},
title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers.},
journal = {PloS one},
volume = {13},
number = {9},
pages = {e0203866},
pmid = {30208106},
issn = {1932-6203},
mesh = {Alleles ; Animals ; Atlantic Ocean ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/genetics ; Gene Flow ; Gene Frequency/genetics ; Genetic Variation ; Genetics, Population/methods ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; },
abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.},
}
@article {pmid30239783,
year = {2018},
author = {Hood, WR and Austad, SN and Bize, P and Jimenez, AG and Montooth, KL and Schulte, PM and Scott, GR and Sokolova, I and Treberg, JR and Salin, K},
title = {The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation.},
journal = {Integrative and comparative biology},
volume = {58},
number = {3},
pages = {480-485},
pmid = {30239783},
issn = {1557-7023},
support = {P30 DK079626/DK/NIDDK NIH HHS/United States ; },
mesh = {*Acclimatization ; Animals ; *Energy Metabolism ; *Life History Traits ; Mitochondria/*physiology ; },
abstract = {Animals display tremendous variation in their rates of growth, reproductive output, and longevity. While the physiological and molecular mechanisms that underlie this variation remain poorly understood, the performance of the mitochondrion has emerged as a key player. Mitochondria not only impact the performance of eukaryotes via their capacity to produce ATP, but they also play a role in producing heat and reactive oxygen species and function as a major signaling hub for the cell. The papers included in this special issue emerged from a symposium titled "Inside the Black Box: The Mitochondrial Basis of Life-history Variation and Animal Performance." Based on studies of diverse animal taxa, three distinct themes emerged from these papers. (1) When linking mitochondrial function to components of fitness, it is crucial that mitochondrial assays are performed in conditions as close as the intracellular conditions experienced by the mitochondria in vivo. (2) Functional plasticity allows mitochondria to retain their performance, as well as that of their host, over a range of exogenous conditions, and selection on mitochondrial and nuclear-derived proteins can optimize the match between the environment and the bioenergetic capacity of the mitochondrion. Finally, (3) studies of wild and wild-derived animals suggest that mitochondria play a central role in animal performance and life history strategy. Taken as a whole, we hope that these papers will foster discussion and inspire new hypotheses and innovations that will further our understanding of the mitochondrial processes that underlie variation in life history traits and animal performance.},
}
@article {pmid30280695,
year = {2018},
author = {Önder, Z and İnci, A and Yıldırım, A and Çiloğlu, A and Düzlü, &#xd6;},
title = {Molecular Characterization of Myiasis-Causing Moth Flies (Diptera: Psychodidae).},
journal = {Turkiye parazitolojii dergisi},
volume = {42},
number = {3},
pages = {223-228},
doi = {10.5152/tpd.2018.5943},
pmid = {30280695},
issn = {2146-3077},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Mitochondria/genetics ; Myiasis/*parasitology ; Phylogeny ; Psychodidae/classification/*genetics ; Sequence Alignment ; Turkey ; },
abstract = {OBJECTIVE: The aim of this study is to examine the molecular characterization of moth flies (Diptera: Psychodidae) based on their mitochondrial DNA sequences and determine the vectorial potential and damage caused by moth flies in future researches.<br><br>METHODS: A total of 240 adult moth flies were collected from toilet, bathroom, and basement walls of houses from different locations of the Kayseri region between May 2016 and April 2017. The polymerase chain reaction (PCR) analyses were performed using primer pairs, specificaly targeting the mitochondrial cytochrome oxidase c subunit I (mt-COI) gene of adult flies.<br><br>RESULTS: In total, five isolates were gel purified and sequenced for molecular characterization and phylogenetic analyses. Two species, namely Telmatoscopus albipunctatus (ERU-Telmatos3 and ERU-Telmatos6) and Psychodidae sp. (ERU-Psycho1,4,5), were successfully identified with the sequence alignment of isolates. According to the phylogenetic analysis, it was determined that the ERU-Telmatos3 and ERU-Telmatos6 isolates are clustered in the haplogroup A, while the ERU-Psycho1,4,5 isolate was clustered within the haplogroup B. The ERU-Psycho1 isolate was characterized as a new haplotype within the haplogroup B.<br><br>CONCLUSION: This study represents the first molecular characterization and phylogenetic status of moth flies in Turkey. The obtained findings should be the first step in the future investigation based on detecting the transmission of bacterial pathogens by moth flies.},
}
@article {pmid30285603,
year = {2018},
author = {Chen, G and Zou, Y and Hu, J and Ding, Y},
title = {Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {720},
pmid = {30285603},
issn = {1471-2164},
support = {31471464//National Nature Science Foundation of China/ ; 2013CB126900//"973" Program of China/ ; },
mesh = {Chromosomes, Plant/genetics ; Droughts ; *Gene Expression Profiling ; Genome, Plant/genetics ; *Genomics ; Intracellular Space/metabolism ; MicroRNAs/genetics ; Oryza/drug effects/*genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Salts/pharmacology ; Stress, Physiological/drug effects/*genetics ; Synteny ; },
abstract = {BACKGROUND: Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is one of the largest families in land plants and play important roles in organelle RNA metabolism and plant development. However, the functions of PPR genes involved in biotic and abiotic stresses of rice (Oryza sativa L.) remain largely unknown.<br><br>RESULTS: In the present study, a comprehensive genome-wide analysis of PPR genes was performed. A total of 491 PPR genes were found in the rice genome, of which 246 PPR genes belong to the P subfamily, and 245 genes belong to the PLS subfamily. Gene structure analysis showed that most PPR genes lack intron. Chromosomal location analysis indicated that PPR genes were widely distributed in all 12 rice chromosomes. Phylogenetic relationship analysis revealed the distinct difference between the P and PLS subfamilies. Many PPR proteins are predicted to target chloroplasts or mitochondria, and a PPR protein (LOC_Os10g34310) was verified to localize in mitochondria. Furthermore, three PPR genes (LOC_Os03g17634,LOC_Os07g40820,LOC_Os04g51350) were verified as corresponding miRNA targets. The expression pattern analysis showed that many PPR genes could be induced under biotic and abiotic stresses. Finally, seven PPR genes were confirmed with their expression patterns under salinity or drought stress.<br><br>CONCLUSIONS: We found 491 PPR genes in the rice genome, and our genes structure analysis and syntenic analysis indicated that PPR genes might be derived from amplification by retro-transposition. The expression pattern present here suggested that PPR proteins have crucial roles in response to different abiotic stresses in rice. Taken together, our study provides a comprehensive analysis of the PPR gene family and will facilitate further studies on their roles in rice growth and development.},
}
@article {pmid30286121,
year = {2018},
author = {Ashrafzadeh, MR and Djan, M and Szendrei, L and Paulauskas, A and Scandura, M and Bagi, Z and Ilie, DE and Kerdikoshvili, N and Marek, P and Soós, N and Kusza, S},
title = {Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204653},
pmid = {30286121},
issn = {1932-6203},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Haplotypes/genetics ; Hares/*genetics ; Hybridization, Genetic/genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.},
}
@article {pmid30291814,
year = {2018},
author = {Lukeš, J and Wheeler, R and Jirsová, D and David, V and Archibald, JM},
title = {Massive mitochondrial DNA content in diplonemid and kinetoplastid protists.},
journal = {IUBMB life},
volume = {70},
number = {12},
pages = {1267-1274},
pmid = {30291814},
issn = {1521-6551},
support = {MOP-115141//CIHR/Canada ; 103261/Z/13/Z//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; },
mesh = {DNA, Mitochondrial/*genetics/isolation &amp; purification/ultrastructure ; Euglenozoa/*genetics ; Kinetoplastida/*genetics ; Mitochondria/*genetics ; Phylogeny ; Trans-Splicing/genetics ; },
abstract = {The mitochondrial DNA of diplonemid and kinetoplastid protists is known for its suite of bizarre features, including the presence of concatenated circular molecules, extensive trans-splicing and various forms of RNA editing. Here we report on the existence of another remarkable characteristic: hyper-inflated DNA content. We estimated the total amount of mitochondrial DNA in four kinetoplastid species (Trypanosoma brucei, Trypanoplasma borreli, Cryptobia helicis, and Perkinsela sp.) and the diplonemid Diplonema papillatum. Staining with 4',6-diamidino-2-phenylindole and RedDot1 followed by color deconvolution and quantification revealed massive inflation in the total amount of DNA in their organelles. This was further confirmed by electron microscopy. The most extreme case is the ∼260 Mbp of DNA in the mitochondrion of Diplonema, which greatly exceeds that in its nucleus; this is, to our knowledge, the largest amount of DNA described in any organelle. Perkinsela sp. has a total mitochondrial DNA content ~6.6× greater than its nuclear genome. This mass of DNA occupies most of the volume of the Perkinsela cell, despite the fact that it contains only six protein-coding genes. Why so much DNA? We propose that these bloated mitochondrial DNAs accumulated by a ratchet-like process. Despite their excessive nature, the synthesis and maintenance of these mtDNAs must incur a relatively low cost, considering that diplonemids are one of the most ubiquitous and speciose protist groups in the ocean. © 2018 IUBMB Life, 70(12):1267-1274, 2018.},
}
@article {pmid30297026,
year = {2018},
author = {Porcelli, V and Vozza, A and Calcagnile, V and Gorgoglione, R and Arrigoni, R and Fontanesi, F and Marobbio, CMT and Castegna, A and Palmieri, F and Palmieri, L},
title = {Molecular identification and functional characterization of a novel glutamate transporter in yeast and plant mitochondria.},
journal = {Biochimica et biophysica acta. Bioenergetics},
volume = {1859},
number = {11},
pages = {1249-1258},
doi = {10.1016/j.bbabio.2018.08.001},
pmid = {30297026},
issn = {1879-2650},
mesh = {Amino Acid Transport System X-AG/*metabolism ; Arabidopsis/*metabolism ; Arabidopsis Proteins/*metabolism ; Gene Deletion ; Glutamic Acid/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Membrane Transport Proteins/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Proteolipids ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Substrate Specificity ; Time Factors ; },
abstract = {The genome of Saccharomyces cerevisiae encodes 35 members of the mitochondrial carrier family (MCF) and 58 MCF members are coded by the genome of Arabidopsis thaliana, most of which have been functionally characterized. Here two members of this family, Ymc2p from S. cerevisiae and BOU from Arabidopsis, have been thoroughly characterized. These proteins were overproduced in bacteria and reconstituted into liposomes. Their transport properties and kinetic parameters demonstrate that Ymc2p and BOU transport glutamate, and to a much lesser extent L-homocysteinesulfinate, but not other amino acids and many other tested metabolites. Transport catalyzed by both carriers was saturable, inhibited by mercuric chloride and dependent on the proton gradient across the proteoliposomal membrane. The growth phenotype of S. cerevisiae cells lacking the genes ymc2 and agc1, which encodes the only other S. cerevisiae carrier capable to transport glutamate besides aspartate, was fully complemented by expressing Ymc2p, Agc1p or BOU. Mitochondrial extracts derived from ymc2Δagc1Δ cells, reconstituted into liposomes, exhibited no glutamate transport at variance with wild-type, ymc2Δ and agc1Δ cells, showing that S. cerevisiae cells grown in the presence of acetate do not contain additional mitochondrial transporters for glutamate besides Ymc2p and Agc1p. Furthermore, mitochondria isolated from wild-type, ymc2Δ and agc1Δ strains, but not from the double mutant ymc2Δagc1Δ strain, swell in isosmotic ammonium glutamate showing that glutamate is transported by Ymc2p and Agc1p together with a H[+]. It is proposed that the function of Ymc2p and BOU is to transport glutamate across the mitochondrial inner membrane and thereby play a role in intermediary metabolism, C1 metabolism and mitochondrial protein synthesis.},
}
@article {pmid30300424,
year = {2018},
author = {Kobayashi, G and Araya, JF},
title = {Southernmost records of Escarpia spicata and Lamellibrachia barhami (Annelida: Siboglinidae) confirmed with DNA obtained from dried tubes collected from undiscovered reducing environments in northern Chile.},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0204959},
pmid = {30300424},
issn = {1932-6203},
mesh = {Animals ; Annelida/classification/*genetics/microbiology ; Bacteria/genetics/isolation &amp; purification ; Chile ; DNA/*chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Hemoglobins/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Protein Subunits/classification/genetics ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {Deep-sea fishing bycatch enables collection of samples of rare species that are not easily accessible, for research purposes. However, these specimens are often degraded, losing diagnostic morphological characteristics. Several tubes of vestimentiferans, conspicuous annelids endemic to chemosynthetic environments, were obtained from a single batch of deep-sea fishing bycatch at depths of around 1,500 m off Huasco, northern Chile, as part of an ongoing study examining bycatch species. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and an intron region within the hemoglobin subunit B2 (hbB2i) were successfully determined using vestimentiferans' dried-up tubes and their degraded inner tissue. Molecular phylogenetic analyses based on DNA sequence identified the samples as Escarpia spicata Jones, 1985, and Lamellibrachia barhami Webb, 1969. These are the southernmost records, vastly extending the geographical ranges of both species from Santa Catalina Island, California to northern Chile for E. spicata (over 8,000 km), and from Vancouver Island Margin to northern Chile for L. barhami (over 10,000 km). We also determined a 16S rRNA sequence of symbiotic bacteria of L. barhami. The sequence of the bacteria is the same as that of E. laminata, Lamellibrachia sp. 1, and Lamellibrachia sp.2 known from the Gulf of Mexico. The present study provides sound evidence forthe presence of reducing environments along the continental margin of northern Chile.},
}
@article {pmid30308027,
year = {2018},
author = {Perdices, A and Ozeren, CS and Erkakan, F and Freyhof, J},
title = {Diversity of spined loaches from Asia Minor in a phylogenetic context (Teleostei: Cobitidae).},
journal = {PloS one},
volume = {13},
number = {10},
pages = {e0205678},
pmid = {30308027},
issn = {1932-6203},
mesh = {Animals ; Cypriniformes/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; Homeodomain Proteins/genetics ; Mitochondria/genetics ; Phylogeny ; Turkey ; },
abstract = {Accurate determination of species diversity in areas of high endemicity, particularly those lacking comprehensive systematic knowledge, represents a challenge for both taxonomists and conservationists. This need is particularly evident in areas greatly affected by anthropogenic disturbances such as the Eastern Mediterranean and its freshwater environments. To improve our knowledge of Eastern Mediterranean freshwater fishes, we phylogenetically studied Western Palearctic Cobitis species, focusing on those found in Turkey. Overall, our results provide a robust framework to assess the number of species of Cobitis. Phylogenetic reconstructions based on mitochondrial (cyt b) and nuclear (RAG1) sequences show seven major clades (Clades 1-7) grouping all Western Palearctic Cobitis species, except C. melanoleuca. In general, each major clade comprises Cobitis species that inhabit geographically close areas and have similar secondary sexual characters. Multiple divergent lineages were identified in our analyses, some of which were highly divergent such as the ones inhabiting Turkish freshwaters. Moreover, in some analyses, several of the identified lineages were incongruent with a priori defined species. Furthermore, our analyses identified eight potentially new candidate species, six that had been suggested in previous studies and two that are reported here for the first time. Our results reveal Turkey as the area with the greatest diversity of spined loaches in the Mediterranean.},
}
@article {pmid30309500,
year = {2018},
author = {Miquel, J and Poonlaphdecha, S and Ribas, A},
title = {Spermatological characteristics of the family Glypthelminthidae (Digenea, Plagiorchioidea) inferred from the ultrastructural study of Glypthelmins staffordi Tubangui, 1928.},
journal = {Tissue &amp; cell},
volume = {54},
number = {},
pages = {114-119},
doi = {10.1016/j.tice.2018.08.013},
pmid = {30309500},
issn = {1532-3072},
mesh = {Animals ; Male ; Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/*ultrastructure ; },
abstract = {The present study describes the ultrastructural organization of the mature spermatozoon of the digenean Glypthelmins staffordi (Glypthelminthidae) by means of transmission electron microscopy. Live digeneans were collected from the Chinese edible frog (Hoplobatrachus rugulosus) in Udon Thani Province (Thailand). The ultrastructural study reveals that the mature spermatozoon of G. staffordi is a filiform cell, which is tapered at both extremities. It exhibits the Bakhoum et al.'s type IV of spermatozoon of digeneans characterized by the 9+'1' axonemes of trepaxonematan Platyhelminthes, the presence of the association "external ornamentation-cortical microtubules", the external ornamentation located in the posterior part of the anterior region, the arrangement of parallel cortical microtubules in two bundles and with its maximum number located in the anterior part of the sperm cell, and the presence of two mitochondria. Other characteristics are the presence of spine-like bodies, a posterior extremity containing only the nucleus, and the presence of a large amount of glycogen granules. Results of the present study are particularly compared with the existing data in other families of the Plagiorchioidea, namely the Brachycoeliidae, the Haematoloechidae, the Omphalometridae and the Plagiorchiidae.},
}
@article {pmid30311911,
year = {2018},
author = {Fischer, J and Müller, SY and Netzker, T and Jäger, N and Gacek-Matthews, A and Scherlach, K and Stroe, MC and García-Altares, M and Pezzini, F and Schoeler, H and Reichelt, M and Gershenzon, J and Krespach, MK and Shelest, E and Schroeckh, V and Valiante, V and Heinzel, T and Hertweck, C and Strauss, J and Brakhage, AA},
title = {Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
pmid = {30311911},
issn = {2050-084X},
support = {SFB-F3703//Austrian Science Fund FWF/Austria ; },
mesh = {Acetylation ; Aspergillus nidulans/genetics/*metabolism ; Chromatin/*metabolism ; Fungal Proteins/genetics/*metabolism ; Gene Expression Regulation, Fungal ; Gene Ontology ; Genome, Fungal ; Histidine/metabolism ; Histones/metabolism ; Lysine/metabolism ; Mitochondria/metabolism ; Multigene Family ; Nitrogen/metabolism ; Phylogeny ; *Secondary Metabolism ; Signal Transduction ; Streptomyces/*metabolism ; Transcription Factors/metabolism ; },
abstract = {The eukaryotic epigenetic machinery can be modified by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. We discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster in the fungus Aspergillus nidulans. Using this model, we aim understanding mechanisms of microbial communication based on bacteria-triggered chromatin modification. Using genome-wide ChIP-seq analysis of acetylated histone H3, we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus and relate changes in the acetylation to that in the fungal transcriptome. Differentially acetylated histones were detected in genes involved in secondary metabolism, in amino acid and nitrogen metabolism, in signaling, and encoding transcription factors. Further molecular analyses identified the Myb-like transcription factor BasR as the regulatory node for transduction of the bacterial signal in the fungus and show its function is conserved in other Aspergillus species.},
}
@article {pmid30313490,
year = {2018},
author = {Katoh, TK and Zhang, G and Zhou, CJ and Gao, JJ},
title = {Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.},
journal = {Zootaxa},
volume = {4422},
number = {3},
pages = {345-365},
doi = {10.11646/zootaxa.4422.3.2},
pmid = {30313490},
issn = {1175-5334},
mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Mitochondria ; Phylogeny ; Tibet ; },
abstract = {The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.},
}
@article {pmid30316921,
year = {2019},
author = {Gao, XM and Mu, DL and Hou, CC and Zhu, JQ and Jin, S and Wang, CL},
title = {Expression and putative functions of KIFC1 for nuclear reshaping and midpiece formation during spermiogenesis of Phascolosoma esculenta.},
journal = {Gene},
volume = {683},
number = {},
pages = {169-183},
doi = {10.1016/j.gene.2018.10.021},
pmid = {30316921},
issn = {1879-0038},
mesh = {Animals ; Binding Sites ; Cell Nucleus/metabolism ; Gene Expression Regulation ; Kinesins/chemistry/*genetics/*metabolism ; Male ; Microtubules/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/genetics/*physiology ; Protein Conformation ; Protein Domains ; Protein Transport ; *Spermatogenesis ; },
abstract = {Kinesin-14 KIFC1 plays an important role in vesicular transport, microtubule organization, and spermiogenesis. In this study, we first investigated the microtubule distribution and expression pattern of KIFC1 during spermiogenesis of P. esculenta. Microtubules are abundant during spermiogenesis of P. esculenta and may be related to the generation and maintenance of pseudopodia-like cytoplasmic protrusions and nuclear reshaping. The Pe-KIFC1 protein is conserved with a motor domain where microtubule and ATP binding sites are predicted, a coiled-coil domain and a divergent tail domain. The Pe-kifc1 gene was extensively expressed and showed the highest expression in coelomic fluid where spermiogenesis occurs. We further observed the expression of kifc1 mRNA and protein and found that Pe-KIFC1 protein primarily co-localized with microtubules during spermiogenesis, indicating that KIFC1 might play several roles during this process via its cargo transport and/or microtubule organization function. In addition, co-localization of mitochondria and KIFC1 was also detected during spermiogenesis, which were located in the midpiece in mature sperm, suggesting that mitochondria might be a cargo of Pe-KIFC1 that participates in the intracellular distribution of mitochondria and formation of the midpiece. Based on our detailed observations of the dynamic distribution of microtubules, KIFC1, and mitochondria during spermiogenesis and the conserved function of KIFC1 in cargo transport and microtubule organization, functional models of Pe-KIFC1 during spermiogenesis are proposed, including the participation of KIFC1 in nuclear reshaping and midpiece formation.},
}
@article {pmid30328804,
year = {2018},
author = {Cao, M and Chen, K and Li, W and Ma, J and Xiao, Z and Wang, H and Gao, J},
title = {Genetic characterization of human-derived hydatid fluid based on mitochondrial gene sequencing in individuals from northern and western China.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e2},
doi = {10.1017/S0022149X18000883},
pmid = {30328804},
issn = {1475-2697},
mesh = {Animals ; China ; Echinococcosis/*parasitology ; Echinococcus/classification/*genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Helminth Proteins/genetics ; Humans ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Tibet ; },
abstract = {This study investigated Echinococcus genotypes in patients with hydatidosis that reside in Inner Mongolia, Tibet or Qinghai Province by partially sequencing the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) genes. Cyst fluids were collected from 23 patients with hydatidosis and DNA was extracted. Portions of the cox1 and nad1 genes were amplified and subsequently sequenced. Sequencing analysis determined that one of the isolates contained Echinococcus multilocularis, and the other 22 isolates contained E. granulosus sensu lato. The isolates were then further classified based on genotype, and E. granulosus sensu stricto (s.s.) G1 (n = 20), E. granulosus s.s. G3 (n = 1) and E. canadensis G6/7 (n = 1) were identified. Additionally, the sequences were concatenated (pcox1 + pnad1) and 11 haplotypes were identified among the E. granulosus s.s. isolates (G1 and G3), with a shared common haplotype (H1) identified. Overall, these findings provide further understanding of the genetic patterns of Echinococcus in western and northern China.},
}
@article {pmid30340785,
year = {2018},
author = {Dos Santos, RF and Quendera, AP and Boavida, S and Seixas, AF and Arraiano, CM and Andrade, JM},
title = {Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA.},
journal = {Progress in molecular biology and translational science},
volume = {159},
number = {},
pages = {101-155},
doi = {10.1016/bs.pmbts.2018.07.005},
pmid = {30340785},
issn = {1878-0814},
mesh = {Animals ; Disease ; Exoribonucleases/chemistry/*metabolism ; Humans ; Open Reading Frames/genetics ; Phylogeny ; RNA, Untranslated/*genetics ; Substrate Specificity ; },
abstract = {3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.},
}
@article {pmid30347227,
year = {2019},
author = {Xin, L and Huang, B and Li, C and Bai, C and Wang, C},
title = {Characterization of a nucleus located mollusc mitoferrin and its response to OsHV-1 infection.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1863},
number = {1},
pages = {255-265},
doi = {10.1016/j.bbagen.2018.10.014},
pmid = {30347227},
issn = {1872-8006},
mesh = {Animals ; Cell Nucleus/*metabolism ; Computational Biology ; Cytosol/metabolism ; DNA Viruses/*physiology ; Female ; Ferritins/metabolism ; Herpesviridae Infections/*veterinary ; Humans ; Immunohistochemistry ; Iron/metabolism ; Membrane Transport Proteins/*chemistry ; Mice ; Mitochondria/metabolism ; Mollusca/*virology ; Phylogeny ; Protein Domains ; Recombinant Proteins/chemistry ; Tissue Distribution ; },
abstract = {Mitoferrin genes as members of SLC25 family are conservatively existed across species, mainly locate on mitochondria and serve an important role in the regulation of whole cellular iron metabolism. Available iron withholding from pathogens presents an important host defense strategy, while the regulation role of mitoferrin against invading pathogens is largely unknown. In this study, a unique mollusc mitoferrin gene was identified in ark clams, named SbmiFn, that showed conserved three-dimensional structure with other mitoferrins, and its iron binding activity was verified by iron chelating assay. Besides cytoplasmic distribution, colocalization between SbmiFn and nuclei was observed by immunohistochemistry assay. Moreover, the response of SbmiFn to viral pathogen OsHV-1 was investigated. The results showed that nucleus located signal of SbmiFn was enhanced, the expressions of SbmiFn and ferritin were coordinately decreased, which might assist host against OsHV-1 replication as the increase of OsHV-1 copies were hardly detected after that. These results refreshed our knowledge on the sequence, structure and functional characteristics of mitoferrin subfamily, and would contribute to further comparative studies on iron metabolism.},
}
@article {pmid30350319,
year = {2018},
author = {Temereva, EN and Kuzmina, TV},
title = {Spermatogenesis in the deep-sea brachiopod Pelagodiscus atlanticus and the phylogenetic significance of spermatozoon structure.},
journal = {Journal of morphology},
volume = {279},
number = {11},
pages = {1579-1589},
doi = {10.1002/jmor.20887},
pmid = {30350319},
issn = {1097-4687},
support = {17-04-00586//Russian Foundation for Basic Research/International ; #14-50-00034//Russian Science Foundation/International ; #18-14-00082//Russian Science Foundation/International ; },
mesh = {Animals ; Invertebrates/*classification/*physiology ; Male ; Models, Biological ; *Phylogeny ; *Spermatogenesis ; Spermatogonia/cytology/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; },
abstract = {Details of spermatogenesis and sperm organization are often useful for reconstructing the phylogeny of closely related groups of invertebrates. Development in general and gametogenesis in particular usually differ in shallow water and deep-sea invertebrates. Here, the spermatogenesis and ultrastructure of sperm were studied in the deep-sea brachiopod Pelagodiscus atlanticus. The testes of P. atlanticus are voluminous sacs located along the lateral sides of the body. Germ cells develop around the blood capillaries, contact the basal lamina, and contain germ plasm, numerous mitochondria, Golgi apparatus, lipid droplets, and centrioles of the rudimentary cilium. During spermatogenesis, several proacrosomal vesicles appear at the posterior pole of the cell; these vesicles then fuse and migrate to the anterior pole. The spermatozoon has a head with an acrosome, nucleus, eight mitochondria, proximal and distal centrioles orthogonally arranged, and a long tail. Comparative analysis suggests that the spermatozoon of P. atlanticus can be considered the most ancestral among all brachiopods. Such an organization indicates that fertilization is external in this deep-sea species. Spermatozoa of other brachiopods should be regarded as derived from this ancestral type. The transformation of brachiopod spermatozoa might have occurred in three different ways that correspond to the three main clades of recent brachiopods: Linguliformea, Craniiformea, and Rhynchonelliformea.},
}
@article {pmid30353148,
year = {2018},
author = {Ng, NSR and Prawiradilaga, DM and Ng, EYX and Suparno, and Ashari, H and Trainor, C and Verbelen, P and Rheindt, FE},
title = {A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {15646},
pmid = {30353148},
issn = {2045-2322},
mesh = {Acoustics ; Animals ; Cytochromes b/genetics ; *Genomics ; Geography ; Indonesia ; Islands ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Principal Component Analysis ; Songbirds/*anatomy &amp; histology/*genetics ; Sound Spectrography ; Species Specificity ; },
abstract = {Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.},
}
@article {pmid30395997,
year = {2019},
author = {López-Rubio, A and Suaza-Vasco, JD and Solari, S and Gutiérez-Builes, L and Porter, C and Uribe, SI},
title = {Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar &amp; Knab 1913, based on mitochondrial and nuclear ribosomal genes.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {67},
number = {},
pages = {183-190},
doi = {10.1016/j.meegid.2018.10.013},
pmid = {30395997},
issn = {1567-7257},
mesh = {Animals ; Anopheles/*classification/*genetics ; Central America/epidemiology ; *Genes, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; South America/epidemiology ; },
abstract = {Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting mangroves and tropical forest in the lowland and coastal areas of the Yucatan Peninsula through the Pacific Ecuadorian coast. This species exhibits epidemiological importance regarding Malaria transmission in natural ecosystems, particularly in rural areas of the Pacific Colombian coast. The results based on phylogenetic networks and Bayesian inference showed no robust evidence supporting the existence of previously suggested cryptic species. Diversification patterns in geographically widespread species such as this one, are complex and therefore could impact malaria control strategies. Further studies focused on behavior, morphology, and phylogenomics will improve the understanding of the evolutionary patterns within An. neivai and its role as a disease vector.},
}
@article {pmid30446790,
year = {2019},
author = {Razzak, MA and Lee, J and Lee, DW and Kim, JH and Yoon, HS and Hwang, I},
title = {Expression of seven carbonic anhydrases in red alga Gracilariopsis chorda and their subcellular localization in a heterologous system, Arabidopsis thaliana.},
journal = {Plant cell reports},
volume = {38},
number = {2},
pages = {147-159},
pmid = {30446790},
issn = {1432-203X},
support = {2016R1E1A1A02922014//Ministry of Fisheries/ ; },
mesh = {Arabidopsis/*genetics ; Carbonic Anhydrases/classification/*metabolism ; Computer Simulation ; Endoplasmic Reticulum/metabolism ; Gene Expression Regulation, Enzymologic ; Glycosylation ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Protoplasts/metabolism ; Rhodophyta/*enzymology ; Subcellular Fractions/metabolism ; Vacuoles/metabolism ; },
abstract = {Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.},
}
@article {pmid30468939,
year = {2019},
author = {Weber, AA and Stöhr, S and Chenuil, A},
title = {Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata).},
journal = {Molecular phylogenetics and evolution},
volume = {131},
number = {},
pages = {138-148},
doi = {10.1016/j.ympev.2018.11.014},
pmid = {30468939},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial ; Discriminant Analysis ; Echinodermata/*classification/*genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Multigene Family ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; Time Factors ; },
abstract = {Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenomenon. The brittle star cryptic species complex Ophioderma longicauda encompasses six mitochondrial lineages, including broadcast spawners and internal brooders, yet the actual species boundaries are unknown. Here, we combined three methods to delimit species in the Ophioderma longicauda complex and to infer its divergence history: (i) unsupervised species discovery based on multilocus genotypes; (ii) divergence time estimation using the multi-species coalescent; (iii) divergence scenario testing (including gene flow) using Approximate Bayesian Computation (ABC) methods. 30 sequence markers (transcriptome-based, mitochondrial or non-coding) for 89 O. longicauda and outgroup individuals were used. First, multivariate analyses revealed six genetic clusters, which globally corresponded to the mitochondrial lineages, yet with many exceptions, suggesting ancient hybridization events and challenging traditional mitochondrial barcoding approaches. Second, multi-species coalescent-based analyses confirmed the occurrence of six species and provided divergence time estimates, but the sole use of this method failed to accurately delimit species, highlighting the power of multilocus genotype clustering to delimit recently diverged species. Finally, Approximate Bayesian Computation showed that the most likely scenario involves hybridization between brooders and broadcasters. Our study shows that despite strong incomplete lineage sorting and past hybridization, accurate species delimitation in Ophioderma was possible using a combination of complementary methods. We propose that these methods, especially multilocus genotype clustering, may be useful to resolve other complex speciation histories.},
}
@article {pmid30474737,
year = {2019},
author = {Guo, J and Miao, X and He, P and Li, M and Wang, S and Cui, J and Huang, C and He, L and Zhao, J},
title = {Babesia gibsoni endemic to Wuhan, China: mitochondrial genome sequencing, annotation, and comparison with apicomplexan parasites.},
journal = {Parasitology research},
volume = {118},
number = {1},
pages = {235-243},
pmid = {30474737},
issn = {1432-1955},
support = {2017YFD0500402//National Key Research and Development Program of China/ ; 2015CB150300//National Basic Science Research Program (973 program) of China/ ; 31772729//National Natural Science Foundation of China/ ; 2017CFA020//Natural Science Foundation of Hubei Province/ ; },
mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/classification/genetics/isolation &amp; purification ; Babesia/classification/genetics/*isolation &amp; purification ; Babesiosis/*parasitology ; China/epidemiology ; Cytochromes b/genetics ; DNA Primers/genetics ; Dog Diseases/*parasitology ; Dogs ; *Genome, Mitochondrial ; Molecular Sequence Annotation ; Phylogeny ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Analysis, DNA ; },
abstract = {Babesia gibsoni (B. gibsoni), an intracellular apicomplexan protozoan, poses great threat to canine health. Currently, little information is available about the B. gibsoni (WH58) endemic to Wuhan, China. Here, the mitochondrial (mt) genome of B. gibsoni (WH58) was amplified by five pairs of primers and sequenced and annotated by alignment with the reported mt genome sequences of Babesia canis (B. canis, KC207822), Babesia orientalis (KF218819), Babesia bovis (AB499088), and Theileria equi (AB499091). The evolutionary relationships were analyzed with the amino acid sequences of cytochrome c oxidase I (cox1) and cytochrome b (cob) genes in apicomplexan parasite species. Additionally, the mt genomes of Babesia, Theileria, and Plasmodium spp. were compared in size, host infection, form, distribution, and direction of the protein-coding genes. The full size of the mt genome of B. gibsoni (WH58) was 5865 bp with a linear form, containing terminal-inverted repeats on both ends, six large subunit ribosomal RNA fragments, and three protein-coding genes: cox1, cob, and cytochrome c oxidase III (cox3). Babesia, Theileria, and Plasmodium spp. had a similar mt genome size of about 6000 bp. The mt genomes of parasites that cause canine babesiosis showed a slightly smaller size than the other species. Moreover, Babesia microti (R1 strain) was about 11,100 bp in size, which was twice larger than that of the other species. The mt form was linear for Babesia and Theileria spp. but circular for Plasmodium falciparum and Plasmodium knowlesi. Additionally, all the species contained the three protein-coding genes of cox1, cox3, and cob except Toxoplasma gondii (RH strain) which only contained the cox1 and cob genes. The phylogenetic analysis indicated that B. gibsoni (WH58) was more identical to B. gibsoni (AB499087), B. canis (KC207822), and Babesia rossi (KC207823) and most divergent from Babesia conradae in Babesia spp. Despite the highest similarity to B. gibsoni (AB499087) reported in Japan, B. gibsoni (WH58) showed notable differences in the sequence of nucleotides and amino acids and the property in virulence to host and in vitro cultivation. This study compared the mt genomes of the two B. gibsoni isolates and other parasites in the phylum Apicomplexa and provided new insights into their differences and evolutionary relationships.},
}
@article {pmid30477329,
year = {2018},
author = {Smith, CF and McGlaughlin, ME and Mackessy, SP},
title = {DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms.},
journal = {BioTechniques},
volume = {65},
number = {6},
pages = {339-345},
doi = {10.2144/btn-2018-0096},
pmid = {30477329},
issn = {1940-9818},
mesh = {Alethinophidia/classification/*genetics ; Animals ; Cell Nucleus/genetics ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Mitochondria/genetics ; Phylogeny ; Snake Venoms/classification/*genetics ; },
abstract = {DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].},
}
@article {pmid30486096,
year = {2018},
author = {Agarwal, I and Mahony, S and Giri, VB and Chaitanya, R and Bauer, AM},
title = {Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India.},
journal = {Zootaxa},
volume = {4524},
number = {5},
pages = {501-535},
doi = {10.11646/zootaxa.4524.5.1},
pmid = {30486096},
issn = {1175-5334},
mesh = {Animals ; *Color ; India ; *Lizards ; Mitochondria ; Myanmar ; Phylogeny ; },
abstract = {We use mitochondrial sequence data to identify divergent lineages within the gekkonid genus Cyrtodactylus in northeast India and use morphological data to describe six new species from within the Indo-Burma clade of Cyrtodactylus. The new species share an irregular colour pattern but differ from described species from the region in morphology and mitochondrial sequence data (>11 % uncorrected pairwise sequence divergence). Three new species are from along the Brahmaputra River and three are from mountains south of the Brahmaputra, including the largest Cyrtodactylus from India and the fifth gecko to be described from a major Indian city, Guwahati.},
}
@article {pmid30486780,
year = {2018},
author = {Fletcher, K and Klosterman, SJ and Derevnina, L and Martin, F and Bertier, LD and Koike, S and Reyes-Chin-Wo, S and Mou, B and Michelmore, R},
title = {Comparative genomics of downy mildews reveals potential adaptations to biotrophy.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {851},
pmid = {30486780},
issn = {1471-2164},
support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; S10 RR026825/RR/NCRR NIH HHS/United States ; Endowed Chair in Genomics//Novozymes Inc./ ; C06 RR012088/RR/NCRR NIH HHS/United States ; },
mesh = {Adaptation, Physiological/*genetics ; *Genomics ; Heterozygote ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Annotation ; Peronospora/*genetics/pathogenicity ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, RNA ; Terminal Repeat Sequences/genetics ; },
abstract = {BACKGROUND: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.<br><br>RESULTS: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 &amp; 880), high contig N50s (48&#xa0;kb &amp; 52&#xa0;kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.<br><br>CONCLUSIONS: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.},
}
@article {pmid30487140,
year = {2019},
author = {Kolli, R and Soll, J and Carrie, C},
title = {OXA2b is Crucial for Proper Membrane Insertion of COX2 during Biogenesis of Complex IV in Plant Mitochondria.},
journal = {Plant physiology},
volume = {179},
number = {2},
pages = {601-615},
pmid = {30487140},
issn = {1532-2548},
mesh = {Arabidopsis/cytology/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Electron Transport Complex IV/genetics/*metabolism ; Genetic Complementation Test ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Organelle Biogenesis ; Phylogeny ; Plant Cells/metabolism ; Protein Domains ; Seeds/genetics/metabolism ; },
abstract = {The evolutionarily conserved YidC/Oxa1/Alb3 proteins are involved in the insertion of membrane proteins in all domains of life. In plant mitochondria, individual knockouts of OXA1a, OXA2a, and OXA2b are embryo-lethal. In contrast to other members of the protein family, OXA2a and OXA2b contain a tetratricopeptide repeat (TPR) domain at the C-terminus. Here, the role of Arabidopsis (Arabidopsis thaliana) OXA2b was determined by using viable mutant plants that were generated by complementing homozygous lethal OXA2b T-DNA insertional mutants with a C-terminally truncated OXA2b lacking the TPR domain. The truncated-OXA2b-complemented plants displayed severe growth retardation due to a strong reduction in the steady-state abundance and enzyme activity of the mitochondrial respiratory chain complex IV. The TPR domain of OXA2b directly interacts with cytochrome c oxidase subunit 2, aiding in efficient membrane insertion and translocation of its C-terminus. Thus, OXA2b is crucial for the biogenesis of complex IV in plant mitochondria.},
}
@article {pmid30496844,
year = {2019},
author = {Boubli, JP and Byrne, H and da Silva, MNF and Silva-Júnior, J and Costa Araújo, R and Bertuol, F and Gonçalves, J and de Melo, FR and Rylands, AB and Mittermeier, RA and Silva, FE and Nash, SD and Canale, G and Alencar, RM and Rossi, RV and Carneiro, J and Sampaio, I and Farias, IP and Schneider, H and Hrbek, T},
title = {On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil.},
journal = {Molecular phylogenetics and evolution},
volume = {132},
number = {},
pages = {117-137},
doi = {10.1016/j.ympev.2018.11.012},
pmid = {30496844},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Brazil ; Cytochromes b/genetics ; Ecosystem ; Endangered Species ; Genome ; Mitochondria/genetics ; Phylogeny ; Pitheciidae/anatomy &amp; histology/*classification/genetics ; Polymorphism, Single Nucleotide ; },
abstract = {The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integrative taxonomic approach that includes phylogenomic analyses, pelage characters, and locality records. A reduced representation genome-wide approach was employed to assess phylogenetic relationships among species of the eastern Amazonian clade of the Plecturocebus moloch group. Using existing records, we calculated the Extent of Occurrence (EOO) of the new species and estimated future habitat loss for the region based on predictive models. We then evaluated the species' conservation status using the IUCN Red list categories and criteria. The new species presents a unique combination of morphological characters: (1) grey agouti colouration on the crown and dorsal parts; (2) entirely bright red-brown venter; (3) an almost entirely black tail with a pale tip; and (4) light yellow colouration of the hair on the cheeks contrasting with bright red-brown hair on the sides of the face. Our phylogenetic reconstructions based on maximum-likelihood and Bayesian methods revealed well-supported species relationships, with the Alta Floresta taxon as sister to P. moloch + P. vieirai. The species EOO is 10,166,653 ha and we predict a total habitat loss of 86% of its original forest habitat under a "business as usual" scenario in the next 24 years, making the newly discovered titi monkey a Critically Endangered species under the IUCN A3c criterion. We give the new titi monkey a specific epithet based on: (1) clear monophyly of this lineage revealed by robust genomic and mitochondrial data; (2) distinct and diagnosable pelage morphology; and (3) a well-defined geographical distribution with clear separation from other closely related taxa. Urgent conservation measures are needed to safeguard the future of this newly discovered and already critically endangered primate.},
}
@article {pmid30584918,
year = {2019},
author = {Lavin, BR and Girman, DJ},
title = {Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae).},
journal = {Molecular phylogenetics and evolution},
volume = {133},
number = {},
pages = {128-140},
doi = {10.1016/j.ympev.2018.12.022},
pmid = {30584918},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Geography ; Lizards/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Probability ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. All major lineages were found to be monophyletic with potential cryptic diversity in some. The Anguinae first appeared in the Eocene and most lineages were present by the beginning of the Miocene. The Anguinae originated in Europe from an Anguidae ancestor that crossed the Thulean land bridge, spreading to Asia after the drying of the Turgai Sea, then across Beringia as the climate permitted. A species tree analyses found support for the major Anguinae lineages and species delimitation supported accepted species.},
}
@article {pmid30586406,
year = {2018},
author = {Zhao, L and Lin, XM and Li, F and Li, KR and He, B and Zhang, LY and Pan, JJ and Wang, QR and Gao, JM and Johnson, N and Yuan, XF and Lv, JZ and Wu, SQ and Liu, YH},
title = {A survey of argasid ticks and tick-associated pathogens in the Peripheral Oases around Tarim Basin and the first record of Argas japonicus in Xinjiang, China.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208615},
pmid = {30586406},
issn = {1932-6203},
mesh = {Anaplasma/classification/genetics/*isolation &amp; purification/pathogenicity ; Animals ; Argas/classification/genetics/*microbiology ; Cattle ; China ; Disease Vectors ; Mitochondria/genetics ; Ornithodoros/classification/genetics/*microbiology ; Phylogeny ; RNA, Ribosomal/classification/genetics/metabolism ; RNA, Ribosomal, 16S/classification/genetics/metabolism ; Rickettsia/classification/genetics/*isolation &amp; purification/pathogenicity ; Sequence Analysis, DNA ; Sheep ; Tick Infestations/parasitology/pathology/veterinary ; },
abstract = {Argasid ticks (Acari: Argasidae) carry and transmit a variety of pathogens of animals and humans, including viruses, bacteria and parasites. There are several studies reporting ixodid ticks (Acari: Ixodidae) and associated tick-borne pathogens in Xinjiang, China. However, little is known about the argasid ticks and argasid tick-associated pathogens in this area. In this study, a total of 3829 adult argasid ticks infesting livestock were collected at 12 sampling sites of 10 counties in the Peripheral Oases, which carry 90% of the livestock and humans population, around the Tarim Basin (southern Xinjiang) from 2013 to 2016. Tick specimens were identified to two species from different genera by morphology and sequences of mitochondrial 16S rRNA and 12S rRNA were derived to confirm the species designation. The results showed that the dominant argasid ticks infesting livestock in southern Xinjiang were Ornithodoros lahorensis (87.86%, 3364/3829). Ornithodoros lahorensis was distributed widely and were collected from 10 counties of southern Xinjiang. Argas japonicus was collected from Xinjiang for the first time. In addition, we screened these ticks for tick-associated pathogens and showed the presence of DNA sequences of Rickettsia spp. of Spotted fever group and Anaplasma spp. in the argasid ticks. This finding suggests the potential role for Argas japonicus as a vector of pathogens to livestock and humans.},
}
@article {pmid30586649,
year = {2019},
author = {Bartáková, V and Bryja, J and Šanda, R and Bektas, Y and Stefanov, T and Choleva, L and Smith, C and Reichard, M},
title = {High cryptic diversity of bitterling fish in the southern West Palearctic.},
journal = {Molecular phylogenetics and evolution},
volume = {133},
number = {},
pages = {1-11},
doi = {10.1016/j.ympev.2018.12.025},
pmid = {30586649},
issn = {1095-9513},
mesh = {Animals ; Asia, Western ; Biodiversity ; Cyprinidae/*classification/genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry ; Demography ; Europe ; Genetic Drift ; Genetic Variation ; Genotype ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; },
abstract = {South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").},
}
@article {pmid30608924,
year = {2019},
author = {Makki, A and Rada, P and Žárský, V and Kereïche, S and Kováčik, L and Novotný, M and Jores, T and Rapaport, D and Tachezy, J},
title = {Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis.},
journal = {PLoS biology},
volume = {17},
number = {1},
pages = {e3000098},
pmid = {30608924},
issn = {1545-7885},
mesh = {Carrier Proteins/genetics/*metabolism/physiology ; Membrane Proteins/metabolism ; Membrane Transport Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Organelles ; Phylogeny ; Protein Transport/physiology ; Trichomonas vaginalis/*metabolism/pathogenicity/physiology ; },
abstract = {Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, an unexpected diversity of subunits between eukaryotic lineages has been predicted. However, experimental knowledge is limited to a few organisms, and so far, it remains unsettled whether the triplet-pore or the twin-pore structure is the generic form of TOM complex. Here, we analysed the TOM complex in hydrogenosomes, a metabolically specialised anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. We demonstrate that the highly divergent β-barrel T. vaginalis TOM (TvTom)40-2 forms a translocation channel to conduct hydrogenosomal protein import. TvTom40-2 is present in high molecular weight complexes, and their analysis revealed the presence of four tail-anchored (TA) proteins. Two of them, Tom36 and Tom46, with heat shock protein (Hsp)20 and tetratricopeptide repeat (TPR) domains, can bind hydrogenosomal preproteins and most likely function as receptors. A third subunit, Tom22-like protein, has a short cis domain and a conserved Tom22 transmembrane segment but lacks a trans domain. The fourth protein, hydrogenosomal outer membrane protein 19 (Homp19) has no known homology. Furthermore, our data indicate that TvTOM is associated with sorting and assembly machinery (Sam)50 that is involved in β-barrel assembly. Visualisation of TvTOM by electron microscopy revealed that it forms three pores and has an unconventional skull-like shape. Although TvTOM seems to lack Tom7, our phylogenetic profiling predicted Tom7 in free-living excavates. Collectively, our results suggest that the triplet-pore TOM complex, composed of three conserved subunits, was present in the last common eukaryotic ancestor (LECA), while receptors responsible for substrate binding evolved independently in different eukaryotic lineages.},
}
@article {pmid30617214,
year = {2019},
author = {Brenner, WG and Mader, M and Müller, NA and Hoenicka, H and Schroeder, H and Zorn, I and Fladung, M and Kersten, B},
title = {High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {3},
pages = {709-717},
pmid = {30617214},
issn = {2160-1836},
mesh = {Gene Expression Profiling ; Mitochondria/genetics/metabolism ; Phylogeny ; *Polymorphism, Single Nucleotide ; Populus/*genetics/metabolism ; *RNA Editing ; RNA, Mitochondrial/*metabolism ; RNA, Plant/metabolism ; Sequence Analysis, RNA ; },
abstract = {RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.},
}
@article {pmid30629584,
year = {2019},
author = {Chiovitti, A and Thorpe, F and Gorman, C and Cuxson, JL and Robevska, G and Szwed, C and Duncan, JC and Vanyai, HK and Cross, J and Siemering, KR and Sumner, J},
title = {A citizen science model for implementing statewide educational DNA barcoding.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0208604},
pmid = {30629584},
issn = {1932-6203},
mesh = {Animals ; Australia ; Base Sequence ; *DNA Barcoding, Taxonomic ; Feedback ; Genetic Variation ; Mitochondria/genetics ; *Models, Educational ; Phylogeny ; Reptiles/classification/genetics ; *Science ; Species Specificity ; Students ; },
abstract = {Our aim was to develop a widely available educational program in which students conducted authentic research that met the expectations of both the scientific and educational communities. This paper describes the development and implementation of a citizen science project based on DNA barcoding of reptile specimens obtained from the Museums Victoria frozen tissue collection. The student program was run by the Gene Technology Access Centre (GTAC) and was delivered as a "one day plus one lesson" format incorporating a one-day wet laboratory workshop followed by a single lesson at school utilising online bioinformatics tools. The project leveraged the complementary resources and expertise of the research and educational partners to generate robust scientific data that could be analysed with confidence, meet the requirements of the Victorian state education curriculum, and provide participating students with an enhanced learning experience. During two 1-week stints in 2013 and 2014, 406 students mentored by 44 postgraduate university students participated in the project. Students worked mainly in pairs to process ~200 tissue samples cut from 53 curated reptile specimens representing 17 species. A total of 27 novel Cytochrome Oxidase subunit 1 (CO1) sequences were ultimately generated for 8 south-east Australian reptile species of the families Scincidae and Agamidae.},
}
@article {pmid30630408,
year = {2019},
author = {Giannoulis, T and Plageras, D and Stamatis, C and Chatzivagia, E and Tsipourlianos, A and Birtsas, P and Billinis, C and Suchentrunk, F and Mamuris, Z},
title = {Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare.},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {17},
pmid = {30630408},
issn = {1471-2148},
mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Exons/genetics ; Gene Frequency/genetics ; Genetic Variation ; Haplotypes ; Hares/*genetics ; *Hybridization, Genetic ; *Islands ; Major Histocompatibility Complex/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; },
abstract = {BACKGROUND: The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.<br><br>RESULTS: Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.<br><br>CONCLUSION: Our results indicate that the Quaternary's climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.},
}
@article {pmid30639162,
year = {2019},
author = {López Rivero, AS and Rossi, MA and Ceccarelli, EA and Catalano-Dupuy, DL},
title = {A bacterial 2[4Fe4S] ferredoxin as redox partner of the plastidic-type ferredoxin-NADP[+] reductase from Leptospira interrogans.},
journal = {Biochimica et biophysica acta. General subjects},
volume = {1863},
number = {4},
pages = {651-660},
doi = {10.1016/j.bbagen.2019.01.004},
pmid = {30639162},
issn = {1872-8006},
mesh = {Amino Acid Sequence ; Ferredoxin-NADP Reductase/chemistry/*metabolism ; Ferredoxins/chemistry/*metabolism ; Leptospira interrogans/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Sequence Alignment ; },
abstract = {BACKGROUND: Ferredoxins are small iron-sulfur proteins that participate as electron donors in various metabolic pathways. They are recognized substrates of ferredoxin-NADP[+] reductases (FNR) in redox metabolisms in mitochondria, plastids, and bacteria. We previously found a plastidic-type FNR in Leptospira interrogans (LepFNR), a parasitic bacterium of animals and humans. Nevertheless, we did not identify plant-type ferredoxins or flavodoxins, the common partners of this kind of FNR.<br><br>METHODS: Sequence alignment, phylogenetical analyses and structural modeling were performed for the identification of a 2[4Fe4S] ferredoxin (LepFd2) as a putative redox partner of LepFNR in L. interrogans. The gene encoding LepFd2 was cloned and the protein overexpressed and purified. The functional properties of LepFd2 and LepFNR-LepFd2 complex were analyzed by kinetic and mutagenesis studies.<br><br>RESULTS: We succeeded in expressing and purifying LepFd2 with its FeS cluster properly bound. We found that LepFd2 exchanges electrons with LepFNR. Moreover, a unique structural subdomain of LepFNR (loop P75-Y91), was shown to be involved in the recognition and binding of LepFd2. This structural subdomain is not found in other FNR homologs.<br><br>CONCLUSIONS: We report for the first time a redox pair in L. interrogans in which a plastidic FNR exchanges electron with a bacterial 2[4Fe4S] ferredoxin. We characterized this reaction and proposed a model for the productive LepFNR-LepFd2 complex.<br><br>GENERAL SIGNIFICANCE: Our findings suggest that the interaction of LepFNR with the iron-sulfur protein would be different from the one previously described for the homolog enzymes. This knowledge would be useful for the design of specific LepFNR inhibitors.},
}
@article {pmid30700787,
year = {2019},
author = {Rusu, I and Modi, A and Radu, C and Mircea, C and Vulpoi, A and Dobrinescu, C and Bodolică, V and Potârniche, T and Popescu, O and Caramelli, D and Kelemen, B},
title = {Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {961},
pmid = {30700787},
issn = {2045-2322},
mesh = {Archaeology ; Bone and Bones/metabolism ; Burial/*history ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; History, Medieval ; Humans ; Male ; Mitochondria/*genetics ; *Phylogeny ; Romania ; },
abstract = {The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.},
}
@article {pmid30731120,
year = {2019},
author = {Brunes, TO and da Silva, AJ and Marques-Souza, S and Rodrigues, MT and Pellegrino, KCM},
title = {Not always young: The first vertebrate ancient origin of true parthenogenesis found in an Amazon leaf litter lizard with evidence of mitochondrial haplotypes surfing on the wave of a range expansion.},
journal = {Molecular phylogenetics and evolution},
volume = {135},
number = {},
pages = {105-122},
doi = {10.1016/j.ympev.2019.01.023},
pmid = {30731120},
issn = {1095-9513},
mesh = {Alleles ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Haplotypes/*genetics ; Hybridization, Genetic ; Lizards/*genetics ; Male ; Mitochondria/*genetics ; Parthenogenesis/*genetics ; Phylogeny ; Phylogeography ; Plant Leaves/*physiology ; },
abstract = {In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. In the Amazon region, parthenogenetic lizards of the Loxopholis percarinatum complex are widely distributed, comprising both diploid and triploid clones. Recently, putative males of L. percarinatum were reported, suggesting the existence of bisexual populations based on morphological data. Here, we used mitochondrial and nuclear data to investigate the origin of parthenogenesis in Loxopholis. Mitochondrial DNA analysis revealed three major lineages: unisexual/2n, unisexual/3n and bisexual, the last of which comprised two sub-lineages placed as the sister taxon to the unisexual/3n lineage. Genetic divergence among the lineages was ∼10% but was lower between the unisexual/3n and bisexual lineages (∼6%). Both mtDNA and nuDNA indicated that individuals from the bisexual lineages might belong to a new species. Nuclear DNA evidence indicates that crossings occasionally occur between unisexual 2n and males from the new bisexual species. Phylogenetic analysis of nuDNA showed L. ferreirai as the closest described bisexual species to the complex. Our results revealed an ancient origin of parthenogenesis in the L. percarinatum complex, in contrast to most young (Pleistocene) parthenogenetic lizards described thus far. Two hybridization events seem to have been involved: the first event occurred in late Miocene, between the ancestral lineage ("A") of the new bisexual species (as a maternal species) and the ancestral lineage of L. ferreirai, as a paternal species of L. percarinatum 2n; and the second event occurred in Pliocene-Pleistocene, in a backcross between L. percarinatum 2n and a male from the common ancestor ("B") of the new bisexual species giving rise to the lineage of L. percarinatum 3n. With these results, we showed that L. percarinatum complex also includes, at least, one undescribed bisexual species in addition to the two known parthenogenetic lineages (2n and 3n). Finally, we present evidence that diploid individuals of L. percarinatum experienced an event of wide demographic expansion over the past million years under an allele surfing model.},
}
@article {pmid30736942,
year = {2019},
author = {Hrazdilová, K and Myśliwy, I and Hildebrand, J and Buńkowska-Gawlik, K and Janaczyk, B and Perec-Matysiak, A and Modrý, D},
title = {Paralogs vs. genotypes? Variability of Babesia canis assessed by 18S rDNA and two mitochondrial markers.},
journal = {Veterinary parasitology},
volume = {266},
number = {},
pages = {103-110},
doi = {10.1016/j.vetpar.2018.12.017},
pmid = {30736942},
issn = {1873-2550},
mesh = {Animals ; Babesia/*genetics ; Babesiosis/blood/diagnosis/parasitology ; Cohort Studies ; DNA, Protozoan/genetics ; Dog Diseases/diagnosis/parasitology ; Dogs ; Europe ; Genetic Markers ; *Genetic Variation ; Genome, Protozoan ; *Genotype ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; },
abstract = {Canine babesiosis caused by Babesia canis sensu stricto became an emerging disease of dogs across Europe calling for attention also in countries where it was an only rare imported disease. An easy accessibility of molecular methods and the growing amount of sequencing data led to the description of intraspecific variability in 18S rDNA sequences designated as "genotypes". Using material from a homogenous cohort of dogs with microscopically confirmed canine babesiosis caused by B. canis, we evaluated Babesia intraspecific variability and amplification sensitivity of three different genes (18S rDNA, COI, Cytb) to assess their potential as diagnostic or phylogenetic markers. In raw sequencing data obtained, we observed at least 3 ambiguous positions in up to 86% of chromatograms within the ∼560 bp fragment of 18S rDNA suggesting the existence of several, not identical copies of this gene. Our COI haplotype analysis resulted in a star-like pattern indicating a recent origin of most haplotypes, but not supporting the existence of two dominant haplotypes. Similarly, the Cytb sequences obtained from samples with all variants of 18S rDNA were identical. We corroborate previous observations from three other European countries and bring the evidence of the existence of 18S rDNA paralogs in B. canis genome replacing currently used "genotype" theory.},
}
@article {pmid30753887,
year = {2019},
author = {Ni, Y and Ma, X and Hu, W and Blair, D and Yin, M},
title = {New lineages and old species: Lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China.},
journal = {Molecular phylogenetics and evolution},
volume = {134},
number = {},
pages = {87-98},
doi = {10.1016/j.ympev.2019.02.007},
pmid = {30753887},
issn = {1095-9513},
mesh = {Alleles ; Animals ; Bayes Theorem ; China ; Cladocera/anatomy &amp; histology/*classification/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Time Factors ; },
abstract = {The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.},
}
@article {pmid30761963,
year = {2019},
author = {Santacruz, A and Ornelas-García, CP and Pérez-Ponce de León, G},
title = {Diversity of Rhabdochona mexicana (Nematoda: Rhabdochonidae), a parasite of Astyanax spp. (Characidae) in Mexico and Guatemala, using mitochondrial and nuclear genes, with the description of a new species.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e34},
doi = {10.1017/S0022149X19000014},
pmid = {30761963},
issn = {1475-2697},
mesh = {Animals ; Cell Nucleus/*genetics ; Characidae/*parasitology ; Fish Diseases/*parasitology ; Guatemala ; Helminth Proteins/genetics ; Mexico ; Mitochondria/*genetics ; Phylogeny ; Spirurida Infections/parasitology/*veterinary ; Spiruroidea/classification/genetics/growth &amp; development/*isolation &amp; purification ; },
abstract = {Among fish parasitic nematodes Rhabdochona is one of the most speciose genera, with c. 100 species. Twelve congeneric species occur in Mexican freshwater fishes, in a region located between the Nearctic and Neotropical biogeographical regions. Host association and biogeographical history have determined the high species richness of Rhabdochona in Mexico. One of these species, Rhabdochona mexicana, is highly specific to the characid genus Astyanax. Characids are a group of freshwater fish with Neotropical affinity. In this paper, we explore the genetic diversity of R. mexicana through samples obtained from populations of Astyanax spp. across river basins of Mexico and Guatemala. Sequences of one mitochondrial and two ribosomal genes were obtained from 38 individuals and analysed using Maximum Likelihood and Bayesian Inference analysis. Phylogenetic analyses using cox1, and a concatenated alignment of 18S + 28S + cox1 recovered two genetic lineages. One of them corresponded with R. mexicana sensu stricto; this lineage included three reciprocally monophyletic subgroups; the other lineage was highly divergent and represented a putative candidate species. A detailed morphological study was conducted to corroborate the molecular findings. We describe a new species herein and discuss the implications of using molecular tools to increase our knowledge about the diversity of a speciose genus such as Rhabdochona.},
}
@article {pmid30763758,
year = {2019},
author = {Jowers, MJ and Sánchez-Ramírez, S and Lopes, S and Karyakin, I and Dombrovski, V and Qninba, A and Valkenburg, T and Onofre, N and Ferrand, N and Beja, P and Palma, L and Godinho, R},
title = {Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards.},
journal = {Molecular phylogenetics and evolution},
volume = {134},
number = {},
pages = {269-281},
doi = {10.1016/j.ympev.2019.02.004},
pmid = {30763758},
issn = {1095-9513},
mesh = {Animals ; Arctic Regions ; Bayes Theorem ; Birds/*genetics ; Climate Change ; DNA, Mitochondrial/genetics ; Demography ; Genetic Markers ; *Genetic Variation ; *Genetics, Population ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Mutation Rate ; *Paleontology ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.},
}
@article {pmid30785686,
year = {2018},
author = {Titov, VN and Aripovskiy, AV and Dmitriev, LF and Medvedev, OS},
title = {[Formation in the phylogenesis of three pulls of cells with expressed different absorption and metabolism of fatty acids. Insulin and medium chains fatty acids.].},
journal = {Klinicheskaia laboratornaia diagnostika},
volume = {63},
number = {12},
pages = {732-740},
doi = {10.18821/0869-2084-2018-63-12-732-740},
pmid = {30785686},
issn = {0869-2084},
mesh = {Animals ; Atherosclerosis ; Diet ; Fatty Acids/*metabolism ; Humans ; Insulin/*metabolism ; Insulin Resistance ; Metabolic Syndrome ; *Phylogeny ; },
abstract = {Somatic cells at the early stages of phylogenesis realized the metabolism of long-chain fatty acids (FA), primarily palmitic saturated FA. It dominated the construction of a bilayer cell membrane and as a substrate for oxidation in mitochondria during energy production. Later, polyene FAs became involved in the construction of the cell membrane, the membranes of intracellular organelles, and became the substrate for the synthesis of biologically active eicosanoids. At later stages of phylogenesis, the metabolism of medium-chain FAs is activated and the formation of ketone bodies as a substrate, which is available for oxidation by the mitochondria of the formed cells of the nervous tissue in the absence of first substrate glucose. In the later stages of phylogenesis, insulin initiated: a) the transformation of carnivorous ancestors of the species Homo sapiens in the ocean into a herbivorous species while living on land; b) the formation of the new biological function of locomotion and c) the dominance of the oleic variant of the metabolism of long-chain fatty acids with higher kinetic parameters of mitochondria oxidation. Metabolites of medium chain FA have become humoral mediators of metabolism and the formation of feedback mechanisms in the function of trophology and cognitive biological function. The formation of an oleic variant of the metabolism of fatty acids under the action of insulin led to the improvement of the energy supply of cells and the high kinetic parameters of many species of herbivorous mammals, including Homo sapiens. The species Homo sapiens was not omnivorous (Omnivores); the insulin's regulatory action during life on land has turned it into a herbivorous species (Herbivore), but with a carnivorous (Carnivore) (fish-eating) past. Seven metabolic pandemics (1. atherosclerosis and atheromatosis; 2. metabolic arterial hypertension; 3. metabolic syndrome; 4. insulin resistance syndrome; 5. obesity; 6. nonalcoholic fatty liver disease and 7. endogenous hyperuricemia) are only functional disorders and can be, in most cases, eliminated. From the standpoint of the phylogenetic theory of general pathology, atherosclerosis and atheromatosis of the arteries have no great future. As soon, as the majority of individuals of the Homo sapiens species realize that in phylogenesis they have formed as herbivores and stop eating excessive amounts of meat food, exogenous palmitic FA, the incidence in the population will begin to decrease. Patients are still obliged to justify the binary, biological name of the species - reasonable man. Prevention and other metabolic pandemics, diseases of civilization, can be discussed. It takes time, an understanding of what happens by the doctors, diligence and the desire of patients to be healthy.},
}
@article {pmid30790556,
year = {2019},
author = {Léveillé, AN and Baneth, G and Barta, JR},
title = {Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences.},
journal = {International journal for parasitology},
volume = {49},
number = {5},
pages = {375-387},
doi = {10.1016/j.ijpara.2018.12.001},
pmid = {30790556},
issn = {1879-0135},
mesh = {Animals ; Apicomplexa/classification/*genetics/isolation &amp; purification ; Apicoplasts/*genetics ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/parasitology ; Dogs ; Genome, Mitochondrial ; *Genome, Plastid ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Protozoan Infections, Animal/parasitology ; },
abstract = {Extrachromosomal genomes of the adeleorinid parasite Hepatozoon canis infecting an Israeli dog were investigated using next-generation and standard sequencing technologies. A complete apicoplast genome and several mitochondrion-associated sequences were generated. The apicoplast genome (31,869 bp) possessed two copies of both large subunit (23S) and small subunit (16S) ribosomal RNA genes (rDNA) within an inverted repeat region, as well as 22 protein-coding sequences, 25 transfer RNA genes (tDNA) and seven open reading frames of unknown function. Although circular-mapping, the apicoplast genome was physically linear according to next-generation data. Unlike other apicoplast genomes, genes encoding ribosomal protein S19 and tDNAs for alanine, aspartic acid, histidine, threonine and valine were not identified. No complete mitochondrial genome was recovered using next-generation data or directed PCR amplifications. Eight mitochondrion-associated (215-3523 bp) contigs assembled from next-generation data encoded a complete cytochrome c oxidase subunit I coding sequence, a complete cytochrome c oxidase subunit III coding sequence, two complete cytochrome B coding sequences, a non-coding, pseudogene for cytochrome B and multiple fragmented mitochondrial rDNA genes (SSUA, SSUB, SSUD, LSUC, LSUG, RNA6, RNA10, RNA14, RNA18). The paucity of NGS reads generating each of the mitochondrion-like sequences suggested that a complete mitochondrial genome at typically high copy number was absent in H. canis. In contrast, the complete nuclear rDNA unit sequence of H. canis (18S rDNA to 28S rDNA, 6977 bp) had >1000-fold next-generation coverage. Multiple divergent (from 93.6% to 99.9% pairwise identities) nuclear 18S rDNA contigs were generated (three types with 10 subtypes total). To our knowledge this is the first apicoplast genome sequenced from any adeleorinid coccidium and the first mitochondrion-associated sequences from this serious pathogen of wild and domestic canids. These newly generated sequences may provide useful genetic loci for high-resolution species-level genotyping that is currently impossible using existing nuclear rDNA targets.},
}
@article {pmid30807709,
year = {2019},
author = {Léveillé, AN and Bland, SK and Carlton, K and Larouche, CB and Kenney, DG and Brouwer, ER and Lillie, BN and Barta, JR},
title = {Klossiella equi Infecting Kidneys of Ontario Horses: Life Cycle Features and Multilocus Sequence-Based Genotyping Confirm the Genus Klossiella Belongs In the Adeleorina (Apicomplexa: Coccidia).},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {29-40},
pmid = {30807709},
issn = {1937-2345},
mesh = {Animals ; Coccidiosis/epidemiology/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eucoccidiida/*classification/genetics/growth &amp; development ; Female ; Genotyping Techniques/veterinary ; Horse Diseases/epidemiology/*parasitology ; Horses ; Kidney/parasitology ; Kidney Diseases/epidemiology/parasitology/*veterinary ; Life Cycle Stages ; Male ; Mitochondria/genetics ; Multilocus Sequence Typing/veterinary ; Ontario/epidemiology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Species in the genus Klossiella Smith and Johnson, 1902 are unique among the suborder Adeleorina because they are monoxenous in mammals exclusively, whereas all other reported members of the Adeleorina use invertebrates as definitive hosts. Unlike other coccidia, all members of the Adeleorina undergo syzygy, the association of microgamonts and macrogamonts before maturation to gametes and syngamy. After fertilization, many members of the Adeleorina produce thin-walled polysporocystic oocysts. Despite being biologically similar to other members of the Adeleorina, the phylogenetic placement of the genus Klossiella has been questioned based on its unique host affinity. In the present study, 2 cases of Klossiella equi were reported from the kidneys of horses in Ontario. Details of the life cycle as well as mitochondrial and nuclear 18S ribosomal DNA (18S rDNA) sequences were analyzed to provide both morphological and molecular evidence for the phylogenetic placement of K. equi. Initially, various stages of the life cycle were identified in histological slides prepared from the kidney tissue, and DNA was isolated from the infected tissue. Polymerase chain reaction and Sanger sequencing were used to generate a complete mitochondrial genome sequence (6,569 bp) and a partial 18S rDNA sequence (1,443 bp). The K. equi 18S rDNA sequence was aligned with various publicly available apicomplexan 18S rDNA sequences. This alignment was used to generate a phylogenetic tree based on Bayesian inference. Multiple K. equi stages were identified including meronts, microgamonts, and macrogamonts associating in syzygy as well as thin-walled oocysts in various stages of sporogonic development. The 18S rDNA sequence of K. equi positioned within the monophyletic Adeleorina clade. The mitochondrial genome of K. equi contained 3 coding sequences for cytochrome c oxidase I, cytochrome c oxidase III, and cytochrome b as well as various fragmented ribosomal sequences. These components were arranged in a unique order that has not been observed in other apicomplexan mitochondrial genomes sequenced to date. Overall, it was concluded that there were sufficient morphological and molecular data to confirm the placement of K. equi and the genus Klossiella among the Adeleorina. The biological and molecular data obtained from these cases may assist with future studies evaluating the prevalence and life history of this seemingly underreported parasite and better define the impact of K. equi on the health of domestic and wild equids.},
}
@article {pmid30807715,
year = {2019},
author = {Matsche, MA and Adams, CR and Blazer, VS},
title = {Newly Described Coccidia Goussia bayae from White Perch Morone americana: Morphology and Phylogenetics Support Emerging Taxonomy of Goussia within Piscine Hosts.},
journal = {The Journal of parasitology},
volume = {105},
number = {1},
pages = {1-10},
pmid = {30807715},
issn = {1937-2345},
mesh = {Animals ; Bass/*parasitology ; Bays ; Bile Ducts, Intrahepatic/parasitology ; Coccidiosis/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Eimeriidae/*classification/genetics/ultrastructure ; Electron Transport Complex IV/genetics ; Female ; Fish Diseases/*parasitology ; Gallbladder/parasitology ; Male ; Maryland ; Mitochondria/genetics ; Oocysts/ultrastructure ; Phylogeny ; Rivers ; Virginia ; },
abstract = {In March and April 2016, 150 white perch (Morone americana) were collected from various localities in Chesapeake Bay and examined for coccidia. A previously undescribed species of coccidia was observed in the hepatic bile ducts and gallbladder of all white perch (100%) examined. We describe this species using morphological characteristics, histology, and gene sequences of the small-subunit ribosomal DNA (rDNA), large-subunit rDNA, and mitochondrial genes cytochrome oxidase 1 (COI), cytochrome oxidase b (Cytb), and cytochrome oxidase 3 (COIII). Oocysts of Goussia bayae n. sp. were subspherical with a single-layered smooth wall and measured (length [L] × width [W]) 26.2 × 21.8 μm, with a L/W ratio of 1.2. A micropyle was present but a micropyle cap, polar granules, and oocyst residuum were absent. Each oocyst contained 4 sporocysts that were ellipsoidal and measured (L × W) 12.6 × 7.8 μm, with a L/W ratio of 1.6. A pair of sporozoites was present, but sporocysts lacked a Stieda body and residuua. Meronts and gamonts were epicellular in biliary epithelial cells and oocysts were coelozoic in hepatic and common bile ducts and gallbladder. This is the first report of Goussia spp. from white perch and the first mitochondrial DNA sequence reported from a Goussia species. Phylogenetic analysis indicates basal placement of G. bayae to Eimeriidae, Choleoeimeria, and Sarcocystidae.},
}
@article {pmid30837540,
year = {2019},
author = {Vai, S and Sarno, S and Lari, M and Luiselli, D and Manzi, G and Gallinaro, M and Mataich, S and Hübner, A and Modi, A and Pilli, E and Tafuri, MA and Caramelli, D and di Lernia, S},
title = {Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {3530},
pmid = {30837540},
issn = {2045-2322},
mesh = {Adult ; Archaeology ; DNA, Mitochondrial/chemistry/classification/genetics ; Female ; Fossils ; Genetic Linkage ; Genome, Mitochondrial ; Haplotypes ; Humans ; Mitochondria/classification/*genetics ; Phylogeny ; Skull/metabolism ; },
abstract = {Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.},
}
@article {pmid30854666,
year = {2019},
author = {Wang, W and Chen, J and Liao, B and Xia, L and Hou, S and Wang, Z and Lu, Y},
title = {Identification and functional characterization of Histone-like DNA-binding protein in Nocardia seriolae (NsHLP) involved in cell apoptosis.},
journal = {Journal of fish diseases},
volume = {42},
number = {5},
pages = {657-666},
doi = {10.1111/jfd.12962},
pmid = {30854666},
issn = {1365-2761},
support = {KY20160207//Shenzhen Dapeng New District special fund for industry development/ ; 2016A050502061//International S&amp;T Cooperation Projects of Guangdong Province/ ; JCYJ20170306161613251//Shenzhen Science and Technology Project/ ; 2017A030313179//Natural Science Foundation of Guangdong Province/ ; C17377//Natural Science Foundation of Guangdong Ocean University/ ; C13454//Natural Science Foundation of Guangdong Ocean University/ ; E10085//Natural Science Foundation of Guangdong Ocean University/ ; },
mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Cyprinidae ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Fish Diseases/microbiology/*physiopathology ; Nocardia/genetics/*physiology ; Nocardia Infections/microbiology/physiopathology/*veterinary ; Phylogeny ; Sequence Alignment/veterinary ; },
abstract = {Nocardia seriolae, a facultative intracellular bacterium, is the main pathogen of fish nocardiosis. Bioinformatic analysis showed that the histone-like DNA-binding protein (HLP) gene of N. seriolae (nshlp) encoded a secreted protein and might target the mitochondria in the host cell. To further study the preliminary function of HLP in N. seriolae (NsHLP), the gene cloning, extracellular products identification, subcellular localization, overexpression and apoptosis detection assay were carried out in this study. Mass spectrometry analysis of the extracellular products from N. seriolae showed that NsHLP was a secreted protein. Subcellular localization of HLP-GFP fusion proteins mainly assembled in the nucleus, which indicated that the NsHLP was co-located with the nucleus rather than mitochondria in fathead minnow (FHM) cells. Notably, the expression of NsHLP had changed the distribution of mitochondria into lumps in the FHM cell. In addition, apoptotic features were found in the transfected FHM cells by overexpression of NsHLP. Quantitative assays of mitochondrial membrane potential value, caspase-3 activity and pro-apoptotic genes mRNA (Bad, Bid and Bax) expression level demonstrated that the cell apoptosis was induced in the transfected FHM cells. All the results presented in this study provided insight on the function of NsHLP, which suggested that it may participate in the cell apoptosis regulation and play an important role in the pathogenesis of N. seriolae.},
}
@article {pmid30870981,
year = {2019},
author = {Du, Z and Ishikawa, T and Liu, H and Kamitani, S and Tadauchi, O and Cai, W and Li, H},
title = {Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences.},
journal = {International journal of molecular sciences},
volume = {20},
number = {5},
pages = {},
pmid = {30870981},
issn = {1422-0067},
support = {31772498//National Natural Science Foundation of China/ ; 2018QC089; 2018QC119//Chinese Universities Scientific Fund/ ; },
mesh = {Animals ; Cell Nucleus/*genetics ; Climate ; DNA, Mitochondrial/*genetics ; Ecosystem ; Asia, Eastern ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; Triatoma/*genetics ; },
abstract = {The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a "dispersal corridor" during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the "Ryukyu Coral Sea Stage" and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids.},
}
@article {pmid30872700,
year = {2019},
author = {Johri, S and Solanki, J and Cantu, VA and Fellows, SR and Edwards, RA and Moreno, I and Vyas, A and Dinsdale, EA},
title = {'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {4476},
pmid = {30872700},
issn = {2045-2322},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; Endangered Species ; Fish Proteins/genetics ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*instrumentation/veterinary ; India ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/instrumentation/veterinary ; Sharks/*classification/genetics ; },
abstract = {Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.},
}
@article {pmid30893316,
year = {2019},
author = {Fregel, R and Ordóñez, AC and Santana-Cabrera, J and Cabrera, VM and Velasco-Vázquez, J and Alberto, V and Moreno-Benítez, MA and Delgado-Darias, T and Rodríguez-Rodríguez, A and Hernández, JC and Pais, J and González-Montelongo, R and Lorenzo-Salazar, JM and Flores, C and Cruz-de-Mercadal, MC and Álvarez-Rodríguez, N and Shapiro, B and Arnay, M and Bustamante, CD},
title = {Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0209125},
pmid = {30893316},
issn = {1932-6203},
mesh = {Africa, Northern/ethnology ; Ethnicity/*genetics ; Europe/ethnology ; Genetic Drift ; Genetics, Population ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Middle East ; Mitochondria/*genetics ; Phylogeography ; Sequence Analysis, DNA ; Spain/ethnology ; Transients and Migrants/*classification ; },
abstract = {The Canary Islands' indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.},
}
@article {pmid30893849,
year = {2019},
author = {Ding, F and Cheng, J and Fu, Y and Chen, T and Li, B and Jiang, D and Xie, J},
title = {Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum.},
journal = {Viruses},
volume = {11},
number = {3},
pages = {},
pmid = {30893849},
issn = {1999-4915},
mesh = {Ascomycota/*genetics/pathogenicity/*virology ; DNA Viruses/*genetics ; *Gene Expression Profiling ; Hyphae/genetics/virology ; Phylogeny ; Sequence Analysis, DNA ; Virion/genetics ; Virulence ; },
abstract = {We previously determined that virions of Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 (SsHADV-1) could directly infect hyphae of Sclerotinia sclerotiorum, resulting in hypovirulence of the fungal host. However, the molecular mechanisms of SsHADV-1 virions disruption of the fungal cell wall barrier and entrance into the host cell are still unclear. To investigate the early response of S. sclerotiorum to SsHADV-1 infection, S. sclerotiorum hyphae were inoculated with purified SsHADV-1 virions. The pre- and post-infection hyphae were collected at one[-]three hours post-inoculation for transcriptome analysis. Further, bioinformatic analysis showed that differentially expressed genes (DEGs) regulated by SsHADV-1 infection were identified in S. sclerotiorum. In total, 187 genes were differentially expressed, consisting of more up-regulated (114) than down-regulated (73) genes. The identified DEGs were involved in several important pathways. Metabolic processes, biosynthesis of antibiotics, and secondary metabolites were the most affected categories in S. sclerotiorum upon SsHADV-1 infection. Cell structure analysis suggested that 26% of the total DEGs were related to membrane tissues. Furthermore, 10 and 27 DEGs were predicted to be located in the cell membrane and mitochondria, respectively. Gene ontology enrichment analyses of the DEGs were performed, followed by functional annotation of the genes. Interestingly, one third of the annotated functional DEGs could be involved in the Ras-small G protein signal transduction pathway. These results revealed that SsHADV-1 virions may be able to bind host membrane proteins and influence signal transduction through Ras-small G protein-coupled receptors during early infection, providing new insight towards the molecular mechanisms of virions infection in S. sclerotiorum.},
}
@article {pmid30897177,
year = {2019},
author = {Liao, L and Dong, T and Liu, X and Dong, Z and Qiu, X and Rong, Y and Sun, G and Wang, Z},
title = {Effect of nitrogen supply on nitrogen metabolism in the citrus cultivar 'Huangguogan'.},
journal = {PloS one},
volume = {14},
number = {3},
pages = {e0213874},
pmid = {30897177},
issn = {1932-6203},
mesh = {Citrus/growth &amp; development/*metabolism ; Cytoplasm/metabolism ; Fruit/metabolism ; Gene Expression Regulation, Plant ; Glutamate Dehydrogenase/classification/genetics/metabolism ; Glutamate-Ammonia Ligase/classification/genetics/metabolism ; Nitrate Reductase/classification/genetics/metabolism ; Nitrogen/*metabolism ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/classification/genetics/*metabolism ; Plant Roots/metabolism ; Seedlings/growth &amp; development/metabolism ; },
abstract = {Nitrogen metabolism in citrus has received increased attention due to its effects on plant growth and productivity. However, little is known about the effects of nitrogen fertilization on nitrogen metabolism in young trees of citrus cultivar 'Huangguogan' (Citrus reticulata × Citrus sinensis). Here, genes encoding nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate dehydrogenase (GDH), and asparagine synthetase (AS), represented as HgNR, HgNiR, HgGS, HgGDH, and HgAS, respectively, were cloned from Huangguogan. Deduced protein sequences were analyzed and proteins were confirmed to be localized in their respective cellular organelles. Moreover, pot-cultured 'Huangguogan' seedlings were fertilized with 0 (N1), 1.36 (N2), 1.81 (N3), 2.26 (N4), or 2.72 (N5) kg N/year, for 12 months. Enzyme activity and enzyme-gene expression were studied in roots, leaves, and fruits at different stages. Finally, the effects of N application rate on root activity, leaf N, soluble protein, yield, and fruit quality at the ripening stage were measured. The results showed that: 1) HgNR, HgNiR, HgGDH, and HgAS gene products were found mainly in the cytoplasm and plasma membrane, while HgGS gene product was found mainly in cytoplasm and mitochondria. 2) Gene expression and enzyme activity differed among plant organs. As the root is in permanent direct contact with the soil we suggest that root gene expression and enzyme activity can be used as reference to determine N application rate. 3) Yield, fruit quality, enzyme activity, and enzyme-related gene expression were considerably lower at low than at high-N supply. However, they were all inhibited by excess nitrogen (i.e., 2.72 kg/year). Therefore, we recommend 1.81 kg N/year as the optimal N application rate for young 'Huangguogan' trees.},
}
@article {pmid30909863,
year = {2019},
author = {Shaari, N'AL and Jaoi-Edward, M and Loo, SS and Salisi, MS and Yusoff, R and Ab Ghani, NI and Saad, MZ and Ahmad, H},
title = {Karyotypic and mtDNA based characterization of Malaysian water buffalo.},
journal = {BMC genetics},
volume = {20},
number = {1},
pages = {37},
pmid = {30909863},
issn = {1471-2156},
mesh = {Animals ; Buffaloes/classification/*genetics ; *DNA, Mitochondrial ; Genetic Variation ; Haplotypes ; Karyotype ; *Karyotyping ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {BACKGROUND: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed.<br><br>RESULTS: Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000&#x2009;&#xb1;&#x2009;0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds.<br><br>CONCLUSION: Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.},
}
@article {pmid30945675,
year = {2019},
author = {Saikia, M and Nath, R and Devi, D},
title = {Genetic diversity and phylogeny analysis of Antheraea assamensis Helfer (Lepidoptera: Saturniidae) based on mitochondrial DNA sequences.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {30945675},
issn = {0973-7731},
mesh = {Animals ; Bombyx/*classification/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Mitochondria ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Antheraea assamensis Helfer, popularly known as Muga silkworm, the golden silk producer of northeast India is economically important and unique among the Saturniid silkworms. In this study, the genetic diversity and phylogeny of semidomesticated and wild morphs of Muga silkwormcollected from different geographical locations of northeast India were investigated based on the sequences of five mitochondrial loci, i.e. 12S rRNA, 16S rRNA, CoxI, Cytb and CR. All the five mitochondrial loci showed a strong bias towards higher 'A' and 'T' contents. Transitional substitutions were found to be more than the transversional substitutions. The rate of nucleotide substitution and average genetic divergence were found to be highest in CR sequences and lowest in 12S rRNA gene sequences among the morphs of Muga silkworm. The morphs collected from same geographical area had identical 12S rRNA, 16S rRNA, CoxI and Cytb gene sequences. Moreover, the 12S rRNA and 16S rRNA gene sequences of somesemi-domesticated and wild morphs collected from different geographical locations were also found to be similar. In the phylogenetic trees generated based on themitochondrial loci, mixing of semi-domesticated and wild morphs was observed as they shared the same group. The information generated in this study will help in formulating strategies to conserve the natural biodiversity present among these unique silkworms in northeast India. In addition, this will be useful in identifying diverse morphs of Muga silkworm, which will help in effective breeding programmes to improve its productivity.},
}
@article {pmid30949694,
year = {2019},
author = {Greiner, S and Lehwark, P and Bock, R},
title = {OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.},
journal = {Nucleic acids research},
volume = {47},
number = {W1},
pages = {W59-W64},
pmid = {30949694},
issn = {1362-4962},
mesh = {Chromosome Mapping ; Genome, Mitochondrial/*genetics ; Genome, Plastid/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Molecular Sequence Annotation ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; *Software ; },
abstract = {Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.},
}
@article {pmid30954588,
year = {2019},
author = {Sajeela, KA and Gopalakrishnan, A and Basheer, VS and Mandal, A and Bineesh, KK and Grinson, G and Gopakumar, SD},
title = {New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {53-64},
doi = {10.1016/j.ympev.2019.04.007},
pmid = {30954588},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Indian Ocean ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Penaeidae/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.},
}
@article {pmid30967590,
year = {2019},
author = {Kehlmaier, C and Zhang, X and Georges, A and Campbell, PD and Thomson, S and Fritz, U},
title = {Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {5841},
pmid = {30967590},
issn = {2045-2322},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Turtles/*genetics ; },
abstract = {Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.},
}
@article {pmid30974201,
year = {2019},
author = {Strong, EE and Whelan, NV},
title = {Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda).},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {87-103},
doi = {10.1016/j.ympev.2019.04.009},
pmid = {30974201},
issn = {1095-9513},
mesh = {Algorithms ; Animal Shells/anatomy &amp; histology ; Animals ; Bayes Theorem ; California ; Cell Nucleus/genetics ; Gastropoda/anatomy &amp; histology/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&amp;P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&amp;P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.},
}
@article {pmid30981810,
year = {2019},
author = {Pazmiño, DA and van Herderden, L and Simpfendorfer, CA and Junge, C and Donnellan, SC and Hoyos-Padilla, EM and Duffy, CAJ and Huveneers, C and Gillanders, BM and Butcher, PA and Maes, GE},
title = {Introgressive hybridisation between two widespread sharks in the east Pacific region.},
journal = {Molecular phylogenetics and evolution},
volume = {136},
number = {},
pages = {119-127},
doi = {10.1016/j.ympev.2019.04.013},
pmid = {30981810},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; California ; Computer Simulation ; DNA, Mitochondrial/genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sample Size ; Sharks/*genetics ; },
abstract = {With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine genetic admixture and introgression between the two species. Using empirical analytical approaches and simulations, we first developed a set of 1873 highly informative SNPs for these two species to evaluate the degree of admixture between them. Overall, results indicate a high discriminatory power of nuclear SNPs (FST = 0.47, p < 0.05) between the two species, unlike mitochondrial DNA (ΦST = 0.00 p > 0.05), which failed to differentiate these species. We identified four hybrid individuals (∼1%) and detected bi-directional introgression between C. galapagensis and C. obscurus in the Gulf of California along the east Pacific coast of the Americas. We emphasize the importance of including a combination of mtDNA and diagnostic nuclear markers to properly assess species identification, detect patterns of hybridisation, and better inform management and conservation of these sharks, especially given the morphological similarities within the genus Carcharhinus.},
}
@article {pmid31017302,
year = {2019},
author = {Escobar L, MD and Ota, RP and Machado-Allison, A and Andrade-López, J and Farias, IP and Hrbek, T},
title = {A new species of Piaractus (Characiformes: Serrasalmidae) from the Orinoco Basin with a redescription of Piaractus brachypomus.},
journal = {Journal of fish biology},
volume = {95},
number = {2},
pages = {411-427},
doi = {10.1111/jfb.13990},
pmid = {31017302},
issn = {1095-8649},
support = {CNPq 490682/2010-3//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; 482662/2013-1 to T.H//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; CNPq/PPG7 5570090/2005-9//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; CNPq/CT-Amazon 575603/2008-9//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; (CAPES 53923790287)//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; CAPES 12002011001P7//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; (306804/2013-3)//CNPq research fellowship/ ; (303646/2010-1)//CNPq research fellowship/ ; },
mesh = {Animal Fins/anatomy &amp; histology ; Animal Scales/anatomy &amp; histology ; Animals ; Brazil ; Characiformes/anatomy &amp; histology/*classification/genetics ; Colombia ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Fisheries/organization &amp; administration ; Lateral Line System/anatomy &amp; histology ; Likelihood Functions ; Maxilla/anatomy &amp; histology ; Mitochondria/genetics ; Phylogeny ; Pigmentation ; Poisson Distribution ; Rivers ; Sequence Alignment ; Software ; Spine/anatomy &amp; histology ; Terminology as Topic ; },
abstract = {Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species.},
}
@article {pmid31018163,
year = {2019},
author = {Torres-Cambas, Y and Ferreira, S and Cordero-Rivera, A and Lorenzo-Carballa, MO},
title = {Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): Vicariance or long-distance dispersal?.},
journal = {Molecular phylogenetics and evolution},
volume = {137},
number = {},
pages = {14-21},
doi = {10.1016/j.ympev.2019.04.018},
pmid = {31018163},
issn = {1095-9513},
mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Cuba ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Odonata/*genetics/*physiology ; Phylogeny ; Species Specificity ; Time Factors ; },
abstract = {We have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear DNA gene fragments were amplified to reconstruct phylogenetic relationships and estimate divergence times in this genus. Hypolestes comprises currently three species, which consist in four geographically and genetically isolated lineages located in Jamaica, Hispaniola, Eastern Cuba and Central Cuba. Results of our analyses suggest that the three species diverged between ∼5.91 and 1.69 mya, and that the separation between the lineages from Central Cuba and Eastern Cuba occurred between ∼2.0 and 0.62 mya. Disjunct distributions in the genus Hypolestes can be better explained by a long-distance dispersal mechanism, since the divergence times of the three species do not coincide with the timeline formation of the geographic barriers between Cuba, Hispaniola and Jamaica. The Cuban lineages of H. trinitatis constitute different molecular operational taxonomic units (MOTU). The elevation of these MOTU to the species category requires the analysis of additional characters.},
}
@article {pmid31018611,
year = {2019},
author = {Crottini, A and Orozco-terWengel, P and Rabemananjara, FCE and Hauswaldt, JS and Vences, M},
title = {Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella.},
journal = {Genes},
volume = {10},
number = {4},
pages = {},
pmid = {31018611},
issn = {2073-4425},
mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Introgression ; Genetics, Population ; Homeodomain Proteins/genetics ; Madagascar ; Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Skin Pigmentation/*genetics ; },
abstract = {Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.},
}
@article {pmid31028468,
year = {2019},
author = {Buddhachat, K and Chontananarth, T},
title = {Is species identification of Echinostoma revolutum using mitochondrial DNA barcoding feasible with high-resolution melting analysis?.},
journal = {Parasitology research},
volume = {118},
number = {6},
pages = {1799-1810},
pmid = {31028468},
issn = {1432-1955},
mesh = {Animals ; Asia, Southeastern ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry/*genetics ; Echinostoma/chemistry/*classification/genetics/*isolation &amp; purification ; Mitochondria/genetics ; Phylogeny ; Thailand ; Transition Temperature ; },
abstract = {The taxonomic evaluation of Echinostoma species is controversial. Echinostoma species are recognized as complex, leading to problems associated with accurate identification of these species. The aim of this study was to test the feasibility of using DNA barcoding of cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) conjugated with high-resolution melting (HRM) analysis to identify Echinostoma revolutum. HRM using COI and ND1 was unable to differentiate between species in the "revolutum complex" but did distinguish between two isolates of 37-collar-spined echinostome species, including E. revolutum (Asian lineage) and Echinostoma sp. A from different genera, e.g., Hypoderaeum conoideum, Haplorchoides mehrai, Fasciola gigantica, and Thapariella anastomusa, based on the Tm values derived from HRM analysis. Through phylogenetic analysis, a new clade of the cryptic species known as Echinostoma sp. A was identified. In addition, we found that the E. revolutum clade of ND1 phylogeny obtained from the Thailand strain was from a different lineage than the Eurasian lineage. These findings reveal the complexity of the clade, which is composed of 37-collar-spined echinostome species found in Southeast Asia. Taken together, the systematic aspects of the complex revolutum group are in need of extensive investigation by integrating morphological, biological, and molecular features in order to clarify them, particularly in Southeast Asia.},
}
@article {pmid31029862,
year = {2020},
author = {Rawal, HC and Kumar, PM and Bera, B and Singh, NK and Mondal, TK},
title = {Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation.},
journal = {Genomics},
volume = {112},
number = {1},
pages = {659-668},
doi = {10.1016/j.ygeno.2019.04.018},
pmid = {31029862},
issn = {1089-8646},
mesh = {Camellia/*genetics ; Chloroplast Proteins/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Chloroplast/genetics ; RNA, Mitochondrial/genetics ; },
abstract = {The NCBI database has >15 chloroplast (cp) genome sequences available for different Camellia species but none for C. assamica. There is no report of any mitochondrial (mt) genome in the Camellia genus or Theaceae family. With the strong believes that these organelle genomes can play a great tool for taxonomic and phylogenetic analysis, we successfully assembled and analyzed cp and mt genome of C. assamica. We assembled the complete mt genome of C. assamica in a single circular contig of 707,441 bp length comprising of a total of 66 annotated genes, including 35 protein-coding genes, 29 tRNAs and two rRNAs. The first ever cp genome of C. assamica resulted in a circular contig of 157,353 bp length with a typical quadripartite structure. Phylogenetic analysis based on these organelle genomes showed that C. assamica was closely related to C. sinensis and C. leptophylla. It also supports Caryophyllales as Superasterids.},
}
@article {pmid31035578,
year = {2019},
author = {Banguera-Hinestroza, E and Ferrada, E and Sawall, Y and Flot, JF},
title = {Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.},
journal = {Genes},
volume = {10},
number = {5},
pages = {},
pmid = {31035578},
issn = {2073-4425},
mesh = {Animals ; Anthozoa/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Ecosystem ; Indian Ocean ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Phylogeography ; Protein Conformation ; Tandem Repeat Sequences/genetics ; },
abstract = {More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.},
}
@article {pmid31068124,
year = {2019},
author = {Wu, Z and Hu, K and Yan, M and Song, L and Wen, J and Ma, C and Shen, J and Fu, T and Yi, B and Tu, J},
title = {Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {348},
pmid = {31068124},
issn = {1471-2164},
support = {31571746//National Natural Science Foundation of China/ ; 2016YFD0100804//National Key Research and Development Program of China/ ; 2662016PY063//the Fundamental Research Funds for the Central Universities/ ; 2016ABA084//Hubei Key Technological Innovation Project/ ; },
mesh = {Cytoplasm/*genetics ; Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mustard Plant/*genetics/physiology ; Open Reading Frames ; Phylogeny ; *Plant Infertility ; Plant Proteins/*genetics ; },
abstract = {BACKGROUND: Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea.<br><br>RESULTS: The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes.<br><br>CONCLUSIONS: On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.},
}
@article {pmid31077734,
year = {2019},
author = {Karagozlu, MZ and An, HE and Park, SH and Shin, SE and Kim, CB},
title = {Comparative analyses of the three complete mitochondrial genomes from forensic important beetle genus Dermestes with phylogenetic relationships.},
journal = {Gene},
volume = {706},
number = {},
pages = {146-153},
doi = {10.1016/j.gene.2019.05.020},
pmid = {31077734},
issn = {1879-0038},
mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Coleoptera/*genetics ; Forensic Sciences/methods ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {Necrophagous Dermestes species have high forensic importance in relation to the estimation of elapsed time since death or death season. To further supplement the genome-level features for related species, the complete mitochondrial genome (mitogenome) of Dermestes species D. essellatocollis, D. frischii and D. coarctatus are amplified, sequenced, annotated, analyzed, and compared with other twelve species of the infraorder Bostrichoidea. The mitochondrial genomes were typical circular molecules with 16,218, 15,873 and 15,873 bp in length, respectively. They included 13 protein coding genes, two rRNAs, and 22 tRNAs, as well as the putative control region. The gene orders and orientations are identical to those of other recorded bostrichiformian species and had the ancestral insect gene composition. Furthermore, phylogenetic analyses based on all the mitochondrial protein coding genes for 13 Bostrichoidea and 16 outgroup taxa were performed using Bayesian and Maximum Likelihood analyses. The inferred trees indicate that the genus Dermestes is monophyletic. The monophyly of infraorder Bostrichiformia is not supported. This study provides genomic data for mitochondrial genome library of the genus Dermestes to investigate evolutionary and systematic studies.},
}
@article {pmid31125665,
year = {2019},
author = {Liu, W and Chen, B and Chen Li, and Yao, J and Liu, J and Kuang, M and Wang, F and Wang, Y and Elkady, G and Lu, Y and Zhang, Y and Liu, X},
title = {Identification of fish CMPK2 as an interferon stimulated gene against SVCV infection.},
journal = {Fish &amp; shellfish immunology},
volume = {92},
number = {},
pages = {125-132},
doi = {10.1016/j.fsi.2019.05.032},
pmid = {31125665},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Fish Diseases/*immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Interferons/metabolism ; Nucleoside-Phosphate Kinase/*genetics/*immunology ; Phylogeny ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary ; Sequence Alignment/veterinary ; Zebrafish/*genetics/*immunology ; Zebrafish Proteins/*genetics/*immunology ; },
abstract = {Cytidine/uridine monophosphate kinase 2 (CMPK2) is known as a nucleoside monophosphate kinase in mitochondria to maintains intracellular UTP/CTP, and could be induced by immunostimulants LPS and Poly (I:C) in mammals, suggesting its potential antiviral and antibacterial role. In this study, CMPK2 was cloned and characterized in Fathead minnow (FHM) cells. In vivo analysis of tissue distribution revealed that CMPK2 transcript was detected in all the tissues of zebrafish (Danio rerio) examined in this study, particularly abundant in liver, spleen and kidney. In addition, indirect immunofluorescence showed that CMPK2 was localized in the cytoplasm of FHM cells. Expression of CMPK2 mRNA was significantly up-regulated following challenge with Spring viraemia of carp virus (SVCV), poly(I:C), or zebrafish IFN1 and IFN3 both in vitro and in vivo. Furthermore, overexpression and RNA interference of CMPK2 in SVCV-infected FHM cells showed significantly antiviral effect. In summary, this study for the first time shows the presence and distribution of CMPK2 in different tissues of zebrafish, but also demonstrates its antiviral potential against SVCV infection in vivo. These new findings could contribute to explain the molecular mechanism of the CMPK2 mediated antiviral function.},
}
@article {pmid31152352,
year = {2019},
author = {Lassance, JM and Svensson, GP and Kozlov, MV and Francke, W and Löfstedt, C},
title = {Pheromones and Barcoding Delimit Boundaries between Cryptic Species in the Primitive Moth Genus Eriocrania (Lepidoptera: Eriocraniidae).},
journal = {Journal of chemical ecology},
volume = {45},
number = {5-6},
pages = {429-439},
pmid = {31152352},
issn = {1573-1561},
mesh = {Animals ; DNA/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Genetic Variation ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/classification/genetics ; Male ; Mitochondria/genetics ; Moths/*genetics ; Phylogeny ; Sex Attractants/*chemistry/metabolism ; },
abstract = {Animal classification is primarily based on morphological characters, even though these may not be the first to diverge during speciation. In many cases, closely related taxa are actually difficult to distinguish based on morphological characters alone, especially when there is no substantial niche separation. As a consequence, the diversity of certain groups is likely to be underestimated. Lepidoptera -moths and butterflies- represent the largest group of herbivorous insects. The extensive diversification in the group is generally assumed to have its origin in the spectacular radiation of flowering plants and the resulting abundance of ecological niches. However, speciation can also occur without strong ecological divergence. For example, reproductive isolation can evolve as the result of divergence in mate preference and the associated pheromone communication system. We combined pheromone trapping and genetic analysis to elucidate the evolutionary relationships within a complex of primitive moth species (Lepidoptera: Eriocraniidae). Mitochondrial and nuclear DNA markers provided evidence that Eriocrania semipurpurella, as currently defined by morphological characters, includes three cryptic species in Northern and Western Europe. Male moths of these cryptic species, as well as of the closely related E. sangii, exhibited relative specificity in terms of their attraction to specific ratios of two major pheromone components, (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol. Our data suggest strong assortative mating in these species in the absence of apparent niche separation, indicating that Eriocrania moths may represent an example of non-ecological speciation. Finally, our study argues in favour of combining pheromone investigations and DNA barcoding as powerful tools for identifying and delimitating species boundaries.},
}
@article {pmid31154527,
year = {2019},
author = {Suleman, and Khan, MS and Heneberg, P and Zhou, CY and Muhammad, N and Zhu, XQ and Ma, J},
title = {Characterization of the complete mitochondrial genome of Uvitellina sp., representative of the family Cyclocoelidae and phylogenetic implications.},
journal = {Parasitology research},
volume = {118},
number = {7},
pages = {2203-2211},
pmid = {31154527},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Birds/parasitology ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Echinostomatidae/classification/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial (mt) DNA has been useful in revealing the phylogenetic relationship of eukaryotic organisms including flatworms. Therefore, the use of mitogenomic data for the comparative and phylogenetic purposes is needed for those families of digenetic trematodes for which the mitogenomic data are still missing. Molecular data with sufficiently rich informative characters that can better resolve species identification, discrimination, and membership in different genera is also required for members of some morphologically difficult families of trematodes bearing few autapomorphic characters among its members. Here, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and the complete mt genome of the trematode Uvitellina sp. (Cyclocoelidae: Haematotrephinae) was determined and annotated. The mt genome of this avian trematode is 14,217 bp in length, containing 36 genes plus a single non-coding region. The ITS rDNA sequences were used for the pairwise sequence comparison of Uvitellina sp. with European cyclocoelid species, and the mitochondrial 12 protein-coding genes (PCGs) and two ribosomal RNA genes were used to evaluate the position of the family within selected trematodes. The ITS rDNA analysis of Uvitellina sp. showed less nucleotide differences with Hyptiasmus oculeus (16.77%) than with other European cyclocoelids (18.63-23.58%). The Bayesian inference (BI) analysis using the 12 mt PCGs and two rRNA genes supported the placement of the family Cyclocoelidae within the superfamily Echinostomatoidea (Plagiorchiida: Echinostmata). The availability of the mt genome sequences of Uvitellina sp. provides a novel resource of molecular markers for phylogenetic studies of Cyclocoelidae and other trematodes.},
}
@article {pmid31168607,
year = {2019},
author = {Hood, WR and Williams, AS and Hill, GE},
title = {An Ecologist's Guide to Mitochondrial DNA Mutations and Senescence.},
journal = {Integrative and comparative biology},
volume = {59},
number = {4},
pages = {970-982},
doi = {10.1093/icb/icz097},
pmid = {31168607},
issn = {1557-7023},
mesh = {Aging/*genetics ; Animals ; DNA, Mitochondrial/*genetics ; *Microsatellite Instability ; Mitochondria/genetics/*physiology ; Mutation/*physiology ; Mutation Rate ; },
abstract = {Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual's age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.},
}
@article {pmid31192351,
year = {2019},
author = {Zhang, D and Zou, H and Hua, CJ and Li, WX and Mahboob, S and Al-Ghanim, KA and Al-Misned, F and Jakovlić, I and Wang, GT},
title = {Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda.},
journal = {Genome biology and evolution},
volume = {11},
number = {7},
pages = {1797-1812},
pmid = {31192351},
issn = {1759-6653},
mesh = {Algorithms ; Animals ; Genome, Mitochondrial/*genetics ; Isopoda/*genetics ; Mitochondria/*genetics ; Mutation/genetics ; Phylogeny ; },
abstract = {The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.},
}
@article {pmid31203477,
year = {2019},
author = {Hu, F and Fan, J and Wu, C and Zhu, M and Zhou, Y and Wang, S and Zhang, C and Tao, M and Zhao, R and Tang, C and Luo, K and Qin, Q and Ma, M and Chen, B and Wang, J and Zhou, A and Bai, L and Liu, S},
title = {Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {21},
number = {4},
pages = {515-525},
pmid = {31203477},
issn = {1436-2236},
support = {31802286//National Natural Science Foundation of China/International ; 31430088//National Natural Science Foundation of China/International ; 31730098//National Natural Science Foundation of China/International ; 2018M642986//Postdoctoral Research Foundation of China/International ; CARS-45//Earmarked Fund for China Agriculture Research System/International ; },
mesh = {Animals ; Chromosomes/*chemistry ; Cyprinidae/classification/*genetics ; Gene Ontology ; *Genome ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Karyotype ; Mitochondria/genetics ; Molecular Sequence Annotation ; Phylogeny ; Ploidies ; Sequence Analysis, DNA ; *Transcriptome ; },
abstract = {Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 50 chromosomes [corrected]. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1-91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma.},
}
@article {pmid31204914,
year = {2019},
author = {Wang, J and Zhou, YA and Su, LP and Li, FM and Chen, M},
title = {[Instability of Mitochondrial DNA D-loop Region Genes in Patients with Leukemia].},
journal = {Zhongguo shi yan xue ye xue za zhi},
volume = {27},
number = {3},
pages = {657-663},
doi = {10.19746/j.cnki.issn.1009-2137.2019.03.005},
pmid = {31204914},
issn = {1009-2137},
mesh = {*DNA, Mitochondrial ; Humans ; *Leukemia ; Mitochondria ; Mutation ; Mutation Rate ; },
abstract = {OBJECTIVE: To study the instability of mitochondrial DNA（mt DNA） D-loop region genes in patients with Leukemia.<br><br>METHODS: The HV-1 and HV-2 regions of D-loop region in 24 patients with leukemia were amplificated and sequenced, then their results were compared with revised Cambridge reference sequence (rCRS) and Databank mtDB. The mutation rate was detected by SPSS 22.0 statistics software.<br><br>RESULTS: The total mutation rate in patients was 95.83% (23/24), the detection showed 82 mutated genes, out of which 47 (57.32%) mutated genes located in HV-1 region, 35 (42.68%) mutated genes in HV-2 region. The comparison showed that the mutation rate in untreated (UT) group and treated (T) group of AML patients was (2.37&#xb1;0.82)&#xd7;10[-3] and (4.76&#xb1;2.45)&#xd7;10[-3] respectively(P&#xff1c;0.01), the mutation rate in PR and CR groups of treated AML patients was (5.10&#xb1;2.56)&#xd7;10[-3] and (4.51&#xb1;2.51)&#xd7;10[-3] respectively (P&#xff1c;0.05), the comparison among M3 group showed that the mutation rates in UT, PR and CR groups were (2.55&#xb1;0.63)&#xd7;10[-3], (5.37&#xb1;3.41)&#xd7;10[-3] and (3.71&#xb1;1.65)&#xd7;10[-3] respectively (P&#xff1e;0.05).<br><br>CONCLUSION: The more high mutation rate and many kinds of mutation types exist in D-loop region, suggesting that the genes in D-loop region display the more strong instability, the chemotherapy may aggravate the instability of genes in D-loop region.},
}
@article {pmid31211668,
year = {2019},
author = {Nascimento, FS and Barta, JR and Whale, J and Hofstetter, JN and Casillas, S and Barratt, J and Talundzic, E and Arrowood, MJ and Qvarnstrom, Y},
title = {Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis.},
journal = {Emerging infectious diseases},
volume = {25},
number = {7},
pages = {1314-1319},
pmid = {31211668},
issn = {1080-6059},
mesh = {Cyclospora/*classification/*genetics ; Cyclosporiasis/*parasitology/transmission ; *DNA, Mitochondrial ; Genetic Markers ; Genetic Variation ; Genotyping Techniques ; Humans ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.},
}
@article {pmid31216623,
year = {2019},
author = {Myszczyński, K and Ślipiko, M and Sawicki, J},
title = {Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends.},
journal = {International journal of molecular sciences},
volume = {20},
number = {12},
pages = {},
pmid = {31216623},
issn = {1422-0067},
support = {Grant No. 2017/01/X/NZ8/01094, Grant No. 2016/21/B/NZ8/03325, Grant No. 2015/19/B/NZ8/03970//Narodowe Centrum Nauki/ ; },
mesh = {Base Composition ; Bryophyta/classification/genetics ; Embryophyta/*classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genomics/methods ; Open Reading Frames ; Phylogeny ; *RNA Editing ; RNA, Messenger/*genetics ; *RNA, Plant ; },
abstract = {RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.},
}
@article {pmid31233550,
year = {2019},
author = {Monteiro, KJL and Calegar, DA and Santos, JP and Bacelar, PAA and Coronato-Nunes, B and Reis, ERC and Boia, MN and Carvalho-Costa, FA and Jaeger, LH},
title = {Genetic diversity of Ascaris spp. infecting humans and pigs in distinct Brazilian regions, as revealed by mitochondrial DNA.},
journal = {PloS one},
volume = {14},
number = {6},
pages = {e0218867},
pmid = {31233550},
issn = {1932-6203},
mesh = {Animals ; Ascariasis/parasitology ; Ascaris lumbricoides/*genetics ; Ascaris suum/*genetics ; Brazil ; Cross-Sectional Studies ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; Swine ; Swine Diseases/parasitology ; },
abstract = {In this study, we assessed the genetic diversity of Ascaris lumbricoides / Ascaris suum circulating in humans and pigs, exploring potential zoonotic cycles in endemic areas in Brazil. We carried out cross-sectional surveys in four municipalities: Santa Isabel do Rio Negro (SIRN-AM) (n = 328); Nossa Senhora de Nazaré (NSN-PI) and Teresina (TER-PI) (n = 605 and n = 297, respectively); and Cachoeiras de Macacu (CAM-RJ) (n = 543). We also studied 61 fecal samples/adult worms obtained from pigs (n = 53 in NSN-PI and n = 8 in TER-PI). A ~450 bp fragment of the Ascaris cytochrome c oxidase subunit 1 (cox1) and ~400 bp of the NADH dehydrogenase subunit 1 (nad1) were amplified and sequenced. Maximum-likelihood (ML) tree and Median-joining (MJ) haplotype network analyses were performed. We also performed scanning electron micrographs of adult specimens. Positivity rates were 93/328 (28.4%) in SIRN-AM, 6/297 (2.0%) in TER-PI, 0/605 (0%) in NSN-PI, and 6/543 (1.1%) in CAM-RJ. In NSN-PI it reached 11/53 (20.7%) in pigs. The MJ network based on cox1 locus (383 bp) revealed three main clusters, one centered around haplotypes H01/H28/H32 and the other around H07/H11. The cox1 haplotypes had a heterogeneous distribution, showing no pattern by geographic region, and high haplotype diversity. The ML trees based on cox1 and nad1 loci showed a similar topology with each other, and with the haplotype networks. Three distinct clusters were observed. Sequences of cox1 and nad1 from humans and animals were distributed throughout the tree and it was not possible to differentiate specimens of human and swine origin. Ascaris populations obtained from humans and swine in different Brazilian regions are not discriminable through the genetic markers used, which indicates the potential for zoonotic transmission and the need for better control of these infections in swine herds, mainly when created in a peridomestic environment.},
}
@article {pmid31233800,
year = {2019},
author = {Bodensohn, US and Simm, S and Fischer, K and Jäschke, M and Groß, LE and Kramer, K and Ehmann, C and Rensing, SA and Ladig, R and Schleiff, E},
title = {The intracellular distribution of the components of the GET system in vascular plants.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {1866},
number = {10},
pages = {1650-1662},
doi = {10.1016/j.bbamcr.2019.06.012},
pmid = {31233800},
issn = {1879-2596},
mesh = {Adenosine Triphosphatases ; Arabidopsis/metabolism ; Bryopsida/metabolism ; Chloroplasts ; Cytoplasm/metabolism ; Cytosol/*metabolism ; Embryophyta ; Endoplasmic Reticulum/metabolism ; Green Fluorescent Proteins ; Guanine Nucleotide Exchange Factors ; Solanum lycopersicum/metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Plants/*metabolism ; Protein Transport/*physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; Seedlings ; },
abstract = {The guided entry of tail-anchored proteins (GET) pathway facilitates targeting and insertion of tail-anchored proteins into membranes. In plants, such a protein insertion machinery for the endoplasmic reticulum as well as constituents within mitochondrial and chloroplasts were discovered. Previous phylogenetic analysis revealed that Get3 sequences of Embryophyta form two clades representing cytosolic ("a") and organellar ("bc") GET3 homologs, respectively. Cellular fractionation of Arabidopsis thaliana seedlings and usage of the self-assembly GFP system in protoplasts verified the cytosolic (ATGet3a), plastidic (ATGet3b) and mitochondrial (ATGet3c) localization of the different homologs. The identified plant homologs of Get1 and Get4 in A. thaliana are localized in ER and cytosol, respectively, implicating a degree of conservation of the GET pathway in A. thaliana. Transient expression of Get3 homologs of Solanum lycopersicum, Medicago × varia or Physcomitrella patens with the self-assembly GFP technique in homologous and heterologous systems verified that multiple Get3 homologs with differing subcellular localizations are common in plants. Chloroplast localized Get3 homologs were detected in all tested plant systems. In contrast, mitochondrial localized Get3 homologs were not identified in S. lycopersicum, or P. patens, while we confirmed on the example of A. thaliana proteins that mitochondrial localized Get3 proteins are properly targeted in S. lycopersicum as well.},
}
@article {pmid31234016,
year = {2019},
author = {Cobley, JN and Noble, A and Jimenez-Fernandez, E and Valdivia Moya, MT and Guille, M and Husi, H},
title = {Catalyst-free Click PEGylation reveals substantial mitochondrial ATP synthase sub-unit alpha oxidation before and after fertilisation.},
journal = {Redox biology},
volume = {26},
number = {},
pages = {101258},
pmid = {31234016},
issn = {2213-2317},
support = {/WT_/Wellcome Trust/United Kingdom ; 212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Click Chemistry/*methods ; Disulfides/chemistry ; Embryo, Nonmammalian ; Female ; Fertilization in Vitro ; Glutathione/metabolism ; Heterocyclic Compounds, 1-Ring/chemistry ; Male ; Mitochondria/*chemistry/enzymology ; Mitochondrial Proton-Translocating ATPases/*chemistry/metabolism ; Ovum/*chemistry/cytology/enzymology ; Oxidation-Reduction ; Phylogeny ; Polyethylene Glycols/*chemistry ; *Protein Processing, Post-Translational ; Protein Subunits/*chemistry/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfhydryl Compounds/chemistry/metabolism ; Xenopus laevis/classification/embryology/metabolism ; },
abstract = {Using non-reducing Western blotting to assess protein thiol redox state is challenging because most reduced and oxidised forms migrate at the same molecular weight and are, therefore, indistinguishable. While copper catalysed Click chemistry can be used to ligate a polyethylene glycol (PEG) moiety termed Click PEGylation to mass shift the reduced or oxidised form as desired, the potential for copper catalysed auto-oxidation is problematic. Here we define a catalyst-free trans-cyclooctene-methyltetrazine (TCO-Tz) inverse electron demand Diels Alder chemistry approach that affords rapid (k ~2000 M[-1] s[-1]), selective and bio-orthogonal Click PEGylation. We used TCO-Tz Click PEGylation to investigate how fertilisation impacts reversible mitochondrial ATP synthase F1-Fo sub-unit alpha (ATP-α-F1) oxidation-an established molecular correlate of impaired enzyme activity-in Xenopus laevis. TCO-Tz Click PEGylation studies reveal substantial (~65%) reversible ATP-α-F1 oxidation at evolutionary conserved cysteine residues (i.e., C[244] and C[294]) before and after fertilisation. A single thiol is, however, preferentially oxidised likely due to greater solvent exposure during the catalytic cycle. Selective reduction experiments show that: S-glutathionylation accounts for ~50-60% of the reversible oxidation observed, making it the dominant oxidative modification type. Intermolecular disulphide bonds may also contribute due to their relative stability. Substantial reversible ATP-α-F1 oxidation before and after fertilisation is biologically meaningful because it implies low mitochondrial F1-Fo ATP synthase activity. Catalyst-free TCO-Tz Click PEGylation is a valuable new tool to interrogate protein thiol redox state in health and disease.},
}
@article {pmid31242450,
year = {2019},
author = {Roy, P and Rout, AK and Maharana, J and Sahoo, DR and Panda, SP and Pal, A and Nayak, KK and Behera, BK and Das, BK},
title = {Molecular characterization, constitutive expression and GTP binding mechanism of Cirrhinus mrigala (Hamilton, 1822) Myxovirus resistance (Mx) protein.},
journal = {International journal of biological macromolecules},
volume = {136},
number = {},
pages = {1258-1272},
doi = {10.1016/j.ijbiomac.2019.06.161},
pmid = {31242450},
issn = {1879-0003},
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cypriniformes/*genetics ; DNA, Complementary/genetics ; Fish Proteins/chemistry/*genetics/*metabolism ; *Gene Expression Regulation ; Guanosine Triphosphate/*metabolism ; Kinetics ; Molecular Dynamics Simulation ; Myxovirus Resistance Proteins/chemistry/*genetics/*metabolism ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Stability ; RNA, Messenger/genetics ; Thermodynamics ; },
abstract = {Myxovirus resistance (Mx) proteins represents the subclass of the dynamin superfamily of large Guanosine triphosphates (GTPases), play esential role in intracellular vesicle trafficking, endocytosis, organelle homeostasis and mitochondria distribution. These proteins are key players of the vertebrate immune system, induced by type-I and type-III interferons (IFN) of infected host and inhibit viral replication by sequestering its nucleoprotein. In the present study, we report the sequencing and characterization of Cirrhinus mrigala Mx protein (CmMx) for the first time and observed its constitutive expression in different tissues for a period of fourteen days. The synthetic peptide, LSGVALPRGTGI, was dissolved in PBS and injected into a rabbit and the antibody raised against CmMx was used to study the level of its expression. The full length of the CmMx cDNA is 2244 bp with a molecular mass of 70.9 kDa and a predicted isoelectric point of 8.25. The 627 amino acids polypeptide formed of three main functional domains: N-terminal GTPase domain (GD), a middle domain (MD) and GTPase effector domain (GED) with carboxy terminal leucine zipper motif. The 3D models of CmMx protein was modeled based on available close structural homologs and further validated through molecular dynamics (MD) simulations. MD study revealed the importance of G-domain responsible for recognition of GTP, which perfectly corroborate with earlier studies. MM/PBSA binding free energy analysis displayed that van der Waals and electrostatic energy were the key driving force behind molecular recognition of GTP by CmMx protein. The results from this study will illuminate more lights into the ongoing research on myxovirus resistance protein and its role in inhibition of viral replication in other eukaryotic system as well.},
}
@article {pmid31247339,
year = {2019},
author = {Laurimäe, T and Kinkar, L and Romig, T and Umhang, G and Casulli, A and Omer, RA and Sharbatkhori, M and Mirhendi, H and Ponce-Gordo, F and Lazzarini, LE and Soriano, SV and Varcasia, A and Rostami-Nejad, M and Andresiuk, V and Maravilla, P and González, LM and Dybicz, M and Gawor, J and Šarkūnas, M and Šnábel, V and Kuzmina, T and Kia, EB and Saarma, U},
title = {Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {74},
number = {},
pages = {103941},
doi = {10.1016/j.meegid.2019.103941},
pmid = {31247339},
issn = {1567-7257},
mesh = {Animals ; Echinococcus granulosus/*classification/genetics ; Genotyping Techniques/*methods ; Helminth Proteins/*genetics ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 and G7 is still limited. An essential first step towards this goal is correct genotype identification, but distinguishing genotypes G6 and G7 has been challenging. A recent analysis based on complete mitogenome data revealed that the conventional sequencing of the cox1 (366 bp) gene fragment mistakenly classified a subset of G7 samples as G6. On the other hand, sequencing complete mitogenomes is not practical if only genotype or haplogroup identification is needed. Therefore, a simpler and less costly method is required to distinguish genotypes G6 and G7. We compared 93 complete mitogenomes of G6 and G7 from a wide geographical range and demonstrate that a combination of nad2 (714 bp) and nad5 (680 bp) gene fragments would be the best option to distinguish G6 and G7. Moreover, this method allows assignment of G7 samples into haplogroups G7a and G7b. However, due to very high genetic variability of G6 and G7, we suggest to construct a phylogenetic network based on the nad2 and nad5 sequences in order to be absolutely sure in genotype assignment. For this we provide a reference dataset of 93 concatenated nad2 and nad5 sequences (1394 bp in total) containing representatives of G6 and G7 (and haplogroups G7a and G7b), which can be used for the reconstruction of phylogenetic networks.},
}
@article {pmid31254562,
year = {2019},
author = {Chen, J and Gong, Y and Zheng, H and Ma, H and Aweya, JJ and Zhang, Y and Chen, X and Li, SK},
title = {SpBcl2 promotes WSSV infection by suppressing apoptotic activity of hemocytes in mud crab, Scylla paramamosain.},
journal = {Developmental and comparative immunology},
volume = {100},
number = {},
pages = {103421},
doi = {10.1016/j.dci.2019.103421},
pmid = {31254562},
issn = {1879-0089},
mesh = {Animals ; Apoptosis/immunology ; Aquaculture ; Arthropod Proteins/immunology/*metabolism ; Brachyura/*immunology/virology ; Cytochromes c/immunology/metabolism ; Disease Resistance/immunology ; Gene Expression Profiling ; Hemocytes/cytology/immunology/pathology ; *Immunity, Innate ; Mitochondria/immunology/metabolism ; Phylogeny ; Proto-Oncogene Proteins c-bcl-2/immunology/*metabolism ; Up-Regulation/immunology ; White spot syndrome virus 1/*immunology ; },
abstract = {White spot syndrome virus (WSSV) is one of the most virulent and widespread pathogens that infect almost all marine crustaceans and therefore cause huge economic losses in aquaculture. The Bcl2 protein plays a key role in the mitochondrial apoptosis pathway, which is a crucial immune response in invertebrates. However, the role of Bcl2 in apoptosis and immunoregulation in mud crab, Scylla paramamosain, is poorly understood. Here, the Bcl2 homolog (SpBcl2) in S. paramamosain was cloned and its role in WSSV infection explored. The expression of SpBcl2 increased at both the transcriptional level and post-transcriptional level after WSSV infection, while the hemocytes apoptosis decreased significantly. Furthermore, there was increase in the level of cytochrome c coupled with an upregulation in the expression of SpBcl2. These results indicated that SpBcl2 suppressed apoptosis by preventing the release of cytochrome c from mitochondria, thereby promoting WSSV replication in mud crab. The findings here therefore provide novel insight into the immune response of mud crabs to WSSV infection.},
}
@article {pmid31278983,
year = {2019},
author = {Taylor, RS and Bolton, M and Beard, A and Birt, T and Deane-Coe, P and Raine, AF and González-Solís, J and Lougheed, SC and Friesen, VL},
title = {Cryptic species and independent origins of allochronic populations within a seabird species complex (Hydrobates spp.).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106552},
doi = {10.1016/j.ympev.2019.106552},
pmid = {31278983},
issn = {1095-9513},
mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Biodiversity ; Breeding ; Charadriiformes/*classification/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Pacific Ocean ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; },
abstract = {Humans are inherently biased towards naming species based on morphological differences, which can lead to reproductively isolated species being mistakenly classified as one if they are morphologically similar. Recognising cryptic diversity is needed to understand drivers of speciation fully, and for accurate estimates of global biodiversity and assessments for conservation. We investigated cryptic species across the range of band-rumped storm-petrels (Hydrobates spp.): highly pelagic, nocturnal seabirds that breed on tropical and sub-tropical islands in the Atlantic and Pacific Oceans. In many breeding colonies, band-rumped storm-petrels have sympatric but temporally isolated (allochronic) populations; we sampled all breeding locations and allochronic populations. Using mitochondrial control region sequences from 754 birds, cytochrome b sequences from 69 birds, and reduced representation sequencing of the nuclear genomes of 133 birds, we uncovered high levels of genetic structuring. Population genomic analyses revealed up to seven unique clusters, and phylogenomic reconstruction showed that these represent seven monophyletic groups. We uncovered up to six independent breeding season switches across the phylogeny, spanning the continuum from genetically undifferentiated temporal populations to full allochronic species. Thus, band-rumped storm-petrels encompass multiple cryptic species, with non-geographic barriers potentially comprising strong barriers to gene flow.},
}
@article {pmid31279710,
year = {2019},
author = {Parhi, J and Tripathy, PS and Priyadarshi, H and Mandal, SC and Pandey, PK},
title = {Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group.},
journal = {Gene},
volume = {713},
number = {},
pages = {143967},
doi = {10.1016/j.gene.2019.143967},
pmid = {31279710},
issn = {1879-0038},
mesh = {Animals ; Cypriniformes/*genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI, COII, COIII, 16S rRNA, 12S rRNA, Cyt b, ATPase 6, D-loop, ND1, ND2, ND3, ND4, ND5, and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b, 12S rRNA, ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction.},
}
@article {pmid31286324,
year = {2019},
author = {Condori-Apfata, JA and Batista-Silva, W and Medeiros, DB and Vargas, JR and Valente, LML and Heyneke, E and Pérez-Diaz, JL and Fernie, AR and Araújo, WL and Nunes-Nesi, A},
title = {The Arabidopsis E1 subunit of the 2-oxoglutarate dehydrogenase complex modulates plant growth and seed production.},
journal = {Plant molecular biology},
volume = {101},
number = {1-2},
pages = {183-202},
pmid = {31286324},
issn = {1573-5028},
support = {306818/2016-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 402511/2016-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CEX - APQ-02985-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; },
mesh = {Arabidopsis/*enzymology/genetics/growth &amp; development ; Arabidopsis Proteins/genetics/metabolism ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Chlorophyll/metabolism ; Ketoglutarate Dehydrogenase Complex/genetics/*metabolism ; Mitochondria/enzymology ; Mutagenesis, Insertional ; Nitrates/metabolism ; Nitrogen/*metabolism ; Phenotype ; Phylogeny ; Plant Leaves/enzymology/genetics/growth &amp; development ; Protein Isoforms ; Protein Subunits ; Seedlings/enzymology/genetics/growth &amp; development ; Seeds/enzymology/genetics/growth &amp; development ; },
abstract = {Isoforms of 2-OGDH E1 subunit are not functionally redundant in plant growth and development of A. thaliana. The tricarboxylic acid cycle enzyme 2-oxoglutarate dehydrogenase (2-OGDH) converts 2-oxoglutarate (2-OG) to succinyl-CoA concomitant with the reduction of NAD[+]. 2-OGDH has an essential role in plant metabolism, being both a limiting step during mitochondrial respiration as well as a key player in carbon-nitrogen interactions. In Arabidopsis thaliana two genes encode for E1 subunit of 2-OGDH but the physiological roles of each isoform remain unknown. Thus, in the present study we isolated Arabidopsis T-DNA insertion knockout mutant lines for each of the genes encoding the E1 subunit of 2-OGDH enzyme. All mutant plants exhibited substantial reduction in both respiration and CO2 assimilation rates. Furthermore, mutant lines exhibited reduced levels of chlorophylls and nitrate, increased levels of sucrose, malate and fumarate and minor changes in total protein and starch levels in leaves. Despite the similar metabolic phenotypes for the two E1 isoforms the reduction in the expression of each gene culminated in different responses in terms of plant growth and seed production indicating distinct roles for each isoform. Collectively, our results demonstrated the importance of the E1 subunit of 2-OGDH in both autotrophic and heterotrophic tissues and suggest that the two E1 isoforms are not functionally redundant in terms of plant growth in A. thaliana.},
}
@article {pmid31300133,
year = {2019},
author = {Mirbadie, SR and Najafi Nasab, A and Mohaghegh, MA and Norouzi, P and Mirzaii, M and Spotin, A},
title = {Molecular phylodiagnosis of Echinococcus granulosus sensu lato and Taenia hydatigena determined by mitochondrial Cox1 and SSU-rDNA markers in Iranian dogs: Indicating the first record of pig strain (G7) in definitive host in the Middle East.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {65},
number = {},
pages = {88-95},
doi = {10.1016/j.cimid.2019.05.005},
pmid = {31300133},
issn = {1878-1667},
mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/diagnosis/*epidemiology ; Dogs/parasitology ; Echinococcosis/diagnosis/epidemiology/*veterinary ; Echinococcus granulosus/genetics ; Feces/parasitology ; Genotype ; Intestinal Diseases, Parasitic/diagnosis/*veterinary ; Iran/epidemiology ; Middle East/epidemiology ; Mitochondria/genetics ; *Phylogeny ; Prevalence ; Swine/parasitology ; Taenia/genetics ; Taeniasis/diagnosis/epidemiology/*veterinary ; },
abstract = {Unawareness of canine parasitic diseases among at-risk hosts and an uncontrolled program of stray dog population have caused that zoonotic parasites received great attention in endemic regions of the Middle East. A total of 552 faecal samples were collected between December 2016 to January 2018 from stray (n = 408) and domestic (n = 144) dogs of Iran. All specimens were coproscopically observed following concentration and flotation techniques. Subsequently, the DNAs of taeniid eggs were extracted, amplified, and sequenced by targeting of mitochondrial cytochrome oxidase subunit 1 and small-subunit ribosomal DNA markers. The overall prevalence of canine intestinal parasites found 53.6%. The following parasites and their total frequencies were identified: taeniid (10.5%), Dicrocoelium dendriticum (0.7%), Trichuris vulpis (1.2%), Capillaria spp. (2.3%), Blastocystis spp. (5.2%), Ancylostoma spp. (2%), Eimeria spp. (13.2%), Dipylidium caninum (2.3%), Toxocara canis (3.8%), Giardia spp. (8.5%), and Toxascaris leonina (3.6%). Stray dogs were characterized more likely to be poliparasitized and indicated a higher prevalence of taeniid (10.9%), T. canis (4.4%) Giardia spp. (10.1%) than domestic dogs (P > 0.05). Phylogenetic and sequence analysis of Cox1 and SSU-rDNA indicated a low genetic diversity (Haplotype diversity; 0 to 0.495) in E. granulosus sensu lato G1, G3, G7 genotypes, and Taenia hydatigena. The pairwise sequence distances between G7 isolates showed an intra-diversity of 0.7%-1.5% and identity of 98.5%-100%. The first occurrence of pig strain (G7) from Iranian dogs might have substantial implications in the drug treatment of infected dogs due to the shorter maturation time of G7 compared with G1 genotype. Thus, the preventive strategies should be noticed to determine the risk factors, the importance of applying the hygienic practices, and well adjusting deworming programs for the Iranian dogs and at-risk individuals.},
}
@article {pmid31311504,
year = {2019},
author = {Wang, L and Zhuang, H and Zhang, Y and Wei, W},
title = {Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS).},
journal = {BMC evolutionary biology},
volume = {19},
number = {1},
pages = {145},
pmid = {31311504},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; China ; Cladocera/*genetics ; DNA, Intergenic/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Zooplankton/genetics ; },
abstract = {BACKGROUND: China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time.<br><br>RESULTS: Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau.<br><br>CONCLUSIONS: This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).},
}
@article {pmid31349101,
year = {2019},
author = {Caro, A and Neiber, MT and Gómez-Moliner, BJ and Madeira, MJ},
title = {Molecular phylogeny and biogeography of the land snail subfamily Leptaxinae (Gastropoda: Hygromiidae).},
journal = {Molecular phylogenetics and evolution},
volume = {139},
number = {},
pages = {106570},
doi = {10.1016/j.ympev.2019.106570},
pmid = {31349101},
issn = {1095-9513},
mesh = {Animals ; Electron Transport Complex IV/chemistry/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/chemistry/classification/genetics ; Snails/*classification/genetics ; Spain ; },
abstract = {The subfamily Leptaxinae is included within the highly diverse land snail family Hygromiidae. In the absence of clear diagnostic morphological differences, the subfamily status is currently based solely on molecular information and includes three disjunctly distributed tribes, Leptaxini, Cryptosaccini and Metafruticicolini. However, the phylogenetic relationships among these tribes are not fully resolved and the clustering of some of the genera to the tribes is not statistically supported. To resolve the relationships within Leptaxinae and their position within Hygromiidae, we reconstructed their phylogeny using a multi-locus approach with two mitochondrial genes and eight nuclear markers. The phylogeny was further calibrated and an analysis of ancestral area estimation was carried out to infer the biogeographic history of the group. We elevated Metafruticicolini to subfamily level (Metafruticicolinae) and we restricted Leptaxinae to Cryptosaccini and Leptaxini. The Lusitanian genus Portugala was moved to Leptaxini, previously containing only the Macaronesian genus Leptaxis. Within Cryptosaccini, a new genus strictly confined to the Sierra de la Cabrera (Spain) is described, Fractanella gen. nov. According to our results, Leptaxinae originated in the Early Miocene in the Iberian Peninsula, from which the Macaronesian Islands were colonized. Due to the old split recovered for the divergence between Macaronesian and Iberian lineages, we hypothesize that this colonization may have occurred via the once emerged seamounts located between the archipelagos and the European and African continents, although this could also have occurred through the oldest now emerged islands of Macaronesia. In the Iberian Peninsula, the climatic shift that began during the Middle Miocene, changing progressively from subtropical climate towards the present-day Mediterranean climate, was identified as an important factor shaping the subfamily's diversification, along with Pleistocene climatic fluctuations.},
}
@article {pmid31382041,
year = {2019},
author = {De, AK and Muthiyan, R and Ponraj, P and Muniswamy, K and Sunder, J and Kundu, A and Karunakaran, D and George, Z and Kundu, MS and Ahmed, SKZ and Malakar, D and Bhattacharya, D},
title = {Mitogenome analysis of Indian isolate of Rhipicephalus microplus clade A sensu (): A first report from Maritime South-East Asia.},
journal = {Mitochondrion},
volume = {49},
number = {},
pages = {135-148},
doi = {10.1016/j.mito.2019.07.014},
pmid = {31382041},
issn = {1872-8278},
mesh = {Animals ; *Genome, Mitochondrial ; India ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rhipicephalus/*genetics ; },
abstract = {This communication reports a comprehensive profile of mitogenome analysis of Rhipicephalus microplus, isolated and identified from Andaman and Nicobar islands, a part of Maritime South East Asia. Complete mitogenome of Indian isolate of R. microplus (MK234703) was 14,903 bp. Mitochondrial (mt.) genome had 13 protein coding genes (PCGs), 22 tRNAs, two ribosomal subunits and two control regions. All PCGs were located on the H-strand except nad1, nad5, nad4 and nad4L. All start codons were ATN codon and abbreviated stop codons were seen in cox-2-3, nad-5 and cytb. A purine rich tick-box motif has been identified. A tandem repeat unit (TTTATT), described as a region alike to nad1 was identified in 130 bp insertion in between nad1 and tRNA-Glu and in nad1 sequence. Presence of two control regions (CRs) proved that, two CRs have evolved in concert rather than independently. Strong biasness towards A and T in Indian isolate of R. microplus is a typical feature for most of the arthropods. Subtracted values of dn and ds suggested that, there was least effect of nt. sequence of cox1 gene when Indian isolate was compared with other isolates of Rhipicephalus. On the basis of phylogenetic analysis, species of the genus Rhipicephalus could be clustered in three groups; ticks of the genera belonging to sub-family Rhipicephalinae could be grouped in a single cluster. Finally, cox1 sequence of MK234703 indicated that the isolate belonged to clade A sensu Burger et al., 2014 which has not been reported earlier from India.},
}
@article {pmid31404610,
year = {2019},
author = {Kanduma, EG and Bishop, RP and Githaka, NW and Skilton, RA and Heyne, H and Mwacharo, JM},
title = {Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya.},
journal = {Molecular phylogenetics and evolution},
volume = {140},
number = {},
pages = {106579},
doi = {10.1016/j.ympev.2019.106579},
pmid = {31404610},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Haplotypes/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Rhipicephalus/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA (12S rDNA) and nuclear ribosomal DNA internal transcriber spacer 2 (ITS2) were analyzed in Rhipicephalus tick populations in Kenya. While the morphological and molecular criteria separated R. e. evertsi, R. pulchellus and R. appendiculatus from other members of the genus, except the morphologically similar sibling species R. zambeziensis, this was not the case for other tick populations. COI sequences of Rhipicephalus ticks from Ruma National Park (RNP) in Southwestern Kenya, that were morphologically similar to R. praetextatus/R. simus, a formed distinct clade and barcode gap group. 12S rDNA haplotypes of this population were 99% identical to a GenBank accession of R. muhsamae which is thought to be endemic in West and Central Africa. However, the ITS2 locus indicated that the RNP samples were genetically closest to ticks identified morphologically as R. praetextatus. The COI and 12S rDNA haplotype sequences of R. praetextatus clustered closely with R. simus reference sequences though the two species occurred in distinct barcode gap groups. Our results suggest that the R. simus/R. praetextatus/R. muhsamae comprise a closely related tick species complex found across sub-Saharan Africa and includes the yet to be described RNP population. More studies on the biology, ecology and genomics of all life stages of tick species in the complex may clarify their taxonomic status. A continent-wide study that combines morphology, DNA marker sequencing and emerging methods, such as mass spectrometry and whole-genome resequencing may reveal the diversity and distribution of taxa within the genus Rhipicephalus in sub-Saharan Africa.},
}
@article {pmid31418651,
year = {2019},
author = {Sato, C and Sasaki, M and Nabeta, H and Tomioka, M and Uga, S and Nakao, M},
title = {A Philophthalmid Eyefluke from a Human in Japan.},
journal = {The Journal of parasitology},
volume = {105},
number = {4},
pages = {619-623},
pmid = {31418651},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Conjunctiva/parasitology ; Conjunctivitis/parasitology ; DNA, Helminth/chemistry ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eye Infections, Parasitic/*parasitology ; Female ; Humans ; Japan ; Middle Aged ; Mitochondria/enzymology ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trematoda/anatomy &amp; histology/classification/genetics/*isolation &amp; purification ; Trematode Infections/*parasitology ; },
abstract = {Philophthalmid eyeflukes are cosmopolitan parasites of birds and occasionally of mammals, including humans. A gravid adult of Philophthalmus sp. was found from the bulbar conjunctiva of a 64-yr-old woman in Japan, who was diagnosed with acute conjunctivitis. The parasite was morphologically most similar to Philophthalmus hegeneri, but distinctive in lacking an esophagus and in having clearly lobed testes. The DNA sequence analysis of genes for nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 supported the identification at generic level. The morphological and molecular analyses strongly suggest that the eyefluke from a human in Japan should be treated as an undescribed species of Philophthalmus. The occurrence of human philophthalmosis is very rare. As far as we know, a total of 11 human cases have been reported worldwide to date.},
}
@article {pmid31448547,
year = {2019},
author = {Derkarabetian, S and Benavides, LR and Giribet, G},
title = {Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.},
journal = {Molecular ecology resources},
volume = {19},
number = {6},
pages = {1531-1544},
doi = {10.1111/1755-0998.13072},
pmid = {31448547},
issn = {1755-0998},
support = {//Harvard Dean's Fund/ ; DEB-1601208//Division of Environmental Biology/ ; DEB-1754278//Division of Environmental Biology/ ; },
mesh = {Animals ; Biodiversity ; Birds/*genetics ; DNA/genetics ; Ethanol/chemistry ; Formaldehyde/chemistry ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Insecta ; Mitochondria/genetics ; Museums ; Phylogeny ; Preservation, Biological/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/methods ; },
abstract = {Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of "fresh" specimens preserved in >95% ethanol and stored at -80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%-80% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.},
}
@article {pmid31482589,
year = {2019},
author = {Chen, J and Xia, L and Wang, W and Wang, Z and Hou, S and Xie, C and Cai, J and Lu, Y},
title = {Identification of a mitochondrial-targeting secretory protein from Nocardia seriolae which induces apoptosis in fathead minnow cells.},
journal = {Journal of fish diseases},
volume = {42},
number = {11},
pages = {1493-1507},
doi = {10.1111/jfd.13062},
pmid = {31482589},
issn = {1365-2761},
support = {2017A030313179//Natural Science Foundation of Guangdong Province/ ; 231419017//Research Projects of Guangdong Ocean University's Top-ranking Discipline Construction/ ; JCYJ20170306161613251//Shenzhen Science and Technology Project/ ; KY20160207//Shenzhen Dapeng New District&#xa0;special fund for industry development/ ; PT201901-06//Shenzhen Dapeng New District&#xa0;special fund for industry development/ ; C17377//Natural Science Foundation of Guangdong Ocean University/ ; C13454//Natural Science Foundation of Guangdong Ocean University/ ; },
mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Bacterial Proteins/chemistry/genetics/immunology ; Base Sequence ; *Cyprinidae ; Fish Diseases/*immunology/microbiology ; Nocardia/*genetics ; Nocardia Infections/immunology/microbiology/*veterinary ; Phylogeny ; Sequence Alignment/veterinary ; Virulence Factors/*genetics/metabolism ; },
abstract = {Nocardia seriolae is the main pathogen responsible for fish nocardiosis. A mitochondrial-targeting secretory protein (MTSP) 3141 with an N-terminal transit peptide (TP) from N. seriolae was predicted by bioinformatic analysis based on the genomic sequence of the N. seriolae strain ZJ0503. However, the function of the MTSP3141 and its homologs remains totally unknown. In this study, mass spectrometry analysis of the extracellular products from N. seriolae proved that MTSP3141 was a secretory protein, subcellular localization research showed the MTSP3141-GFP fusion protein co-localized with mitochondria in fathead minnow (FHM) cells, the TP played an important role in mitochondria targeting, and only the TP located at N-terminus but not C-terminus can lead to mitochondria directing. Moreover, quantitative assays of mitochondrial membrane potential (ΔΨm) value, caspase-3 activity and apoptosis-related gene (Bcl-2, Bax, Bad, Bid and p53) mRNA expression suggested that cell apoptosis was induced in FHM cells by the overexpression of both MTSP3141 and MTSP3141ΔTP (with the N-terminal TP deleted) proteins. Taken together, the results of this study indicated that the MTSP3141 of N. seriolae was a secretory protein, might target mitochondria, induce apoptosis in host cells and function as a virulence factor.},
}
@article {pmid31484671,
year = {2019},
author = {Yang, H and Deng, L and Liu, H and Fan, S and Hua, W and Liu, J},
title = {Overexpression of BnaAOX1b Confers Tolerance to Osmotic and Salt Stress in Rapeseed.},
journal = {G3 (Bethesda, Md.)},
volume = {9},
number = {10},
pages = {3501-3511},
pmid = {31484671},
issn = {2160-1836},
mesh = {Abscisic Acid ; Amino Acid Sequence ; Brassica napus/*physiology ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Germination/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics ; Osmoregulation/*genetics ; Oxidoreductases/chemistry/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Transport ; Salt Tolerance/*genetics ; Seedlings/genetics ; Alternative Oxidase ; },
abstract = {Alternative oxidases (AOXs) are the terminal oxidase in the cyanide-resistant respiration pathway in plant mitochondria, which play an important role in abiotic stress and are proposed as a functional marker for high tolerant breeding. In this study, ten AOX genes (BnaAOXs) were identified, and CysI and CysII of AOX isoforms were highly conserved in rapeseed. Among them, Bna.AOX1b was mainly expressed in the ovule and displayed varying expression between rapeseed cultivars which showed different salt resistance in seed germination. We identified its mitochondrial localization of this gene. To investigate the function of BnaAOX1b in rapeseed, transgenic rapeseed lines with overexpressed BnaAOX1b were created and seed germination and seedling establishment assays were performed under osmotic, salt, and ABA treatment. The results indicated that overexpression of BnaAOX1b significantly improved seed germination under osmotic and salt stress and weakened ABA sensitivity. In addition, post-germination seedling growth was improved under high salt condition, but showed hypersensitivity to ABA. RNA-sequencing analysis indicated that the genes involved in electron transport or energy pathway were induced and a number of gene responses to salt stress and ABA were regulated in Bna.AOX1b overexpressing seeds. Taken together, our results imply that Bna.AOX1b confers tolerance to osmotic and salt stress in terms of seed germination and seedling establishment by regulating stress responsive genes and the response to ABA, and could be utilized as a candidate gene in transgenic breeding.},
}
@article {pmid31486889,
year = {2019},
author = {Wang, J and Gao, X and Zheng, X and Hou, C and Xie, Q and Lou, B and Zhu, J},
title = {Expression and potential functions of KIF3A/3B to promote nuclear reshaping and tail formation during Larimichthys polyactis spermiogenesis.},
journal = {Development genes and evolution},
volume = {229},
number = {5-6},
pages = {161-181},
pmid = {31486889},
issn = {1432-041X},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Nucleus/metabolism ; Cloning, Molecular ; Fish Proteins/chemistry/genetics/*metabolism ; Fishes/*physiology ; Humans ; Kinesins/chemistry/genetics/*metabolism ; Male ; Phylogeny ; Sequence Alignment ; *Spermatogenesis ; Spermatozoa/*cytology/metabolism ; },
abstract = {KIF3A and KIF3B are homologous motor subunits of the Kinesin II protein family. KIF3A, KIF3B, and KAP3 form a heterotrimeric complex and play a significant role in spermatogenesis. Here, we first cloned full-length kif3a/3b cDNAs from Larimichthys polyactis. Lp-kif3a/3b are highly related to their homologs in other animals. The proteins are composed of three domains, an N-terminal head domain, a central stalk domain, and a C-terminus tail domain. Lp-kif3a/3b mRNAs were found to be ubiquitously expressed in the examined tissues, with high expression in the testis. Fluorescence in situ hybridization (FISH) was used to analyze the expression of Lp-kif3a/3b mRNAs during spermiogenesis. The results showed that Lp-kif3a/3b mRNAs had similar expression pattern and were continuously expressed during spermiogenesis. From middle spermatid to mature sperm, Lp-kif3a/3b mRNAs gradually localized to the side of the spermatid where the midpiece and tail form. In addition, we used immunofluorescence (IF) to observe that Lp-KIF3A protein co-localizes with tubulin during spermiogenesis. In early spermatid, Lp-KIF3A protein and microtubule signals were randomly distributed in the cytoplasm. In middle spermatid, however, the protein was detected primarily around the nucleus. In late spermatid, the protein migrated primarily to one side of the nucleus where the tail forms. In mature sperm, Lp-KIF3A and microtubules accumulated in the midpiece. Moreover, Lp-KIF3A co-localized with the mitochondria. In mature sperm, Lp-KIF3A and mitochondria were present in the midpiece. Therefore, Lp-KIF3A/KIF3B may be involved in spermiogenesis in L. polyactis, particularly during nuclear reshaping and tail formation.},
}
@article {pmid31504759,
year = {2019},
author = {Mignerot, L and Nagasato, C and Peters, AF and Perrineau, MM and Scornet, D and Pontheaux, F and Djema, W and Badis, Y and Motomura, T and Coelho, SM and Cock, JM},
title = {Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus.},
journal = {Molecular biology and evolution},
volume = {36},
number = {12},
pages = {2778-2789},
doi = {10.1093/molbev/msz186},
pmid = {31504759},
issn = {1537-1719},
mesh = {*Genes, Mitochondrial ; Genome, Mitochondrial ; Life History Traits ; Parthenogenesis/genetics ; Phaeophyceae/*genetics ; Recombination, Genetic ; },
abstract = {Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.},
}
@article {pmid31511073,
year = {2019},
author = {Honeycutt, RL and Proudfoot, GA and Silvy, NJ},
title = {Mitochondrial DNA variation of the ruffed grouse (Bonasa umbellus).},
journal = {BMC research notes},
volume = {12},
number = {1},
pages = {570},
pmid = {31511073},
issn = {1756-0500},
support = {DEB 9615163//National Science Foundation/ ; },
mesh = {Animals ; Canada ; DNA, Mitochondrial/*genetics ; Galliformes/classification/*genetics ; Gene Frequency ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA/methods ; United States ; },
abstract = {OBJECTIVE: The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitochondrial DNA (mtDNA) variation in the ruffed grouse across western, central, and eastern parts of its distribution. We compare patterns of mtDNA variation to those characterized by morphology and ecology. Additionally, we evaluate the demographic history of the species based on mitochondrial haplotype diversity.<br><br>RESULTS: Patterns of mtDNA variation revealed geographic subdivision, with populations of ruffed grouse subdivided into 3 to 4 genetically distinct groups. This subdivision partially coincided with the ranges of described subspecies. Behavioral traits prohibiting long-distance movement and barriers to dispersal in response to physiography and unsuitable habitat help explain these patterns of subdivision. Historically, the ruffed grouse probably experienced a population expansion, possibly in response to changes during the Pleistocene.},
}
@article {pmid31513293,
year = {2020},
author = {Liu, S and Li, J and Zhang, Y and Liu, N and Viljoen, A and Mostert, D and Zuo, C and Hu, C and Bi, F and Gao, H and Sheng, O and Deng, G and Yang, Q and Dong, T and Dou, T and Yi, G and Ma, LJ and Li, C},
title = {Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4.},
journal = {The New phytologist},
volume = {225},
number = {2},
pages = {913-929},
pmid = {31513293},
issn = {1469-8137},
mesh = {Apoptosis/drug effects ; Biosynthetic Pathways/drug effects/genetics ; Cell Death/drug effects ; Fusaric Acid/biosynthesis/*pharmacology ; Fusarium/drug effects/*pathogenicity ; Gene Expression Regulation, Plant/drug effects ; Mitochondria/drug effects/metabolism ; Models, Biological ; Multigene Family ; Musa/*microbiology ; Phenotype ; Phylogeny ; Plant Stems/microbiology ; Protoplasts/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Virulence/drug effects ; },
abstract = {Fusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in decreased disease symptoms and reduced fungal biomass in the host banana plants. When pretreated with FSA, both banana leaves and pseudostems exhibited increased sensitivity to Foc TR4 invasion. Banana embryogenic cell suspensions (ECSs) treated with FSA exhibited a lower rate of O2 uptake, loss of mitochondrial membrane potential, increased reactive oxygen species (ROS) accumulation, and greater nuclear condensation and cell death. Consistently, transcriptomic analysis of FSA-treated ECSs showed that FSA may induce plant cell death through regulating the expression of genes involved in mitochondrial functions. The results herein demonstrated that the FSA from Foc TR4 functions as a positive virulence factor and acts at the early stage of the disease development before the appearance of the fungal hyphae in the infected tissues.},
}
@article {pmid31542425,
year = {2019},
author = {Zheng, F and Colasante, C and Voncken, F},
title = {Characterisation of a mitochondrial iron transporter of the pathogen Trypanosoma brucei.},
journal = {Molecular and biochemical parasitology},
volume = {233},
number = {},
pages = {111221},
doi = {10.1016/j.molbiopara.2019.111221},
pmid = {31542425},
issn = {1872-9428},
support = {BB/G00448X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Cation Transport Proteins/chemistry/genetics/metabolism ; Genes, Fungal ; Genes, Protozoan ; Iron/*metabolism ; Iron-Binding Proteins/chemistry/genetics/metabolism ; Mitochondria/metabolism ; *Mitochondrial Membrane Transport Proteins/chemistry/genetics/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Trypanosoma brucei brucei/*metabolism ; },
abstract = {Similar to higher eukaryotes, the protist parasite T. brucei harbours several iron-containing proteins that regulate DNA and protein processing, oxidative stress defence and mitochondrial respiration. The synthesis of these proteins occurs either in the cytoplasm or within the mitochondrion. For mitochondrial iron cluster protein synthesis, iron needs to be transported across the solute impermeable mitochondrial membrane. In T. brucei we previously identified 24 mitochondrial carrier proteins (TbMCPs) sharing conserved structural and functional features with those from higher eukaryotes. One of these carriers (TbMCP17) displayed high similarity with the iron carriers MRS3, MRS4 from yeast and mitoferrin from mammals, insects and plants. In the present study we demonstrated that TbMCP17 functions as an iron carrier by complementation studies using MRS3/4-deficient yeast. Depletion of TbMCP17 in procyclic form T. brucei resulted in growth deficiency, increased sensitivity to iron deprivation, and lowered mitochondrial iron content. Taken together our results suggest that TbMCP17 functions as a mitochondrial iron transporter in the parasite T. brucei.},
}
@article {pmid31554701,
year = {2019},
author = {Dell'Aglio, E and Giustini, C and Kraut, A and Couté, Y and Costa, A and Decros, G and Gibon, Y and Mazars, C and Matringe, M and Finazzi, G and Curien, G},
title = {Identification of the Arabidopsis Calmodulin-Dependent NAD[+] Kinase That Sustains the Elicitor-Induced Oxidative Burst.},
journal = {Plant physiology},
volume = {181},
number = {4},
pages = {1449-1458},
pmid = {31554701},
issn = {1532-2548},
mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology ; Arabidopsis Proteins/chemistry/*metabolism ; Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Flagellin/metabolism ; Kinetics ; Mitochondria/metabolism ; Models, Biological ; Peptides/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*metabolism ; Photosynthesis ; Phylogeny ; Protein Binding ; Protein Domains ; *Respiratory Burst ; Seedlings/metabolism ; },
abstract = {NADP(H) is an essential cofactor of multiple metabolic processes in all living organisms, and in plants, NADP(H) is required as the substrate of Ca[2+]-dependent NADPH oxidases, which catalyze a reactive oxygen species burst in response to various stimuli. While NADP[+] production in plants has long been known to involve a calmodulin (CaM)/Ca[2+]-dependent NAD[+] kinase, the nature of the enzyme catalyzing this activity has remained enigmatic, as has its role in plant physiology. Here, we used proteomic, biochemical, molecular, and in vivo analyses to identify an Arabidopsis (Arabidopsis thaliana) protein that catalyzes NADP[+] production exclusively in the presence of CaM/Ca[2+] This enzyme, which we named NAD kinase-CaM dependent (NADKc), has a CaM-binding peptide located in its N-terminal region and displays peculiar biochemical properties as well as different domain organization compared with known plant NAD[+] kinases. In response to a pathogen elicitor, the activity of NADKc, which is associated with the mitochondrial periphery, contributes to an increase in the cellular NADP[+] concentration and to the amplification of the elicitor-induced oxidative burst. Based on a phylogenetic analysis and enzymatic assays, we propose that the CaM/Ca[2+]-dependent NAD[+] kinase activity found in photosynthetic organisms is carried out by NADKc-related proteins. Thus, NADKc represents the missing link between Ca[2+] signaling, metabolism, and the oxidative burst.},
}
@article {pmid31561566,
year = {2019},
author = {Varré, JS and D'Agostino, N and Touzet, P and Gallina, S and Tamburino, R and Cantarella, C and Ubrig, E and Cardi, T and Drouard, L and Gualberto, JM and Scotti, N},
title = {Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome.},
journal = {International journal of molecular sciences},
volume = {20},
number = {19},
pages = {},
pmid = {31561566},
issn = {1422-0067},
mesh = {Amino Acid Sequence ; *Gene Expression Profiling ; *Genome, Mitochondrial ; *Genomics/methods ; Open Reading Frames ; Phylogeny ; RNA Editing ; Solanum tuberosum/*genetics ; *Whole Genome Sequencing ; },
abstract = {Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.},
}
@article {pmid31575774,
year = {2019},
author = {Murante, D and Hogan, DA},
title = {New Mitochondrial Targets in Fungal Pathogens.},
journal = {mBio},
volume = {10},
number = {5},
pages = {},
pmid = {31575774},
issn = {2150-7511},
support = {R01 AI127548/AI/NIAID NIH HHS/United States ; },
mesh = {*Candida albicans ; Humans ; *Mitochondria ; Phylogeny ; Saccharomyces cerevisiae ; },
abstract = {In eukaryotic cells, mitochondria are responsible for the synthesis of ATP using power generated by the electron transport chain (ETC). While much of what is known about mitochondria has been gained from a study of a small number of model species, including the yeast Saccharomyces cerevisiae, the general mechanisms of mitochondrial respiration have been recognized as being highly conserved across eukaryotes. Now, Sun et al. (N. Sun, R. S. Parrish, R. A. Calderone, and W. A. Fonzi, mBio 10:e00300-19, 2019, https://doi.org/10.1128/mBio.00300-19) take the next steps in understanding mitochondrial function by identifying proteins that are unique to a smaller phylogenetic group of microbes. Using the combination of in silico, biochemical, and microbiological assays, Sun and colleagues identified seven genes that are unique to the CTG fungal clade, which contains multiple important human pathogens, including Candida albicans, and showed that they are required for full ETC function during respiratory metabolism. Because respiratory metabolism is critical for fungal pathogenesis, these clade-specific mitochondrial factors may represent novel therapeutic targets.},
}
@article {pmid31580785,
year = {2019},
author = {Achatz, TJ and Curran, SS and Patitucci, KF and Fecchio, A and Tkach, VV},
title = {Phylogenetic Affinities of Uvulifer Spp. (Digenea: Diplostomidae) in the Americas with Description of Two New Species from Peruvian Amazon.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {704-717},
pmid = {31580785},
issn = {1937-2345},
support = {R15 AI092622/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bayes Theorem ; Bird Diseases/*parasitology ; Birds ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Intestine, Small/parasitology ; Mitochondria/enzymology ; Peru ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 28S/genetics ; Rivers ; Sequence Alignment/veterinary ; Trematoda/anatomy &amp; histology/*classification/genetics ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Uvulifer Yamaguti, 1934, is a genus of diplostomoidean digeneans that parasitizes kingfishers worldwide. Species have a Neascus-type metacercaria that encysts in or on fish intermediate hosts, often causing black spot disease. Only 3 prior studies published DNA sequence data for Uvulifer species with only 1 including a single named species (Uvulifer spinatus López-Jiménez, Pérez-Ponce de León, &amp; García-Varela, 2018). Herein we describe 2 new species of Uvulifer from the green-and-rufous kingfisher, Chloroceryle inda (Linnaeus), collected in Peru (Uvulifer batesi n. sp. and Uvulifer pequenae n. sp.). Both new species are readily differentiated from their New World congeners by a combination of morphological characters including distribution of vitelline follicles and prosoma:opisthosoma length ratios. In addition, we used newly generated nuclear 28S rRNA and mitochondrial COI gene sequence data to differentiate among species and examine phylogenetic affinities of Uvulifer. This includes the 2 new species and Uvulifer ambloplitis (Hughes, 1927), as well as Uvulifer elongatus Dubois, 1988 , Uvulifer prosocotyle (Lutz, 1928), and Uvulifer weberi Dubois, 1985 , none of which have been part of prior molecular phylogenetic studies. Our data on Uvulifer revealed 0.1-2.2% interspecific divergence in 28S sequences and 9.3-15.3% in COI sequences. Our 28S phylogeny revealed at least 6 well-supported clades within the genus. In contrast, the branch topology in the COI phylogenetic tree was overall less supported, indicating that although COI sequences are a great tool for species differentiation, they should be used with caution for phylogenetic inference at higher taxonomic levels. Our 28S phylogeny did not reveal any clear patterns of host association between Uvulifer and particular species of kingfishers; however, it identified 2 well-supported clades uniting Uvulifer species from distant geographical locations and more than 1 biogeographic realm, indicating at least 2 independent dispersal events in the evolutionary history of the New World Uvulifer. Our results clearly demonstrate that the diversity of Uvulifer in the New World has been underestimated.},
}
@article {pmid31580787,
year = {2019},
author = {Velázquez-Urrieta, Y and Oceguera-Figueroa, A and León-Règagnon, V},
title = {Two New Species of Haematoloechus (Digenea: Plagiorchidae) Parasitizing Rana brownorum (Amphibia: Ranidae) from Southeast Mexico.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {724-732},
pmid = {31580787},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Lung/parasitology ; Mexico ; Mitochondria/enzymology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Sequence Alignment/veterinary ; Trematoda/anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {In an ongoing investigation on the helminths of amphibians in southeastern Mexico, specimens of 2 undescribed species of Haematoloechus were collected from Rana brownorum. Haematoloechus ceciliae n. sp. is morphologically most similar to Haematoloechus meridionalis, but differs in the shape of the oral sucker, in the nature of the acetabulum, and in the distribution of the glandular cells in the pharyngeal region; Haematoloechus celestunensis n. sp. closely resembles Haematoloechus floedae, but differs in the form and size of the testes and measurements of acetabulum. COI and 28S DNA sequences of both new species show high divergence compared to other species of the genus. In the phylogenetic trees, H. ceciliae appears most closely related to Haematoloechus danbrooksi and H. celestunensis to Haematoloechus veracruzanus.},
}
@article {pmid31585116,
year = {2019},
author = {Betgiri, AA and Jadhav, SN and Pawde, M and Shukla, A and Mote, C and Pawar, PD and Shanmugam, D and Kundu, K},
title = {Mitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs.},
journal = {Experimental parasitology},
volume = {206},
number = {},
pages = {107771},
doi = {10.1016/j.exppara.2019.107771},
pmid = {31585116},
issn = {1090-2449},
mesh = {Animals ; Babesia/classification/genetics/*isolation &amp; purification ; Babesiosis/*diagnosis/parasitology ; Base Sequence ; Cross Reactions ; DNA, Ribosomal Spacer/chemistry ; Dog Diseases/*diagnosis/parasitology ; Dogs ; Electron Transport Complex IV/*genetics ; Erythrocytes/parasitology ; Likelihood Functions ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Predictive Value of Tests ; RNA, Ribosomal, 18S/analysis ; Sensitivity and Specificity ; Sequence Alignment/veterinary ; },
abstract = {A PCR targeting mitochondrial cytochrome oxidase subunit III (cox3) for molecular detection of Babesia gibsoni infection in dogs has been developed in this study. Fifty blood samples from suspected clinical cases from dogs, brought to the veterinary college clinics, were examined for presence of B. gibsoni using conventional diagnosis by microscopic examination of Giemsa stained thin blood smears. In addition, species specific PCRs targeting ITS-1 region (BgITS-1 PCR) and nested PCR targeting 18S ribosomal RNA gene (Bg18SnPCR) were carried out. A 634 bp PCR fragment of B. gibsoni cox3 gene was amplified in positive samples from three geographical locations of Satara, Wai and Pune in Maharashtra state of India. From analysis of the sequence of the B. gibsoni cox3 gene, we found that the Indian isolate had 96-98% similarity to the isolate from Japan and China. Post sequencing, de-novo diagnostic primer pair for species specific amplification of 164 bp fragment of B. gibsonicox3 was designed and the PCR was standardized. The diagnostic results of de-novo Bgcox3 PCR were compared with BgITS-1 PCR and Bg18S nPCR. Thin blood smears detected 22% (11/50) samples positive for small form of Babesia species. The BgITS-1 PCR detected 25% samples (15/50) as positive and Bg18S nPCR detected 80% (40/50) B. gibsoni positive samples. The de-novo Bgcox3 PCR detected 66% (33/50) samples positive for B. gibsoni (at 95% CI). The analytical sensitivity of cox3 PCR was evaluated as 0.000003% parasitaemia or 09 parasites in 100 μl of blood. The de-novo diagnostic cox3 PCR did not cross react with control positive DNA from other haemoprotozoa and rickettsia like B. vogeli, Hepatozoon canis, Trypanosoma evansi, Ehrlichia canis and Anaplasma platys. Statistically, cox3 PCR had better diagnostic efficiency than ITS-1 PCR in terms of sensitivity (p = 0.0006). No statistically significant difference between results of cox3 PCR and 18S nPCR was observed (p = 0.1760). Kappa values estimated for each test pair showed fair to moderate agreement between the observations. Specificity of Bgcox3 PCR was 100% when compared with microscopy or BgITS-1 PCR. Sensitivity of Bgcox3 PCR was 100% when compared with that of Bg18S nPCR.},
}
@article {pmid31598902,
year = {2020},
author = {Baysal, C and Pérez-González, A and Eseverri, &#xc1; and Jiang, X and Medina, V and Caro, E and Rubio, L and Christou, P and Zhu, C},
title = {Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria.},
journal = {Transgenic research},
volume = {29},
number = {1},
pages = {37-52},
pmid = {31598902},
issn = {1573-9368},
support = {OPP1143172.//Bill and Melinda Gates Foundation/International ; },
mesh = {Amino Acid Motifs ; Arabidopsis/genetics/metabolism ; Cell Nucleus/genetics/*metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/genetics/*metabolism ; Oryza/genetics/*metabolism ; Peptide Fragments/genetics/*metabolism ; *Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Sorting Signals ; Protein Transport ; Recombinant Proteins/genetics/*metabolism ; Nicotiana/genetics/metabolism ; },
abstract = {Mitochondria fulfil essential functions in respiration and metabolism as well as regulating stress responses and apoptosis. Most native mitochondrial proteins are encoded by nuclear genes and are imported into mitochondria via one of several receptors that recognize N-terminal signal peptides. The targeting of recombinant proteins to mitochondria therefore requires the presence of an appropriate N-terminal peptide, but little is known about mitochondrial import in monocotyledonous plants such as rice (Oryza sativa). To gain insight into this phenomenon, we targeted nuclear-encoded enhanced green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origins, and investigated their effectiveness by immunoblot analysis as well as confocal and electron microscopy. We found that the ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (Arabidopsis thaliana) and OsSCSb (Oryza sativa) peptides successfully directed most of the eGFP to the mitochondria, whereas the MTS2 peptide (Nicotiana plumbaginifolia) showed little or no evidence of targeting ability even though it is a native plant sequence. Our data therefore indicate that the presence of particular recognition motifs may be required for mitochondrial targeting, whereas the phylogenetic origin of the pre-sequences probably does not play a key role in the success of mitochondrial targeting in dedifferentiated rice callus and plants.},
}
@article {pmid31601645,
year = {2019},
author = {Ivanova, A and Gill-Hille, M and Huang, S and Branca, RM and Kmiec, B and Teixeira, PF and Lehtiö, J and Whelan, J and Murcha, MW},
title = {A Mitochondrial LYR Protein Is Required for Complex I Assembly.},
journal = {Plant physiology},
volume = {181},
number = {4},
pages = {1632-1650},
pmid = {31601645},
issn = {1532-2548},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; DNA, Bacterial/genetics ; Electron Transport Complex I/*metabolism ; Gene Deletion ; Gene Expression Regulation, Plant ; Holoenzymes/metabolism ; Iron-Sulfur Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Biological ; Organelle Biogenesis ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Subunits/metabolism ; Saccharomyces cerevisiae/metabolism ; Up-Regulation/genetics ; },
abstract = {Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.},
}
@article {pmid31610813,
year = {2019},
author = {Motoki, MT and Fonseca, DM and Miot, EF and Demari-Silva, B and Thammavong, P and Chonephetsarath, S and Phommavanh, N and Hertz, JC and Kittayapong, P and Brey, PT and Marcombe, S},
title = {Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People's Democratic Republic.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {477},
pmid = {31610813},
issn = {1756-3305},
mesh = {Aedes/classification/genetics/*physiology/virology ; Algorithms ; Animals ; Asia, Southeastern ; Bayes Theorem ; Cluster Analysis ; DNA/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Asia, Eastern ; Female ; Genetic Variation ; Genetics, Population ; Haplotypes ; Italy ; Laos ; Mitochondria/enzymology ; Mosquito Control ; Mosquito Vectors/classification/genetics/*physiology/virology ; Phylogeny ; Sequence Analysis, DNA ; Tropical Climate ; United States ; },
abstract = {BACKGROUND: The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR.<br><br>METHODS: We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA.<br><br>RESULTS: We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions.<br><br>CONCLUSIONS: Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.},
}
@article {pmid31648074,
year = {2020},
author = {Wu, H and Li, R and Liu, Y and Zhang, X and Zhang, J and Ma, E},
title = {A second intracellular copper/zinc superoxide dismutase and a manganese superoxide dismutase in Oxya chinensis: Molecular and biochemical characteristics and roles in chlorpyrifos stress.},
journal = {Ecotoxicology and environmental safety},
volume = {187},
number = {},
pages = {109830},
doi = {10.1016/j.ecoenv.2019.109830},
pmid = {31648074},
issn = {1090-2414},
mesh = {Animals ; Chlorpyrifos/*metabolism ; Copper/metabolism ; Grasshoppers/classification/*enzymology ; Insect Proteins/chemistry/genetics/metabolism/*physiology ; Manganese/metabolism ; Metals, Heavy/*metabolism ; Phylogeny ; Superoxide Dismutase/chemistry/genetics/metabolism/*physiology ; Zinc/metabolism ; },
abstract = {A second intracellular copper/zinc superoxide dismutase (icCuZnSOD2) and manganese SOD (MnSOD) were cloned and characterized in Oxya chinensis. The open reading frame (ORF) of OcicCuZnSOD2 and OcMnSOD are 462 and 672 bp encoding 153 and 223 amino acids, respectively. OcicCuZnSOD2 contains two signature sequences, one potential N-glycosylation site, and seven copper/zinc binding sites. OcMnSOD includes a mitochondria targeting sequence of 7 amino acids at N-terminal, one signature sequence, two N-glycosylation sites, and four manganese binding sites. The secondary structure and homology model of OcicCuZnSOD2 include nine β sheets, two Greek-key motifs, and one electrostatic loop. OcMnSOD contains nine α-helices and three β-sheets. Phylogenetic analysis shows that OcMnSOD is evolutionarily conserved while OcicCuZnSOD2 may be gene duplication and is paralogous to OcicCuZnSOD1. OcMnSOD expressed widely in all tissues and developmental stages. OcicCuZnSOD2 showed testis-specific expression and expressed highest in the 5th-instar nymph and the adult. The optimum temperatures and pH values of the recombinant OcicCuZnSOD2 and OcMnSOD were 40 °C and 8.0. They were stable at 25-55 °C and at pH 5.0-12.0 and pH 6.0-12.0, respectively. The activity and mRNA expression of each OcSOD were assayed after chlorpyrifos treatments. Total SOD and CuZnSOD activities first increased then declined under chlorpyrifos stress. Chlorpyrifos induced the mRNA expression and activity of OcMnSOD as a dose-dependent manner and inhibited OcicCuZnSOD2 transcription. The role of each OcSOD gene in chlorpyrifos stress was investigated using RNAi and disc diffusion assay with Escherichia coli overexpressing OcSOD proteins. Silencing of OcMnSOD significantly increased ROS content in chlorpyrifos-exposed grasshoppers. Disc diffusion assay showed that the plates with E. coli overexpressing OcMnSOD had the smaller inhibition zones around the chlorpyrifos-soaked filter discs. These results implied that OcMnSOD played a significant role in defense chlorpyrifos-induced oxidative stress.},
}
@article {pmid31665278,
year = {2019},
author = {Kortsinoglou, AM and Korovesi, AG and Theelen, B and Hagen, F and Boekhout, T and Kouvelis, VN},
title = {The mitochondrial intergenic regions nad1-cob and cob-rps3 as molecular identification tools for pathogenic members of the genus Cryptococcus.},
journal = {FEMS yeast research},
volume = {19},
number = {8},
pages = {},
doi = {10.1093/femsyr/foz077},
pmid = {31665278},
issn = {1567-1364},
mesh = {Cryptococcosis/microbiology ; Cryptococcus/*genetics/*pathogenicity ; DNA, Fungal/*genetics ; *DNA, Intergenic ; DNA, Ribosomal/genetics ; *Genes, Mitochondrial ; Humans ; Membrane Glycoproteins/genetics ; Mitochondria/genetics ; Mycological Typing Techniques ; NADH Dehydrogenase/genetics ; Phylogeny ; Ribosomal Proteins/genetics ; },
abstract = {Cryptococcus spp. are fungal species belonging to Tremellomycetes, Agaricomycotina, Basidiomycota, and several members are responsible for cryptococcosis, one of the most ubiquitous human mycoses. Affecting mainly immunosuppressed patients, but also immunocompetent ones, the members of this genus present a high level of genetic diversity. In this study, two mitochondrial intergenic regions, i.e. nad1-cob and cob-rps3, were tested for the intra- or interspecies discrimination and identification of strains and species of the genus Cryptococcus. Phylogenetic trees were constructed based on individual and concatenated sequences from representative pathogenic strains of the Cryptococcus neoformans/Cryptococcus gattii complex, representing serotypes and AFLP genotypes of all newly introduced species of this complex. Using both intergenic regions, as well as the concatenated dataset, the strains clustered in accordance with the new taxonomy. These results suggest that identification of Cryptococcus strains is possible by employing these mitochondrial intergenic regions using PCR amplification as a quick and effective method to elucidate genotypic and taxonomic differences. Thus, these regions may be applicable to a broad range of clinical studies, leading to a rapid recognition of the clinical profiles of patients.},
}
@article {pmid31670613,
year = {2019},
author = {Achatz, TJ and Dmytrieva, I and Kuzmin, Y and Tkach, VV},
title = {Phylogenetic Position of Codonocephalus Diesing, 1850 (Digenea, Diplostomoidea), an Unusual Diplostomid with Progenetic Metacercariae.},
journal = {The Journal of parasitology},
volume = {105},
number = {5},
pages = {821-826},
pmid = {31670613},
issn = {1937-2345},
mesh = {Animals ; Bayes Theorem ; DNA, Helminth/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Life Cycle Stages ; Metacercariae/classification/genetics ; Microscopy, Electron, Scanning/veterinary ; Mitochondria/enzymology ; *Phylogeny ; RNA, Helminth/genetics ; RNA, Nuclear/genetics ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Trematoda/*classification/genetics/ultrastructure ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Codonocephalus is a monotypic genus of diplostomid digeneans and is the only genus in the sub-family Codonocephalinae. The type-species Codonocephalus urniger has an unusual progenetic metacercaria that uses frogs as intermediate hosts and can use snakes as paratenic hosts. Adult C. urniger parasitize ardeid wading birds in the Palearctic. Despite the broad distribution of Codonocephalus, no DNA sequence data are currently available for the genus. In this study, we generated sequence data for nuclear ribosomal and mitochondrial DNA from progenetic metacercaria of the type-species C. urniger from marsh frog, Pelophylax ridibundus, collected in Ukraine. We used partial sequences of the nuclear ribosomal 28S gene to examine for the first time the phylogenetic position of Codonocephalus among the Diplostomoidea.},
}
@article {pmid31673019,
year = {2019},
author = {Stjelja, S and Fogelqvist, J and Tellgren-Roth, C and Dixelius, C},
title = {The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {15753},
pmid = {31673019},
issn = {2045-2322},
mesh = {Cell Nucleus/*genetics ; *Genome, Mitochondrial ; *Genome, Protozoan ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Plant Diseases/genetics/parasitology ; Plasmodiophorida/*genetics ; },
abstract = {Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.},
}
@article {pmid31673867,
year = {2019},
author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K},
title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {35},
number = {11},
pages = {176},
pmid = {31673867},
issn = {1573-0972},
support = {16KT0032//Japan Society for the Promotion of Science/ ; },
mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.},
}
@article {pmid31679533,
year = {2019},
author = {Li, Y and Ma, XX and Lv, QB and Hu, Y and Qiu, HY and Chang, QC and Wang, CR},
title = {Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae.},
journal = {Journal of helminthology},
volume = {94},
number = {},
pages = {e101},
doi = {10.1017/S0022149X19000932},
pmid = {31679533},
issn = {1475-2697},
mesh = {Animals ; Base Sequence ; Genome, Helminth ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Trematoda/classification/*genetics/isolation &amp; purification ; },
abstract = {Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.},
}
@article {pmid31706020,
year = {2020},
author = {Prous, M and Lee, KM and Mutanen, M},
title = {Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106670},
doi = {10.1016/j.ympev.2019.106670},
pmid = {31706020},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Flow ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics ; Hymenoptera/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).},
}
@article {pmid31715688,
year = {2019},
author = {Jeon, HK and Eom, KS},
title = {Mitochondrial DNA Sequence Variability of Spirometra Species in Asian Countries.},
journal = {The Korean journal of parasitology},
volume = {57},
number = {5},
pages = {481-487},
pmid = {31715688},
issn = {1738-0006},
support = {2017K1A3A1A09085607//National Research Foundation of Korea/ ; },
mesh = {Animals ; Cestode Infections/*parasitology ; China ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Helminth Proteins/genetics ; Humans ; Japan ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Republic of Korea ; Spirometra/classification/*genetics/isolation &amp; purification ; },
abstract = {Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.},
}
@article {pmid31716329,
year = {2019},
author = {Macià, R and Mally, R and Ylla, J and Gastón, J and Huertas, M},
title = {Integrative revision of the Iberian species of Coscinia Hübner, [1819] sensu lato and Spiris Hübner, [1819], (Lepidoptera: Erebidae, Arctiinae).},
journal = {Zootaxa},
volume = {4615},
number = {3},
pages = {zootaxa.4615.3.1},
doi = {10.11646/zootaxa.4615.3.1},
pmid = {31716329},
issn = {1175-5334},
mesh = {Animals ; Female ; Genitalia ; Male ; Mitochondria ; *Moths ; *Mustelidae ; Phylogeny ; },
abstract = {The Iberian species of the genera Coscinia Hübner, [1819] and Spiris Hübner, [1819], as well as three other species from the Mediterranean area, are revised based on morphological and molecular genetic data. Our results suggest the separation into four morphologically and phylogenetically different genera: Coscinia Hübner, [1819], Lerautia Kemal Koçak, 2006 stat. rev., Sagarriella Macià, Mally, Ylla, Gastón Huertas gen. nov. and Spiris Hübner, [1819]. We conclude that there are eight species of the Coscinia genus group present in the studied area: Coscinia cribraria (Linnaeus, 1758), Coscinia chrysocephala (Hübner, [1810]) stat. rev., Coscinia mariarosae Expósito, 1991, Sagarriella libyssa caligans (Turati, 1907) comb. nov., Sagarriella romei (Sagarra, 1924) (= romeii sensu auctorum) comb. nov., Spiris striata Hübner, [1819], Spiris slovenica (Daniel, 1939) and Lerautia bifasciata (Rambur, 1832) comb. rev. We consider Coscinia cribraria benderi (Marten, 1957) stat. nov., Coscinia c. rippertii (Boisduval, 1834) and Coscinia c. ibicenca Kobes, 1991 stat. rev. to be subspecies of C. cribraria. COI Barcodes of C. cribraria diverge by up to 7.99%, and the investigated specimens group into six different COI Barcode BINs. Both the phylogenetic analysis of mitochondrial and nuclear DNA and the morphological examination of different specimens corroborate the changes in taxonomic status and justify the proposed taxonomic categories. We present images of adults and genitalia of both sexes, the immature stages of some of the species and the subspecies studied, as well as phylogenetic results from the analysis of genetic data. We also include data on life history, foodplants and geographical distribution.},
}
@article {pmid31716534,
year = {2019},
author = {Braun, MP and Datzmann, T and Arndt, T and Reinschmidt, M and Schnitker, H and Bahr, N and Sauer-Gürth, H and Wink, M},
title = {A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications.},
journal = {Zootaxa},
volume = {4563},
number = {3},
pages = {zootaxa.4563.3.8},
doi = {10.11646/zootaxa.4563.3.8},
pmid = {31716534},
issn = {1175-5334},
mesh = {Animals ; Base Sequence ; Mitochondria ; *Parrots ; Phylogeny ; *Psittaciformes ; *Psittacula ; },
abstract = {The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species.},
}
@article {pmid31716895,
year = {2019},
author = {Tominaga, A and Matsui, M and Tanabe, S and Nishikawa, K},
title = {A revision of Hynobius stejnegeri, a lotic breeding salamander from western Japan, with a description of three new species (Amphibia, Caudata, Hynobiidae).},
journal = {Zootaxa},
volume = {4651},
number = {3},
pages = {zootaxa.4651.3.1},
doi = {10.11646/zootaxa.4651.3.1},
pmid = {31716895},
issn = {1175-5334},
mesh = {Animals ; Breeding ; Japan ; Mitochondria ; Phylogeny ; Tooth ; *Caudata ; },
abstract = {A lotic-breeding salamander Hynobius stejnegeri, formerly called H. yatsui, from western Japan is revised based on genetic and morphological evidence, and three species are described: H. guttatus sp. nov. from Chubu-Kinki districts of Honshu Island, H. tsurugiensis sp. nov. from east highland of Shikoku Island, and H. kuishiensis sp. nov. from other parts of Shikoku Island. Thus, H. stejnegeri sensu stricto is restricted to Kyushu Island. Of these four species, H. kuishiensis sp. nov. contains two distinct mitochondrial lineages, but this split is not reflected in differentiation of allozyme (nuclear genome) markers. These species are morphologically similar to each other but can be differentiated by several characteristics, especially in combination of dorsal coloration, the number of vomerine, upper, and lower jaw teeth, and depth of vomerine teeth series. In coloration, H. guttatus sp. nov. is brown or dark brown mostly with tiny white to brownish white marking, while H. tsurugiensis sp. nov. is dark brown with bright yellow continuous markings. Hynobius kuishiensis sp. nov. is reddish purple or dark brown with small to continuous brownish white markings, in contrast to reddish purple or dark brown with small to large brownish white markings in H. stejnegeri.},
}
@article {pmid31719597,
year = {2019},
author = {Hao, Y and Ruiz, R and Yang, L and Neto, AG and Amin, MR and Kelly, D and Achlatis, S and Roof, S and Bing, R and Kannan, K and Brown, SM and Pei, Z and Branski, RC},
title = {Mitochondrial somatic mutations and the lack of viral genomic variation in recurrent respiratory papillomatosis.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16625},
pmid = {31719597},
issn = {2045-2322},
support = {R21 DE025352/DE/NIDCR NIH HHS/United States ; R01 AI110372/AI/NIAID NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; R01 CA204113/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; DNA, Viral/genetics ; Female ; Genetic Variation/genetics ; Genome, Viral/*genetics ; Human papillomavirus 11/*genetics ; Human papillomavirus 6/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mouth/virology ; Multiplex Polymerase Chain Reaction ; Mutation/genetics ; Papillomavirus Infections/diagnosis/genetics/*virology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Respiratory Tract Infections/diagnosis/genetics/*virology ; },
abstract = {Recurrent Respiratory Papillomatosis (RRP) is a rare disease of the aerodigestive tract caused by the Human Papilloma Virus (HPV) that manifests as profoundly altered phonatory and upper respiratory anatomy. Current therapies are primarily symptomatic; enhanced insight regarding disease-specific biology of RRP is critical to improved therapeutics for this challenging population. Multiplex PCR was performed on oral rinses collected from twenty-three patients with adult-onset RRP every three months for one year. Twenty-two (95.6%) subjects had an initial HPV positive oral rinse. Of those subjects, 77.2% had an additional positive oral rinse over 12 months. A subset of rinses were then compared to tissue samples in the same patient employing HPViewer to determine HPV subtype concordance. Multiple HPV copies (60-787 per human cell) were detected in RRP tissue in each patient, but a single dominant HPV was found in individual samples. These data confirm persistent oral HPV infection in the majority of patients with RRP. In addition, three novel HPV6 isolates were found and identical HPV strains, at very low levels, were identified in oral rinses in two patients suggesting potential HPV subtype concordance. Finally, somatic heteroplasmic mtDNA mutations were observed in RRP tissue with 1.8 mutations per sample and two nonsynonymous variants. These data provide foundational insight into both the underlying pathophysiology of RRP, but also potential targets for intervention in this challenging patient cohort.},
}
@article {pmid31727366,
year = {2020},
author = {Li, J and Xue, C and Gao, Q and Tan, J and Wan, Z},
title = {Mitochondrial DNA heteroplasmy rises in substantial nigra of aged PINK1 KO mice.},
journal = {Biochemical and biophysical research communications},
volume = {521},
number = {4},
pages = {1024-1029},
doi = {10.1016/j.bbrc.2019.10.112},
pmid = {31727366},
issn = {1090-2104},
mesh = {Aging/genetics ; Animals ; Brain/metabolism ; DNA Copy Number Variations/genetics ; DNA, Mitochondrial/*genetics ; Gene Frequency/genetics ; Mice, Knockout ; Mutation Rate ; Protein Kinases/*deficiency/genetics/metabolism ; Substantia Nigra/*metabolism ; PTEN-Induced Putative Kinase ; },
abstract = {Mutations in PINK1 and Parkin result in early-onset autosomal recessive Parkinson's disease (PD). PINK1/Parkin pathway maintain mitochondrial function by mediating the clearance of damaged mitochondria. However, the role of PINK1/Parkin in maintaining the balance of mtDNA heteroplasmy is still unknown. Here, we isolated mitochondrial DNA (mtDNA) from cortex, striatum and substantia nigra of wildtype (WT), PINK1 knockout (PINK1 KO) and Parkin knockout (Parkin KO) mice to analyze mtDNA heteroplasmy induced by PINK1/Parkin deficiency or aging. Our results showed that the Single Nucleotide Variants (SNVs) of late-onset somatic variants mainly increased with aging. Conversely, the early-onset somatic variants exhibited significant increase in the cortex and substantia nigra of PINK1 KO mice than WT mice of the same age. Increased average variant allele frequency was observed in aged PINK1 KO mice and in substantial nigra of aged Parkin KO mice than in WT mice. Cumulative variant allele frequency in the substantia nigra of PINK1 KO mice was significantly higher than that in WT mice, further supporting the pivotal role of PINK1 in mtDNA maintenance. This study presented a new evidence for PINK1 and Parkin in participating in mitochondrial quality control and provided clues for further revealing the role of PINK1 and Parkin in the pathogenesis of PD.},
}
@article {pmid31742484,
year = {2019},
author = {Woodyard, ET and Stilwell, JM and Camus, AC and Rosser, TG},
title = {Molecular and Histopathological Data on Levisunguis subaequalis Curran, Overstreet, Collins &amp; Benz, 2014 (Pentastomida: Eupentastomida: Porocephalida: Porocephaloidea: Sebekidae: Sebekinae) from Gambusia affinis in Alabama, USA.},
journal = {The Journal of parasitology},
volume = {105},
number = {6},
pages = {827-839},
pmid = {31742484},
issn = {1937-2345},
mesh = {Alabama/epidemiology ; Animals ; Bayes Theorem ; Cyprinodontiformes/*parasitology ; DNA/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Fish Diseases/epidemiology/*parasitology ; Likelihood Functions ; Lung/parasitology ; Mitochondria/enzymology ; Nymph/anatomy &amp; histology ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Pentastomida/anatomy &amp; histology/classification/*genetics ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Turtles/parasitology ; },
abstract = {Levisunguis subaequalis Curran, Overstreet, Collins &amp; Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.},
}
@article {pmid31747540,
year = {2020},
author = {Anderson, K and Braoudakis, G and Kvist, S},
title = {Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species.},
journal = {Molecular phylogenetics and evolution},
volume = {143},
number = {},
pages = {106688},
doi = {10.1016/j.ympev.2019.106688},
pmid = {31747540},
issn = {1095-9513},
mesh = {Animals ; Annelida/classification/*genetics ; Biodiversity ; Canada ; Electron Transport Complex IV/classification/genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; },
abstract = {Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification processes, molecular approaches have, in recent years, been employed to illuminate the relationships within this family, and DNA barcoding has been employed for identification purposes. However, an understanding of the levels of genetic variation across the geographic distributions of members of the genus is still lacking. Herein, we sequence the mitochondrial COI locus for 249 newly collected North American individuals, representing 5 species, as well as mitochondrial 12S rDNA, nuclear 18S rDNA, and nuclear 28S rDNA for a select subset of these. Our COI dataset was leveraged to detect potential cryptic species, and to calculate genetic distances as a proxy for the degree of gene flow between populations. Augmented by numerous sequences from GenBank, the multilocus dataset was used to reconstruct a phylogenetic hypothesis for worldwide members of the genus. Beyond corroborating previous overarching phylogenetic frameworks, our results show that an undescribed species that is morphologically and genetically similar to Erpobdella punctata exists in sympatry with this species - the new species has likely been overlooked in previous studies due to its morphological similarity with Erpobdella punctata. Erpobdella bucera is reported from Canada for the first time; and Erpobdella microstoma is newly reported from Saskatchewan and placed in a phylogeny for the first time. Finally, we find evidence for genetic structure in both E. cf. punctata and Erpobdella obscura that is correlated with major river drainage basin boundaries in North America.},
}
@article {pmid31758495,
year = {2020},
author = {Magallón-Gayón, E and Del Río-Portilla, M&#xc1; and de Los Angeles Barriga-Sosa, I},
title = {The complete mitochondrial genomes of two octopods of the eastern Pacific Ocean: Octopus mimus and 'Octopus' fitchi (Cephalopoda: Octopodidae) and their phylogenetic position within Octopoda.},
journal = {Molecular biology reports},
volume = {47},
number = {2},
pages = {943-952},
pmid = {31758495},
issn = {1573-4978},
support = {UAM-147.09.01//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 04//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 07//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 14713349//SEP-PRODEP/ ; },
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Octopodiformes/*genetics ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {The complete mitochondrial genomes of two important octopus species from the eastern Pacific were sequenced, obtaining their complete nucleotide sequences. Octopus mimus is the most important commercially catched species along the eastern Pacific, from Mexico to Chile, whereas 'Octopus' fitchi is a pigmy species with uncertain taxonomic genus. The mitogenomes of Octopus mimus and 'Octopus' fitchi were 15,696 and 15,780 base pairs (bp) in length with an A + T composition of 75.5% and 75.8%, respectively. Each genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, as well as a control region. Gene order is maintained as reported for other species of the Octopodidae. The phylogenetic analysis based on the concatenated thirteen protein-coding genes confirms that O. mimus belongs to the genus Octopus, which is supported by the genetic distance (11-16%) whereas the position of 'O'. fitchi within this group it is not supported. The analysis also indicated that the phylogenetic position of 'O'. fitchi is closer to Callistoctopus than to the Cistopus or the Amphioctopus clades. Based on the tree topology and the high genetic distance observed (24-25%), we suggest that 'O'. fitchi might represent a different genus.},
}
@article {pmid31762360,
year = {2020},
author = {Phukuntsi, MA and Du Plessis, M and Dalton, DL and Jansen, R and Cuozzo, FP and Sauther, ML and Kotze, A},
title = {Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {1},
pages = {1-10},
doi = {10.1080/24701394.2019.1694015},
pmid = {31762360},
issn = {2470-1408},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Galago/*genetics ; Genetic Variation/genetics ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Male ; Phylogeny ; South Africa ; },
abstract = {Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.},
}
@article {pmid31767814,
year = {2019},
author = {Kumar De, A and Ponraj, P and Malakar, D and Muthiyan, R and Kundu, A and Bhattacharya, D},
title = {Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {31767814},
issn = {0973-7731},
mesh = {Animals ; Base Composition ; Buffaloes/*genetics ; China ; Codon, Initiator ; Codon, Terminator ; Genes, Mitochondrial/*genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; India ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.},
}
@article {pmid31767817,
year = {2019},
author = {Abou-Shaara, HF},
title = {Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies.},
journal = {Journal of genetics},
volume = {98},
number = {},
pages = {},
pmid = {31767817},
issn = {0973-7731},
mesh = {Africa ; Animals ; Base Sequence ; Bees/*classification/*genetics ; *Computational Biology ; DNA Primers ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Multigene Family ; Open Reading Frames ; Phylogeny ; Sequence Analysis ; },
abstract = {Various honey bees, especially subspecies Apis mellifera, occur in Africa and are distribute across the continent. The genetic relationships and identical genetic characteristics between honey bee subspecies in Africa (African bee subspecies) have not been widely investigated using sequence analysis. On the other hand, bioinformatics are developed rapidly and have diverse applications. It is anticipated that bioinformatics can show the genetic relationships and similarities among subspecies. These points have high importance, especially subspecies with identical genetic characteristics can be infected with the same group of pathogens, which have implications on honey bee health. In this study, the mitochondrial DNA sequences of four African subspecies and Africanized bees were subjected to the analyses of base composition, phylogeny, shared gene clusters, enzymatic digestion, and open reading frames. High identical base composition was detected in the studied subspecies, and high identical results from all tests were found between A. m. scutellata and A. m. capensis followed by A. m. intermissa and A. m. monticola. The least genetic relationships were found between A. m. lamarckii and the other subspecies. This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m. capensis. Additionally, specific primers to identify these subspecies were designed and tested.},
}
@article {pmid31767921,
year = {2019},
author = {Kehlmaier, C and Graciá, E and Campbell, PD and Hofmeyr, MD and Schweiger, S and Martínez-Silvestre, A and Joyce, W and Fritz, U},
title = {Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.).},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17487},
pmid = {31767921},
issn = {2045-2322},
mesh = {Animals ; DNA, Mitochondrial/*analysis ; Fossils ; Indian Ocean ; Mauritius ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Reunion ; Sequence Analysis, DNA/*methods ; Turtles/*classification/genetics ; },
abstract = {The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage that diverged as early as the late Eocene. Diversification of Cylindraspis commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, Cylindraspis likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna.},
}
@article {pmid31772306,
year = {2019},
author = {Barbour, AG and Shao, H and Cook, VJ and Baldwin-Brown, J and Tsao, JI and Long, AD},
title = {Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {17618},
pmid = {31772306},
issn = {2045-2322},
support = {R01 AI037248/AI/NIAID NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R21 AI136523/AI/NIAID NIH HHS/United States ; S10 OD021718/OD/NIH HHS/United States ; R21 AI126037/AI/NIAID NIH HHS/United States ; S10 RR025496/RR/NCRR NIH HHS/United States ; },
mesh = {Animals ; Animals, Laboratory/genetics ; Animals, Wild/genetics ; Arachnid Vectors/microbiology ; Borrelia ; Borrelia Infections/genetics/microbiology ; Borrelia burgdorferi/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; *Disease Reservoirs ; Female ; Gene Expression Profiling ; *Genome ; Haplotypes ; Ixodes/microbiology ; Lyme Disease/microbiology/transmission/veterinary ; Muridae/classification/genetics ; Organ Specificity ; Peromyscus/classification/*genetics/microbiology ; Phylogeny ; Pseudogenes ; Rodent Diseases/epidemiology/microbiology/parasitology ; Sequence Homology, Nucleic Acid ; Species Specificity ; Tick Bites/microbiology/veterinary ; United States ; },
abstract = {The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.},
}
@article {pmid31773863,
year = {2020},
author = {Gao, H and Li, N and Huang, Y and Qiao, F and Li, J and Li, Z and Li, Y and Wang, Z and Teng, L and Liu, Z},
title = {Taxonomic status of Chinese blue sheep (Pseudois nayaur): new evidence of a distinct subspecies.},
journal = {Integrative zoology},
volume = {15},
number = {3},
pages = {202-212},
doi = {10.1111/1749-4877.12422},
pmid = {31773863},
issn = {1749-4877},
mesh = {Animals ; China ; Genetic Variation ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Ruminants/*classification/genetics ; Sequence Analysis, DNA/veterinary ; Sheep/classification/genetics ; },
abstract = {The blue sheep is an endemic species to the Qinghai-Tibet Plateau and surrounding regions. It has been regarded as having 2 subspecies: Pseudois nayaur nayaur and P. n. szechuanensis. However, such a classification remains controversial. Herein, we analyze 10 microsatellite loci and part of the mitochondrial control region for clarification in such taxonomic debates. We use samples from 168 individuals from 6 geographic populations covering almost all the distribution areas of the species in China to carry out comparisons. Phylogenetic trees derived from both the microsatellite and mitochondrial markers combined with the discriminant analysis of principal components (DAPC) and the STRUCTURE analysis reveal that the individuals in the Helan Mountains are well grouped with a distinct evolutionary lineage and are significantly different from the other populations of P. n. szechuanensis according to Fst values, implying that this isolated population should be categorized as a valid subspecies; namely, Pseudois nayaur alashanicus. The isolation-by-distance (IBD) analysis shows a significant positive relationship between genetic and geographical distances among the populations.},
}
@article {pmid31781636,
year = {2019},
author = {Owuor, SA and Mamati, EG and Kasili, RW},
title = {Origin, Genetic Diversity, and Population Structure of Rabbits (Oryctolagus cuniculus) in Kenya.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {7056940},
pmid = {31781636},
issn = {2314-6141},
mesh = {Animals ; Breeding/methods ; DNA, Mitochondrial/genetics ; Europe ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Kenya ; Mitochondria/genetics ; Phylogeny ; Rabbits/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {To evaluate the origin, genetic diversity, and population structure of domesticated rabbits in Kenya, a 263-base pair region of mtDNA D-loop region of 111 rabbits sampled from Kakamega, Vihiga, and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region, and Kitui, Machakos, and Makueni in the eastern region of the country were analyzed. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity of domesticated rabbits in Kenya. This study resolved 5 unique haplotypes in the mtDNA D-loop region. A population genetic structure distinguishing Europe grouping and domesticated rabbits in Kenya was obtained on incorporating 32 known haplotypes. Domesticated rabbits in Kenya clustered together with rabbits from other geographic regions, suggesting common origin. The results suggested that the Kenyan domesticated rabbits may have originated from Europe. Integration of exotic breeds into breeding programmes could have contributed to the low genetic diversity. These results provide useful information for breeding and conservation decisions by the relevant stakeholders in the agriculture industry in Kenya.},
}
@article {pmid31787045,
year = {2020},
author = {Schaack, S and Ho, EKH and Macrae, F},
title = {Disentangling the intertwined roles of mutation, selection and drift in the mitochondrial genome.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1790},
pages = {20190173},
pmid = {31787045},
issn = {1471-2970},
support = {R15 GM132861/GM/NIGMS NIH HHS/United States ; },
mesh = {*Genetic Drift ; *Genome, Mitochondrial ; *Mutation ; *Selection, Genetic ; },
abstract = {Understanding and quantifying the rates of change in the mitochondrial genome is a major component of many areas of biological inquiry, from phylogenetics to human health. A critical parameter in understanding rates of change is estimating the mitochondrial mutation rate (mtDNA MR). Although the first direct estimates of mtDNA MRs were reported almost 20 years ago, the number of estimates has not grown markedly since that time. This is largely owing to the challenges associated with time- and labour-intensive mutation accumulation (MA) experiments. But even MA experiments do not solve a major problem with estimating mtDNA MRs-the challenge of disentangling the role of mutation from other evolutionary forces acting within the cell. Now that it is widely understood that any newly generated mutant allele in the mitochondria will initially be at very low frequency (1/N, where N is the number of mtDNA molecules in the cell), the importance of understanding the effective population size (Ne) of the mtDNA and the size of genetic bottlenecks during gametogenesis and development has come into the spotlight. In addition to these factors regulating the role of genetic drift, advances in our understanding of mitochondrial replication and turnover allow us to more easily envision how natural selection within the cell might favour or purge mutations in multi-copy organellar genomes. Here, we review the unique features of the mitochondrial genome that pose a challenge for accurate MR estimation and discuss ways to overcome those challenges. Estimates of mtDNA MRs remain one of the most widely used parameters in biology, thus accurate quantification and a deeper understanding of how and why they may vary within and between individuals, populations and species is an important goal. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.},
}
@article {pmid31797315,
year = {2020},
author = {Suk, HY and Bae, HG and Kim, DY and Won, H and Baek, HJ and Lee, CH and Kim, DY and Go, YM and Song, JY and Lee, H and Min, MS},
title = {Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula.},
journal = {Genes &amp; genomics},
volume = {42},
number = {2},
pages = {165-178},
pmid = {31797315},
issn = {2092-9293},
mesh = {Animals ; *Endangered Species ; Genetic Variation ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Republic of Korea ; Caudata/classification/*genetics ; },
abstract = {BACKGROUND: The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions.<br><br>OBJECTIVES: To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius.<br><br>METHODS: Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus.<br><br>RESULTS: A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used.<br><br>CONCLUSION: Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.},
}
@article {pmid31802201,
year = {2020},
author = {Yang, J and Khan, MAK and Zhang, H and Zhang, Y and Certik, M and Garre, V and Song, Y},
title = {Mitochondrial Citrate Transport System in the Fungus Mucor circinelloides: Identification, Phylogenetic Analysis, and Expression Profiling During Growth and Lipid Accumulation.},
journal = {Current microbiology},
volume = {77},
number = {2},
pages = {220-231},
pmid = {31802201},
issn = {1432-0991},
support = {31670064//National Natural Science Foundation of China/ ; tscy 20160101//TaiShan Industrial Experts Programme/ ; 2018GNC110039//Key Technology Research and Development Program of Shandong/ ; },
mesh = {Biological Transport ; Citrates/*metabolism ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Lipid Metabolism ; Lipids/*biosynthesis ; Mitochondria/*metabolism ; Mucor/*classification/*metabolism ; *Phylogeny ; },
abstract = {The mitochondrial citrate transport system, composed of citrate and malate transporters (MTs), can regulate the citrate efflux from mitochondria to cytosol, and then citrate is cleaved into OAA and acetyl-CoA which can be used for fatty acid (FA) biosynthesis. However, in the fungus Mucor circinelloides the molecular mechanism of citrate efflux from the mitochondria by this system and its role in FA synthesis is unclear. In the present study, we have analyzed the genome of high lipid-producing strain WJ11 and the low lipid-producing strain CBS 277.49 to find the potential genes involving in this system. Five potential genes are present in the genome of WJ11. These genes encode one citrate transport protein (CT), one tricarboxylate carrier (TCT), one MT, and two 2-oxoglutarate:malate antiporters (SoDIT-a and SoDIT-b). However, the genome of CBS 277.49 contains the same set of genes, except for the presence of just one SoDIT. The proteins from WJ11 had similar properties as their counterparts in CBS 277.49. Moreover, phylogenetic analyses revealed the evolutionary relationship of these proteins and illuminated their typical motifs related to potential functions. Additionally, the expression of these genes was analyzed to predict the possible functions in lipid metabolism in M. circinelloides. This is the first study to report the in silico analysis of structures and functions of the mitochondrial citrate transport system in M. circinelloides. This work showed a new strategy for research for the selection of candidate genes for further detailed functional investigation of the mitochondrial citrate transport system in lipid accumulation.},
}
@article {pmid31809841,
year = {2020},
author = {Ju, Y and Liu, H and He, J and Wang, L and Xu, J and Liu, H and Dong, Y and Zhang, R and Zhao, P and Xing, X},
title = {Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications.},
journal = {Gene},
volume = {733},
number = {},
pages = {144271},
doi = {10.1016/j.gene.2019.144271},
pmid = {31809841},
issn = {1879-0038},
mesh = {Animals ; China ; Conservation of Natural Resources/methods ; DNA, Mitochondrial/*genetics ; Finland ; Genetic Variation/genetics ; Haplotypes ; Introduced Species ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Reindeer/*genetics ; },
abstract = {Aoluguya Reindeer is the only reindeer population in China. In recent years, habitat loss and inbreeding have led to population decline, and population growth has been slow, maintaining a thousand or so. To better protect the Aoluguya Reindeer and improve its fecundity, we have introduced reindeer from Finland, crossbreeding help us to reach this goal. However, it is lacking in the study of genetic diversity of reindeer in China and Finland. Therefore, we used the partial sequences of the D-loop region of mitochondrial DNA to analyze the genetic diversity of Chinese reindeer (Aoluguya Reindeer) and the introduced Finnish reindeer, and identified twenty-six haplotypes, including nineteen in China, five in Finland, and two in Russia. There is no shared haplotype among them. The nucleotide diversity of Aoluguya Reindeer is 0.00752, which is significantly lower than that of reindeer in Finland and other countries. The haplotype and phylogenetic analysis show that reindeer from different geographical origins are not clustered completely according to geographical distribution. Aoluguya Reindeer populations and the introduced reindeer herds from Finland are all closely related to the reindeer from Russia. AMOVA analysis showed that there was significant differentiation between reindeer populations in China and Finland, and mismatch analysis showed that both populations had not experienced expansion. In this study, we identified the genetic diversity of Aoluguya Reindeer and the introduced reindeer, and provided a scientific basis for the conservation and breeding of Aoluguya Reindeer resources.},
}
@article {pmid31823814,
year = {2019},
author = {Dubin, A and Jørgensen, TE and Jakt, LM and Johansen, SD},
title = {The mitochondrial transcriptome of the anglerfish Lophius piscatorius.},
journal = {BMC research notes},
volume = {12},
number = {1},
pages = {800},
pmid = {31823814},
issn = {1756-0500},
mesh = {Adenosine Triphosphatases/genetics ; Animals ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/genetics ; Fishes/*genetics/metabolism ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Intracellular Signaling Peptides and Proteins/genetics ; Mitochondria/*genetics/metabolism ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Antisense/genetics ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; RNA, Mitochondrial/genetics ; RNA, Ribosomal/genetics ; Transcriptome/*genetics ; },
abstract = {OBJECTIVE: Analyze key features of the anglerfish Lophius piscatorius mitochondrial transcriptome based on high-throughput total RNA sequencing.<br><br>RESULTS: We determined the complete mitochondrial DNA and corresponding transcriptome sequences of L. piscatorius. Key features include highly abundant mitochondrial ribosomal RNAs (10-100 times that of mRNAs), and that cytochrome oxidase mRNAs appeared&#x2009;>&#x2009;5 times more abundant than both NADH dehydrogenase and ATPase mRNAs. Unusual for a vertebrate mitochondrial mRNA, the polyadenylated COI mRNA was found to harbor a 75 nucleotide 3' untranslated region. The mitochondrial genome expressed several non-canonical genes, including the long noncoding RNAs lncCR-H, lncCR-L and lncCOI. Whereas lncCR-H and lncCR-L mapped to opposite strands in a non-overlapping organization within the control region, lncCOI appeared novel among vertebrates. We found lncCOI to be a highly abundant mitochondrial RNA in antisense to the COI mRNA. Finally, we present the coding potential of a humanin-like peptide within the large subunit ribosomal RNA.},
}
@article {pmid31830457,
year = {2020},
author = {Liu, W and Cai, Y and Zhang, Q and Chen, L and Shu, F and Ma, X and Bian, Y},
title = {The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences.},
journal = {International journal of biological macromolecules},
volume = {143},
number = {},
pages = {373-381},
doi = {10.1016/j.ijbiomac.2019.12.056},
pmid = {31830457},
issn = {1879-0003},
mesh = {Ascomycota/classification/*genetics ; Genome, Mitochondrial/*genetics ; Introns/genetics ; Mitochondria/genetics ; *Molecular Sequence Annotation ; Open Reading Frames/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; },
abstract = {The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.},
}
@article {pmid31841396,
year = {2020},
author = {Showmaker, KC and Cobb, MB and Johnson, AC and Yang, W and Garrett, MR},
title = {Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat.},
journal = {Physiological genomics},
volume = {52},
number = {1},
pages = {56-70},
pmid = {31841396},
issn = {1531-2267},
support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; P20 GM104357/GM/NIGMS NIH HHS/United States ; P30 GM103328/GM/NIGMS NIH HHS/United States ; R01 HL137673/HL/NHLBI NIH HHS/United States ; P20 GM121334/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Chromosomes, Mammalian/genetics ; Disease Models, Animal ; *Genetic Association Studies ; *Genetic Predisposition to Disease ; Genome ; Genome, Mitochondrial ; Introns/genetics ; Mitochondria/genetics ; Nephrons/*embryology ; Organogenesis/*genetics ; Phylogeny ; Proto-Oncogene Proteins c-kit/metabolism ; Rats ; Urogenital Abnormalities/*genetics ; Vesico-Ureteral Reflux/*genetics ; *Whole Genome Sequencing ; },
abstract = {The HSRA rat is a model of congenital abnormalities of the kidney and urogenital tract (CAKUT). Our laboratory has used this model to investigate the role of nephron number (functional unit of the kidney) in susceptibility to develop kidney disease as 50-75% offspring are born with a single kidney (HSRA-S), while 25-50% are born with two kidneys (HSRA-C). HSRA-S rats develop increased kidney injury and hypertension with age compared with nephrectomized two-kidney animals (HSRA-UNX), suggesting that even slight differences in nephron number can be an important driver in decline in kidney function. The HSRA rat was selected and inbred from a family of outbred heterogeneous stock (NIH-HS) rats that exhibited a high incidence of CAKUT. The HS model was originally developed from eight inbred strains (ACI, BN, BUF, F344, M520, MR, WKY, and WN). The genetic make-up of the HSRA is therefore a mosaic of these eight inbred strains. Interestingly, the ACI progenitor of the HS model exhibits CAKUT in 10-15% of offspring with the genetic cause being attributed to the presence of a long-term repeat (LTR) within exon 1 of the c-Kit gene. Our hypothesis is that the HSRA and ACI share this common genetic cause, but other alleles in the HSRA genome contribute to the increased penetrance of CAKUT (75% HSRA vs. 15% in ACI). To facilitate genetic studies and better characterize the model, we sequenced the whole genome of the HSRA to a depth of ~50×. A genome-wide variant analysis of high-impact variants identified a number of novel genes that could be linked to CAKUT in the HSRA model. In summary, the identification of new genes/modifiers that lead to CAKUT/loss of one kidney in the HSRA model will provide greater insight into association between kidney development and susceptibility to develop cardiovascular disease later in life.},
}
@article {pmid31851687,
year = {2019},
author = {Barbosa, AD and Austen, J and Portas, TJ and Friend, JA and Ahlstrom, LA and Oskam, CL and Ryan, UM and Irwin, PJ},
title = {Sequence analyses at mitochondrial and nuclear loci reveal a novel Theileria sp. and aid in the phylogenetic resolution of piroplasms from Australian marsupials and ticks.},
journal = {PloS one},
volume = {14},
number = {12},
pages = {e0225822},
pmid = {31851687},
issn = {1932-6203},
mesh = {Animals ; Australia ; DNA, Protozoan/genetics ; Genetic Loci ; Marsupialia/*parasitology ; Mitochondria/*genetics ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/*genetics ; *Theileria/classification/genetics/isolation &amp; purification ; Theileriasis/*parasitology ; Ticks/*parasitology ; },
abstract = {The order Piroplasmida encompasses two main families: Babesiidae and Theileriidae, containing tick-borne pathogens of veterinary and medical importance worldwide. While only three genera (Babesia, Cytauxzoon and Theileria) comprising piroplasm parasites are currently recognised, phylogenetic studies at the 18S rRNA (18S) gene suggest that these organisms represent at least ten lineages, one of which comprises the relatively unique and highly diverse Theileria spp. from Australian marsupials and ticks. As an alternative to analysing 18S sequences alone, sequencing of mitochondrial genes has proven to be useful for the elucidation of evolutionary relationships amongst some groups of piroplasms. This research aimed to characterise piroplasms from Australian native mammals and ticks using multiple genetic markers (18S, cytochrome c, oxidase subunit III (cox3) and cytochrome B (cytB)) and microscopy. For this, nearly complete piroplasm-18S sequences were obtained from 32 animals belonging to six marsupial species: eastern bettong (Bettongia gaimardi), eastern quoll (Dasyurus viverrinus), eastern grey kangaroo (Macropus giganteus), swamp wallaby (Wallabia bicolor), quokka (Setonix brachyurus) and Gilbert's potoroo (Potorous gilbertii). The organisms detected represented eight novel Theileria genotypes, which formed five sub-clades within the main marsupial clade containing previously reported Australian marsupial and tick-derived Theileria spp. A selection of both novel and previously described Australian piroplasms at the 18S were also successfully characterised, for the first time, at the cox3 and cytB loci, and corroborated the position of Australian native theilerias in a separate, well-supported clade. Analyses of the cox3 and cytB genes also aided in the taxonomic resolution within the clade of Australian Piroplasmida. Importantly, microscopy and molecular analysis at multiple loci led to the discovery of a unique piroplasm species that clustered with the Australian marsupial theilerias, for which we propose the name Theileria lupei n. sp.},
}
@article {pmid31865652,
year = {2019},
author = {Hamamcı, B and Açıkgöz, G and Kılıç, E and Karaaslan, K and Çetinkaya, &#xdc; and Durgun Yetim, T and Yetim, &#x130;},
title = {Biochemical Analysis of Germinal Membrane and Cyst Fluid by Raman Spectroscopy in Echinococcosis.},
journal = {Turkiye parazitolojii dergisi},
volume = {43},
number = {4},
pages = {175-181},
doi = {10.4274/tpd.galenos.2019.6293},
pmid = {31865652},
issn = {2146-3077},
mesh = {Animals ; Cyst Fluid/chemistry ; DNA, Helminth/chemistry ; Echinococcosis, Hepatic/*diagnostic imaging/parasitology ; Echinococcus granulosus/*classification/genetics ; Electron Transport Complex IV/genetics ; Humans ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction ; Spectrum Analysis, Raman ; Zoonoses/*diagnostic imaging/parasitology ; },
abstract = {OBJECTIVE: Hydatidosis is a zoonotic parasitic infection caused by the larval stage of Echinococcus granulosus. The aim of this study was to investigate the biochemical structures of germinal membrane and cyst fluids obtained from patients with liver involvement during surgery, by Raman spectroscopy at the molecular level.<br><br>METHODS: Molecular characterization of germinal membrane and cyst fluid according to mitochondrial gene region was determined and phylogenetic analysis was performed. Raman spectroscopy was used in samples and spectral bands between 300 and 1800 cm[-1] were examined.<br><br>RESULTS: As a result of PCR, approximately 400 bp DNA band was obtained from germinal membranes and cyst fluids gathered from patients. Peaks were observed at 780, 880, 970, 1151, 1200, 1270 cm[-1] for germinal membrane and at 780 and 1200 cm[-1] for cyst fluid. The highest spectral bands were obtained at 1333-1335 cm[-1] and were determined to be modes indicating the CH3CH2 collagen and polynucleotide chain.<br><br>CONCLUSION: In the identification of microorganisms and biochemical analysis of biological tissues; different diagnostic methods such as molecular, serological and conventional methods are used. In addition to these methods, Raman spectroscopy has been shown in studies to be a fast, non-destructive and noninvasive method. Therefore, it is thought to be an alternative method for analyzing the basic biochemical components of microorganisms at molecular level.},
}
@article {pmid31881988,
year = {2019},
author = {Liu, Y and Qu, J and Zhang, L and Xu, X and Wei, G and Zhao, Z and Ren, M and Cao, M},
title = {Identification and characterization of the TCA cycle genes in maize.},
journal = {BMC plant biology},
volume = {19},
number = {1},
pages = {592},
pmid = {31881988},
issn = {1471-2229},
support = {2016YFD0101206//National Key Research and Development Program of China/ ; NASC2019TI13//Chengdu Agricultural Science and Technology Center local financial special fund project/ ; 19-001-09//Fundamental Research Funds for the Central Institutes/ ; },
mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Citric Acid Cycle/*genetics ; Computational Biology ; *Genes, Plant ; Solanum lycopersicum/genetics ; Phylogeny ; Plant Proteins/genetics ; Sequence Alignment ; Transcriptome ; Zea mays/*genetics/metabolism ; },
abstract = {BACKGROUND: The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear.<br><br>RESULTS: In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (&#x3b1;-ketoglutarate dehydrogenase, &#x3b1;KGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility.<br><br>CONCLUSION: Sequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.},
}
@article {pmid31888438,
year = {2019},
author = {Lichtblau, D},
title = {Alignment-free genomic sequence comparison using FCGR and signal processing.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {742},
pmid = {31888438},
issn = {1471-2105},
mesh = {Animals ; Genomics/*methods ; Humans ; Influenza A virus/classification ; Mitochondria/classification ; Phylogeny ; *Software ; },
abstract = {BACKGROUND: Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing "nearby" species in a reference data set, or for constructing phylogenetic trees.<br><br>RESULTS: We describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of this approach on several benchmark test sets.<br><br>CONCLUSIONS: The tandem of FCGR and dimension reductions using Fourier-type transforms and SVD provides a powerful approach for alignment-free genomic comparison. Results compare favorably and often surpass best results reported in prior literature. Good scalability is also observed.},
}
@article {pmid31914665,
year = {2020},
author = {Draper, ACE and Wilson, Z and Maile, C and Faccenda, D and Campanella, M and Piercy, RJ},
title = {Species-specific consequences of an E40K missense mutation in superoxide dismutase 1 (SOD1).},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {34},
number = {1},
pages = {458-473},
doi = {10.1096/fj.201901455R},
pmid = {31914665},
issn = {1530-6860},
mesh = {Adenosine Triphosphate/*metabolism ; Amyotrophic Lateral Sclerosis/genetics/metabolism/*pathology ; Animals ; Dogs ; Horses ; Humans ; Mitochondria/*metabolism/pathology ; *Mutation, Missense ; Phylogeny ; Species Specificity ; Superoxide Dismutase-1/*genetics ; Transgenes/*physiology ; },
abstract = {A glutamic acid to lysine (E40K) residue substitution in superoxide dismutase 1 (SOD1) is associated with canine degenerative myelopathy: the only naturally occurring large animal model of amyotrophic lateral sclerosis (ALS). The E40 residue is highly conserved across mammals, except the horse, which naturally carries the (dog mutant) K40 residue. Here we hypothesized that in vitro expression of mutant dog SOD1 would recapitulate features of human ALS (ie, SOD1 protein aggregation, reduced cell viability, perturbations in mitochondrial morphology and membrane potential, reduced ATP production, and increased superoxide ion levels); further, we hypothesized that an equivalent equine SOD1 variant would share similar perturbations in vitro, thereby explain horses' susceptibility to certain neurodegenerative diseases. As in human ALS, expression of mutant dog SOD1 was associated with statistically significant increased aggregate formation, raised superoxide levels (ROS), and altered mitochondrial morphology (increased branching (form factor)), when compared to wild-type dog SOD1-expressing cells. Similar deficits were not detected in cells expressing the equivalent horse SOD1 variant. Our data helps explain the ALS-associated cellular phenotype of dogs expressing the mutant SOD1 protein and reveals that species-specific sequence conservation does not necessarily predict pathogenicity. The work improves understanding of the etiopathogenesis of canine degenerative myelopathy.},
}
@article {pmid31919449,
year = {2020},
author = {De Pierri, CR and Voyceik, R and Santos de Mattos, LGC and Kulik, MG and Camargo, JO and Repula de Oliveira, AM and de Lima Nichio, BT and Marchaukoski, JN and da Silva Filho, AC and Guizelini, D and Ortega, JM and Pedrosa, FO and Raittz, RT},
title = {SWeeP: representing large biological sequences datasets in compact vectors.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {91},
pmid = {31919449},
issn = {2045-2322},
mesh = {Algorithms ; Bacterial Proteins/genetics/*metabolism ; Computational Biology/*methods ; Datasets as Topic ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phylogeny ; Proteome/*analysis ; Sequence Alignment ; *Software ; },
abstract = {Vectoral and alignment-free approaches to biological sequence representation have been explored in bioinformatics to efficiently handle big data. Even so, most current methods involve sequence comparisons via alignment-based heuristics and fail when applied to the analysis of large data sets. Here, we present "Spaced Words Projection (SWeeP)", a method for representing biological sequences using relatively small vectors while preserving intersequence comparability. SWeeP uses spaced-words by scanning the sequences and generating indices to create a higher-dimensional vector that is later projected onto a smaller randomly oriented orthonormal base. We constructed phylogenetic trees for all organisms with mitochondrial and bacterial protein data in the NCBI database. SWeeP quickly built complete and accurate trees for these organisms with low computational cost. We compared SWeeP to other alignment-free methods and Sweep was 10 to 100 times quicker than the other techniques. A tool to build SWeeP vectors is available at https://sourceforge.net/projects/spacedwordsprojection/.},
}
@article {pmid31939618,
year = {2020},
author = {Ding, Y and Ye, YF and Li, MY and Xia, BH and Leng, JH},
title = {Mitochondrial tRNAAla 5601C&gt;T variant may affect the clinical expression of the LHON‑related ND4 11778G&gt;A mutation in a family.},
journal = {Molecular medicine reports},
volume = {21},
number = {1},
pages = {201-208},
pmid = {31939618},
issn = {1791-3004},
mesh = {Adolescent ; Adult ; Asian People/genetics ; Child ; Computational Biology ; DNA, Mitochondrial/*genetics ; Family ; Female ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mutation ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/blood/*genetics/metabolism/pathology ; Pedigree ; Penetrance ; Phylogeny ; Polymorphism, Genetic ; RNA, Transfer, Ala/chemistry/*genetics ; },
abstract = {Certain mutations in mitochondrial DNA (mtDNA) are associated with Leber's hereditary optic neuropathy (LHON). In particular, the well‑known NADH dehydrogenase 4 (ND4) m.11778G>A mutation is one of the most common LHON‑associated primary mutations worldwide. However, how specific mtDNA mutations, or variants, affect LHON penetrance is not fully understood. The aim of the current study was to explore the relationship between mtDNA mutations and LHON, and to provide useful information for early detection and prevention of this disease. Following the molecular characterization of a Han Chinese family with maternally inherited LHON, four out of eight matrilineal relatives demonstrated varying degrees of both visual impairment and age of onset. Through PCR amplification of mitochondrial genomes and direct Sanger sequencing analysis, a homoplasmic mitochondrial‑encoded ND4 m.11778G>A mutation, alongside a set of genetic variations belonging to human mtDNA haplogroup B5b1 were identified. Among these sequence variants, alanine transfer RNA (tRNA)Ala m.5601C>T was of particular interest. This variant occurred at position 59 in the TψC loop and altered the base pairing, which led to mitochondrial RNA (mt‑RNA) metabolism failure and defects in mitochondrial protein synthesis. Bioinformatics analysis suggested that the m.5601C>T variant altered tRNAAla structure. Therefore, impaired mitochondrial functions caused by the ND4 m.11778G>A mutation may be enhanced by the mt‑tRNAAla m.5601C>T variant. These findings suggested that the tRNAAla m.5601C>T variant might modulate the clinical manifestation of the LHON‑associated primary mutation.},
}
@article {pmid31940908,
year = {2020},
author = {Liu, W and Cai, Y and Zhang, Q and Shu, F and Chen, L and Ma, X and Bian, Y},
title = {Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes.},
journal = {International journal of molecular sciences},
volume = {21},
number = {2},
pages = {},
pmid = {31940908},
issn = {1422-0067},
mesh = {Ascomycota/genetics/*growth &amp; development ; Chromosome Mapping/*methods ; Gene Expression Regulation, Fungal ; Genome Size ; Genome, Fungal ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.},
}
@article {pmid31945484,
year = {2020},
author = {Huo, LJ and Yang, MC and Wang, JX and Shi, XZ},
title = {Mitochondrial ATPase inhibitor factor 1, MjATPIF1, is beneficial for WSSV replication in kuruma shrimp (Marsupenaeus japonicus).},
journal = {Fish &amp; shellfish immunology},
volume = {98},
number = {},
pages = {245-254},
doi = {10.1016/j.fsi.2020.01.019},
pmid = {31945484},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/genetics/*metabolism ; Gene Expression Regulation ; Hemocytes/metabolism ; Mitochondria/metabolism ; NF-kappa B/genetics/metabolism ; Penaeidae/classification/genetics/*virology ; Phylogeny ; Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism/pharmacology ; Sequence Alignment ; Superoxides/metabolism ; Survival Rate ; Tissue Distribution ; Virus Replication/drug effects ; White spot syndrome virus 1/*physiology ; ATPase Inhibitory Protein ; },
abstract = {ATPase Inhibitory Factor 1 (IF1) is a mitochondrial protein that functions as a physiological inhibitor of F1F0-ATP synthase. In the present study, a mitochondrial ATPase inhibitor factor 1 (MjATPIF1) was identified from kuruma shrimp (Marsupenaeus japonicus), which was demonstrated to participate in the viral immune reaction of white spot syndrome virus (WSSV). MjATPIF1 contained a mitochondrial ATPase inhibitor (IATP) domain, and was widely distributed in hemocytes, heart, hepatopancreas, gills, stomach, and intestine of shrimp. MjATPIF1 transcription was upregulated in hemocytes and intestines by WSSV. WSSV replication decreased after MjATPIF1 knockdown by RNA interference and increased following recombinant MjATPIF1 protein injection. Further study found that MjATPIF1 promoted the production of superoxide and activated the transcription factor nuclear factor kappa B (NF-κB, Dorsal) to induce the transcription of WSSV RNAs. These results demonstrate that MjATPIF1 benefits WSSV replication in kuruma shrimp by inducing superoxide production and NF-κB activation.},
}
@article {pmid31952167,
year = {2020},
author = {Kleymann, A and Becker, AAMJ and Malik, YS and Kobayashi, N and Ghosh, S},
title = {Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code.},
journal = {Viruses},
volume = {12},
number = {1},
pages = {},
pmid = {31952167},
issn = {1999-4915},
mesh = {Animals ; Feces/virology ; *Genetic Code ; Genetic Variation ; *Genome, Viral ; Genotype ; Herpestidae/*virology ; Host Specificity ; Mitochondria/genetics ; Phylogeny ; Picobirnavirus/classification/*genetics/isolation &amp; purification ; RNA Virus Infections/*veterinary ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Saint Kitts and Nevis ; },
abstract = {We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3'-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.},
}
@article {pmid31953445,
year = {2020},
author = {Pascual-Itoiz, MA and Peña-Cearra, A and Martín-Ruiz, I and Lavín, JL and Simó, C and Rodríguez, H and Atondo, E and Flores, JM and Carreras-González, A and Tomás-Cortázar, J and Barriales, D and Palacios, A and García-Cañas, V and Pellón, A and Fullaondo, A and Aransay, AM and Prados-Rosales, R and Martín, R and Anguita, J and Abecia, L},
title = {The mitochondrial negative regulator MCJ modulates the interplay between microbiota and the host during ulcerative colitis.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {572},
pmid = {31953445},
issn = {2045-2322},
support = {R21 AI115091/AI/NIAID NIH HHS/United States ; },
mesh = {ADAM17 Protein/genetics ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Colitis, Ulcerative/*genetics/microbiology ; Disease Models, Animal ; Dysbiosis/*genetics ; Gene Deletion ; Gene Expression Regulation ; HSP40 Heat-Shock Proteins/*genetics ; Humans ; Mice ; Microbiota ; Mitochondrial Proteins/*genetics ; Molecular Chaperones/*genetics ; Phylogeny ; Receptors, Tumor Necrosis Factor, Type I/genetics ; Severity of Illness Index ; Tissue Inhibitor of Metalloproteinase-3/genetics ; Tumor Necrosis Factor-alpha/genetics ; },
abstract = {Recent evidences indicate that mitochondrial genes and function are decreased in active ulcerative colitis (UC) patients, in particular, the activity of Complex I of the electron transport chain is heavily compromised. MCJ is a mitochondrial inner membrane protein identified as a natural inhibitor of respiratory chain Complex I. The induction of experimental colitis in MCJ-deficient mice leads to the upregulation of Timp3 expression resulting in the inhibition of TACE activity that likely inhibits Tnf and Tnfr1 shedding from the cell membrane in the colon. MCJ-deficient mice also show higher expression of Myd88 and Tlr9, proinflammatory genes and disease severity. Interestingly, the absence of MCJ resulted in distinct microbiota metabolism and composition, including a member of the gut community in UC patients, Ruminococcus gnavus. These changes provoked an effect on IgA levels. Gene expression analyses in UC patients showed decreased levels of MCJ and higher expression of TIMP3, suggesting a relevant role of mitochondrial genes and function among active UC. The MCJ deficiency disturbs the regulatory relationship between the host mitochondria and microbiota affecting disease severity. Our results indicate that mitochondria function may be an important factor in the pathogenesis. All together support the importance of MCJ regulation during UC.},
}
@article {pmid31954510,
year = {2020},
author = {Eberle, J and Ahrens, D and Mayer, C and Niehuis, O and Misof, B},
title = {A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy.},
journal = {Trends in ecology &amp; evolution},
volume = {35},
number = {4},
pages = {336-345},
doi = {10.1016/j.tree.2019.12.003},
pmid = {31954510},
issn = {1872-8383},
mesh = {Animals ; *DNA ; *DNA Barcoding, Taxonomic ; Mitochondria ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The ease of sequencing DNA barcodes promoted a species identification system universally applicable across animal phyla. However, relying on a single mitochondrial DNA fragment has a number of drawbacks that can mislead species delimitation and identification. Implementation of multiple nuclear markers would mitigate the limits of the current barcoding system if these markers are universally applicable across species, carry sufficient information to discriminate between closely related species, and if sequencing and analyzing these markers can be automatized. As sequencing costs continue to fall, we believe that the time is right to extend DNA barcoding. Here we argue that nearly universal single-copy nuclear protein-coding genes deliver the desired characteristics and could be used to reliably delimit and identify animal species.},
}
@article {pmid31960780,
year = {2020},
author = {Kumari, K and M, MH and Sinha, A and Koushlesh, SK and Das Sarkar, S and Borah, S and BaItha, R and Behera, BK and Das, BK},
title = {Genetic differentiation and phylogenetic relationship of 11 Asian Sisorinae genera (Siluriformes: Sisoridae) with new record of Pseudolaguvia foveolata.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {1},
pages = {35-41},
doi = {10.1080/24701394.2020.1714605},
pmid = {31960780},
issn = {2470-1408},
mesh = {Animals ; Catfishes/*genetics/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Electron Transport Complex IV/*genetics/metabolism ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/*genetics/metabolism ; Phylogeny ; },
abstract = {Studies on Sisorinae systematics have been largely restricted to morphological data with few studies on examination of phylogenetic relations. However, no study has been done to evaluate genetic distance of the genera under Sisorinae sub-family and detailed phylogenetic relations within it. We used nuclear recombination activating 2 (rag2) gene and mitochondrial cytochrome c oxidase I (COI) gene from 64 species to examine genetic differentiation and phylogenetic relationships within 11 Asian Sisorinae genera. The range of interspecies K2P distance for rag2 was 0-0.061 and COI was 0-0.204. Phylogenetic analysis based on maximum likelihood (ML) and Bayesian (BI) approaches for each locus individually and for the concatenated rag2 and COI sequences revealed three major subclades viz. Bagariini, Sisorini and Erethistini under subfamily Sisorinae. The analysis based on COI gene showed ((Sisorini, Bagariini), Erethistini) relationship. Rag2 and combined rag2 and COI showed ((Sisorini, Erethistini), Bagariini) relationship. Combined rag2 and COI analyses resulted into better resolved trees with a good bootstrap support. In this study, new record of Pseudolaguvia foveolata (Erethistini) has been documented based on 13 specimens collected from Torsa River, Jaldapara, Alipurduar district, West Bengal, India (26°43'44.66″ N and 89°19'32.34″ E), extending its distribution range in Brahmaputra drainage, India. The genetic distance between the P. foveolata new record and the reported P. foveolata (holotype: UMMZ 244867) was 0.00 at both rag2 and COI locus and it was further grouped with P. foveolata Type specimen (holotype: UMMZ 244867) with 100% bootstrap support. This report gives additional information on occurrence of the species P. foveolata, along with discussion on morphometric, meristic and molecular (COI and rag2 gene) data.},
}
@article {pmid31974502,
year = {2020},
author = {Capt, C and Bouvet, K and Guerra, D and Robicheau, BM and Stewart, DT and Pante, E and Breton, S},
title = {Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1087},
pmid = {31974502},
issn = {2045-2322},
mesh = {Animals ; Bivalvia/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Female ; Genome ; Genome, Mitochondrial ; Inheritance Patterns ; Male ; Mitochondria ; Mytilidae/classification/genetics ; Phylogeny ; Species Specificity ; },
abstract = {In animals, strictly maternal inheritance (SMI) of mitochondria is the rule, but one exception (doubly uniparental inheritance or DUI), marked by the transmission of sex-specific mitogenomes, has been reported in bivalves. Associated with DUI is a frequent modification of the mitochondrial cox2 gene, as well as additional sex-specific mitochondrial genes not involved in oxidative phosphorylation. With the exception of freshwater mussels (for 3 families of the order Unionida), these DUI-associated features have only been shown in few species [within Mytilidae (order Mytilida) and Veneridae (order Venerida)] because of the few complete sex-specific mitogenomes published for these orders. Here, we present the complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida, Scrobicularia plana (Semelidae) and Limecola balthica (Tellinidae). These species display the largest differences in genome size between sex-specific mitotypes in DUI species (>10 kb), as well as the highest mtDNA divergences (sometimes reaching >50%). An important in-frame insertion (>3.5 kb) in the male cox2 gene is partly responsible for the differences in genome size. The S. plana cox2 gene is the largest reported so far in the Kingdom Animalia. The mitogenomes may be carrying sex-specific genes, indicating that general mitochondrial features are shared among DUI species.},
}
@article {pmid31978488,
year = {2020},
author = {Souza, DS and Marinoni, L and Monné, ML and Gómez-Zurita, J},
title = {Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae).},
journal = {Molecular phylogenetics and evolution},
volume = {145},
number = {},
pages = {106736},
doi = {10.1016/j.ympev.2020.106736},
pmid = {31978488},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Coleoptera/*classification ; Electron Transport Complex IV/genetics ; Insect Proteins/chemistry/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Ribosome Subunits, Large/genetics ; },
abstract = {Lamiinae is the most diverse subfamily of longhorned beetles, with about 20,000 described species classified into 80 tribes. Most of the tribes of Lamiinae were proposed during the 19th century and the suprageneric classification of the subfamily has never been assessed under phylogenetic criteria. In this study, we present the first tribal-level phylogeny of Lamiinae, inferred from 130 terminals (representing 46 tribes, prioritizing generic type species of the tribes) and fragments of two mitochondrial and three nuclear markers (cox1, rrnL, Wg, CPS and LSU; 5,024 aligned positions in total). Analyses were performed under Maximum Likelihood and Bayesian methods based on two datasets: a dataset including all taxa available for the study, and a reduced dataset with 111 terminals where taxa only contributing with mitochondrial markers were excluded from the matrix. The monophyly of Lamiinae was corroborated in three of the four analyses and 11 of the 35 tribes with more than one species represented in the analyses were consistently recovered as monophyletic. However, 15 tribes were not retrieved as monophyletic, requiring a revision of their boundaries: Acanthocinini, Acanthoderini, Agapanthiini, Apomecynini, Desmiphorini, Dorcaschematini, Enicodini, Hemilophini, Monochamini, Onciderini, Parmenini, Phytoeciini, Pogonocherini, Pteropliini and Saperdini. Based on these results, when strong support values for paraphyly were recovered, we argue a number of tribe synonymies, including Moneilemini as synonym of Acanthocinini; Onocephalini of Onciderini; Dorcadionini, Gnomini, Monochamini and Rhodopinini of Lamiini; and Obereini and Phytoeciini of Saperdini. Other taxonomic changes proposed in this study based on the criterion of monophyly and supported by morphological characters include the transfer of Tricondyloides and Stenellipsis to Enicodini, and of Dylobolus stat. rest., which is removed as subgenus of Mecas and restituted as genus, to Hemilophini. Furthermore, our analyses suggest that Ostedes and Neohoplonotus should be removed from Acanthocinini and Parmenini, respectively, and Colobotheini should be redefined to encompass several genera currently placed in Acanthocinini.},
}
@article {pmid31992373,
year = {2020},
author = {Le, TH and Pham, LTK and Doan, HTT and Le, XTK and Saijuntha, W and Rajapakse, RPVJ and Lawton, SP},
title = {Comparative mitogenomics of the zoonotic parasite Echinostoma revolutum resolves taxonomic relationships within the 'E. revolutum' species group and the Echinostomata (Platyhelminthes: Digenea).},
journal = {Parasitology},
volume = {147},
number = {5},
pages = {566-576},
pmid = {31992373},
issn = {1469-8161},
mesh = {Animals ; Echinostoma/*genetics ; Echinostomatidae/*classification/genetics ; Genome ; Mitochondria/genetics ; Phylogeny ; Trematoda ; },
abstract = {The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.},
}
@article {pmid32018005,
year = {2020},
author = {Wu, H and Liu, Y and Shi, X and Zhang, X and Ye, C and Zhu, KY and Zhu, F and Zhang, J and Ma, E},
title = {Transcriptome analysis of antennal cytochrome P450s and their transcriptional responses to plant and locust volatiles in Locusta migratoria.},
journal = {International journal of biological macromolecules},
volume = {149},
number = {},
pages = {741-753},
doi = {10.1016/j.ijbiomac.2020.01.309},
pmid = {32018005},
issn = {1879-0003},
mesh = {Animals ; Cytochrome P-450 Enzyme System/classification/*genetics/*metabolism ; Cytochrome P450 Family 2/metabolism ; Cytochrome P450 Family 3/metabolism ; Cytochrome P450 Family 4/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Inactivation, Metabolic ; Locusta migratoria/drug effects/*genetics/*metabolism ; Mitochondria/metabolism ; Odorants ; Phylogeny ; Transcriptome ; Volatile Organic Compounds/pharmacology ; },
abstract = {Cytochrome P450 monooxygenases (P450s) constitute a large superfamily of heme-thiolate proteins that are involved in the biosynthesis or degradation of endogenous compounds and detoxification of exogenous chemicals. It has been reported that P450s could serve as odorant-degrading enzymes (ODEs) to inactivate odorants to avoid saturating the antennae. However, there is little information about P450s in the antennae of Locusta migratoria. In the current work, we conducted an antenna transcriptome analysis and identified 92 P450s, including 68 full-length and 24 partial sequences. Phylogenetic analysis showed that 68 full-length P450s were grouped into four clans: CYP2, CYP3, CYP4, and mitochondria clans. Tissue, stage, and sex-dependent expressions of these 68 P450s were investigated. The results showed that 4 P450s were antenna-specific, whereas others were antenna-rich but also expressed in other tissues, implying their various potential roles in the antennae. In addition, the responses of seven selected P450s to five gramineous plant volatiles and four locust volatiles were determined. CYP6MU1 could be induced by almost all compounds tested, suggesting its important roles in odorant processing. Different P450s exhibited diverse responses to odorants, indicating that specific regulation of P450 expression by odorants might modulate the sensitivity of the olfactory responses to various chemicals.},
}
@article {pmid32039475,
year = {2020},
author = {Donin, LM and Ferrer, J and Carvalho, TP},
title = {Taxonomical study of Trichomycterus (Siluriformes: Trichomycteridae) from the Ribeira de Iguape River basin reveals a new species recorded in the early 20th century.},
journal = {Journal of fish biology},
volume = {96},
number = {4},
pages = {886-904},
doi = {10.1111/jfb.14278},
pmid = {32039475},
issn = {1095-8649},
support = {//CNPq/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; },
mesh = {Animals ; Brazil ; Catfishes/anatomy &amp; histology/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Rivers ; Species Specificity ; },
abstract = {A new species of Trichomycterus endemic to the Ribeira de Iguape River basin, southeastern Brazil, was studied based on morphological and molecular evidence. This species had an outer layer of coloration composed of scattered, round, black or dark-brown spots smaller or equivalent in size to the circumference of the eye; eight pectoral-fin rays; 28-29 opercular odontodes; 54-56 interopercular odontodes; and supraorbital line of the laterosensory system not interrupted, with pores s2 absent. Two other species of Trichomycterus from the Ribeira de Iguape River basin are recorded, and their taxonomic status is discussed: Trichomycterus alternatus and Trichomycterus jacupiranga were not differentiated using molecular analysis but may be consistently distinguished based on morphology. The phylogenetic relationships of the co-occurring species, T. alternatus and Cambeva zonata, were inferred using mitochondrial data, reinforcing the taxonomic status of these recently revised species that have a complex taxonomy. In addition, a new combination for Trichomycterus taroba with its inclusion in the genus Cambeva is recommended.},
}
@article {pmid32041545,
year = {2020},
author = {Bhowal, B and Singla-Pareek, SL and Sopory, SK and Kaur, C},
title = {From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {145},
pmid = {32041545},
issn = {1471-2164},
support = {IFA-14/LSPA-24//Department of Science and Technology, Ministry of Science and Technology/ ; },
mesh = {Genome-Wide Association Study ; Lactate Dehydrogenases/classification/*genetics ; Lactoylglutathione Lyase/classification/*genetics ; Phylogeny ; Plant Proteins/classification/*genetics ; Pyruvaldehyde/*metabolism ; Pyruvic Acid/*metabolism ; Sorghum/*enzymology/genetics ; Stress, Physiological/genetics ; Thiolester Hydrolases/classification/*genetics ; Hydroxyacylglutathione Hydrolase ; },
abstract = {BACKGROUND: The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes.<br><br>RESULT: Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive.<br><br>CONCLUSION: This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.},
}
@article {pmid32050506,
year = {2020},
author = {Li, Z and Li, X and Song, N and Tang, H and Yin, X},
title = {The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles.},
journal = {Genes},
volume = {11},
number = {2},
pages = {},
pmid = {32050506},
issn = {2073-4425},
mesh = {Animals ; Bayes Theorem ; Coleoptera/classification/*genetics ; Genes, rRNA ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; },
abstract = {Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.},
}
@article {pmid32083134,
year = {2020},
author = {Li, K and Wu, L and Liu, J and Lin, W and Qi, Q and Zhao, T},
title = {Maternally Inherited Diabetes Mellitus Associated with a Novel m.15897G&gt;A Mutation in Mitochondrial tRNA[Thr] Gene.},
journal = {Journal of diabetes research},
volume = {2020},
number = {},
pages = {2057187},
pmid = {32083134},
issn = {2314-6753},
mesh = {Adult ; Aged ; Asian People/genetics ; Blotting, Northern ; Blotting, Western ; China ; Diabetes Mellitus, Type 2/*genetics/metabolism ; Electron Transport Chain Complex Proteins/metabolism ; Electrophoresis, Polyacrylamide Gel ; Female ; Genome, Mitochondrial ; Humans ; Male ; Maternal Inheritance ; Membrane Potential, Mitochondrial/genetics ; Middle Aged ; Mitochondria/metabolism ; Pedigree ; Phylogeny ; Point Mutation ; RNA, Transfer, Thr/*genetics ; Reactive Oxygen Species/metabolism ; },
abstract = {We report here the clinical, genetic, and molecular characteristics of type 2 diabetes in a Chinese family. There are differences in the severity and age of onset in diabetes among these families. By molecular analysis of the complete mitochondrial genome in this family, we identified the homoplasmic m.15897G>A mutation underwent sequence analysis of whole mitochondrial DNA genome, which localized at conventional position ten of tRNA[Thr], and distinct sets of mtDNA polymorphisms belonging to haplogroup D4b1. This mutation has been implicated to be important for tRNA identity and stability. Using cybrid cell models, the decreased efficiency of mitochondrial tRNA[Thr] levels caused by the m.15897G>A mutation results in respiratory deficiency, protein synthesis and assembly, mitochondrial ATP synthesis, and mitochondrial membrane potential. These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cell lines. These data provide a direct evidence that a novel tRNA mutation was associated with T2DM. Thus, our findings provide a new insight into the understanding of pathophysiology of maternally inherited diabetes.},
}
@article {pmid32093074,
year = {2020},
author = {Zhou, J and Wang, Y and Liang, X and Xie, C and Liu, W and Miao, W and Kang, Z and Zheng, L},
title = {Molecular Characterization of a Novel Ourmia-Like Virus Infecting Phoma matteucciicola.},
journal = {Viruses},
volume = {12},
number = {2},
pages = {},
pmid = {32093074},
issn = {1999-4915},
mesh = {Amino Acid Sequence ; Fungal Viruses/*classification/isolation &amp; purification ; *Genome, Viral ; Nucleic Acid Conformation ; Open Reading Frames ; Phoma/*virology ; Phylogeny ; RNA Viruses/*genetics/isolation &amp; purification ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {Here, we report a novel (+) ssRNA mycovirus, Phoma matteucciicola ourmia-like virus 1 (PmOLV1), isolated from Phoma matteucciicola strain LG915-1. The genome of PmOLV1 was 2603 nucleotides long and contained a single open reading frame (ORF), which could be translated into a product of RNA-dependent RNA polymerase (RdRp) by both standard and mitochondrial genetic codons. Cellular fractionation assay indicated that PmOLV1 RNAs are likely more enriched in mitochondria than in cytoplasm. Phylogenetic analysis indicated that PmOLV1 is a new member of the genus Penoulivirus (recently proposed) within the family Botourmiaviridae.},
}
@article {pmid32114398,
year = {2020},
author = {Chernyshev, AV and Neznanova, SY and Yurchenko, OV},
title = {Spermatozoa ultrastructure of two basal pilidiophoran nemerteans, Hubrechtella juliae and Sonnenemertes cantelli (Nemertea, Pilidiophora).},
journal = {Micron (Oxford, England : 1993)},
volume = {133},
number = {},
pages = {102853},
doi = {10.1016/j.micron.2020.102853},
pmid = {32114398},
issn = {1878-4291},
mesh = {Acrosome/ultrastructure ; Animals ; Invertebrates/*anatomy &amp; histology/classification ; Male ; Microscopy, Electron, Scanning ; Phylogeny ; Spermatozoa/*ultrastructure ; },
abstract = {Nemertea is a phylum of worms with a simple internal morphology; nemerteans' spermatozoon morphology can be used for their classification and phylogenetic analyses. The aim of the present study was to describe spermatozoa of the nemerteans Hubrechtella juliae and Sonnenemertes cantelli from the basal groups of the class Pilidiophora at the ultrastructure level. Both species have primitive ('compact-head' sensu Stricker and Folsom, 1998) spermatozoa with ovoid head and five mitochondria in the midpiece, but differ in the structure of acrosomal complex: in Hubrechtella juliae, the single lens-shaped acrosomal vesicle contains an area of moderate electron density not enclosed by a separate membrane; in Sonnenemertes cantelli, the acrosome shows a unique morphology and contains a few electron-dense vesicles with irregular shapes and positions and one more electron-lucent elongated vesicle. Such a pattern of the acrosomal complex organization is described for Nemertea for the first time. An assumption is made that the states "two or more mitochondria" and "posterior acrosomal ring component" may be synapomorphies of Hubrechtiiformes+Heteronemertea (class Pilidiophora), whereas "the posterior margin of the acrosomes forms an acrosomal ring component" is presumably an autapomorphy of the family Lineidae s.l. The results suggest that spermatozoa provide a useful source of characters for nemertean systematics.},
}
@article {pmid32121321,
year = {2020},
author = {Duran, DP and Laroche, RA and Gough, HM and Gwiazdowski, RA and Knisley, CB and Herrmann, DP and Roman, SJ and Egan, SP},
title = {Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype.},
journal = {Genes},
volume = {11},
number = {3},
pages = {},
pmid = {32121321},
issn = {2073-4425},
mesh = {Animals ; Classification/*methods ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; Genome, Insect/genetics ; Haplotypes/genetics ; Life History Traits ; Mitochondria/genetics ; Phenotype ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidiapolitula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These patterns are incongruous with the phenotypic variation that informed prior taxonomy, and most subspecies were not supported as distinct evolutionary lineages. One of the nominal subspecies was found to be a cryptic species; consequently, we elevate C. p.laetipennis (Horn, 1913) to a full species. Although nuclear and mtDNA datasets recovered broadly similar evolutionary units, mito-nuclear discordance was more common than expected, being observed between nearly all geographically overlapping taxonomic pairs. Additionally, a pattern of 'mitochondrial displacement' was observed, where mitochondria from one species unidirectionally displace others. Overall, we found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading.},
}
@article {pmid32140958,
year = {2020},
author = {Kobayashi, G},
title = {Small-scale population genetic structure of the sand bubbler crab Scopimera ryukyuensis in the Ryukyu Islands, Japan.},
journal = {Molecular biology reports},
volume = {47},
number = {4},
pages = {2619-2626},
pmid = {32140958},
issn = {1573-4978},
mesh = {Animals ; Brachyura/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Islands ; Japan ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Generally, the gene flow of marine organisms is well maintained, but some local populations of coastal species are genetically differentiated even on a small scale (genetic patchiness). Small-scale isolation can be crucial for understanding genetic diversity within a species. The present study examined the population genetic structure of the sand bubbler crab Scopimera ryukyuensis, which is endemic to the Ryukyu Islands in the northwestern Pacific. A total of 52 haplotypes of mitochondrial cytochrome c oxidase subunit I were recovered from 197 specimens collected from four islands. The haplotype and nucleotide diversities were relatively high in the central Ryukyus (Amami-Oshima and Okinawa Islands) with some exceptions but were low at the southern edge of the geographical distribution of the species, i.e., the southern Ryukyus (Ishigaki and Iriomote Islands). Pairwise FST analysis suggested that the gene flow of S. ryukyuensis was largely restricted. The local populations of the species are differentiated among islands, except for stations on Ishigaki Island and a station on Iriomote Island. Moreover, a clear intra-island population genetic structure was observed within Amami-Oshima and Iriomote Islands, e.g., only 20 km between stations. Small-scale isolation among local populations may be a common tendency for coastal species in the Ryukyu Islands, considering the results of previous studies on corals.},
}
@article {pmid32142937,
year = {2020},
author = {Mehmood, N and Muqaddas, H and Arshad, M and Ullah, MI and Khan, ZI},
title = {Comprehensive study based on mtDNA signature (nad1) providing insights on Echinococcus granulosus s.s. genotypes from Pakistan and potential role of buffalo-dog cycle.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {81},
number = {},
pages = {104271},
doi = {10.1016/j.meegid.2020.104271},
pmid = {32142937},
issn = {1567-7257},
mesh = {Animals ; Buffaloes/*parasitology ; Cattle ; Cattle Diseases/*parasitology ; DNA, Helminth/genetics ; DNA, Mitochondrial/*genetics ; Echinococcosis/parasitology ; Echinococcus granulosus/*genetics ; Genetic Variation/genetics ; Genotype ; Goat Diseases/parasitology ; Goats/parasitology ; Haplotypes/genetics ; Mitochondria/*genetics ; Pakistan ; Phylogeny ; Sheep/parasitology ; Sheep Diseases/parasitology ; },
abstract = {Pakistan has long been considered neglected endemic region for Echinococcus granulosus. Limited surveillance studies have failed to epidemiologically draw complete picture on geographical presence and etiological agents of cystic echinococcosis. Amidst such lacunae, current study explored main transmission routes of this disease through molecular characterization of hydatid cyst isolates obtained from sheep (n = 35), goats (n = 26), cattle (n = 30) and buffalo (n = 30) from the four provinces of Pakistan. Two strains of E. granulosus sensu stricto, G1/G3, and their haplotypes were observed to be cycling in sympatry in the domestic ungulate populations. G3 genotype had higher prevalence (66.94%) in the hosts compared to G1 genotype (33.06%) which was not surprising, considering the large buffalo population in Pakistan. Haplotypic analysis revealed presence of 9 different haplotypes configured in a double clustered network with two centrally positioned haplotypes referred to as G3 (PKH1) and G1 (PKH6). Population demographics and genetic variability indices suggested expanding parasitic population in multiple host spectrum. Elucidating local transmission patterns of E. granulosus sensu stricto, buffalo-dog cycle emerged as one of the dominant causes of G3 dispersal in contrary to other global studies. Adaptability of G3 to environmental conditions of Pakistan and high affinity for buffaloes emphasize on heterogeneous nature of this strain in contrast to G1. However, more studies involving larger datasets and mitochondrial sequences could confirm this hypothetically formulated inference.},
}
@article {pmid32143704,
year = {2020},
author = {Cinar, HN and Gopinath, G and Murphy, HR and Almeria, S and Durigan, M and Choi, D and Jang, A and Kim, E and Kim, R and Choi, S and Lee, J and Shin, Y and Lee, J and Qvarnstrom, Y and Benedict, TK and Bishop, HS and da Silva, A},
title = {Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing.},
journal = {Parasites &amp; vectors},
volume = {13},
number = {1},
pages = {122},
pmid = {32143704},
issn = {1756-3305},
mesh = {Base Sequence ; Cluster Analysis ; Computational Biology ; Cyclospora/classification/*genetics/*isolation &amp; purification ; Cyclosporiasis/*diagnosis/parasitology ; DNA, Protozoan/genetics ; Feces/parasitology ; Genome, Mitochondrial/*genetics ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Molecular Typing/*methods ; Oocysts/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing.<br><br>METHODS: We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3&#xa0;kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline.<br><br>RESULTS: This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study.<br><br>CONCLUSIONS: Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.},
}
@article {pmid32145731,
year = {2020},
author = {Ran, R and Zhao, Q and Abuzeid, AMI and Huang, Y and Liu, Y and Sun, Y and He, L and Li, X and Liu, J and Li, G},
title = {Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis).},
journal = {The Korean journal of parasitology},
volume = {58},
number = {1},
pages = {73-79},
pmid = {32145731},
issn = {1738-0006},
support = {31672541//National Natural Science Foundation of China/ ; 2014A020214005//the Science and Technology Planning Project of Guangdong Province, China/ ; },
mesh = {Animals ; Birds/*parasitology ; Echinostoma/*genetics ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing ; },
abstract = {Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.},
}
@article {pmid32148763,
year = {2019},
author = {Pichon, J and Luscombe, NM and Plessy, C},
title = {Widespread use of the "ascidian" mitochondrial genetic code in tunicates.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {2072},
pmid = {32148763},
issn = {2046-1402},
mesh = {Animals ; Base Sequence ; *Genetic Code ; Mitochondria ; *Phylogeny ; *Urochordata/genetics ; },
abstract = {Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.},
}
@article {pmid32178369,
year = {2020},
author = {Lu, K and Policar, T and Song, X and Rahimnejad, S},
title = {Molecular Characterization of PGC-1β (PPAR Gamma Coactivator 1β) and its Roles in Mitochondrial Biogenesis in Blunt Snout Bream (Megalobrama amblycephala).},
journal = {International journal of molecular sciences},
volume = {21},
number = {6},
pages = {},
pmid = {32178369},
issn = {1422-0067},
support = {B17162//Outstanding Young Scientific Research Talents Program of Fujian province/ ; 31801969//National Nature Science Foundation of China/ ; LM2018099//Ministry of Education, Youth and Sports of the Czech Republic, project CENAKVA/ ; QK1710310//Ministry of Agriculture of the Czech Republic, project NAZV/ ; },
mesh = {Amino Acids ; Animals ; Cyprinidae/*genetics/*physiology ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/genetics ; Hepatocytes/physiology ; Liver ; Mitochondria/*genetics/*physiology ; Mitochondrial Proteins/genetics ; Organelle Biogenesis ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/*genetics ; Phylogeny ; Signal Transduction/genetics ; Transcription Factors/genetics ; },
abstract = {This study aimed at achieving the molecular characterization of peroxisome proliferator-activated receptor-gamma coactivator 1β (PGC-1β) and exploring its modulatory roles in mitochondria biogenesis in blunt snout bream (Megalobrama amblycephala). A full-length cDNA of PGC-1β was cloned from liver which covered 3110 bp encoding 859 amino acids. The conserved motifs of PGC-1β family proteins were gained by MEME software, and the phylogenetic analyses showed motif loss and rearrangement of PGC-1β in fish. The function of PGC-1β was evaluated through overexpression and knockdown of PGC-1β in primary hepatocytes of blunt snout bream. We observed overexpression of PGC-1β along with enhanced mitochondrial transcription factor A (TFAM) expression and mtDNA copies in hepatocytes, and its knockdown led to slightly reduced NRF1 expression. However, knockdown of PGC-1β did not significantly influence TFAM expression or mtDNA copies. The alterations in mitochondria biogenesis were assessed following high-fat intake, and the results showed that it induces downregulation of PGC-1β. Furthermore, significant decreases in mitochondrial respiratory chain activities and mitochondria biogenesis were observed by high-fat intake. Our findings demonstrated that overexpression of PGC-1β induces the enhancement of TFAM expression and mtDNA amount but not NRF-1. Therefore, it could be concluded that PGC-1β is involved in mitochondrial biogenesis in blunt snout bream but not through PGC-1β/NRF-1 pathway.},
}
@article {pmid32179772,
year = {2020},
author = {Naik, VCB and Pusadkar, PP and Waghmare, ST and K P, R and Kranthi, S and Kumbhare, S and Nagrare, VS and Kumar, R and Prabhulinga, T and Gokte-Narkhedkar, N and Waghmare, VN},
title = {Evidence for population expansion of Cotton pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) in India.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {4740},
pmid = {32179772},
issn = {2045-2322},
mesh = {Animals ; Bacillus thuringiensis Toxins ; DNA, Mitochondrial ; Endotoxins ; Genetic Variation ; *Genetics, Population ; Gossypium/*parasitology ; *Haplotypes ; Hemolysin Proteins ; India ; Lepidoptera/*genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Pink bollworm, Pectinophora gossypiella (Saunders) infestation on Bt cotton is a major concern to cotton production in India. The genetic diversity and phylogeographic structure of the insect in light of PBW resistance needs to be revisited. The objective of this study was to identify different haplotypes of pink bollworm and their distribution in India. To achieve this we studied the population structure in 44 cotton growing districts of India. The partial mitochondrial COI sequence analyses of 214 pink bollworm populations collected from 44 geographical locations representing 9 cotton growing states of India were analysed. Genetic diversity analysis exhibited presence of 27 haplotypes, among them Pg_H1 and Pg_H2 were the most common and were present in 143 and 32 populations, respectively. Distributions of pairwise differences obtained with partial COI gene data from the overall Indian populations are unimodal, suggesting population expansion in India. Significant neutrality test on the basis of Tajima' D and Fu's Fs presented a star-shaped haplotype network together with multiple haplotypes. The unimodal mismatch distribution, rejection of neutrality test with significant negative values supported the theory of demographic expansion in cotton pink bollworm populations in India. Genetic data not only provides us with a perspective of population genetics, but also that the two populations of pink bollworm, those occurring early in the season are genetically close to the late season populations with respect to their partial CO1 region. Resistance to Cry toxins does not seem to have had an impact on this region of the mt DNA in populations of pink bollworm.},
}
@article {pmid32183692,
year = {2020},
author = {Wang, H and Liu, C and Liu, Z and Wang, Y and Ma, L and Xu, B},
title = {The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering.},
journal = {BMC microbiology},
volume = {20},
number = {1},
pages = {61},
pmid = {32183692},
issn = {1471-2180},
support = {CARS-45//Agriculture Research System of China/International ; 31572470//Innovative Research Group Project of the National Natural Science Foundation of China/International ; },
mesh = {Animals ; Bacteria/*classification/drug effects/isolation &amp; purification ; Bees/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Sugars/*adverse effects ; Gastrointestinal Microbiome/drug effects ; High Fructose Corn Syrup/adverse effects ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Sucrose/adverse effects ; },
abstract = {BACKGROUND: The health of honeybee colonies is critical for bee products and agricultural production, and colony health is closely associated with the bacteria in the guts of honeybees. Although colony loss in winter is now the primary restriction in beekeeping, the effects of different sugars as winter food on the health of honeybee colonies are not well understood. Therefore, in this study, the influence of different sugar diets on honeybee gut bacteria during overwintering was examined.<br><br>RESULTS: The bacterial communities in honeybee midguts and hindguts before winter and after bees were fed honey, sucrose, and high-fructose syrup as winter-food were determined by targeting the V3-V4 region of 16S rDNA using the Illumina MiSeq platform. The dominant microbiota in honeybee guts were the phyla Proteobacteria (63.17%), Firmicutes (17.61%; Lactobacillus, 15.91%), Actinobacteria (4.06%; Bifidobacterium, 3.34%), and Bacteroidetes (1.72%). The dominant taxa were conserved and not affected by season, type of overwintering sugar, or spatial position in the gut. However, the relative abundance of the dominant taxa was affected by those factors. In the midgut, microbial diversity of the sucrose group was higher than that of the honey and high-fructose syrup groups, but in the hindgut, microbial diversity of the honey and high-fructose groups was higher than that in the sucrose group. Sucrose increased the relative abundance of Actinobacteria (Bifidobacteriales Bifidobacteriaceae) and Alphaproteobacteria (Rhizobiales and Mitochondria) of honeybee midgut, and honey enriched the Bacteroidetes and Gammaproteobacteria (Pasteurellales) in honeybee hindgut. High-fructose syrup increased the relative abundance of Betaproteobacteria (Neisseriales: Neisseriaceae) of the midgut.<br><br>CONCLUSION: The type of sugar used as winter food affected the relative abundance of the dominant bacterial communities in honeybee guts, not the taxa, which could affect the health and safety of honeybee colonies during overwintering. The presence of the supernal Alphaproteobacteria, Bifidobacteriales, and Lactobacillaceae in the gut of honeybees fed sucrose and cheaper than honey both indicate that sucrose is very suitable as the overwintering food for honeybees.},
}
@article {pmid32186219,
year = {2020},
author = {Zhang, WJ and Wang, JJ and Li, C and Chen, JQ and Li, W and Jiang, SY and Hsu, KC and Zhao, M and Lin, HD and Zhao, J},
title = {Spatial genetic structure of Opsariichthys hainanensis in South China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {3},
pages = {98-107},
doi = {10.1080/24701394.2020.1741564},
pmid = {32186219},
issn = {2470-1408},
mesh = {Animals ; China ; Cyprinidae/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Genes, Mitochondrial/genetics ; Genetic Structures/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Rivers ; Sequence Analysis, DNA/methods ; },
abstract = {South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.},
}
@article {pmid32202195,
year = {2020},
author = {Yang, C and Zhu, EJ and He, QJ and Yi, CH and Wang, XB and Hu, SJ and Wei, SJ},
title = {Strong genetic differentiation among populations of Cheirotonus gestroi (Coleoptera: Euchiridae) in its native area sheds lights on species conservation.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {3},
pages = {108-119},
doi = {10.1080/24701394.2020.1741565},
pmid = {32202195},
issn = {2470-1408},
mesh = {Animals ; China ; Coleoptera/*genetics ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Ecosystem ; Endangered Species ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Geography ; Haplotypes/genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The long-armed scarab (Cheirotonus gestroi) is an endangered large insect in southwestern China and neighboring countries; however, limited information is available regarding its population genetics, hindering conservation efforts. Therefore, we investigated the population genetic structure and evolutionary history of C. gestroi in southwestern China. Twenty-five haplotypes were obtained from 47 specimens across five populations. The Dawei Mountain (DWS) population differed from other populations by a high genetic distance. Population structure analysis generated three distinct clades, corresponding to Hengduan Mountains (HM), Ailao Mountains (AM), and Dawei Mountains (DM), and high-level genetic diversity was found in two HM populations. Collectively, the strong genetic differentiation among populations might be due to limited gene flow, geographical isolation, and habitat fragmentation. Therefore, while developing a conservation strategy, HM, AM, and DM groups should be defined as separate management units. Additionally, the DWS population should be given priority protection due to its uniqueness and low genetic diversity.},
}
@article {pmid32212876,
year = {2020},
author = {Kim, JS and Park, J and Fong, JJ and Zhang, YP and Li, SR and Ota, H and Min, SH and Min, MS and Park, D},
title = {Genetic diversity and inferred dispersal history of the Schlegel's Japanese Gecko (Gekko japonicus) in Northeast Asia based on population genetic analyses and paleo-species distribution modelling.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {3},
pages = {120-130},
doi = {10.1080/24701394.2020.1742332},
pmid = {32212876},
issn = {2470-1408},
mesh = {Alleles ; Animals ; China ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Japan ; Lizards/*genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/*genetics ; Phylogeny ; Phylogeography/methods ; Republic of Korea ; Sequence Analysis, DNA/methods ; },
abstract = {To understand the genetic diversity and dispersal history of Schlegel's Japanese gecko (Gekko japonicus), we performed genetic analyses and paleo-species distributional modelling. For the genetic analysis, we analyzed mitochondrial DNA (mtDNA) (cytochrome b [Cytb] and NADH dehydrogenase 2 [ND2]) and seven microsatellite loci of 353 individuals from 11 populations (2 east coast China, 4 west and central coast Japan and 5 Korea). For the paleo-species distribution modelling, we used 432 occurrence data points (125 China, 291 Japan and 16 Korea) over the Pleistocene and Holocene. China is inferred to be the source population, which had higher genetic diversity (mtDNA) and more private alleles (mtDNA) compared to Japanese and Korean populations. Differences between the three counties were very small in the mtDNA haplotype network despite some genetic structure among the three countries. Microsatellite analysis inferred that genetic exchange has actively occurred among the Chinese, Japanese and Korean populations. Suitable habitats in Japan should have been plentiful by the mid-Holocene, but have only recently become available in Korea. These results suggest that dispersal of G. japonicus occurred after the Holocene warming from the east coast of China to the west and central coasts of Japan and Korea, and gene flow is actively occurring among the three countries.},
}
@article {pmid32230306,
year = {2020},
author = {Ceríaco, LMP and Agarwal, I and Marques, MP and Bauer, AM},
title = {A review of the genus Hemidactylus Goldfuss, 1820 (Squamata: Gekkonidae) from Angola, with the description of two new species.},
journal = {Zootaxa},
volume = {4746},
number = {1},
pages = {zootaxa.4746.1.1},
doi = {10.11646/zootaxa.4746.1.1},
pmid = {32230306},
issn = {1175-5334},
mesh = {Angola ; Animals ; *Lizards ; Mitochondria ; Phylogeny ; },
abstract = {The genus Hemidactylus in Angola is represented by six species, all of them part of taxonomically and nomenclaturally challenging species complexes. We present a detailed taxonomic revision of the group in the region and describe two new species, Hemidactylus nzingae sp. nov. and Hemidactylus paivae sp. nov., both occuring in and potentially endemic to the highlands of Angola. Phylogenetic analysis using a combination of mitochondrial (ND2) and nuclear (MXRA5, PDC, RAG1) markers, as well as morphological and scalation data support the recognition of the new species. In addition, data support the revalidation of Hemidactylus bayonii Bocage, 1893, and Hemidactylus benguellensis Bocage, 1893. We also provide a redefinition of Hemidactylus longicephalus Bocage, 1873 with which we synonymize Hemidactylus mabouia molleri Bedriaga, 1892, from São Tomé in the Gulf of Guinea. Given that the type material of H. bayonii, H. benguellensis, H. longicephalus and H. mabouia molleri have all been lost or destroyed, we designate neotypes for all of these nomina for purposes of nomenclatural stability. The description of the new species and the revision and revalidation of the Angolan species already described contributes to a better understanding of the taxonomy and biogeography of West and Central African Hemidactylus, as well as to the general biogeographic and evolutionary patterns of Angolan fauna. A key to the Angolan species is also presented.},
}
@article {pmid32243910,
year = {2020},
author = {Muhammad, N and Suleman, and Khan, MS and Li, L and Zhao, Q and Ullah, H and Zhu, XQ and Ma, J},
title = {Characterization of the complete mitogenome of Centrorhynchus clitorideus (Meyer, 1931) (Palaeacanthocephala: Centrorhynchidae), the largest mitochondrial genome in Acanthocephala, and its phylogenetic implications.},
journal = {Molecular and biochemical parasitology},
volume = {237},
number = {},
pages = {111274},
doi = {10.1016/j.molbiopara.2020.111274},
pmid = {32243910},
issn = {1872-9428},
mesh = {Acanthocephala/classification/*genetics/isolation &amp; purification ; Animals ; Base Sequence ; Bayes Theorem ; Falconiformes/parasitology ; *Genes, Helminth ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Pakistan ; *Phylogeny ; Strigiformes/parasitology ; Whole Genome Sequencing ; },
abstract = {Species of Centrorhynchus (Polymorphida: Centrorhynchidae) commonly parasitize various falconiform and strigiform birds worldwide. In the present study, the complete mitochondrial (mt) genome sequences of Centrorhynchus clitorideus was sequenced and annotated for the first time based on specimens collected from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. The complete mt genome sequences of C. clitorideus is 15,884 bp in length, and contained 36 genes [two rRNA genes (rrnL and rrnS), 22 tRNA genes and 12 protein-coding genes (PCGs) (lacking atp8)] and two non-coding regions (NCR1 and NCR2), which represents the largest mt genome of acanthocephalan reported so far. In order to assess the systematic position of C. clitorideus and the interrelationship of the family Centrorhynchidae and the other families in order Polymorphida, the phylogenetic tree was constructed using Bayesian inference (BI) based on amino acid sequences of 12 PCGs. Phylogenetic results supported C. clitorideus formed a sister relationship to C. milvus in Centrorhynchidae, which has a sister relationship to the representatives of Polymorphidae + Plagiorhynchidae. Our results revealed the monophyly of Polymorphida and paraphyly of Echinorhynchida in the class Palaeacanthocephala. The validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) was also challenged by our phylogenetic results, which seems to be a synonym of Centrorhynchus. Moreover, the present phylogenetic analysis indicated that the family Quadrigyridae and subfamily Pallisentinae (A. cheni and P. celatus) are polyphyletic.},
}
@article {pmid32268201,
year = {2020},
author = {Bolívar-Leguizamón, SD and Silveira, LF and Derryberry, EP and Brumfield, RT and Bravo, GA},
title = {Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients.},
journal = {Molecular phylogenetics and evolution},
volume = {148},
number = {},
pages = {106810},
doi = {10.1016/j.ympev.2020.106810},
pmid = {32268201},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Environment ; Genetic Variation ; Genetics, Population ; Geography ; Information Theory ; Mitochondria/genetics ; Passeriformes/*classification/genetics ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; South America ; Species Specificity ; Time Factors ; },
abstract = {The Neotropics show a wealth of distributional patterns shared by many co-distributed species. A distinctive pattern is the so-called "circum-Amazonian distribution," which is observed in species that do not occur in Amazonia but rather along a belt of forested habitats spanning south and east of Amazonia, the Andean foothills, and often into the Venezuelan Coastal Range and the Tepuis. Although this pattern is widespread across animals and plants, its underlying biogeographic mechanisms remain poorly understood. The Variable Antshrike (Thamnophilus caerulescens) is a sexually dimorphic suboscine passerine that exhibits extreme plumage variation and occurs along the southern portion of the circum-Amazonian belt. We describe broad-scale phylogeographic patterns of T. caerulescens and assess its demographic history using DNA sequences from the mitochondrion and ultraconserved elements (UCEs). We identified three genomic clusters: a) northern Atlantic Forest; b) southeastern Cerrado and central-southern Atlantic Forest, and c) Chaco and Andes. Our results were consistent with Pleistocene divergence followed by gene flow, mainly between the latter two clusters. There were no genetic signatures of rapid population expansions or bottlenecks. The population from the northern Atlantic Forest was the most genetically divergent group within the species. The demographic history of T. caerulescens was probably affected by series of humid and dry periods throughout the Quaternary that generated subtle population expansions and contractions allowing the intermittent connection of habitats along the circum-Amazonian belt. Recognizing the dynamic history of climate-mediated forest expansions, contractions, and connections during the South American Pleistocene is central toward a mechanistic understanding of circum-Amazonian distributions.},
}
@article {pmid32278863,
year = {2020},
author = {Vargas-Ramírez, M and Caballero, S and Morales-Betancourt, MA and Lasso, CA and Amaya, L and Martínez, JG and das Neves Silva Viana, M and Vogt, RC and Farias, IP and Hrbek, T and Campbell, PD and Fritz, U},
title = {Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography.},
journal = {Molecular phylogenetics and evolution},
volume = {148},
number = {},
pages = {106823},
doi = {10.1016/j.ympev.2020.106823},
pmid = {32278863},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Calibration ; Colombia ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; *Genomics ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; Probability ; Species Specificity ; Time Factors ; Turtles/classification/*genetics ; },
abstract = {The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.},
}
@article {pmid32282807,
year = {2020},
author = {Sun, X and Yu, D and Xie, Z and Dong, J and Ding, Y and Yao, H and Greenslade, P},
title = {Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection.},
journal = {PloS one},
volume = {15},
number = {4},
pages = {e0230827},
pmid = {32282807},
issn = {1932-6203},
mesh = {Animals ; Arthropods/*classification/*genetics ; *Genome, Mitochondrial ; *Phylogeny ; },
abstract = {Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.},
}
@article {pmid32291084,
year = {2020},
author = {Eom, KS and Rim, HJ and Jeon, HK},
title = {Taenia asiatica: Historical overview of taeniasis and cysticercosis with molecular characterization.},
journal = {Advances in parasitology},
volume = {108},
number = {},
pages = {133-173},
doi = {10.1016/bs.apar.2019.12.004},
pmid = {32291084},
issn = {2163-6079},
mesh = {Animals ; Cysticercosis/*parasitology ; Genes, Helminth/genetics ; Humans ; Phylogeny ; Taenia/anatomy &amp; histology/classification/*genetics ; Taeniasis/*parasitology ; },
abstract = {Asian Taenia is a human-infecting Taenia tapeworm known as Taenia asiatica following morphological examination of adult and larval stages of the tapeworm by Eom and Rim (1993). The life cycle of T. asiatica differs from that of T. saginata in its intermediate host (pigs versus cattle) as well as in the infected organs (liver versus muscle). T. asiatica can be differentiated from T. solium and T. saginata by examination of morphological characteristics such as the scolex, mature and gravid proglottids in the adult stage, and the scolex and bladder surface in the larval stage. T. asiatica has been identified in Korea, Taiwan, the Philippines, China, Thailand, Indonesia, Vietnam, Japan, Lao PDR, Nepal and India. The molecular tools employed for T. asiatica identification have been developed to differentiate T. asiatica from other human-infecting Taenia tapeworms based on genetic information such as nucleotide sequence of mitochondrial genes, nuclear ribosomal genes and nuclear genes that lead to development of the subsequent molecular techniques, such as PCR-RFLP, PCR-RAPD, BESST-base, LAMP and qPCR. Investigation of the phylogenetic relationships among human Taenia species revealed that T. asiatica is a sister species with T. saginata, which is genetically more similar than other Taenia species in terms of the nucleotide sequences of cox1, nad1 and 28S rDNA. The mitochondrial genomes of human Taenia tapeworms comprise 13,703bp (T. asiatica), 13,670bp (T. saginata) and 13,709bp (T. solium), and contain 36 genes including 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Sequence differences in the full genome of T. asiatica and T. saginata mitochondria is 4.6%, while T. solium differs by 11%. Hox gene orthology in T. asiatica was established by comparative analysis with Platyhelminthes Hox genes. T. asiatica Hox revealed six Hox orthologs including two lab/Hox1, two Hox3, one Dfd/Hox4 and one Lox/Lox4. Hybridization between T. asiatica and T. saginata was definitely observed in these species which are sympatrically endemic in the regions of Korea, Thailand, China and Lao PDR. Comparative analyses of T. asiatica, T. saginata and T. solium genomes were also reported with genome features. Taenia asiaticus nomen novum was proposed for T. asiaticaEom and Rim, 1993 which is a homonym of T. asiatica Linstow, 1901 (Davaineidae).},
}
@article {pmid32326478,
year = {2020},
author = {Shu, B and Zhang, J and Veeran, S and Zhong, G},
title = {Pro-Apoptotic Function Analysis of the Reaper Homologue IBM1 in Spodoptera frugiperda.},
journal = {International journal of molecular sciences},
volume = {21},
number = {8},
pages = {},
pmid = {32326478},
issn = {1422-0067},
support = {31572335//National Natural Science Foundation of China/ ; },
mesh = {Amino Acid Chloromethyl Ketones/pharmacology ; Amino Acid Sequence ; Animals ; Apoptosis/drug effects/*genetics/radiation effects ; Baculoviral IAP Repeat-Containing 3 Protein/pharmacology ; Camptothecin/pharmacology ; Caspase Inhibitors/*pharmacology ; Gene Expression Regulation, Developmental ; Insect Proteins/genetics/*metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics/*metabolism ; Limonins/pharmacology ; Mitochondria/drug effects/*metabolism/radiation effects ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sf9 Cells ; Spodoptera/genetics/growth &amp; development/*metabolism/radiation effects ; Ultraviolet Rays ; Up-Regulation ; },
abstract = {As an important type of programmed cell death, apoptosis plays a critical role in lepidopteran insects in response to various internal and external stresses. It is controlled by a network of genes such as those encoding the inhibitor of apoptosis proteins. However, there are few studies on apoptosis-related genes in Spodoptera frugiperda. In this study, an orthologue to the Drosophila reaper gene, named Sf-IBM1, was identified from S. frugiperda, and a full-length sequence was obtained by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends PCR (RACE-PCR). The expression pattern of Sf-IBM1 was determined in different developmental stages and various tissues. Apoptotic stimuli including azadirachtin, camptothecin, and ultraviolet radiation (UV) induced the expression of Sf-IBM1 at both transcript and protein levels. Overexpression of Sf-IBM1 induced apoptosis in Sf9 cells, and the Sf-IBM1 protein was localized in mitochondria. The apoptosis induced by Sf-IBM1 could be blocked by the caspase universal inhibitor carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone (Z-VAD-FMK) and Sf-IAP1. Our results provide valuable information that should contribute to a better understanding of the molecular events that lead to apoptosis in lepidopterans.},
}
@article {pmid32349679,
year = {2020},
author = {Anwar, A and She, M and Wang, K and Ye, X},
title = {Cloning and molecular characterization of Triticum aestivum ornithine amino transferase (TaOAT) encoding genes.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {187},
pmid = {32349679},
issn = {1471-2229},
support = {31771788//National Natural Science Foundation of China/ ; 2019BBF02020//General Key Program of Science and Technology Department of Ningxia/ ; },
mesh = {Chromosomes, Plant ; Droughts ; *Genes, Plant ; Ornithine-Oxo-Acid Transaminase/*genetics ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Polyethylene Glycols/pharmacology ; Polyploidy ; Promoter Regions, Genetic ; Sodium Chloride/pharmacology ; Transcriptome ; Triticum/drug effects/*genetics ; },
abstract = {BACKGROUND: Ornithine aminotransferase (OAT, EC:2.6.1.13), alternatively known as ornithine delta aminotransferase (δOAT), is a pyridoxal phosphate (PLP)-dependent enzyme involved in the conversion of ornithine into glutamyl-5-semi-aldehyde (GSA) and vice versa. Up till now, there has been no study on OAT in wheat despite the success of its isolation from rice, maize, and sorghum. This study focuses on identification and molecular characterization of OAT in wheat.<br><br>RESULTS: In total, three homeologous OAT genes in wheat genome were found on chromosome group 5, named as TaOAT-5AL, TaOAT-5BL, and TaOAT-5DL. Sequence alignment between gDNA and its corresponding cDNA obtained a total of ten exons and nine introns. A phylogenetic tree was constructed and results indicated that OATs shared highly conserved domains between monocots and eudicots, which was further illustrated by using WebLogo to generate a sequence logo. Further subcellular localization analysis indicated that they functioned in mitochondria. Protein-protein interactions supported their role in proline biosynthesis through interactions with genes, such as delta 1-pyrroline-5-carboxylate synthetase (P5CS) and pyrroline-5-carboxylate reductase (P5CR), involved in the proline metabolic pathway. Promoter analysis exposed the presence of several stress responsive elements, implying their involvement in stress regulation. Expression profiling illustrated that TaOAT was highly induced in the wheat plants exposed to drought or salt stress condition. Upregulated expression of TaOATs was observed in stamens and at the heading stage. A potential role of TaOAT genes during floret development was also revealed. Furthermore, the transgenic plants overexpressing TaOAT showed enhanced tolerance to drought stress by increasing proline accumulation. In addition, salt tolerance of the transgenic plants was also enhanced.<br><br>CONCLUSION: TaOATs genes were involved in proline synthesis and nitrogen remobilization because they interacted with genes related to proline biosynthesis enzymes and arginine catabolism. In addition, TaOAT genes had a role in abiotic stress tolerance and a potential role in floret development. The results of this study may propose future research in the improvement of wheat resistance to abiotic stresses.},
}
@article {pmid32371258,
year = {2020},
author = {Sun, L and Zhou, F and Shao, Y and Lv, Z and Li, C},
title = {The iron-sulfur protein subunit of succinate dehydrogenase is critical in driving mitochondrial reactive oxygen species generation in Apostichopus japonicus.},
journal = {Fish &amp; shellfish immunology},
volume = {102},
number = {},
pages = {350-360},
doi = {10.1016/j.fsi.2020.04.060},
pmid = {32371258},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Iron-Sulfur Proteins/*genetics/metabolism ; Lipopolysaccharides/pharmacology ; Mitochondria/metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Sequence Alignment ; Stichopus/enzymology/*genetics/*immunology/*metabolism ; Succinate Dehydrogenase/genetics/*metabolism ; Vibrio/physiology ; },
abstract = {Succinate dehydrogenase (SDH) is a mitochondrial enzyme with the unique ability to participate in both the tricarboxylic acid cycle and the electron transport chain to produce reactive oxygen species (ROS). The B subunit of SDH is required for succinate oxidation, which is critical for pro-inflammatory response. In this study, we cloned the iron-sulfur protein subunit of SDH from Apostichopus japonicus (denoted as AjSDHB) via RACE technology and explored its role in the immune system as a response to pathogen infection. The full-length cDNA of AjSDHB was 1442 bp with a complete open reading frame of 858 bp encoding 286 amino acids. Simple modular architecture research tool analysis revealed that AjSDHB contained two conserved domains, including a 2Fe-2S iron-sulfur cluster binding domain and a 4Fe-4S dicluster domain, without a signal peptide. Multiple sequence alignment demonstrated that AjSDHB shared a high degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates. Phylogenetic analysis supported the finding that AjSDHB is a new member of the SDHB protein subfamily. Tissue distribution analysis revealed that AjSDHB was expressed in all examined tissues and particularly highly expressed in the muscles. AjSDHB transcripts were markedly induced in coelomocytes both by Vibrio splendidus challenge in vivo and lipopolysaccharide exposure in vitro. Function analysis showed that siRNA-mediated AjSDHB knockdown could substantially reduce the mitochondrial membrane potential (ΔΨm) and further decrease mitochondrial ROS production in A. japonicus coelomocytes. By contrast, AjSDHB overexpression considerably increased ΔΨm and mitochondrial ROS production of A. japonicus coelomocytes. These results supported the idea that AjSDHB is involved in the innate immunity of A. japonicus through its participation in mitochondrial ROS generation.},
}
@article {pmid32380284,
year = {2020},
author = {Xu, L and Liu, P and Wang, X and Van Damme, K and Du, F},
title = {Phylogenetic relationships and cryptic species in the genus Sthenoteuthis (Cephalopoda: Ommastrephidae) in the South China Sea.},
journal = {Molecular phylogenetics and evolution},
volume = {149},
number = {},
pages = {106846},
doi = {10.1016/j.ympev.2020.106846},
pmid = {32380284},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; China ; DNA, Mitochondrial/genetics ; Decapodiformes/*classification/genetics ; Genetic Variation ; Geography ; Haplotypes/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Oceans and Seas ; *Phylogeny ; Species Specificity ; },
abstract = {Large squids of the genus Sthenoteuthis are commercially relevant species that include two truly oceanic squids. They are large nektonic predators being widely distributed throughout tropical and subtropical waters of the Atlantic and Indo-Pacific Ocean. The present study investigates different morphs varying in size at maturity, and assesses the genetic divergence in Sthenotheutis in relation to geographic patterns in the South China Sea. We obtained sequences using a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (Histone H3) gene marker from 111 individuals in 23 locations of the South China Sea. In combination with sequences available in public databases, we performed tests on DNA taxonomy, mostly based on molecular phylogenies. Our results suggest that the genus Sthenoteuthis includes at least three species. The Indo-Pacific purpleback squid Sthenoteuthis oualaniensis contains at least two genetically distinct lineages that can be considered separate species, a dwarf species and a medium-sized species, separated by both the mitochondrial marker and the more conserved nuclear marker. We also assessed whether the few cases of mitonuclear discordance could be the result of genetic introgression and past hybridization or incongruence lineage sorting. The medium-sized species is more widely distributed and dominant in the South China Sea than the dwarf species. The medium-sized species inhabits the whole South China Sea, whereas the dwarf species is restricted to the equatorial waters of the South China Sea. The medium-sized species has two further genetic clades, one distributed in the East Pacific Ocean and the other in the South China Sea. This high level of genetic differentiation is in agreement with the discriminant analysis on the morphological measurements, clearly separating the dwarf and medium-sized species, indicating the presence of a complex of pseudo-cryptic species in S. oualaniensis, clearly identifiable by differences in DNA sequences and in body size, and statistically differentiated in their body measurements.},
}
@article {pmid32429841,
year = {2020},
author = {Chang, H and Nie, Y and Zhang, N and Zhang, X and Sun, H and Mao, Y and Qiu, Z and Huang, Y},
title = {MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects.},
journal = {BMC evolutionary biology},
volume = {20},
number = {1},
pages = {57},
pmid = {32429841},
issn = {1471-2148},
support = {31872217, 30970346//National Science Foundation of China/International ; 2018JQ8003//Natural Science Basic Research Plan in Shaanxi Province of China/International ; },
mesh = {Amino Acid Sequence ; Amino Acid Substitution/*genetics ; Animals ; Confidence Intervals ; Databases, Genetic ; Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/*genetics ; *Models, Genetic ; Orthoptera/classification/*genetics ; Phylogeny ; *Software ; },
abstract = {BACKGROUND: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthoptera-specific mitochondrial amino acid empirical model.<br><br>RESULTS: We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data.<br><br>CONCLUSIONS: The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.},
}
@article {pmid32468258,
year = {2020},
author = {Leelagud, P and Kongsila, S and Vejchasarn, P and Darwell, K and Phansenee, Y and Suthanthangjai, A and Uparang, C and Kawichai, R and Yajai, P and Boonsa-Nga, K and Chamarerk, V and Jairin, J},
title = {Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M.},
journal = {Molecular biology reports},
volume = {47},
number = {6},
pages = {4273-4283},
pmid = {32468258},
issn = {1573-4978},
support = {Project No. 27363//Rice Department/ ; },
mesh = {Animals ; Chromosome Mapping/methods ; Cyclooxygenase 1/*genetics/metabolism ; Diptera/genetics ; Genes, Mitochondrial/genetics ; Genetic Linkage/genetics ; Genetic Loci/genetics ; Genetic Markers/genetics ; Genetic Variation/genetics ; Mitochondria/enzymology/genetics ; Nematocera/*genetics ; Oryza/*genetics/parasitology ; Phylogeny ; Plant Diseases/genetics ; },
abstract = {The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F2 plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.},
}
@article {pmid32483282,
year = {2020},
author = {Ajene, I and Khamis, FM and Pietersen, G and van Asch, B},
title = {Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {8893},
pmid = {32483282},
issn = {2045-2322},
mesh = {Animals ; Citrus/*parasitology ; Ethiopia ; Europe ; *Genetic Variation ; Genome Size ; Genome, Mitochondrial ; Haplotypes ; Hemiptera/*classification/genetics ; Kenya ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; South Africa ; Uganda ; Whole Genome Sequencing/*veterinary ; },
abstract = {Trioza erytreae is the main vector for 'Candidatus Liberibacter africanus', the causative agent of African Citrus Greening disease. The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences for T. erytreae, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes of T. erytreae from Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure of T. erytreae was assessed using genetic clustering and pairwise distances, based on a dataset of public COI sequences recorded as T. erytreae. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya on Clausena anisata belonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified as T. erytreae belong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity of T. erytreae, with potential implications for the epidemiology of African Citrus Greening disease.},
}
@article {pmid32497832,
year = {2020},
author = {Klabacka, RL and Wood, PL and McGuire, JA and Oaks, JR and Grismer, LL and Grismer, JL and Aowphol, A and Sites, JW},
title = {Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex.},
journal = {Molecular phylogenetics and evolution},
volume = {150},
number = {},
pages = {106861},
doi = {10.1016/j.ympev.2020.106861},
pmid = {32497832},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Biodiversity ; Brain-Derived Neurotrophic Factor/classification/genetics ; Indochina ; Lizards/*classification/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Phylogeography ; Protein Subunits/classification/genetics ; RNA, Ribosomal/classification/genetics ; },
abstract = {Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.},
}
@article {pmid32534184,
year = {2020},
author = {Pozzi, L and Penna, A and Bearder, SK and Karlsson, J and Perkin, A and Disotell, TR},
title = {Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex.},
journal = {Molecular phylogenetics and evolution},
volume = {150},
number = {},
pages = {106887},
doi = {10.1016/j.ympev.2020.106887},
pmid = {32534184},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; Forests ; Galagidae/anatomy &amp; histology/*classification/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; },
abstract = {The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.},
}
@article {pmid32534185,
year = {2020},
author = {Mao, X and Rossiter, SJ},
title = {Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis).},
journal = {Molecular phylogenetics and evolution},
volume = {150},
number = {},
pages = {106886},
doi = {10.1016/j.ympev.2020.106886},
pmid = {32534185},
issn = {1095-9513},
support = {310482/ERC_/European Research Council/International ; },
mesh = {Animals ; Cell Nucleus/genetics ; Chiroptera/*classification/genetics ; DNA, Mitochondrial/classification/genetics ; Gene Flow ; Genome ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; },
abstract = {Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.},
}
@article {pmid32552121,
year = {2020},
author = {Kim, P and Han, JH and An, SL},
title = {Genetic identification of species and natural hybridization determination based on mitochondrial DNA and nuclear DNA of genus Zacco in Korea.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {6},
pages = {221-227},
doi = {10.1080/24701394.2020.1777994},
pmid = {32552121},
issn = {2470-1408},
mesh = {Animals ; Breeding ; Cell Nucleus/*genetics ; Chimera ; Cyprinidae/*classification/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Female ; Genes, RAG-1/genetics ; Genetic Variation ; Male ; Mitochondria/*genetics ; Phylogeny ; Republic of Korea ; },
abstract = {Genus Zacco specimens collected in this study were classified genetically as five species, Zacco platypus, Z. temminckii, Z. koreanus and two unidentified species, using DNA barcoding analysis based on 655 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene. Two of unidentified species (Z. sp.1 and Z. sp.2) were considered to be unrecorded or new species of genus Zacco according to genetic distances between Zacco species. In addition, we determined a natural hybrid based on polymorphic base at the diagnostic positions displayed on nuclear recombination activating gene 1 (RAG1) gene (965 bp), and estimated paternal and maternal species of natural hybrid comparing phylogenetic tree between COI and RAG1, and Z. sp.1♀ × Z. koreanus♂, Z. sp.2♀ × Z. koreanus♂ and Z. koreanus♀ × Z. sp.1♂ individuals were confirmed. The habitat of natural hybrids of Z. koreanus between Z. sp.1 and Z. sp.2 was identified as Geum and Yeongsan River, respectively. In our data, only F1 hybrid generation was identified; however, generations after F1 hybrid or backcross were not demonstrated.},
}
@article {pmid32561724,
year = {2020},
author = {Nong, W and Cao, J and Li, Y and Qu, Z and Sun, J and Swale, T and Yip, HY and Qian, PY and Qiu, JW and Kwan, HS and Bendena, W and Tobe, S and Chan, TF and Yip, KY and Chu, KH and Ngai, SM and Tsim, KY and Holland, PWH and Hui, JHL},
title = {Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {3051},
pmid = {32561724},
issn = {2041-1723},
mesh = {Animals ; Developmental Biology ; *Genes, Homeobox ; Genome ; Genome, Mitochondrial ; Hormones/genetics ; MicroRNAs/genetics ; Mitochondria/genetics ; *Multigene Family ; Phylogeny ; Plastids/genetics ; RNA/*genetics ; RNA, Small Interfering/genetics ; Scyphozoa/*genetics/*physiology ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome ; },
abstract = {The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.},
}
@article {pmid32579605,
year = {2020},
author = {Pyrih, J and Rašková, V and Škodová-Sveráková, I and Pánek, T and Lukeš, J},
title = {ZapE/Afg1 interacts with Oxa1 and its depletion causes a multifaceted phenotype.},
journal = {PloS one},
volume = {15},
number = {6},
pages = {e0234918},
pmid = {32579605},
issn = {1932-6203},
mesh = {Biotinylation ; Down-Regulation ; Electron Transport Complex I/metabolism ; Electron Transport Complex IV/metabolism ; Eukaryota/genetics ; *Gene Deletion ; Genome, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Phenotype ; Phylogeny ; Protein Binding ; Protozoan Proteins/*metabolism ; Trypanosoma brucei brucei/*metabolism ; },
abstract = {ZapE/Afg1 is a component of the inner cell membrane of some eubacteria and the inner mitochondrial membrane of eukaryotes. This protein is involved in FtsZ-dependent division of eubacteria. In the yeast and human mitochondrion, ZapE/Afg1 likely interacts with Oxa1 and facilitates the degradation of mitochondrion-encoded subunits of respiratory complexes. Furthermore, the depletion of ZapE increases resistance to apoptosis, decreases oxidative stress tolerance, and impacts mitochondrial protein homeostasis. It remains unclear whether ZapE is a multifunctional protein, or whether some of the described effects are just secondary phenotypes. Here, we have analyzed the functions of ZapE in Trypanosoma brucei, a parasitic protist, and an important model organism. Using a newly developed proximity-dependent biotinylation approach (BioID2), we have identified the inner mitochondrial membrane insertase Oxa1 among three putative interacting partners of ZapE, which is present in two paralogs. RNAi-mediated depletion of both ZapE paralogs likely affected the function of respiratory complexes I and IV. Consistently, we show that the distribution of mitochondrial ZapE is restricted only to organisms with Oxa1, respiratory complexes, and a mitochondrial genome. We propose that the evolutionarily conserved interaction of ZapE with Oxa1, which is required for proper insertion of many inner mitochondrial membrane proteins, is behind the multifaceted phenotype caused by the ablation of ZapE.},
}
@article {pmid32647112,
year = {2020},
author = {Lubośny, M and Przyłucka, A and Śmietanka, B and Burzyński, A},
title = {Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11256},
pmid = {32647112},
issn = {2045-2322},
mesh = {Alleles ; Animals ; DNA, Mitochondrial/*genetics ; Female ; Fresh Water ; Genome ; Genome, Mitochondrial ; Heredity ; High-Throughput Nucleotide Sequencing ; *Inheritance Patterns ; Male ; Mitochondria/metabolism ; Models, Genetic ; Mytilus/*genetics ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; RNA/genetics ; Sex Determination Processes ; },
abstract = {Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic mussel Semimytilus algosus (Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.},
}
@article {pmid32667908,
year = {2020},
author = {Arbeithuber, B and Hester, J and Cremona, MA and Stoler, N and Zaidi, A and Higgins, B and Anthony, K and Chiaromonte, F and Diaz, FJ and Makova, KD},
title = {Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues.},
journal = {PLoS biology},
volume = {18},
number = {7},
pages = {e3000745},
pmid = {32667908},
issn = {1545-7885},
support = {R01 GM116044/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; },
mesh = {Aging/*genetics ; Animals ; DNA Mutational Analysis ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency/genetics ; Genetic Drift ; Germ Cells/metabolism ; Inheritance Patterns/genetics ; Logistic Models ; Male ; Mammals/*genetics ; Mice ; Mitochondria/*genetics ; Models, Genetic ; Mutation/*genetics ; Mutation Rate ; Nucleotides/genetics ; Oocytes/*metabolism ; Organ Specificity/*genetics ; Pedigree ; },
abstract = {Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.},
}
@article {pmid32681023,
year = {2020},
author = {Folgueira, I and Lamas, J and Sueiro, RA and Leiro, JM},
title = {Molecular characterization and gene expression modulation of the alternative oxidase in a scuticociliate parasite by hypoxia and mitochondrial respiration inhibitors.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {11880},
pmid = {32681023},
issn = {2045-2322},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Respiration/*drug effects ; Female ; Gene Expression ; Genome, Protozoan ; Genomics/methods ; Hypoxia/*metabolism ; Male ; Mitochondria/*drug effects/metabolism/ultrastructure ; Mitochondrial Proteins/chemistry/*genetics ; Models, Molecular ; Oligohymenophorea/classification/*enzymology/*genetics ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Conformation ; Structure-Activity Relationship ; Alternative Oxidase ; },
abstract = {Philasterides dicentrarchi is a marine benthic microaerophilic scuticociliate and an opportunistic endoparasite that can infect and cause high mortalities in cultured turbot (Scophthalmus maximus). In addition to a cytochrome pathway (CP), the ciliate can use a cyanide-insensitive respiratory pathway, which indicates the existence of an alternative oxidase (AOX) in the mitochondrion. Although AOX activity has been described in P. dicentrarchi, based on functional assay results, genetic evidence of the presence of AOX in the ciliate has not previously been reported. In this study, we conducted genomic and transcriptomic analysis of the ciliate and identified the AOX gene and its corresponding mRNA. The AOX gene (size 1,106 bp) contains four exons and three introns that generate an open reading frame of 915 bp and a protein with a predicted molecular weight of 35.6 kDa. The amino acid (aa) sequence of the AOX includes an import signal peptide targeting the mitochondria and the protein is associated with the inner membrane of the mitochondria. Bioinformatic analysis predicted that the peptide is a homodimeric glycoprotein, although monomeric forms may also appear under native conditions, with EXXH motifs associated with the diiron active centers. The aa sequences of the AOX of different P. dicentrarchi isolates are highly conserved and phylogenetically closely related to AOXs of other ciliate species, especially scuticociliates. AOX expression increased significantly during infection in the host and after the addition of CP inhibitors. This confirms the important physiological roles of AOX in respiration under conditions of low levels of O2 and in protecting against oxidative stress generated during infection in the host.},
}
@article {pmid32693123,
year = {2020},
author = {Xu, H and Wu, Y and Wang, Y and Liu, Z},
title = {Comparative analysis of five mitogenomes of Osmylinae (Neuroptera: Osmylidae) and their phylogenetic implications.},
journal = {International journal of biological macromolecules},
volume = {164},
number = {},
pages = {447-455},
doi = {10.1016/j.ijbiomac.2020.07.150},
pmid = {32693123},
issn = {1879-0003},
mesh = {Animals ; Base Composition ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Neoptera/*classification/genetics ; Phylogeny ; RNA Folding ; RNA, Transfer/chemistry ; Sequence Analysis, DNA/*methods ; },
abstract = {In this study, five mitogenomes of Osmylinae species were sequenced: Osmylus fulvicephalus, Osmylus lucalatus, Plethosmylus atomatus, Plethosmylus zheanus, and Plethosmylus sp. These mitogenomes vary from 15,401 bp to 17,136 bp in size. The nucleotide compositions of Osmylinae mitogenomes are biased towards A/T. The gene arrangement of five mitogenomes is congruent with the putative ancestral pattern of the insects. Most of PCGs initiate with typical start codon ATN and terminate with TAA as the stop codon. All tRNA genes are folded into the typical cloverleaf secondary structure with an exception of tRNA[Ser(AGN)]. The phylogenetic relationship was reconstructed by both maximum likelihood and Bayesian methods based on 13 PCGs and two rRNA genes. The sister group relationships between Osmylinae and the clade of Spilosmylinae and Protosmylinae were recovered as expected. The monophyly of Osmylinae was corroborated, but within the subfamily, three species (P. atomatus, P. zheanus, and Plethosmylus sp.) originally belonging to Plethosmylus (transferred to Osmylus by Winterton) were restored as a clade and sister to the clade of Osmylus. The current results implied that it is necessary to reassess the systematic status of Plethosmylus in the future.},
}
@article {pmid32722672,
year = {2020},
author = {Fernando, HSD and Hapugoda, M and Perera, R and Black Iv, WC and De Silva, BGDNK},
title = {Mitochondrial metabolic genes provide phylogeographic relationships of global collections of Aedes aegypti (Diptera: Culicidae).},
journal = {PloS one},
volume = {15},
number = {7},
pages = {e0235430},
pmid = {32722672},
issn = {1932-6203},
mesh = {Aedes/classification/*genetics ; Africa ; Africa, Eastern ; Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gene Flow ; Genes, Mitochondrial/genetics ; Haplotypes ; India ; Mitochondria/*genetics/metabolism ; Pakistan ; Phylogeny ; *Phylogeography ; Sri Lanka ; },
abstract = {Phylogeographic relationships among global collections of the mosquito Aedes aegypti were evaluated using the mitochondrial Cytochrome C Oxidase 1 (CO1) and NADH dehydrogenase subunit 4 (ND4) genes including new sequences from Sri Lanka. Phylogeographic analysis estimated that Ae. aegypti arose as a species ~614 thousand years ago (kya) in the late Pleistocene. At 545 kya an "early" East African clade arose that continued to differentiate in East Africa, and eventually gave rise to three lineages one of which is distributed throughout all tropical and subtropical regions, a second that contains Southeast Asian/Sri Lankan mosquitoes and a third that contains mostly New World mosquitoes. West African collections were not represented in this early clade. The late clade continued to differentiate throughout Africa and gave rise to a lineage that spread globally. The most recent branches of the late clade are represented by South-East Asia and India/Pakistan collections. Analysis of migration rates suggests abundant gene flow between India/Pakistan and the rest of the world with the exception of Africa.},
}
@article {pmid32735957,
year = {2020},
author = {Harasgama, JC and Kasthuriarachchi, TDW and Kwon, H and Wan, Q and Lee, J},
title = {Molecular and functional characterization of a mitochondrial glutathione reductase homolog from redlip mullet (Liza haematocheila): Disclosing its antioxidant properties in the fish immune response mechanism.},
journal = {Developmental and comparative immunology},
volume = {113},
number = {},
pages = {103785},
doi = {10.1016/j.dci.2020.103785},
pmid = {32735957},
issn = {1879-0089},
mesh = {Animals ; Antioxidants/*metabolism ; Cloning, Molecular ; Fish Proteins/*genetics/metabolism ; Gills/*metabolism ; Glutathione Reductase/*genetics/metabolism ; Homeostasis ; Immunity, Innate ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Phylogeny ; Sequence Alignment ; Smegmamorpha/*immunology ; Transcriptome ; },
abstract = {Glutathione reductase (GSHR) is a biologically important enzyme involved in the conversion of oxidized glutathione (GSSG) into its reduced form, reduced glutathione (GSH), with the catalytic activity of NADPH. Most animals and aquatic organisms, including fish, possess high levels of this enzyme system to neutralize oxidative stress in cells. The current study was conducted to broaden our knowledge of GSHR in fish by identifying a mitochondrial isoform of this enzyme (LhGSHRm) in redlip mullet, Liza haematocheila, and clarifying its structure and function. The complete open reading frame of LhGSHRm consists of 1527 base pairs, encoding 508 amino acids, with a predicted molecular weight of 55.43 kDa. Multiple sequence alignment revealed the conservation of important amino acids in this fish. Phylogenetic analysis demonstrated the closest evolutionary relationship between LhGSHRm and other fish GSHRm counterparts. In tissue distribution analysis, the highest mRNA expression of LhGSHRm was observed in the gill tissue under normal physiological conditions. Following pathogenic challenges, the LhGSHRm transcription level was upregulated in a time-dependent manner in the gill and liver tissues, which may modulate the immune reaction against pathogens. rLhGSHRm showed considerable glutathione reductase activity in an enzyme assay. Further, the biological activity of rLhGSHRm in balancing cellular oxidative stress was observed in both disk diffusion and DPPH assays. Collectively, these results support that LhGSHRm has profound effects on modulating the immune reaction in fish to sustain precise redox homeostasis.},
}
@article {pmid32771550,
year = {2020},
author = {Kornilios, P and Jablonski, D and Sadek, RA and Kumlutaş, Y and Olgun, K and Avci, A and Ilgaz, C},
title = {Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex.},
journal = {Molecular phylogenetics and evolution},
volume = {152},
number = {},
pages = {106922},
doi = {10.1016/j.ympev.2020.106922},
pmid = {32771550},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; *Molecular Typing ; *Phylogeny ; Snakes/*classification/*genetics ; Species Specificity ; },
abstract = {Scolecophidia (worm snakes) are a vertebrate group with high ecomorphological conservatism due to their burrowing lifestyle. The Eurasian or Greek blindsnake Xerotyphlops vermicularis is their only European representative, a species-complex with an old diversification history. However, its systematics and taxonomy has remained untouched. Here, we extend previous work that relied heavily on mitochondrial markers, following a multi-locus approach and applying several species-delimitation methods, including a Bayesian coalescence-based approach (STACEY). Four "species" delimitation analyses based on the mtDNA (ABGD, bGMYC, mPTP, parsimony networks) returned 14, 11, 9 and 10 clusters, respectively. By mitotyping twice as many specimens as before, we have a complete picture of each cluster's distribution. With the exception of the highly-divergent Levantine lineage, the three independent nuclear markers did not help with phylogenetic resolution, as demonstrated in haplotype networks, concatenated and species-trees, a result of incomplete lineage sorting. The prevailing model from the coalescence-based species-delimitation identified two species: the lineage from the Levant and all others. We formally recognize them as distinct species and resurrect Xerotyphlops syriacus (Jan, 1864) to include the Levantine blindsnakes. Finally, X. vermicularis and X. syriacus may represent species-complexes themselves, since they include high levels of cryptic diversity.},
}
@article {pmid32822607,
year = {2020},
author = {Deng, J and Xie, XL and Wang, DF and Zhao, C and Lv, FH and Li, X and Yang, J and Yu, JL and Shen, M and Gao, L and Yang, JQ and Liu, MJ and Li, WR and Wang, YT and Wang, F and Li, JQ and Hehua, E and Liu, YG and Shen, ZQ and Ren, YL and Liu, GJ and Chen, ZH and Gorkhali, NA and Rushdi, HE and Salehian-Dehkordi, H and Esmailizadeh, A and Nosrati, M and Paiva, SR and Caetano, AR and Štěpánek, O and Olsaker, I and Weimann, C and Erhardt, G and Curik, I and Kantanen, J and Mwacharo, JM and Hanotte, O and Bruford, MW and Ciani, E and Periasamy, K and Amills, M and Lenstra, JA and Han, JL and Zhang, HP and Li, L and Li, MH},
title = {Paternal Origins and Migratory Episodes of Domestic Sheep.},
journal = {Current biology : CB},
volume = {30},
number = {20},
pages = {4085-4095.e6},
doi = {10.1016/j.cub.2020.07.077},
pmid = {32822607},
issn = {1879-0445},
mesh = {Animals ; Breeding ; Cell Lineage/genetics ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Genome/*genetics ; Male ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Sheep ; Sheep, Domestic/classification/*genetics ; Whole Genome Sequencing ; Y Chromosome/*genetics ; },
abstract = {The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.},
}
@article {pmid32824295,
year = {2020},
author = {Yamada, M and Akashi, K and Ooka, R and Miyado, K and Akutsu, H},
title = {Mitochondrial Genetic Drift after Nuclear Transfer in Oocytes.},
journal = {International journal of molecular sciences},
volume = {21},
number = {16},
pages = {},
pmid = {32824295},
issn = {1422-0067},
mesh = {Gene Editing/methods ; *Genes, Mitochondrial ; *Genetic Drift ; Humans ; Mitochondrial Replacement Therapy/adverse effects/*methods ; Nuclear Transfer Techniques/*adverse effects ; Oocytes/*metabolism ; },
abstract = {Mitochondria are energy-producing intracellular organelles containing their own genetic material in the form of mitochondrial DNA (mtDNA), which codes for proteins and RNAs essential for mitochondrial function. Some mtDNA mutations can cause mitochondria-related diseases. Mitochondrial diseases are a heterogeneous group of inherited disorders with no cure, in which mutated mtDNA is passed from mothers to offspring via maternal egg cytoplasm. Mitochondrial replacement (MR) is a genome transfer technology in which mtDNA carrying disease-related mutations is replaced by presumably disease-free mtDNA. This therapy aims at preventing the transmission of known disease-causing mitochondria to the next generation. Here, a proof of concept for the specific removal or editing of mtDNA disease-related mutations by genome editing is introduced. Although the amount of mtDNA carryover introduced into human oocytes during nuclear transfer is low, the safety of mtDNA heteroplasmy remains a concern. This is particularly true regarding donor-recipient mtDNA mismatch (mtDNA-mtDNA), mtDNA-nuclear DNA (nDNA) mismatch caused by mixing recipient nDNA with donor mtDNA, and mtDNA replicative segregation. These conditions can lead to mtDNA genetic drift and reversion to the original genotype. In this review, we address the current state of knowledge regarding nuclear transplantation for preventing the inheritance of mitochondrial diseases.},
}
@article {pmid32861874,
year = {2020},
author = {Marotta, R and Chin, J and Chiotis, M and Shuey, N and Collins, SJ},
title = {Long-term screening for primary mitochondrial DNA variants associated with Leber hereditary optic neuropathy: incidence, penetrance and clinical features.},
journal = {Mitochondrion},
volume = {54},
number = {},
pages = {128-132},
doi = {10.1016/j.mito.2020.08.007},
pmid = {32861874},
issn = {1872-8278},
mesh = {Adolescent ; Adult ; Case-Control Studies ; DNA, Mitochondrial/genetics ; Female ; Genetic Predisposition to Disease ; Humans ; Incidence ; Male ; Middle Aged ; Mutation Rate ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Penetrance ; *Polymorphism, Single Nucleotide ; },
abstract = {Leber hereditary optic neuropathy (LHON) is a neurodegenerative disorder characterised by bilateral, painless, subacute, central vision loss caused by pathogenic sequence variants in mitochondrial DNA (mtDNA). Over the course of 20 years, 734 people were systematically screened by our diagnostic laboratory for suspected LHON or for being at risk of LHON, with 98 found to harbour one of the three primary pathogenic mtDNA variants. Detection incidences were: 0.95% for NC_012920.1(MT-ND1):m.3460G>A; 9.4% for (MT-ND4):m.11778G>A; and 2.9% for (MT-ND6):m.14484T>C. The median age for symptomatic males was 27.3 years and for females 29.5 years, with a male to female ratio of 4.4:1 (62 males; 14 females). Most pathogenic variant carriers were propositi with the other individuals belonging to one of 14 pedigrees with noteworthy intra-family variability of clinical severity of the disease.},
}
@article {pmid32891682,
year = {2020},
author = {Darriba, S and Lee, RS and López, C},
title = {Mikrocytos mytilicoli n.sp. (Cercozoa, Mikrocytida, Mikrocytiidae) infecting the copepod Mytilicola intestinalis (Arthropoda, Cyclopoida, Mytilicolidae), a symbiont of Mytilus galloprovincialis in Galicia (NW Spain).},
journal = {Journal of invertebrate pathology},
volume = {176},
number = {},
pages = {107460},
doi = {10.1016/j.jip.2020.107460},
pmid = {32891682},
issn = {1096-0805},
mesh = {Animals ; Cercozoa/*classification/cytology/genetics/ultrastructure ; Copepoda/*parasitology/physiology ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; *Host-Parasite Interactions ; Microscopy ; Microscopy, Electron, Transmission ; Mytilus/physiology ; Phylogeny ; RNA, Ribosomal, 18S/analysis ; RNA, Ribosomal, 28S/analysis ; Spain ; Symbiosis ; },
abstract = {During a histopathological survey of Mytilus galloprovincialis in Galicia (NW Spain), microcells were observed infecting several organs of the symbiont copepod Mytilicola intestinalis. Positive results of PCR assay with specific primers for genus Mikrocytos and a clear signal of in situ hybridization with MACKINI-1 digoxigenin- labelled DNA probe (DIG-ISH) indicated a protozoan parasite of Mikrocytos genus. The ultrastructural study revealed intra and extracellular locations, polymorphic nuclei, intracellular round vesicles in the cytoplasm and absence of mitochondria. The present paper reports the characterization of the Mikrocytos sp. infecting M. intestinalis and proposes a novel species in the genus: Mikrocytos mytilicoli n. sp. A sequence of 18S-28S rDNA was obtained with 95.6% maximum identity (query cover 100%) with Mikrocytos mackini. Phylogenetic analysis showed that M. mytilicoli n. sp. and M. mackini share a common ancestor. However, comparison of the ITS1 rDNA region showed low similarity (75.8%) with M. mackini, which, combined with differences in ultrastructural details, host and geographic location, support the designation of a new species. This is the first description of a microcytid parasite of the genus Mikrocytos from a non-bivalve host.},
}
@article {pmid32896572,
year = {2021},
author = {Gupta, A and Shrivastava, D and Shakya, AK and Gupta, K and Pratap, JV and Habib, S},
title = {PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum.},
journal = {International journal for parasitology},
volume = {51},
number = {1},
pages = {23-37},
doi = {10.1016/j.ijpara.2020.07.010},
pmid = {32896572},
issn = {1879-0135},
mesh = {DNA-Directed RNA Polymerases/genetics ; Mitochondria/genetics ; *Mitochondrial Proteins/genetics ; Peptide Initiation Factors ; Phylogeny ; *Plasmodium falciparum/genetics ; RNA, Mitochondrial ; Transcription Factors/genetics ; },
abstract = {The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein-protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.},
}
@article {pmid32916006,
year = {2020},
author = {Gueuning, M and Frey, JE and Praz, C},
title = {Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees.},
journal = {Molecular ecology},
volume = {29},
number = {21},
pages = {4203-4220},
doi = {10.1111/mec.15629},
pmid = {32916006},
issn = {1365-294X},
mesh = {Animals ; Bees/genetics ; Biodiversity ; Cell Nucleus ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Genomics ; *Mitochondria/genetics ; Phylogeny ; },
abstract = {Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.},
}
@article {pmid32917087,
year = {2020},
author = {Teske, D and Peters, A and Möllers, A and Fischer, M},
title = {Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {49},
pages = {14323-14333},
doi = {10.1021/acs.jafc.0c03001},
pmid = {32917087},
issn = {1520-5118},
mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; *Genome, Plant ; Genomics ; Phylogeny ; Plants/classification/*genetics ; },
abstract = {Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.},
}
@article {pmid32920905,
year = {2020},
author = {Ghifari, AS and Teixeira, PF and Kmiec, B and Pružinská, A and Glaser, E and Murcha, MW},
title = {A mitochondrial prolyl aminopeptidase PAP2 releases N-terminal proline and regulates proline homeostasis during stress response.},
journal = {The Plant journal : for cell and molecular biology},
volume = {104},
number = {5},
pages = {1182-1194},
doi = {10.1111/tpj.14987},
pmid = {32920905},
issn = {1365-313X},
mesh = {Amino Acid Motifs ; Aminopeptidases/genetics/*metabolism ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cellular Senescence/physiology ; Darkness ; Green Fluorescent Proteins/genetics ; Loss of Function Mutation ; Mitochondria/metabolism ; Phylogeny ; Plants, Genetically Modified ; Pollen/physiology ; Proline/*metabolism ; Stress, Physiological/*physiology ; Transcription Factors/genetics/*metabolism ; },
abstract = {Most mitochondrial proteins are synthesised in the cytosol and targeted into the organelle via N-terminal targeting peptides that are cleaved upon import. The free targeting peptide is subsequently processed in a stepwise manner, with single amino acids released as final products. Here, we have characterised a proline-cleaving aminopeptidase in Arabidopsis thaliana, prolyl aminopeptidase-2 (PAP2, At3g61540). Activity assays show that PAP2 has a preferred activity to hydrolyse N-terminal proline. Protein localisation studies revealed that PAP2 is exclusively targeted to mitochondria. Characterisation of pap2 mutants show defective pollen, enhanced dark-induced senescence and increased susceptibility to abiotic stresses, which are likely attributed to a reduced level of accumulated free proline. Taken together, these results demonstrate the role of PAP2 in proline cleavage from mitochondrial peptides and proline homeostasis, which is required for the development of male gametophyte, tolerance to abiotic stresses, and leaf senescence.},
}
@article {pmid32934270,
year = {2020},
author = {Simaika, JP and Ware, JL and Garrison, RW and Samways, MJ},
title = {Phylogeny of the Synlestidae (Odonata: Zygoptera), with an emphasis on Chlorolestes Selys and Ecchlorolestes Barnard.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {15088},
pmid = {32934270},
issn = {2045-2322},
mesh = {Animals ; Cell Nucleus/genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; South Africa ; },
abstract = {The Synlestidae (Odonata: Zygoptera) of southern Africa comprise some highly localized species. All but one species are endemic to South Africa, and many to the Cape Floristic Region. Here we present the first phylogenetic reconstruction of the southern African Synlestidae using nuclear and mitochondrial molecular data. The genera Ecchlorolestes and Chlorolestes are monophyletic, and we propose that the Neotropical family Perilestidae consisting of two genera, Perilestes and Perissolestes, be sunk within Synlestidae. We discuss the intra-familial relationships for the southern African Synlestidae.},
}
@article {pmid32935660,
year = {2021},
author = {Li, H and Qiao, H and Liu, Y and Li, S and Tan, J and Hao, D},
title = {Characterization, expression profiling, and thermal tolerance analysis of heat shock protein 70 in pine sawyer beetle, Monochamus alternatus hope (Coleoptera: Cerambycidae).},
journal = {Bulletin of entomological research},
volume = {111},
number = {2},
pages = {217-228},
doi = {10.1017/S0007485320000541},
pmid = {32935660},
issn = {1475-2670},
mesh = {Animals ; *Coleoptera/genetics/metabolism ; Genes, Insect ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; Larva/genetics/metabolism ; Phylogeny ; Thermotolerance/*genetics ; },
abstract = {Monochamus alternatus Hope (Coleoptera: Cerambycidae) warrants attention as a dominant transmission vector of the pinewood nematode, and it exhibits tolerance to high temperature. Heat shock protein 70 (HSP70) family members, including inducible HSP70 and heat shock cognate protein 70 (HSC70), are major contributors to the molecular chaperone networks of insects under heat stress. In this regard, we specifically cloned and characterized three MaltHSP70s and three MaltHSC70s. Bioinformatics analysis on the deduced amino acid sequences showed these genes, having close genetic relationships with HSP70s of Coleopteran species, collectively shared conserved signature structures and ATPase domains. Subcellular localization prediction revealed the HSP70s of M. alternatus were located not only in the cytoplasm and endoplasmic reticulum but also in the nucleus and mitochondria. The transcript levels of MaltHSP70s and MaltHSC70s in each state were significantly upregulated by exposure to 35-50°C for early 3 h, while MaltHSP70s reached a peak after exposure to 45°C for 2-3 h in contrast to less-upregulated MaltHSC70s. In terms of MaltHSP70s, the expression threshold in females was lower than that in males. Also, both fat bodies and Malpighian tubules were the tissues most sensitive to heat stress in M. alternatus larvae. Lastly, the ATPase activity of recombinant MaltHSP70-2 in vitro remained stable at 25-40°C, and this recombinant availably enhanced the thermotolerance of Escherichia coli. Overall, our findings unraveled HSP70s might be the intrinsic mediators of the strong heat tolerance of M. alternatus due to their stabilized structure and bioactivity.},
}
@article {pmid32949792,
year = {2020},
author = {Cihlar, JC and Strobl, C and Lagacé, R and Muenzler, M and Parson, W and Budowle, B},
title = {Distinguishing mitochondrial DNA and NUMT sequences amplified with the precision ID mtDNA whole genome panel.},
journal = {Mitochondrion},
volume = {55},
number = {},
pages = {122-133},
doi = {10.1016/j.mito.2020.09.001},
pmid = {32949792},
issn = {1872-8278},
mesh = {Cell Nucleus/*genetics ; Computational Biology/methods ; DNA, Mitochondrial/*classification/isolation &amp; purification ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing/*methods ; },
abstract = {Nuclear mitochondrial DNA segments (NUMTs) are generated via transfer of portions of the mitochondrial genome into the nuclear genome. Given their common origin, there is the possibility that both the mitochondrial and NUMT segments may co-amplify using the same set of primers. Thus, analysis of the variation of the mitochondrial genome must take into account this co-amplification of mitochondrial and NUMT sequences. The study herein builds on data from the study by Strobl et al. (Strobl et al., 2019), in which multiple point heteroplasmies were called with an "N" to prevent labeling NUMT sequences mimicking mitochondrial heteroplasmy and being interpreted as true mitochondrial in origin sequence variants. Each of these point heteroplasmies was studied in greater detail, both molecularly and bioinformatically, to determine whether NUMT or true mitochondrial DNA variation was present. The bioinformatic and molecular tools available to help distinguish between NUMT and mitochondrial DNA and the effect of NUMT sequences on interpretation were discussed.},
}
@article {pmid32998193,
year = {2020},
author = {Marshall, C and Sturk-Andreaggi, K and Ring, JD and Dür, A and Parson, W},
title = {Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting.},
journal = {Genes},
volume = {11},
number = {10},
pages = {},
pmid = {32998193},
issn = {2073-4425},
mesh = {*Algorithms ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Mitochondrial ; *Haplotypes ; Humans ; Mitochondria/*genetics/metabolism/pathology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.},
}
@article {pmid33002605,
year = {2020},
author = {Pacheco, MA and Ceríaco, LMP and Matta, NE and Vargas-Ramírez, M and Bauer, AM and Escalante, AA},
title = {A phylogenetic study of Haemocystidium parasites and other Haemosporida using complete mitochondrial genome sequences.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {85},
number = {},
pages = {104576},
doi = {10.1016/j.meegid.2020.104576},
pmid = {33002605},
issn = {1567-7257},
mesh = {Africa ; Biodiversity ; DNA, Protozoan ; *Genome, Mitochondrial ; *Genomics/methods ; Haemosporida/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; South America ; },
abstract = {Haemosporida are diverse vector-borne parasites associated with terrestrial vertebrates. Driven by the interest in species causing malaria (genus Plasmodium), the diversity of avian and mammalian haemosporidian species has been extensively studied, relying mostly on mitochondrial genes, particularly cytochrome b. However, parasites from reptiles have been neglected in biodiversity surveys. Reptilian haemosporidian parasites include Haemocystidium, a genus that shares morphological features with Plasmodium and Haemoproteus. Here, the first complete Haemocystidium mitochondrial DNA (mtDNA) genomes are studied. In particular, three mtDNA genomes from Haemocystidium spp. sampled in Africa, Oceania, and South America, are described. The Haemocystidium mtDNA genomes showed a high A + T content and a gene organization, including an extreme fragmentation of the rRNAs, found in other Haemosporida. These Haemocystidium mtDNA genomes were incorporated in phylogenetic and molecular clock analyses together with a representative sample of haemosporidian parasites from birds, mammals, and reptiles. The recovered phylogeny supported Haemocystidium as a monophyletic group apart from Plasmodium and other Haemosporida. Both the phylogenetic and molecular clock analyses yielded results consistent with a scenario in which haemosporidian parasites radiated with modern birds. Haemocystidium, like mammalian parasite clades, seems to originate from host switches by avian Haemosporida that allowed for the colonization of new vertebrate hosts. This hypothesis can be tested by investigating additional parasite species from all vertebrate hosts, particularly from reptiles. The mtDNA genomes reported here provide baseline data that can be used to scale up studies in haemosporidian parasites of reptiles using barcode approaches.},
}
@article {pmid33030077,
year = {2020},
author = {Han, L and Zhang, JT and Wang, MM and Zhu, KX and Wang, XY},
title = {Mitochondrial DNA diversity and population structure of Laodelphax striatellus across a broad geographic area in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {31},
number = {8},
pages = {346-354},
doi = {10.1080/24701394.2020.1830075},
pmid = {33030077},
issn = {2470-1408},
mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Hemiptera/*classification/genetics ; Mitochondria/*genetics ; Pest Control ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) gene. Overall, 83 haplotypes were detected in 1253 mtDNA COI sequences. High levels of genetic variability (Hd = 0.756 ± 0.009, π = 0.00416 ± 0.00011) and genetic differentiation (FST = 0.262, p < .001) were observed. Bayesian inference phylogenetic and median-joining haplotype network analyses indicated no obvious geographical distribution pattern among haplotypes. Hierarchical AMOVA and SAMOVA revealed no genetically distinct groups and lack of obvious phylogeographic structure. Isolation by distance (IBD) analysis results demonstrated no correlation between genetic differentiation and geographic distance. Finally, the demographic history of SBPH examined by neutrality tests and mismatch distribution analyses illustrated a sudden population expansion at the large spatial scale in China.},
}
@article {pmid33032063,
year = {2020},
author = {Chen, C and Meng, Y and Shopan, J and Whelan, J and Hu, Z and Yang, J and Zhang, M},
title = {Identification and characterization of Arabidopsis thaliana mitochondrial F1F0-ATPase inhibitor factor 1.},
journal = {Journal of plant physiology},
volume = {254},
number = {},
pages = {153264},
doi = {10.1016/j.jplph.2020.153264},
pmid = {33032063},
issn = {1618-1328},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Green Fluorescent Proteins ; Mitochondria/enzymology/metabolism ; Phylogeny ; Proteins/genetics/*metabolism ; Proton-Translocating ATPases/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; ATPase Inhibitory Protein ; },
abstract = {Mitochondrial F1F0-ATP synthase (F1F0-ATPase) inhibitor factor 1 (IF1) has been extensively characterized as an endogenous inhibitor that prevents the hydrolysis of adenosine-5'-triphosphate (ATP) by mitochondrial ATPases in mammals and yeasts; however, IF1's functions in plants remain unclear. Here, a comprehensive bioinformatic analysis was performed to identify plant mitochondrial F1F0-ATPase IF1 orthologs. Plant IF1s contain a conserved F1F0-ATPase inhibitory domain, but lack the antiparallel α-helical coiled-coil structure compared with mammalian IF1s. A subcellular localization analysis in Arabidopsis thaliana revealed that AtIF1-green fluorescent protein was present only in mitochondria. Additionally, AtIF1 was widely expressed in diverse organs and intense β-glucuronidase staining was observed in reproductive tissues and germinating seeds. Compared with the wild-type and p35S:AtIF1-if1 etiolated seedlings, the ATP/ADP ratio was significantly lower in the AtIF1 T-DNA knockout seedlings (if1 mutant) growing under dark conditions, suggesting that AtIF1 can influence the energy state of cells. A significant reduction in seed yield and strong growth retardation under dark conditions were observed in the if1 mutant line. Furthermore, if1 plants exhibited a substantially decreased sensitivity to abscisic acid. Thus, the A. thaliana mitochondrial IF1, which is a conserved F1F0-ATPase inhibitor, is crucial for plant growth and responses to abscisic acid.},
}
@article {pmid33035389,
year = {2021},
author = {Novo, N and Ferreira, P and Medina, M},
title = {The apoptosis-inducing factor family: Moonlighting proteins in the crosstalk between mitochondria and nuclei.},
journal = {IUBMB life},
volume = {73},
number = {3},
pages = {568-581},
doi = {10.1002/iub.2390},
pmid = {33035389},
issn = {1521-6551},
mesh = {Animals ; Apoptosis ; Apoptosis Inducing Factor/*chemistry/genetics/*metabolism ; Apoptosis Regulatory Proteins/genetics/metabolism ; Cell Death ; Cell Nucleus/*metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Diseases/genetics/*metabolism/pathology ; Mitochondrial Proteins/genetics/metabolism ; Multigene Family ; Neoplasms/metabolism/pathology ; Phylogeny ; },
abstract = {In Homo sapiens, the apoptosis-inducing factor (AIF) family is represented by three different proteins, known as AIF, AMID and AIFL, that have in common the mitochondrial localisation in healthy cells, the presence of FAD- and NADH-dependent domains involved in an -albeit yet not well understood- oxidoreductase function and their capability to induce programmed cell death. AIF is the best characterised family member, while the information about AMID and AIFL is much scarcer. Nonetheless, available data support different roles as well as mechanisms of action of their particular apoptogenic and redox domains regarding both pro-apoptotic and anti-apoptotic activities. Moreover, diverse cellular functions, to date far from fully clarified, are envisaged for the transcripts corresponding to these three proteins. Here, we review the so far available knowledge on the moonlighting human AIF family from their molecular properties to their relevance in health and disease, through the evaluation of their potential cell death and redox functions in their different subcellular locations. This picture emerging from the current knowledge of the AIF family envisages its contribution to regulate signalling and transcription machineries in the crosstalk among mitochondria, the cytoplasm and the nucleus.},
}
@article {pmid33056243,
year = {2020},
author = {GÓmez-Zurita, J and Platania, L and Cardoso, A},
title = {A new species of the genus Tricholapita nom. nov. and stat. nov. (Coleoptera: Chrysomelidae, Eumolpinae) from New Caledonia.},
journal = {Zootaxa},
volume = {4858},
number = {1},
pages = {zootaxa.4858.1.5},
doi = {10.11646/zootaxa.4858.1.5},
pmid = {33056243},
issn = {1175-5334},
mesh = {Animals ; *Coleoptera ; Mitochondria ; New Caledonia ; Phylogeny ; },
abstract = {Tricholapita Gómez-Zurita and Cardoso nom. nov. is proposed as the replacement name for the leaf beetle taxon Lapita Gómez-Zurita and Cardoso, 2014, nec Bickel, 2002. Moreover, the rank of Tricholapita stat. nov. is elevated from subgenus of Taophila Heller, 1916 to generic status. Phylogenetic evidence based on mtDNA rrnS sequences and diagnostic morphological characters reveals a new species from the south of Grande Terre in New Caledonia, which is described: Tricholapita reidi sp. nov.},
}
@article {pmid33056981,
year = {2020},
author = {Brady, SW and Liu, Y and Ma, X and Gout, AM and Hagiwara, K and Zhou, X and Wang, J and Macias, M and Chen, X and Easton, J and Mulder, HL and Rusch, M and Wang, L and Nakitandwe, J and Lei, S and Davis, EM and Naranjo, A and Cheng, C and Maris, JM and Downing, JR and Cheung, NV and Hogarty, MD and Dyer, MA and Zhang, J},
title = {Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations.},
journal = {Nature communications},
volume = {11},
number = {1},
pages = {5183},
pmid = {33056981},
issn = {2041-1723},
support = {R01 CA216391/CA/NCI NIH HHS/United States ; R35 CA220500/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P30 CA021765/CA/NCI NIH HHS/United States ; U10 CA180899/CA/NCI NIH HHS/United States ; U10 CA180886/CA/NCI NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Age Factors ; Anaplastic Lymphoma Kinase/genetics ; Biomarkers, Tumor/*genetics ; Child ; Child, Preschool ; Cohort Studies ; DNA Copy Number Variations ; DNA Mutational Analysis ; Datasets as Topic ; Electron Transport/genetics ; Exome/genetics ; Female ; *Gene Expression Regulation, Neoplastic ; Humans ; Infant ; Infant, Newborn ; Male ; Mitochondrial Ribosomes ; Mutation ; Neuroblastoma/*genetics/pathology ; Receptor, Fibroblast Growth Factor, Type 1/genetics ; Ribosomal Proteins/genetics ; Transcriptome/genetics ; Whole Genome Sequencing ; Young Adult ; },
abstract = {Neuroblastoma is a pediatric malignancy with heterogeneous clinical outcomes. To better understand neuroblastoma pathogenesis, here we analyze whole-genome, whole-exome and/or transcriptome data from 702 neuroblastoma samples. Forty percent of samples harbor at least one recurrent driver gene alteration and most aberrations, including MYCN, ATRX, and TERT alterations, differ in frequency by age. MYCN alterations occur at median 2.3 years of age, TERT at 3.8 years, and ATRX at 5.6 years. COSMIC mutational signature 18, previously associated with reactive oxygen species, is the most common cause of driver point mutations in neuroblastoma, including most ALK and Ras-activating variants. Signature 18 appears early and is continuous throughout disease evolution. Signature 18 is enriched in neuroblastomas with MYCN amplification, 17q gain, and increased expression of mitochondrial ribosome and electron transport-associated genes. Recurrent FGFR1 variants in six patients, and ALK N-terminal structural alterations in five samples, identify additional patients potentially amenable to precision therapy.},
}
@article {pmid33059067,
year = {2021},
author = {Bocalini, F and Bolívar-Leguizamón, SD and Silveira, LF and Bravo, GA},
title = {Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest.},
journal = {Molecular phylogenetics and evolution},
volume = {154},
number = {},
pages = {106973},
doi = {10.1016/j.ympev.2020.106973},
pmid = {33059067},
issn = {1095-9513},
mesh = {Animals ; Brazil ; Demography ; *Forests ; Gene Flow ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Passeriformes/*classification/genetics ; Phylogeny ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.},
}
@article {pmid33086570,
year = {2020},
author = {Piłsyk, S and Mieczkowski, A and Golan, MP and Wawrzyniak, A and Kruszewska, JS},
title = {Internalization of the Aspergillus nidulans AstA Transporter into Mitochondria Depends on Growth Conditions, and Affects ATP Levels and Sulfite Oxidase Activity.},
journal = {International journal of molecular sciences},
volume = {21},
number = {20},
pages = {},
pmid = {33086570},
issn = {1422-0067},
mesh = {Adenosine Triphosphate/*metabolism ; Aspergillus nidulans/*growth &amp; development/*metabolism ; Endocytosis ; Endophytes/metabolism ; Fungal Proteins/*metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/*metabolism ; Models, Biological ; Oxidation-Reduction ; Phenotype ; Phylogeny ; Sulfite Oxidase/*metabolism ; Sulfur/metabolism ; },
abstract = {The astA gene encoding an alternative sulfate transporter was originally cloned from the genome of the Japanese Aspergillus nidulans isolate as a suppressor of sulfate permease-deficient strains. Expression of the astA gene is under the control of the sulfur metabolite repression system. The encoded protein transports sulfate across the cell membrane. In this study we show that AstA, having orthologs in numerous pathogenic or endophytic fungi, has a second function and, depending on growth conditions, can be translocated into mitochondria. This effect is especially pronounced when an astA-overexpressing strain grows on solid medium at 37 °C. AstA is also recruited to the mitochondria in the presence of mitochondria-affecting compounds such as menadione or antimycin A, which are also detrimental to the growth of the astA-overexpressing strain. Disruption of the Hsp70-Porin1 mitochondrial import system either by methylene blue, an Hsp70 inhibitor, or by deletion of the porin1-encoding gene abolishes AstA translocation into the mitochondria. Furthermore, we observed altered ATP levels and sulfite oxidase activity in the astA-overexpressing strain in a manner dependent on sulfur sources. The presented data indicate that AstA is also involved in the mitochondrial sulfur metabolism in some fungi, and thereby indirectly manages redox potential and energy state.},
}
@article {pmid33108945,
year = {2022},
author = {Fadhil, IA and Al-Shuhaib, MBS},
title = {Phylogenetic differentiation between Awassi and Hamdani sheep using the mitochondrial 12S rRNA.},
journal = {Animal biotechnology},
volume = {33},
number = {5},
pages = {801-809},
doi = {10.1080/10495398.2020.1837146},
pmid = {33108945},
issn = {1532-2378},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation/genetics ; Haplotypes/genetics ; Phylogeny ; *RNA, Ribosomal/genetics ; Sheep/genetics ; },
abstract = {This study was conducted to assess the role of the mitochondrial 12S rRNA variations in the phylogenetic discrimination between two Iraqi breeds of sheep that differ in geographical distribution. A total of 122 animals (68 Awassi and 54 Hamdani) were included in the study. Direct sequencing of amplicons followed by the construction of a median-joining network and several trees were performed to identify the possible phylogenetic differences between both involved breeds. Genetic diversity, relative frequencies, and analysis of molecular variance (AMOVA) were performed to assess the genetic correlation between both populations. The median-joining network and minimized tree values showed that all observed haplotypes were separated into two groups according to their breed. Comprehensive phylogenetic data revealed only one Asian ancestor for all observed haplotypes. As indicated by AMOVA, the observed diversity was mostly due to between-population variation (1.24836%), while within-population variation (0.91221%) accounted for much less. The currently investigated rRNA amplicons exhibited different mitochondrial manifestations between Awassi and Hamdani breeds. Due to the ability of these 12S rRNA amplicons to mimic the geographical diversity for the currently investigated breeds, it is highly recommended to be used as potent mitochondrial genetic markers among broader ovine sequences.},
}
@article {pmid33127981,
year = {2020},
author = {Zhang, N and Jiang, H and Meng, X and Qian, K and Liu, Y and Song, Q and Stanley, D and Wu, J and Park, Y and Wang, J},
title = {Broad-complex transcription factor mediates opposing hormonal regulation of two phylogenetically distant arginine kinase genes in Tribolium castaneum.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {631},
pmid = {33127981},
issn = {2399-3642},
mesh = {Animals ; Arginine Kinase/*genetics/metabolism ; Cloning, Molecular ; Ecdysterone/metabolism ; Female ; Fertility/genetics ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Insect Proteins/*genetics/metabolism ; Juvenile Hormones/metabolism ; Male ; Metamorphosis, Biological/genetics ; Phylogeny ; Pupa/genetics ; Stress, Physiological ; Transcription Factors/*genetics/metabolism ; Tribolium/*genetics/*metabolism ; },
abstract = {The phosphoarginine-arginine kinase shuttle system plays a critical role in maintaining insect cellular energy homeostasis. Insect molting and metamorphosis are coordinated by fluctuations of the ecdysteroid and juvenile hormone. However, the hormonal regulation of insect arginine kinases remain largely elusive. In this report, we comparatively characterized two arginine kinase genes, TcAK1 and TcAK2, in Tribolium castaneum. Functional analysis using RNAi showed that TcAK1 and TcAK2 play similar roles in adult fertility and stress response. TcAK1 was detected in cytoplasm including mitochondria, whereas TcAK2 was detected in cytoplasm excluding mitochondria. Interestingly, TcAK1 expression was negatively regulated by 20-hydroxyecdysone and positively by juvenile hormone, whereas TcAK2 was regulated by the opposite pattern. RNAi, dual-luciferase reporter assays and electrophoretic mobility shift assay further revealed that the opposite hormonal regulation of TcAK1 and TcAK2 was mediated by transcription factor Broad-Complex. Finally, relatively stable AK activities were observed during larval-pupal metamorphosis, which was generally consistent with the constant ATP levels. These results provide new insights into the mechanisms underlying the ATP homeostasis in insects by revealing opposite hormonal regulation of two phylogenetically distant arginine kinase genes.},
}
@article {pmid33130297,
year = {2021},
author = {Raphalo, EM and Cole, ML and Daniels, SR},
title = {Climatic oscillations during the Mio/Pliocene epochs induced cladogenesis in the terrestrial snail genus Gittenedouardia (Mollusca: Gastropoda: Cerastidae) from South Africa.},
journal = {Molecular phylogenetics and evolution},
volume = {155},
number = {},
pages = {107000},
doi = {10.1016/j.ympev.2020.107000},
pmid = {33130297},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; *Climate ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genetics, Population ; Geography ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*classification/genetics ; South Africa ; Time Factors ; },
abstract = {In South Africa, the terrestrial snail genus Gittenedouardia is the most species-rich member of the Cerastidae, where it is primarily distributed in the highly fragmented Afrotemperate and Indian Ocean coastal belt (IOCB) forest biomes. Phylogenetic relationships and cladogenetic events within the genus remain unstudied. In this respect, we reconstructed a dated phylogeny for eight Gittenedouardia species, and two populations identified to genus level using a combined mitochondrial (16S rRNA and COI) DNA sequencing dataset analysed using Bayesian inference and Maximum Likelihood framework. Furthermore, we investigated the population genetic substructure of the three widely distributed species (Gittenedouardia spadicea, G. natalensis and G. arenicola) for the COI locus, while also subsampling these species using the nuclear DNA ITS-2 locus. Phylogenetic results based on the combined mtDNA dataset supported the monophyly of Gittenedouardia and revealed three major clades and deep genetic structure among the three widely distributed species. Divergence-time estimates suggest that diversification within Gittenedouardia occurred during the middle Miocene/late Pliocene, a period characterised by a decrease in precipitation and the contraction of the Afrotemperate and IOCB forest biomes. We used two species delimitation methods, (PTP and STACEY) to infer putative species in G. spadicea, G. natalensis and G. arenicola. The two methods recovered a large number of evolutionary distinct units, with minimal consensus in the exact number of lineages. Our findings suggest the presence of undescribed diversity, necessitating the need for taxonomic revisionary work on Gittenedouardia. We discuss the climatic factors which may have contributed to the observed cladogenesis and compare our results with other studies of forest dwelling faunal taxa.},
}
@article {pmid33135056,
year = {2020},
author = {Ji, J and Day, A},
title = {Construction of a highly error-prone DNA polymerase for developing organelle mutation systems.},
journal = {Nucleic acids research},
volume = {48},
number = {21},
pages = {11868-11879},
pmid = {33135056},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/*genetics/metabolism ; Binding Sites ; Chloroplasts/*genetics/*metabolism ; Cloning, Molecular ; DNA Polymerase gamma/chemistry/*genetics/metabolism ; DNA Replication ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Mitochondria/*genetics/metabolism ; Models, Molecular ; Mutation ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Polymorphism, Single Nucleotide ; Porins/chemistry/*genetics/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Receptors, Virus/chemistry/*genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Selection, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Nicotiana/classification/*genetics/metabolism ; },
abstract = {A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation of 3'-5' exonuclease function resulted in a modest 5-8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.},
}
@article {pmid33164622,
year = {2021},
author = {Iketani, G and Pimentel, L and Torres, EDS and Rêgo, PSD and Sampaio, I},
title = {Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {1},
pages = {1-11},
doi = {10.1080/24701394.2020.1844677},
pmid = {33164622},
issn = {2470-1408},
mesh = {Animals ; Arthropod Proteins/genetics ; Brazil ; Cell Nucleus/*genetics ; Cloning, Molecular ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetics, Population ; Heteroplasmy ; Mitochondria/*genetics ; Palaemonidae/*classification/genetics ; Paraguay ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.},
}
@article {pmid33179562,
year = {2021},
author = {Khan, S and Nisar, A and Ahmad, H and Mehmood, SA and Hameed, M and Zhao, X and Yang, X and Feng, X},
title = {Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {32},
number = {1},
pages = {34-42},
doi = {10.1080/24701394.2020.1845323},
pmid = {33179562},
issn = {2470-1408},
mesh = {Animals ; Chickens/*classification/genetics ; DNA, Mitochondrial/*genetics ; Feathers/chemistry ; Gene Pool ; Genetic Markers/*genetics ; Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Pakistan ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA/*methods ; },
abstract = {Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10[-6] mutations/site/year (95% HPD interval: 2.28 × 10[-8] to 9.32 × 10[-6]) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.},
}
@article {pmid33222011,
year = {2021},
author = {Liu, H and Liu, M and Zhu, H and Zhong, J and Liao, X and Zhou, Q},
title = {Molecular characterization of a novel mitovirus from the plant‑pathogenic fungus Botryosphaeria dothidea.},
journal = {Archives of virology},
volume = {166},
number = {2},
pages = {633-637},
pmid = {33222011},
issn = {1432-8798},
support = {2018JJ3220//Hunan Provincial Natural Science Fund/ ; CX20190522//Hunan Provincial Innovation Foundation for Postgraduate/ ; },
mesh = {Amino Acids/genetics ; Ascomycota/*virology ; Genome, Viral/*genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; Plants/*microbiology ; RNA Viruses/*genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase ; Viral Proteins/genetics ; },
abstract = {Here, a novel mycovirus, Botryosphaeria dothidea mitovirus 1 (BdMV1), was isolated from a phytopathogenic fungus, Botryosphaeria dothidea, and its molecular characteristics were determined. BdMV1 has a genome of 2,667 nt that contains a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 727 amino acids with a molecular mass of 81.64 kDa. BLASTp analysis revealed that the RdRp domain of BdMV1 has 39.59% and 39.18% sequence identity to Plasmopara viticola associated mitovirus 43 and Setosphaeria turcica mitovirus 1, respectively. Phylogenetic analysis further suggested that BdMV1 is a new member of the genus Mitovirus within the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in B. dothidea.},
}
@article {pmid33231829,
year = {2021},
author = {Mirahmadi, H and Behravan, M and Raz, A and Tasa, D and Namaei, MH and Solgi, R},
title = {Genotyping of the Echinococcus granulosus in Paraffin-Embedded Human Tissue Samples from Iran.},
journal = {Acta parasitologica},
volume = {66},
number = {2},
pages = {535-542},
pmid = {33231829},
issn = {1896-1851},
support = {5303//Birjand University of Medical Sciences/ ; },
mesh = {Animals ; *Echinococcus granulosus/genetics ; Genotype ; Humans ; Iran/epidemiology ; Paraffin Embedding ; Phylogeny ; Sheep ; },
abstract = {PURPOSE: Cystic Echinococcosis (CE) is a medically important disease that is caused by the metacestodes of Echinococcus granulosus. Human hydatid is considered an endemic disease in specific regions of Iran. The goal of the present study was to determine the genetic diversity of E. granulosus from the paraffin-embedded human tissue samples which were collected from the endemic regions of Iran.<br><br>METHODS: Fifty-five formalin-fixed and paraffin-embedded hydatid cysts (FFPE) of humans, which had been removed surgically, were obtained from the South Khorasan and Sistan and Baluchistan provinces. These regions are related to the East and Southeast regions of Iran, respectively. The cox1 and nad1 genes from mitochondria were amplified from the extracted DNA and sequenced. The sequences were edited using the BioEdit software. Furthermore, phylogenetic and genetic diversity analyses were performed.<br><br>RESULTS: Sequencing of the cox1 and nad1 genes from the 44 CE samples was done successfully. Genetic analysis revealed that 38 (86.3%) and 6 (13.6%) of the isolates were G1- and G6-genotypes, respectively. In general, eight and six haplotypes were identified by cox1 and nad1 genes analysis, respectively. For G1 strains, the haplotype diversity index was higher for the cox1 gene (0.6&#x2009;&#xb1;&#x2009;0.07) in comparison with the nad1 gene (0.4&#x2009;&#xb1;&#x2009;0.09).<br><br>CONCLUSION: The findings of the present study showed that the sheep strain (G1) and the less important camel strain (G6) play the main roles in the transmission cycle of CE in the East and Southeast regions of Iran. Therefore, these results could be useful for managing the hydatid disease control programs in the studied and other similar areas.},
}
@article {pmid33245800,
year = {2021},
author = {Wang, W and Hou, S and Chen, G and Xia, L and Chen, J and Wang, Z and Lu, Y},
title = {Characterization and function study of a glutamyl endopeptidase homolog from Nocardia seriolae.},
journal = {Journal of fish diseases},
volume = {44},
number = {6},
pages = {813-821},
doi = {10.1111/jfd.13311},
pmid = {33245800},
issn = {1365-2761},
support = {KJYF202001-08//Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District/ ; JCYJ20180306173022502//Shenzhen Science and Technology Project/ ; JCYJ20180507183240459//Shenzhen Science and Technology Project/ ; 231419017//Research Projects of Guangdong Ocean University's Top-ranking Discipline Construction/ ; },
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Fish Diseases/microbiology ; Nocardia/*genetics/metabolism ; Nocardia Infections/microbiology/veterinary ; Phylogeny ; Sequence Alignment ; Serine Endopeptidases/chemistry/*genetics/metabolism ; },
abstract = {Glutamic endopeptidases (Glu), belonging to the class of serine proteases, are a subfamily of chymotrypsin-like proteolytic enzymes, which are regarded as important virulence factors in bacteria. However, the roles of glutamic endopeptidases of Nocardia seriolae in pathogenic process still remain uncertain. Here, a glutamic endopeptidase homolog from N. seriolae (GluNS) was cloned and its function was elucidated. GluNS encoded a 414-aa protein which shared 93% identity to N. concava. In the phylogenetic tree, the glutamic endopeptidases of genus Nocardia clustered together firstly and then clustered with Streptomyces species. Moreover, GluNS was identified to be a secreted protein of N. seriolae and localized in the mitochondria of FHM cells. The transient overexpression of GluNS significantly induced increase in caspase-3 activity and decrease in ΔΨm values in FHM cells. The number of apoptotic bodies was remarkably higher than that in control group. Taken together, GluNS overexpression induced apoptotic characteristics in FHM cells. This study provided new insights into the function of glutamic endopeptidase from N. seriolae.},
}
@article {pmid33247794,
year = {2021},
author = {Bagherfard, S and Najafi, N and Gharzi, A and Akmali, V},
title = {Lack of intraspecific variations of the mitochondrial cytochrome b gene in the greater mouse-tailed bat Rhinopoma microphyllum (Chiroptera: Rhinopomatidae) in Iran.},
journal = {Genetica},
volume = {149},
number = {1},
pages = {37-45},
pmid = {33247794},
issn = {1573-6857},
mesh = {Animals ; Chiroptera/classification/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeography ; Species Specificity ; },
abstract = {Rhinopoma microphyllum is one of the species of bats that lives in arid and semi-arid areas of Iran. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni based on their morphological characteristics has been questioned on the basis of small differences between the populations. Later, other researchers assigned Iranian populations of this species to one or two subspecies based on their morphological and molecular characteristics. The present study provides a phylogeographical analysis of this species using 687 bp of the mitochondrial cytochrome b in 81 bats in Iran, Jordan, Levant and Ethiopia. Based on mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. microphyllum (π = 0.0025), which shows a close relationship between the haplotypes. The analysis of genetic distance (0.15-1.93%), phylogenetic trees, and statistical parsimony network showed that all Iranian samples were grouped in the same clade, while Levant, Jordan and Ethiopian samples belonged to a different clade. Molecular dating suggested the Iranian R. microphyllum lineage split from the R. microphyllum of the Levant and Jordan clade during the Pliocene 3.18 (2.11-4.32 Ma). Taking these results into consideration, we can conclude that all Iranian specimens belong to the same subspecies as R. m. harrisoni since molecular results indicate that Iranian samples are differ from Levant subspecies (R. m. microphyllum).},
}
@article {pmid33248045,
year = {2021},
author = {Song, L and Gao, C and Xue, T and Yang, N and Fu, Q and Zhu, Q and Ge, X and Li, C},
title = {Characterization and expression analysis of mitochondrial localization molecule: NOD-like receptor X1 (Nlrx1) in mucosal tissues of turbot (Scophthalmus maximus) following bacterial challenge.},
journal = {Developmental and comparative immunology},
volume = {116},
number = {},
pages = {103944},
doi = {10.1016/j.dci.2020.103944},
pmid = {33248045},
issn = {1879-0089},
mesh = {Amino Acid Sequence ; Animals ; Cytoplasm/metabolism ; Fish Diseases/immunology/microbiology ; Fish Proteins/genetics/metabolism ; Flatfishes/*immunology/microbiology ; Gene Expression Profiling ; HEK293 Cells ; Humans ; Mitochondrial Proteins/genetics/*immunology/metabolism ; Mucous Membrane/*immunology/microbiology ; Phylogeny ; Protein Interaction Maps ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Streptococcus iniae/physiology ; Vibrio/physiology ; },
abstract = {The NOD-like receptor X1 (NLRX1) is a member of highly conserved nucleotide-binding domain (NBD)- and leucine-rich-repeat (LRR)-containing family (known as NLR), that localizes to the mitochondrial outer membrane and regulate the innate immunity by interacting with mitochondrial antiviral-signaling protein (MAVS). As one of cytoplasmic PRRs, NLRX1 plays key roles for pathogen recognition, autophagy and regulating of subsequent immune signaling pathways. In this study, we identified the nlrx1 in turbot as well as its expression profiles in mucosal surfaces following bacterial infection. In our results, the full-length nlrx1 transcript consists of an open reading frame (ORF) of 4,886 bp encoding the putative peptide of 966 amino acids. The phylogenetic analysis revealed the SmNlrx1 showed the closest relationship to Cynoglossus semilaevis. In addition, the Nlrx1 mRNA expression could be detected in all the examined tissues, with the most abundant expression level in head kidney, and the lowest expression level in liver. Moreover, Nlrx1 showed similar expression patterns following Vibrio anguillarum and Streptococcus iniae infection, that were both significantly up-regulated following challenge, especially post S. iniae challenge. Finally, fluorescence microscopy unveiled that the SmNlrx1 localized to mitochondria in HEK293T by N-terminal mitochondrial targeting sequence. Characterization of Nlrx1 might have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity and will probably contribute to the development of novel intervention strategies for farming turbot.},
}
@article {pmid33255957,
year = {2020},
author = {King, MS and Tavoulari, S and Mavridou, V and King, AC and Mifsud, J and Kunji, ERS},
title = {A Single Cysteine Residue in the Translocation Pathway of the Mitosomal ADP/ATP Carrier from Cryptosporidium parvum Confers a Broad Nucleotide Specificity.},
journal = {International journal of molecular sciences},
volume = {21},
number = {23},
pages = {},
pmid = {33255957},
issn = {1422-0067},
support = {MC_UU_00015/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/7/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Atractyloside/analogs &amp; derivatives/chemistry ; Bongkrekic Acid/chemistry ; Cryptosporidium parvum/*metabolism ; Cysteine/*metabolism ; Lactococcus lactis/metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/*chemistry/*metabolism ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Nucleotides/*metabolism ; Phylogeny ; Protein Translocation Systems/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; },
abstract = {Cryptosporidiumparvum is a clinically important eukaryotic parasite that causes the disease cryptosporidiosis, which manifests with gastroenteritis-like symptoms. The protist has mitosomes, which are organelles of mitochondrial origin that have only been partially characterized. The genome encodes a highly reduced set of transport proteins of the SLC25 mitochondrial carrier family of unknown function. Here, we have studied the transport properties of one member of the C. parvum carrier family, demonstrating that it resembles the mitochondrial ADP/ATP carrier of eukaryotes. However, this carrier has a broader substrate specificity for nucleotides, transporting adenosine, thymidine, and uridine di- and triphosphates in contrast to its mitochondrial orthologues, which have a strict substrate specificity for ADP and ATP. Inspection of the putative translocation pathway highlights a cysteine residue, which is a serine in mitochondrial ADP/ATP carriers. When the serine residue is replaced by cysteine or larger hydrophobic residues in the yeast mitochondrial ADP/ATP carrier, the substrate specificity becomes broad, showing that this residue is important for nucleotide base selectivity in ADP/ATP carriers.},
}
@article {pmid33270708,
year = {2020},
author = {Dell, AC and Curry, MC and Yarnell, KM and Starbuck, GR and Wilson, PB},
title = {Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0243247},
pmid = {33270708},
issn = {1932-6203},
mesh = {Animals ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Variation/genetics ; Haplotypes/genetics ; Horses/*genetics ; Maternal Inheritance/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods/veterinary ; },
abstract = {Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes (Fig 2) shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only five domestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.},
}
@article {pmid33278586,
year = {2021},
author = {Lee, Y and Ni, G and Shin, J and Kim, T and Kern, EMA and Kim, Y and Kim, SC and Chan, B and Goto, R and Nakano, T and Park, JK},
title = {Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance.},
journal = {Molecular phylogenetics and evolution},
volume = {157},
number = {},
pages = {107037},
doi = {10.1016/j.ympev.2020.107037},
pmid = {33278586},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/*genetics ; Mytilidae/*genetics ; Pacific Ocean ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; Time Factors ; },
abstract = {The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.},
}
@article {pmid33297963,
year = {2020},
author = {Ren, RC and Yan, XW and Zhao, YJ and Wei, YM and Lu, X and Zang, J and Wu, JW and Zheng, GM and Ding, XH and Zhang, XS and Zhao, XY},
title = {The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize.},
journal = {BMC plant biology},
volume = {20},
number = {1},
pages = {553},
pmid = {33297963},
issn = {1471-2229},
support = {91735301//National Natural Science Foundation of China/ ; 2016ZX08003-003//The National Plant Transgenic Program/ ; ts201712024//Taishan Scholar Project of Shandong Province/ ; SYL2017YSTD03//Shandong "Double Tops" Program/ ; dxkt201707//the project from State Key Laboratory of Crop Biology/ ; },
mesh = {Base Sequence ; Binding Sites/genetics ; Electron Transport Complex I/*genetics/metabolism ; Gene Expression Regulation, Plant ; Introns/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/classification/genetics/metabolism ; Mutation ; NADH Dehydrogenase/*genetics/metabolism ; Phylogeny ; Plant Proteins/classification/*genetics/metabolism ; Plants, Genetically Modified ; *RNA Editing ; *RNA Splicing ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/metabolism ; Zea mays/*genetics/metabolism ; },
abstract = {BACKGROUND: Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown.<br><br>RESULTS: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at +&#x2009;449&#x2009;bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291).<br><br>CONCLUSIONS: Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.},
}
@article {pmid33301090,
year = {2021},
author = {Duminil, J and Besnard, G},
title = {Utility of the Mitochondrial Genome in Plant Taxonomic Studies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2222},
number = {},
pages = {107-118},
pmid = {33301090},
issn = {1940-6029},
mesh = {*DNA Barcoding, Taxonomic ; *Genome, Mitochondrial ; *Genomics/methods ; Phylogeny ; Phylogeography ; Plants/*classification/*genetics ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; },
abstract = {Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.},
}
@article {pmid33301927,
year = {2021},
author = {Jaimes Díaz, H and Martínez Covarrubias, EI and Murcia Garzón, JE and Flores Valdez, M and Muñoz Ramírez, ZY and Ramírez Calzada, CA and Bohra, R and Méndez Tenorio, A},
title = {Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints.},
journal = {Mitochondrion},
volume = {57},
number = {},
pages = {294-299},
doi = {10.1016/j.mito.2020.11.016},
pmid = {33301927},
issn = {1872-8278},
mesh = {Animals ; Computer Simulation ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/classification/*genetics ; Genomics/*methods ; Haplotypes ; Humans ; Mitochondria/*classification/genetics ; Neanderthals/genetics ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Phylogeny ; },
abstract = {In the present study, we evaluated the ability of the Virtual Analysis Method for Phylogenomic fingerprint Estimation (VAMPhyRE) toolkit to classify human mitochondrial DNA (mtDNA) haplogroups. In total, 357 random mtDNA sequences were obtained from different haplogroups, based on the classification of PhyloTree. Additionally, we included a control group of five sequences (Pan paniscus, Pan troglodytes, Homo sapiens neanderthalensis, Yoruba15, and the revised Cambridge reference sequence). VAMPhyRE employs a virtual hybridization technique, using probes that specifically bind to their complementary sequences in the genome. We used 65,536 probes of 8 nucleotides to identify potential sites where hybridization occurs between the mtDNA and the specific probe, forming different heteroduplexes and thus, creating a unique and specific genomic fingerprint for each sequence. Genomic fingerprints were compared, and a table of distances was calculated to obtain a mitochondrial phylogenomic tree with the macrohaplogroups, L, N, M, and R, and their corresponding haplogroups, according to universal nomenclature. The results obtained suggest an accuracy of 97.25% for the distribution of the 357 mtDNA sequences in the four macrohaplogroups and their corresponding haplogroups when compared with other mtDNA classification tools that require reference sequences and do not offer an analysis based on an evolutionary approach. These data are available online at http://biomedbiotec.encb.ipn.mx/VAMPhyRE/.},
}
@article {pmid33310361,
year = {2021},
author = {Bi, YH and Du, AY and Li, JL and Zhou, ZG},
title = {Isolation and characterization of a γ-carbonic anhydrase localized in the mitochondria of Saccharina japonica.},
journal = {Chemosphere},
volume = {266},
number = {},
pages = {129162},
doi = {10.1016/j.chemosphere.2020.129162},
pmid = {33310361},
issn = {1879-1298},
mesh = {Carbon Dioxide ; *Carbonic Anhydrases/genetics ; Escherichia coli ; Mitochondria ; Phylogeny ; },
abstract = {Saccharina japonica is an ecologically and economically important seaweed that is dominant in the rocky shores of cold-temperate regions, forms the major component of productive beds, and affects marine environments. S. japonica exhibits a high photosynthetic efficiency in natural seawater with low dissolved CO2 concentration, thus suggesting the presence of its carbon-concentrating mechanism (CCM). However, the genes, proteins, and pathways involved in the CCM of S. japonica have not been fully identified and characterized. Carbonic anhydrase (CA) is a crucial component of CCM in macroalgae. In this study, the cloning, characterization, and subcellular localization of a specific CA were described. Multisequence alignment and phylogenetic analysis indicated that this CA belonged to the gamma (Sjγ-CA) class. This enzyme has a full-length cDAN of 1370 bp, encodes a protein with 246 amino acids (aa; ca. 25.7 kDa), and contains the mitochondrial transit peptide of 16 aa and LbH_gama_CA_like domain of 159 aa that defined the γ-CA region. The Sjγ-CA was successfully expressed in E. coli BL21 and purified as an active recombinant CA. Immunogold electron microscopy and fluorescence localization illustrated that this enzyme is localized in the mitochondria, and its transcription level is up-regulated by low CO2 concentration. These findings showed that Sjγ-CA is a possible component of the CCM in S. japonica. This work is the first to report about the mtCA of macroalgae and provides a basis for further analysis on seaweed CCM.},
}
@article {pmid33311144,
year = {2020},
author = {Vasconcelos, R and KÖhler, G and Geniez, P and Crochet, PA},
title = {A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde.},
journal = {Zootaxa},
volume = {4878},
number = {3},
pages = {zootaxa.4878.3.4},
doi = {10.11646/zootaxa.4878.3.4},
pmid = {33311144},
issn = {1175-5334},
mesh = {Animals ; Cabo Verde ; Islands ; *Lizards ; Mitochondria ; Phylogeny ; },
abstract = {A new species of gecko of the genus Hemidactylus (Squamata: Gekkonidae) is described from São Nicolau Island, Cabo Verde Archipelago, and the Sal and Boavista island populations of Hemidactylus boavistensis (i.e., Hemidactylus boavistensis boavistensis comb. nov. and Hemidactylus boavistensis chevalieri comb. nov.) are recognized as subspecies. Hemidactylus nicolauensis sp. nov. is genetically distinct from H. bouvieri, to which it has previously been referred, and from all other closely related endemic Hemidactylus from Cabo Verde Islands in mitochondrial (12S cyt b) and nuclear (RAG2, MC1R) markers. It is characterized morphologically by its distinct colouration and a diagnostically different arrangement of digital lamellae. With the description of this new species, São Nicolau is now known to harbour three single-island endemic gecko species, and the documented reptile diversity in Cabo Verde is raised to 23 endemic species. As a result of our taxonomic changes, existing conservation regulations should be updated and the conservation status of these taxa should be re-evaluated.},
}
@article {pmid33314286,
year = {2021},
author = {Mutti, LD and Ivanov, VA},
title = {Ultrastructure of the rhyncheal apparatus and other structures of the scolex of Grillotia (Christianella) carvajalregorum (Cestoda: Trypanorhyncha).},
journal = {Journal of morphology},
volume = {282},
number = {2},
pages = {309-324},
doi = {10.1002/jmor.21305},
pmid = {33314286},
issn = {1097-4687},
mesh = {Animals ; Cestoda/*anatomy &amp; histology/cytology/*ultrastructure ; Histocytochemistry ; Phylogeny ; Sensory Receptor Cells/cytology/ultrastructure ; },
abstract = {The scolex ultrastructure was studied in Grillotia (Christianella) carvajalregorum (Cestoda: Trypanorhyncha) using histochemistry and transmission electron microscopy. We show for the first time the presence of scolex glands arranged in two longitudinal acini at the pars vaginalis parenchyma. These glands, along with those scattered in bothrial parenchyma, produce potentially adhesive glycoprotein secretions that are discharged via ducts to the bothrial grooves and apex. A particular type of sensory receptor was found around frontal gland pores, with a possible function in regulating their secretion activity. The internal structure of microtriches varies according to their morphotype and distribution on the scolex, this study providing the first description of the ultrastructure of serrate lanceolate spinitriches. The projections that form serrate margins are an extension of the medulla, differing from similar projections of other spinitriches. The large caps observed in serrate lanceolate spinitriches may reflect their specialization in attachment to and abrasion of intestinal mucosa, while the short caps and large bases of acicular filitriches may reflect their involvement in nutrient absorption. We also describe the rhyncheal apparatus ultrastructure, showing a similar basic structure of tentacular walls than that of other trypanorhynchs. Some differences among species in the number of fibrous layers, composition of the apical cytoplasm and presence of microvilli-like projections were discussed. Finally, our study describes in detail the internal ultrastructure of hollow hooks, evidencing the presence of cytoplasm, mitochondria and fibrils. The location of these fibrils may increase the area of contact surface of hooks on tentacles, possibly allowing for a higher tensile strength than that of solid hooks. We consider that gland location and shape, composition of tentacular wall layers, and hook internal structure may serve as useful characters for the taxonomy and phylogeny of Trypanorhyncha. RESEARCH HIGHLIGHTS: This is the first description of scolex internal ultrastructure in Grillotia carvajalregorum, showing the presence of glands arranged in two longitudinal acini at the pars vaginalis parenchyma, with potentially adhesive functions. The internal ultrastructure of serrate lanceolate spinitriches and acicular filitriches may reflect their specialization in attachment to the host intestinal mucosa and their involvement in nutrient absorption, respectively. Internally, hollow hooks have cytoplasm with mitochondria and fibrils, which are more widely distributed than in solid hooks, possibly increasing their tensile strength.},
}
@article {pmid33338660,
year = {2021},
author = {Cairns, NA and Cicchino, AS and Stewart, KA and Austin, JD and Lougheed, SC},
title = {Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {156},
number = {},
pages = {107042},
doi = {10.1016/j.ympev.2020.107042},
pmid = {33338660},
issn = {1095-9513},
mesh = {Animals ; Anura/*genetics ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; *Genetic Variation ; Geography ; Linear Models ; Male ; Mitochondria/genetics ; North America ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; },
abstract = {Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.},
}
@article {pmid33359125,
year = {2021},
author = {Liu, H and Ju, Y and Tamate, H and Wang, T and Xing, X},
title = {Phylogeography of sika deer (Cervus nippon) inferred from mitochondrial cytochrome-b gene and microsatellite DNA.},
journal = {Gene},
volume = {772},
number = {},
pages = {145375},
doi = {10.1016/j.gene.2020.145375},
pmid = {33359125},
issn = {1879-0038},
mesh = {Animals ; Cell Nucleus/genetics ; China ; Cytochromes b/*genetics ; Deer/*classification/genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Japan ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; },
abstract = {The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.},
}
@article {pmid33422563,
year = {2021},
author = {Pabis, K},
title = {Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan.},
journal = {Mechanisms of ageing and development},
volume = {194},
number = {},
pages = {111429},
doi = {10.1016/j.mad.2021.111429},
pmid = {33422563},
issn = {1872-6216},
mesh = {Age Factors ; Aging/*genetics/metabolism/pathology ; Animals ; DNA/*genetics/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; G-Quadruplexes ; *Gene Deletion ; Humans ; Longevity/*genetics ; Models, Genetic ; *Mutation ; Nucleic Acid Conformation ; *Nucleotide Motifs ; Phylogeny ; Species Specificity ; },
abstract = {The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.},
}
@article {pmid33432342,
year = {2021},
author = {Harada, R and Inagaki, Y},
title = {Phage Origin of Mitochondrion-Localized Family A DNA Polymerases in Kinetoplastids and Diplonemids.},
journal = {Genome biology and evolution},
volume = {13},
number = {2},
pages = {},
pmid = {33432342},
issn = {1759-6653},
mesh = {Bacteriophages/enzymology/*genetics ; DNA-Directed DNA Polymerase/classification/*genetics ; Euglenozoa/enzymology/*genetics ; *Gene Transfer, Horizontal ; Kinetoplastida/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; },
abstract = {Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting that the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies have revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as "PolIBCD+") have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via nonvertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.},
}
@article {pmid33436634,
year = {2021},
author = {Bit, A and Thakur, M and Singh, SK and Joshi, BD and Singh, VK and Sharma, LK and Tripathy, B and Chandra, K},
title = {Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {730},
pmid = {33436634},
issn = {2045-2322},
mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; *Phylogeny ; Ursidae/classification/*genetics ; },
abstract = {The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.},
}
@article {pmid33442829,
year = {2021},
author = {Zhang, K and Liu, Y and Chen, J and Zhang, H and Gong, L and Jiang, L and Liu, L and Lü, Z and Liu, B},
title = {Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes.},
journal = {Molecular biology reports},
volume = {48},
number = {1},
pages = {677-689},
pmid = {33442829},
issn = {1573-4978},
support = {NO.41806156//National Natural Science Foundation of China/ ; LMB20201005//State Key Laboratory of Microbial Resources (CN)/ ; No.2019J00048//Starting Research Fund from the Zhejiang Ocean University; Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes/ ; 2020C21016//Science and Technology Project of Zhoushan/ ; 31702321//National Natural Science Foundation of China/ ; LY20C190008//Zhejiang Provincial Natural Science Foundation of China/ ; },
mesh = {Animals ; Base Composition ; Catfishes/classification/*genetics ; Chromosome Mapping ; DNA, Circular/genetics ; DNA, Mitochondrial/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Open Reading Frames ; Phylogeny ; RNA, Ribosomal/classification/genetics ; RNA, Transfer/classification/genetics ; Whole Genome Sequencing ; },
abstract = {The vertebrate mitochondrial genome is typically circular molecules made up of 14,000 to 16,000 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12 s rRNA and 16 s rRNA) and a control region. Compared with nuclear DNA, mitochondrial DNA has a higher mutation rate, so it is one of the most effective and reliable molecular markers in fish phylogeny. Macrotocinclus affinis was the only species in Macrotocinclus (it was classified as Otocinclus in the past) and currently lacks genetic information. Most of the current researches are based on the mitochondrial Cytb gene and RAG1 and RAG2 nuclear genes to study the phylogenetic analysis of Siluriformes. So, the study provides the characteristic features of the Macrotocinclus affinis mitochondrial genome and this is the first time that the phylogenetic relationship of Siluriformes has been reconstructed based on COI. We aimed to sequence the entire mitochondrial genome of Macrotocinclus affinis using conventional PCR techniques and to clarify its phylogenetic status in Siluriformes by using the COI sequence of mitochondria. In this study, we sequenced the whole mitochondrial genome of this species yielding a 16,632 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes A (30.07%), T (24.43%), C (29.43%) and G (16.01%). The genome composition is A + T biased (54.5%), and exhibits AT-skew (0.1036) and GC-skew (-0.2962). Moreover, the 13 PCGs encode 3850 amino acids in total. The result of the phylogenetic tree supports Macrotocinclus affinis has a closest relationship with Otocinclus cf. hoppei far. These results will help to understand the characteristics of the mitochondrial genome of Macrotocinclus affinis and provide molecular basis for the evolutionary relationship of Loricariidae.},
}
@article {pmid33482382,
year = {2021},
author = {Irwin, AR and Strong, EE and Kano, Y and Harper, EM and Williams, ST},
title = {Eight new mitogenomes clarify the phylogenetic relationships of Stromboidea within the caenogastropod phylogenetic framework.},
journal = {Molecular phylogenetics and evolution},
volume = {158},
number = {},
pages = {107081},
doi = {10.1016/j.ympev.2021.107081},
pmid = {33482382},
issn = {1095-9513},
mesh = {Animals ; Gastropoda/classification/*genetics ; *Genome, Mitochondrial ; Mitochondria/classification/*genetics ; Mitochondrial Proteins/classification/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 18S/classification/genetics ; RNA, Transfer/chemistry ; },
abstract = {Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in tropical and subtropical waters. Although a few strombid mitochondrial genomes have been sequenced, data for the other four Recent families in Stromboidea are lacking. In this study we report seven new stromboid mitogenomes obtained from transcriptomic and genomic data, with taxonomic representation from each Recent stromboid family, including the first mitogenomes for Aporrhaidae, Rostellariidae, Seraphsidae and Struthiolariidae. We also report a new mitogenome for the family Xenophoridae. We use these data, along with published sequences, to investigate the relationships among these and other caenogastropod groups. All analyses undertaken in this study support monophyly of Stromboidea as redefined here to include Xenophoridae, a finding consistent with morphological and behavioural data. Consistent with previous morphological and molecular analyses, including those based on mitogenomes, monophyly of Hypsogastropoda is confirmed but monophyly of Littorinimorpha is again rejected.},
}
@article {pmid33498264,
year = {2021},
author = {Gladyck, S and Aras, S and Hüttemann, M and Grossman, LI},
title = {Regulation of COX Assembly and Function by Twin CX9C Proteins-Implications for Human Disease.},
journal = {Cells},
volume = {10},
number = {2},
pages = {},
pmid = {33498264},
issn = {2073-4409},
support = {W81XWH-16-1-0516//U.S. Department of Defense/ ; R01 GM116807/GF/NIH HHS/United States ; HHSN275201300006C/HD/NICHD NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; *Disease ; Electron Transport Complex IV/*chemistry/*metabolism ; Humans ; Phylogeny ; Protein Binding ; Protein Subunits/chemistry/metabolism ; },
abstract = {Oxidative phosphorylation is a tightly regulated process in mammals that takes place in and across the inner mitochondrial membrane and consists of the electron transport chain and ATP synthase. Complex IV, or cytochrome c oxidase (COX), is the terminal enzyme of the electron transport chain, responsible for accepting electrons from cytochrome c, pumping protons to contribute to the gradient utilized by ATP synthase to produce ATP, and reducing oxygen to water. As such, COX is tightly regulated through numerous mechanisms including protein-protein interactions. The twin CX9C family of proteins has recently been shown to be involved in COX regulation by assisting with complex assembly, biogenesis, and activity. The twin CX9C motif allows for the import of these proteins into the intermembrane space of the mitochondria using the redox import machinery of Mia40/CHCHD4. Studies have shown that knockdown of the proteins discussed in this review results in decreased or completely deficient aerobic respiration in experimental models ranging from yeast to human cells, as the proteins are conserved across species. This article highlights and discusses the importance of COX regulation by twin CX9C proteins in the mitochondria via COX assembly and control of its activity through protein-protein interactions, which is further modulated by cell signaling pathways. Interestingly, select members of the CX9C protein family, including MNRR1 and CHCHD10, show a novel feature in that they not only localize to the mitochondria but also to the nucleus, where they mediate oxygen- and stress-induced transcriptional regulation, opening a new view of mitochondrial-nuclear crosstalk and its involvement in human disease.},
}
@article {pmid33507977,
year = {2021},
author = {Dryomov, SV and Nazhmidenova, AM and Starikovskaya, EB and Shalaurova, SA and Rohland, N and Mallick, S and Bernardos, R and Derevianko, AP and Reich, D and Sukernik, RI},
title = {Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244228},
pmid = {33507977},
issn = {1932-6203},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {DNA, Mitochondrial/chemistry/classification/genetics/history ; Genetic Linkage ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Mitochondria/*genetics ; Phylogeny ; Siberia ; },
abstract = {The Central Siberian Plateau was the last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through a comprehensive dataset of mitochondrial DNA (mtDNA) genomes retained in the remnats of earlier ("Old") Siberians, primarily the Ket, Tofalar, and Todzhi, we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia (best represented by the Yukaghir) over the last 10,000 years. We generated 218 new complete mtDNA sequences and placed them into compound phylogenies with 7 newly obtained and 70 published ancient mitochondrial genomes. We have considerably extended the mtDNA sequence diversity (at the entire mtDNA genome level) of autochthonous Siberians, which remain poorly sampled, and these new data may have a broad impact on the study of human migration. We compared present-day mtDNA diversity in these groups with complete mitochondrial genomes from ancient samples from the region and placed the samples into combined genealogical trees. The resulting components were used to clarify the origins and expansion history of mtDNA lineages that evolved in the refugia of south-central Siberia and beyond, as well as multiple phases of connection between this region and distant parts of Eurasia.},
}
@article {pmid33510193,
year = {2021},
author = {Zhang, K and Zhu, K and Liu, Y and Zhang, H and Gong, L and Jiang, L and Liu, L and Lü, Z and Liu, B},
title = {Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {2411},
pmid = {33510193},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; Codon ; Eels/*classification/*genetics ; *Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genomics/methods ; Nucleic Acid Conformation ; *Phylogeny ; },
abstract = {The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.},
}
@article {pmid33513437,
year = {2021},
author = {Li, W and Cao, Y and Chen, Z and Tan, Y and Dai, Y and Wei, J and Xiao, J and Feng, H},
title = {Black carp TRADD suppresses MAVS/IFN signaling during the innate immune activation.},
journal = {Fish &amp; shellfish immunology},
volume = {111},
number = {},
pages = {83-93},
doi = {10.1016/j.fsi.2021.01.006},
pmid = {33513437},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Carps/*genetics/*immunology ; Cell Line ; Fish Diseases/*immunology ; Fish Proteins/chemistry/genetics/immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; HEK293 Cells ; Humans ; Immunity, Innate/*genetics ; Lipopolysaccharides/pharmacology ; Phylogeny ; Poly I-C/pharmacology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary ; Sequence Alignment/veterinary ; TNF Receptor-Associated Death Domain Protein/chemistry/*genetics/*immunology ; },
abstract = {Tumor necrosis factor receptor 1 (TNFR1) associated death domain protein (TRADD) is a pivotal adaptor in TNF signaling pathway and up-regulates MAVS/IFN signaling pathway in human and mammal. However, the role of TRADD in teleost fish remains obscure. To reveal the function of teleost TRADD in the innate immune response, the TRADD homologue (bcTRADD) of black carp (Mylopharyngodon piceus) has been cloned and the function of bcTRADD is investigated in this study, which shares similar functional domain to its mammalian counterpart. bcTRADD mRNA expression level increased in response to different stimuli, including LPS, poly (I:C) and virus infection in host cells. bcTRADD activated the transcriptional activity of NF-κB promoter in the reporter assay; however, showed hardly any effect on the transcriptional activity of IFN promoter. It was interesting that black carp mitochondria antiviral signaling protein (bcMAVS)-activated IFN promoter transcription were dramatically depressed by bcTRADD and the C-terminal death domain of bcTRADD was indispensable for its regulation of bcMAVS. Accordingly, the plaque assay result showed that EPC cells co-expressing bcMAVS and bcTRADD presented much attenuated antiviral activity than EPC cells expressing bcMAVS alone. Knockdown of bcTRADD slightly promoted the antiviral ability of the host cells against SVCV. The current data support the conclusion that bcTRADD suppresses MAVS-mediated antiviral signaling, which is different to its mammalian counterpart.},
}
@article {pmid33521839,
year = {2021},
author = {Schumm, YR and Bakaloudis, D and Barboutis, C and Cecere, JG and Eraud, C and Fischer, D and Hering, J and Hillerich, K and Lormée, H and Mader, V and Masello, JF and Metzger, B and Rocha, G and Spina, F and Quillfeldt, P},
title = {Prevalence and genetic diversity of avian haemosporidian parasites in wild bird species of the order Columbiformes.},
journal = {Parasitology research},
volume = {120},
number = {4},
pages = {1405-1420},
pmid = {33521839},
issn = {1432-1955},
mesh = {Animal Migration ; Animals ; Bird Diseases/*epidemiology/parasitology ; Columbidae/parasitology ; Columbiformes/*parasitology ; Cytochromes b/genetics ; Genetic Variation ; Global Warming ; Haemosporida/classification/*genetics/growth &amp; development ; Host Specificity ; Mitochondria/genetics ; Multiplex Polymerase Chain Reaction/veterinary ; Phylogeny ; Plasmodium/genetics ; Polymerase Chain Reaction/veterinary ; Prevalence ; Protozoan Infections, Animal/*epidemiology/parasitology ; },
abstract = {Diseases can play a role in species decline. Among them, haemosporidian parasites, vector-transmitted protozoan parasites, are known to constitute a risk for different avian species. However, the magnitude of haemosporidian infection in wild columbiform birds, including strongly decreasing European turtle doves, is largely unknown. We examined the prevalence and diversity of haemosporidian parasites Plasmodium, Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus in six species of the order Columbiformes during breeding season and migration by applying nested PCR, one-step multiplex PCR assay and microscopy. We detected infections in 109 of the 259 screened individuals (42%), including 15 distinct haemosporidian mitochondrial cytochrome b lineages, representing five H. (Haemoproteus), two H. (Parahaemoproteus), five Leucocytozoon and three Plasmodium lineages. Five of these lineages have never been described before. We discriminated between single and mixed infections and determined host species-specific prevalence for each parasite genus. Observed differences among sampled host species are discussed with reference to behavioural characteristics, including nesting and migration strategy. Our results support previous suggestions that migratory birds have a higher prevalence and diversity of blood parasites than resident or short-distance migratory species. A phylogenetic reconstruction provided evidence for H. (Haemoproteus) as well as H. (Parahaemoproteus) infections in columbiform birds. Based on microscopic examination, we quantified parasitemia, indicating the probability of negative effects on the host. This study provides a large-scale baseline description of haemosporidian infections of wild birds belonging to the order Columbiformes sampled in the northern hemisphere. The results enable the monitoring of future changes in parasite transmission areas, distribution and diversity associated with global change, posing a potential risk for declining avian species as the European turtle dove.},
}
@article {pmid33542272,
year = {2021},
author = {Sucháčková Bartoňová, A and Konvička, M and Marešová, J and Wiemers, M and Ignatev, N and Wahlberg, N and Schmitt, T and Faltýnek Fric, Z},
title = {Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {3019},
pmid = {33542272},
issn = {2045-2322},
mesh = {Animals ; Butterflies/*genetics/microbiology/ultrastructure ; DNA, Mitochondrial/genetics ; Mitochondria/genetics/microbiology/*ultrastructure ; *Phylogeny ; Wolbachia/*genetics/pathogenicity ; },
abstract = {The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.},
}
@article {pmid33554278,
year = {2021},
author = {Ohari, Y and Matsuo, K and Yoshida, A and Nonaka, N and Sato, H and Itagaki, T},
title = {Genetic diversity and population structure analyses based on microsatellite DNA of parthenogenetic Fasciola flukes obtained from cattle and sika deer in Japan.},
journal = {Parasitology research},
volume = {120},
number = {4},
pages = {1341-1350},
pmid = {33554278},
issn = {1432-1955},
mesh = {Animals ; Cattle ; Cattle Diseases/epidemiology/*parasitology ; DNA, Helminth/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Deer/*parasitology ; Fasciola/*genetics/physiology ; Fascioliasis/parasitology/*veterinary ; *Genetic Variation ; Haplotypes ; Helminth Proteins/genetics ; Japan/epidemiology ; Microsatellite Repeats ; Mitochondria/enzymology ; NADH Dehydrogenase/genetics ; Parthenogenesis ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {Understanding the population structure of Fasciola flukes in domestic and wild animals is important for determining the extent of cross-infection between them. Although the parthenogenetic Fasciola flukes in Japan have been shown to comprise five genetic types based on the ribosomal internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1) regions, these genetic regions are not suitable for analyzing their population structure. In the present study, the genetic diversity and population structure of the parthenogenetic Fasciola flukes in Japan were studied using microsatellite DNA, ITS1, and nad1 regions. A total of 144 parthenogenetic Fasciola flukes, obtained from cattle and sika deer in 16 localities, were individually analyzed using PCR-RFLP for ITS1, PCR-direct sequence analysis for nad1, and post-labeling PCR and capillary electrophoresis for microsatellite DNA regions. The flukes showed higher genetic diversity in the microsatellite DNA regions than ITS1 and nad1. The population structures of parthenogenetic Fasciola flukes were unclear, however, it was suggested that the flukes are more diverse populations. We hypothesized that their distribution throughout Japan is closely related to livestock movement dependent on human activity. Moreover, it is considered that cross-infection of the flukes between cattle and sika deer possibly has occurred in the past.},
}
@article {pmid33557932,
year = {2021},
author = {Pilgrim, J and Siozios, S and Baylis, M and Venter, G and Garros, C and Hurst, GDD},
title = {Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {100},
pmid = {33557932},
issn = {1756-3305},
support = {BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; H2020-MSCA-IF-2014//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; },
mesh = {Animals ; Bacterial Infections/*transmission ; Bacteroidetes/genetics ; Ceratopogonidae/*genetics/*microbiology ; DNA, Mitochondrial/chemistry/*genetics ; Gene Flow ; Horses ; Insect Vectors/*microbiology ; Mediterranean Region ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; South Africa ; *Symbiosis ; },
abstract = {BACKGROUND: Culicoides imicola (Diptera: Ceratopogonidae) is an important Afrotropical and Palearctic vector of disease, transmitting viruses of animal health and economic significance including African horse sickness and bluetongue viruses. Maternally inherited symbiotic bacteria (endosymbionts) of arthropods can alter the frequency of COI (cytochrome c oxidase subunit I) mitochondrial haplotypes (mitotypes) in a population, masking the true patterns of host movement and gene flow. Thus, this study aimed to assess the mtDNA structure of C. imicola in relation to infection with Candidatus Cardinum hertigii (Bacteroides), a common endosymbiont of Culicoides spp.<br><br>METHODS: Using haplotype network analysis, COI Sanger sequences from Cardinium-infected and -uninfected C. imicola individuals were first compared in a population from South Africa. The network was then extended to include mitotypes from a geographic range where Cardinium infection has previously been investigated.<br><br>RESULTS: The mitotype network of the South African population demonstrated the presence of two broad mitotype groups. All Cardinium-infected specimens fell into one group (Fisher's exact test, P&#x2009;=&#x2009;0.00071) demonstrating a linkage disequilibrium between endosymbiont and mitochondria. Furthermore, by extending this haplotype network to include other C. imicola populations from the Mediterranean basin, we revealed mitotype variation between the Eastern and Western Mediterranean basins (EMB and WMB) mirrored Cardinium-infection heterogeneity.<br><br>CONCLUSIONS: These observations suggest that the linkage disequilibrium of Cardinium and mitochondria reflects endosymbiont gene flow within the Mediterranean basin but may not assist in elucidating host gene flow. Subsequently, we urge caution on the single usage of the COI marker to determine population structure and movement in C. imicola and instead suggest the complementary utilisation of additional molecular markers.},
}
@article {pmid33581918,
year = {2021},
author = {Zheng, X and Gao, X and Wang, J and Du, C and Hou, C and Xie, Q and Lou, B and Liu, F and Zhu, J},
title = {KIFC1 functions in nuclear reshaping and midpiece formation during the spermatogenesis of small yellow croaker Larimichthys polyactis.},
journal = {Animal reproduction science},
volume = {226},
number = {},
pages = {106702},
doi = {10.1016/j.anireprosci.2021.106702},
pmid = {33581918},
issn = {1873-2232},
mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/physiology ; Cloning, Molecular ; DNA, Complementary/genetics ; Fishes/genetics/*physiology ; Gene Expression Regulation/physiology ; Kinesins/genetics/*metabolism ; Male ; Microtubules/physiology ; Mitochondria/physiology ; Phylogeny ; Protein Conformation ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Spermatogenesis/*physiology ; Spermatozoa/*cytology/*physiology ; Testis/*physiology ; Tubulin/genetics/metabolism ; },
abstract = {The C-terminal kinesin motor protein (KIFC1) has essential functions in spermatogenesis. To evaluate molecular mechanisms of KIFC1 during teleost fish spermatogenesis, there was cloning and sequencing the kifc1 cDNA in the testis of Larimichthys polyactis. Quantitative PCR results indicated there were Lp-kifc1 mRNA transcripts in the testes. Results from conducting fluorescence in situ hybridization and immunofluorescence procedures indicated there were trends in relative abundance changes in Lp-kifc1 mRNA transcripts that were associated with abundance of Lp-KIFC1 protein during spermatogenesis. The Lp-KIFC1 protein was detected at all stages of spermatogenesis. There was minimal Lp-KIFC1 in the cytoplasm of spermatogonia, with content being greater and concentrated in the perinuclear region in spermatocytes and during early/mid-stages of development of spermatids. There were large abundances of Lp-KIFC1 in spermatids at the mid-developmental stage. In late-developing spermatids, Lp-KIFC1 content was less and concentrated in the bottom of the nucleus, where the midpiece formed. There was a small Lp-KIFC1 in the midpiece of mature sperm. These findings indicate Lp-KIFC1 may have functions in L. polyactis spermatogenesis. Results from conducting immunofluorescence procedures indicated Lp-KIFC1 was co-localized microtubules and mitochondria throughout spermatogenesis. There were large abundances of Lp-KIFC1 and tubulin in spermatids during the mid-developmental stage, when there is a decrease in size and reshaping of the nucleus. During midpiece formation, there was co-localization of the Lp-KIFC1 and mitochondria in the spermatid perinuclear region to the midpiece. These findings indicate Lp-KIFC1 is involved in nuclear reshaping and midpiece formation during spermatogenesis in L. polyactis.},
}
@article {pmid33612083,
year = {2022},
author = {Ma, ZJ and Li, GZ and Chen, SM and Han, JL and Hanif, Q},
title = {Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus).},
journal = {Animal biotechnology},
volume = {33},
number = {6},
pages = {1382-1386},
doi = {10.1080/10495398.2021.1884567},
pmid = {33612083},
issn = {1532-2378},
mesh = {Cattle/genetics ; Animals ; Phylogeny ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Genetic Variation/genetics ; },
abstract = {Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai-Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.},
}
@article {pmid33652602,
year = {2021},
author = {Prieto, C and Montecinos, J and Jiménez, G and Riquelme, C and Garrido, D and Hernández, S and Loyola, A and Villanueva, RA},
title = {Phosphorylation of Phylogenetically Conserved Amino Acid Residues Confines HBx within Different Cell Compartments of Human Hepatocarcinoma Cells.},
journal = {Molecules (Basel, Switzerland)},
volume = {26},
number = {5},
pages = {},
pmid = {33652602},
issn = {1420-3049},
mesh = {Amino Acid Sequence/genetics ; Carcinoma, Hepatocellular/*genetics/pathology/virology ; Conserved Sequence/genetics ; Gene Expression Regulation, Viral/genetics ; Genome, Viral/genetics ; Hep G2 Cells ; Hepatitis B/*genetics/pathology/virology ; Hepatitis B virus/genetics/pathogenicity ; Humans ; Liver Neoplasms/*genetics/pathology/virology ; Phosphorylation/genetics ; Phylogeny ; Trans-Activators/*genetics ; Viral Regulatory and Accessory Proteins/*genetics ; },
abstract = {Hepatitis B virus (HBV) is a circular, and partially double-stranded DNA virus. Upon infection, the viral genome is translocated into the cell nucleus, generating the covalently closed circular DNA (cccDNA) intermediate, and forming a mini chromosome. HBV HBx is a small protein displaying multiple roles in HBV-infected cells, and in different subcellular locations. In the nucleus, the HBx protein is required to initiate and maintain viral transcription from the viral mini chromosome. In contrast, HBx also functions in the cytoplasm, where it is able to alter multiple cellular functions such as mitochondria metabolism, apoptosis and signal transduction pathways. It has been reported that in cultured cells, at low expression levels, the HBx protein is localized in the nucleus, whereas at high expression levels, it accumulates in the cytoplasm. This dynamic subcellular distribution of HBx might be essential to exert its multiple roles during viral infection. However, the mechanism that regulates different subcellular localizations of the HBx protein is unknown. We have previously taken a bioinformatics approach to investigate whether HBx might be regulated via post-translational modification, and we have proposed that the multiple nucleocytoplasmic functions of HBx might be regulated by an evolutionarily conserved mechanism via phosphorylation. In the current study, phylogenetically conserved amino acids of HBx with a high potential of phosphorylation were targeted for site-directed mutagenesis. Two conserved serine (Ser25 and Ser41), and one conserved threonine (Thr81) amino acids were replaced by either alanine or aspartic acid residues to simulate an unphosphorylated or phosphorylated state, respectively. Human hepatoma cells were transfected with increasing amounts of the HBx DNA constructs, and the cells were analyzed by fluorescence microscopy. Together, our results show that the nucleocytoplasmic distribution of the HBx protein could be regulated by phosphorylation since some of the modified proteins were mainly confined to distinct subcellular compartments. Remarkably, both HBx Ser41A, and HBx Thr81D proteins were predominantly localized within the nuclear compartment throughout the different expression levels of HBx mutants.},
}
@article {pmid33678114,
year = {2021},
author = {Huang, F and Ye, X and Wang, Z and Ding, Y and Cai, X and Yu, L and Waseem, M and Abbas, F and Ashraf, U and Chen, X and Ke, Y},
title = {The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses.},
journal = {GM crops &amp; food},
volume = {12},
number = {1},
pages = {535-550},
pmid = {33678114},
issn = {2164-5701},
mesh = {Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genome, Plant ; *Solanum lycopersicum/genetics/metabolism ; Multigene Family ; Phylogeny ; Plant Growth Regulators ; Plant Proteins/genetics/metabolism ; Prohibitins ; Stress, Physiological/genetics ; },
abstract = {The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as Arabidopsis, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in Solanum lycopersicum. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive cis-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.},
}
@article {pmid33684992,
year = {2021},
author = {Song, JY and Kim, KY and Choi, SW},
title = {Occurrence and Molecular Identification of Microcotyle sebastis Isolated from Fish Farms of the Korean Rockfish, Sebastes schlegelii.},
journal = {The Korean journal of parasitology},
volume = {59},
number = {1},
pages = {89-95},
pmid = {33684992},
issn = {1738-0006},
support = {R2021065//National Institute of Fisheries Science/ ; },
mesh = {Animals ; Electron Transport Complex IV/genetics ; Fish Diseases/*epidemiology/*parasitology ; *Fisheries ; Microscopy, Electron, Scanning ; Mitochondria/enzymology/genetics ; Phylogeny ; RNA, Ribosomal, 28S ; Republic of Korea/epidemiology ; Trematoda/*genetics/*isolation &amp; purification/ultrastructure ; Trematode Infections/epidemiology/*parasitology/*veterinary ; },
abstract = {Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.},
}
@article {pmid33711786,
year = {2021},
author = {Srivastava, PN and Narwal, SK and Mishra, S},
title = {Mitochondrial apurinic/apyrimidinic endonuclease Apn1 is not critical for the completion of the Plasmodium berghei life cycle.},
journal = {DNA repair},
volume = {101},
number = {},
pages = {103078},
doi = {10.1016/j.dnarep.2021.103078},
pmid = {33711786},
issn = {1568-7856},
mesh = {Amino Acid Sequence ; DNA Damage ; DNA Repair ; DNA, Mitochondrial/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry/genetics/*metabolism ; *Life Cycle Stages ; Mitochondria/*enzymology ; Models, Molecular ; Phylogeny ; Plasmodium berghei/*enzymology/growth &amp; development ; Protein Conformation ; Sequence Alignment ; Sequence Analysis, Protein ; },
abstract = {Mitochondrion is an essential organelle in malaria parasite and its DNA must be maintained for optimal function during its complex life cycle. Base excision repair is one of the major pathways by which this is achieved. Apurinic/apyrimidinic (AP) endonucleases are important components of this pathway as they create a nick at the 5'-phosphodiester bond in the AP site and generate free 5'-phosphate and 3'-hydroxyl groups. Two class II AP endonucleases (Apn1 and Ape1) have been annotated in the Plasmodium berghei genome. Using reverse genetic approaches, we provide direct evidence that Apn1 is exclusively localized to the mitochondria of P. berghei. Surprisingly, our gene deletion study revealed a completely dispensable role of Apn1 for the entirety of the P. berghei life cycle. Apn1[-] parasites were found to successfully grow in the blood. They were transmitted normally to the mosquito midguts and salivary glands. Sporozoites obtained from the salivary glands were infective and achieved similar patency as WT. Our results help emphasize the non-availability of this enzyme as a plausible drug target. We also emphasize the importance of genetic validation of antimalarial drug targets before furthering them down the drug discovery pipeline.},
}
@article {pmid33720930,
year = {2021},
author = {Londoño-Burbano, A and Reis, RE},
title = {A combined molecular and morphological phylogeny of the Loricariinae (Siluriformes: Loricariidae), with emphasis on the Harttiini and Farlowellini.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247747},
pmid = {33720930},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Catfishes/anatomy &amp; histology/classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Fish Proteins/*genetics ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; },
abstract = {We present a combined molecular and morphological phylogenetic analysis of the Loricariinae, with emphasis on the Harttiini (Cteniloricaria, Harttia, and Harttiella) and Farlowellini (Aposturisoma, Farlowella, Lamontichthys, Pterosturisoma, Sturisoma, and Sturisomatichthys). Character sampling comprised seven molecular markers (the mitochondrial Cytb, nd2, 12S and 16S, and the nuclear MyH6, RAG1 and RAG2) and 196 morphological characters. A total of 1,059 specimens, and 159 tissue samples were analized, representing 100 species. A Bayesian Inference analysis was performed using the concatenated data matrix, which is comprised of 6,819 characters. The Loricariinae were found to comprise the tribes (Hartiini (Loricariini, Farlowellini)), the latter two elevated from subtribes. A Maximum Parsimony analysis was also performed using the same data matrix in order to reveal phenotypical synapomorphies to diagnose each clade. Two MP trees were found with a length of 14,704 steps, consistency index of 0.29 and retention index of 0.61, which were summarized in a strict consensus tree. Harttiini includes (Harttiella (Cteniloricaria, Harttia), and Farlowellini includes (Lamontichthys (Pterosturisoma (Sturisoma (Sturisomatichthys, Farlowella)))). Aposturisoma was recovered nested within Farlowella and is synonymyzed to the latter. Sturisoma was corroborated as strictly cis-Andean, while Sturisomatichthys encompasses, besides the valid species already included in the genus, the trans-Andean species once belonging to Sturisoma sensu lato. Identification keys and phylogenetic diagnoses of family-group taxa and genera of both the Harttiini and the Farlowellini are provided.},
}
@article {pmid33735257,
year = {2021},
author = {Liu, Y and Yao, L and Ci, Y and Cao, X and Zhao, M and Li, Y and Zhang, X},
title = {Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0248102},
pmid = {33735257},
issn = {1932-6203},
mesh = {Animals ; Cytochromes b/*genetics ; *Gene Flow ; Genes, Mitochondrial ; *Genetic Drift ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Rats/*genetics ; },
abstract = {Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima's D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.},
}
@article {pmid33741537,
year = {2021},
author = {Bober, S and Glaubrecht, M and Hausdorf, B and Neiber, MT},
title = {One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data.},
journal = {Molecular phylogenetics and evolution},
volume = {161},
number = {},
pages = {107153},
doi = {10.1016/j.ympev.2021.107153},
pmid = {33741537},
issn = {1095-9513},
mesh = {*Amplified Fragment Length Polymorphism Analysis ; Animals ; *DNA Barcoding, Taxonomic ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Snails/*anatomy &amp; histology/classification/*genetics ; Spain ; },
abstract = {Hemicycla mascaensis and H. diegoi are short-range endemics that occur allopatrically in small areas in the Teno Mountains in the western part of Tenerife (Canary Islands). Both taxa have been recognised as distinct species based on differences in shell morphology and genital anatomy. Preliminary molecular analyses using mitochondrial markers suggested a potential paraphyly of H. diegoi with regard to H. mascaensis. We here use multilocus AFLP data and ddRADseq data as well as distribution data, data on shell morphology and genital anatomy to assess the status of these taxa using phylogenetic analyses, species tree reconstruction and molecular species delimitation based on the multispecies coalescent as implemented in BFD* and BPP in an integrative approach. Our analyses show that, based on the analysis of multilocus data, the two taxa are reciprocally monophyletic. Species delimitation methods, however, tend to recognise all investigated populations as distinct species, albeit neither lending unambiguous support to any of the species hypotheses. The comparison of the anatomy of distal genital organs further suggests differentiation within H. mascaensis. This highlights the need for a balanced weighting of arguments from different lines of evidence to determine species status and calls for cautious interpretations of the results of molecular species delimitation analyses, especially in organisms with low active dispersal capacities and expected distinct population structuring such as land snails. Taking all available evidence into account, we favour to recognise H. mascaensis and H. diegoi as distinct species, acknowledging, though, that the recognition of both taxa as subspecies (with possibly a third yet undescribed) would also be an option as morphological differentiation is within the limits of other land snail species that are traditionally subdivided into subspecies.},
}
@article {pmid33743097,
year = {2021},
author = {Ressaissi, Y and Amills, M and Noce, A and Ben Hamouda, M},
title = {Characterizing the Mitochondrial Diversity of Arbi Goats from Tunisia.},
journal = {Biochemical genetics},
volume = {59},
number = {5},
pages = {1225-1232},
pmid = {33743097},
issn = {1573-4927},
support = {AGL2016-76108-R//Ministerio de Econom&#xed;a y Competitividad/ ; },
mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Variation ; Goats ; *Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Tunisia ; },
abstract = {Arbi is one of the main local goat breeds in Tunisia, representing an important economic resource in arid and hot areas where cattle and sheep cannot thrive successfully. In the current work, we have characterized the mitochondrial diversity of 26 Arbi goats by partially sequencing the mitochondrial D-loop region. These sequences plus 10 retrieved from GenBank were analyzed with the DnaSP v.5.10.1, evidencing the existence of 12 different haplotypes. Nucleotide and haplotype diversities were 0.02 and 0.96. Moreover, median-joining network analysis showed that all D-loop sequences from Arbi goats correspond to haplogroup A and that in general they do not cluster with sequences from other goat breeds. The high diversity that has been observed in North African goats is compatible with the maritime diffusion of the Neolithic package 10,000-7000 YBP. Moreover, there are evidences that local Tunisian breeds have been extensively crossed with highly productive transboundary breeds in order to improve meat and milk yields. These uncontrolled crossing practices may lead to the loss of alleles that play key roles in the adaptation of Tunisian local breeds to a harsh environment.},
}
@article {pmid33750312,
year = {2021},
author = {Cheng, Y and He, X and Priyadarshani, SVGN and Wang, Y and Ye, L and Shi, C and Ye, K and Zhou, Q and Luo, Z and Deng, F and Cao, L and Zheng, P and Aslam, M and Qin, Y},
title = {Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {167},
pmid = {33750312},
issn = {1471-2164},
support = {31671267//National Natural Science Foundation of China/ ; 31970333//National Natural Science Foundation of China/ ; },
mesh = {*Chenopodiaceae/genetics ; Genome Size ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; },
abstract = {BACKGROUND: Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored.<br><br>RESULTS: The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330&#x2009;bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes.<br><br>CONCLUSIONS: In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.},
}
@article {pmid33798681,
year = {2021},
author = {Ennis, CC and Haeffner, NN and Keyser, CD and Leonard, ST and Macdonald-Shedd, AC and Savoie, AM and Cronin, TJ and Veldsman, WP and Barden, P and Chak, STC and Baeza, JA},
title = {Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps.},
journal = {Gene},
volume = {786},
number = {},
pages = {145624},
doi = {10.1016/j.gene.2021.145624},
pmid = {33798681},
issn = {1879-0038},
mesh = {Animals ; Codon Usage ; Decapoda/*classification/genetics ; Genome Size ; Genome, Mitochondrial ; Genomics/*methods ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Selection, Genetic ; },
abstract = {The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.},
}
@article {pmid33807111,
year = {2021},
author = {Maár, K and Varga, GIB and Kovács, B and Schütz, O and Maróti, Z and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Varga, S and Költő, L and Raskó, I and Török, T and Neparáczki, E},
title = {Maternal Lineages from 10-11th Century Commoner Cemeteries of the Carpathian Basin.},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33807111},
issn = {2073-4425},
mesh = {Cemeteries ; DNA, Mitochondrial/*genetics ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; History, Medieval ; Humans ; Hungary/ethnology ; Maternal Inheritance ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; Transients and Migrants/*history ; },
abstract = {Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10-11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10-11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians).},
}
@article {pmid33808521,
year = {2021},
author = {Gînguță, A and Rusu, I and Mircea, C and Ioniță, A and Banciu, HL and Kelemen, B},
title = {Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania).},
journal = {Genes},
volume = {12},
number = {3},
pages = {},
pmid = {33808521},
issn = {2073-4425},
mesh = {Asia/ethnology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics/*history ; Genetics, Population ; History, Medieval ; Humans ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Romania/ethnology ; White People/*genetics ; },
abstract = {The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.},
}
@article {pmid33848317,
year = {2021},
author = {Postic, E and Outreman, Y and Derocles, S and Granado, C and Le Ralec, A},
title = {Genetics of wild and mass-reared populations of a generalist aphid parasitoid and improvement of biological control.},
journal = {PloS one},
volume = {16},
number = {4},
pages = {e0249893},
pmid = {33848317},
issn = {1932-6203},
mesh = {Animals ; Aphids/classification/*genetics ; Discriminant Analysis ; Electron Transport Complex IV/genetics ; Fragaria/parasitology ; Genetic Variation ; Genetics, Population ; Haplotypes ; Host-Parasite Interactions ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Pest Control, Biological ; Phylogeny ; Principal Component Analysis ; },
abstract = {Due to their ability to parasitize various insect species, generalist parasitoids are widely used as biological control agents. They can be mass-reared and released in agroecosystems to control several pest species in various crops. However, the existence of genetic differentiation among populations of generalist parasitoid species is increasingly recognized and this can be associated with an adaptation to local conditions or to a reduced range of host species. Moreover, constraints of mass-rearing conditions can alter genetic variation within parasitoid populations released. These features could be associated with a reduced efficiency of the control of targeted pest species. Here, we focused on strawberry greenhouses where the control of aphids with the generalist parasitoid Aphidius ervi appears to be inefficient. We investigated whether this inefficiency may have both genetic and ecological bases comparing wild and commercial populations of A. ervi. We used two complementary genetic approaches: one based on the mitochondrial marker COI and one based on microsatellite markers. COI analysis showed a genetic differentiation within the A. ervi species, but the structure was neither associated with the commercial/wild status nor with host species factors. On the other hand, using microsatellite markers, we showed a genetic differentiation between commercial and wild A. ervi populations associated with a loss of genetic diversity within the mass-reared populations. Our ecological genetics study may potentially explain the weak efficiency of biological control of aphids in protected strawberry crops and enable to provide some insights to improve biological control.},
}
@article {pmid33859247,
year = {2021},
author = {Louro, M and Kuzmina, TA and Bredtmann, CM and Diekmann, I and de Carvalho, LMM and von Samson-Himmelstjerna, G and Krücken, J},
title = {Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {8245},
pmid = {33859247},
issn = {2045-2322},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/analysis ; Genetic Variation ; Germany ; Horse Diseases/parasitology ; Horses/parasitology ; Intestinal Diseases, Parasitic ; Mitochondria/*genetics ; Parasite Egg Count/veterinary ; Phylogeny ; Sequence Analysis, DNA ; *Strongyloidea/classification/genetics ; Ukraine ; },
abstract = {Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. In this study, the nucleotide sequences of the nuclear second internal transcribed spacer (ITS-2) and the mitochondrial partial cytochrome c oxidase subunit I (COI) were determined for adults of six cyathostomin species (Coronocyclus coronatus, Coronocyclus labiatus, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus longibursatus, Cylicostephanus minutus) collected from different equine species within two geographic regions. Maximum likelihood trees were calculated for ITS-2, COI, and concatenated data. No obvious differentiation was observed between geographic regions or equine host species. As previously reported, Coronocyclus coronatus and Cylicostephanus calicatus revealed a close relationship. Cryptic species were detected in Cylicostephanus minutus and Cylicostephanus calicatus. Cylicocyclus nassatus and Coronocyclus labiatus showed diverse mitochondrial and nuclear haplotypes occurring in different combinations, while Cylicostephanus longibursatus was comparatively homogenous. In conclusion, a combined analysis of nuclear and mitochondrial haplotypes improved resolution of the phylogeny and should be applied to the remaining cyathostomin species and across additional equine host species and geographic regions.},
}
@article {pmid33891583,
year = {2021},
author = {Edwards, DM and Røyrvik, EC and Chustecki, JM and Giannakis, K and Glastad, RC and Radzvilavicius, AL and Johnston, IG},
title = {Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck.},
journal = {PLoS biology},
volume = {19},
number = {4},
pages = {e3001153},
pmid = {33891583},
issn = {1545-7885},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Arabidopsis ; DNA, Mitochondrial/genetics ; Drosophila ; Eukaryota/classification/*genetics ; Gene Expression Regulation, Developmental ; Genetic Speciation ; Germ Cells/*metabolism ; Germ-Line Mutation/physiology ; Humans ; Mice ; Mitochondria/genetics ; Mitochondrial Dynamics/genetics ; Models, Genetic ; Mutagenesis/physiology ; Mutation/*physiology ; Mutation Rate ; Organelle Biogenesis ; Organelles/*genetics/physiology ; },
abstract = {Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic "bottleneck" increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller's ratchet-the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller's ratchet is avoided in different eukaryotes.},
}
@article {pmid33929506,
year = {2021},
author = {Liao, Z and Schelcher, C and Smirnov, A},
title = {YbeY, éminence grise of ribosome biogenesis.},
journal = {Biochemical Society transactions},
volume = {49},
number = {2},
pages = {727-745},
doi = {10.1042/BST20200669},
pmid = {33929506},
issn = {1470-8752},
mesh = {Amino Acid Sequence ; Animals ; GTP-Binding Proteins/*metabolism ; Humans ; Phylogeny ; Protein Binding ; RNA-Binding Proteins/*metabolism ; Ribonucleases/classification/genetics/*metabolism ; Ribosomal Proteins/*metabolism ; Ribosomes/*metabolism ; Sequence Homology, Amino Acid ; },
abstract = {YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.},
}
@article {pmid33951769,
year = {2021},
author = {Ndosi, BA and Park, H and Lee, D and Choe, S and Kang, Y and Nath, TC and Bia, MM and Eamudomkarn, C and Jeon, HK and Eom, KS},
title = {Mitochondrial Genome of Spirometra theileri Compared with Other Spirometra Species.},
journal = {The Korean journal of parasitology},
volume = {59},
number = {2},
pages = {139-148},
pmid = {33951769},
issn = {1738-0006},
support = {//International Parasite Resource Bank/ ; 2020-0042//Inclusive Business Solution (IBS) project, Korea/ ; },
mesh = {Animals ; Genome, Helminth ; *Genome, Mitochondrial ; Male ; Panthera/parasitology ; Phylogeny ; Spirometra/classification/*genetics/isolation &amp; purification ; Tanzania ; },
abstract = {This study was carried out to provide information on the taxonomic classification and analysis of mitochondrial genomes of Spirometra theileri. One strobila of S. theileri was collected from the intestine of an African leopard (Panthera pardus) in the Maswa Game Reserve, Tanzania. The complete mtDNA sequence of S. theileri was 13,685 bp encoding 36 genes including 12 protein genes, 22 tRNAs and 2 rRNAs with absence of atp8. Divergences of 12 protein-coding genes were as follow: 14.9% between S. theileri and S. erinaceieuropaei, 14.7% between S. theileri and S. decipiens, and 14.5% between S. theileri with S. ranarum. Divergences of 12 proteins of S. theileri and S. erinaceieuropaei ranged from 2.3% in cox1 to 15.7% in nad5, while S. theileri varied from S. decipiens and S. ranarum by 1.3% in cox1 to 15.7% in nad3. Phylogenetic relationship of S. theileri with eucestodes inferred using the maximum likelihood and Bayesian inferences exhibited identical tree topologies. A clade composed of S. decipiens and S. ranarum formed a sister species to S. erinaceieuropaei, and S. theileri formed a sister species to all species in this clade. Within the diphyllobothridean clade, Dibothriocephalus, Diphyllobothrium and Spirometra formed a monophyletic group, and sister genera were well supported.},
}
@article {pmid33958611,
year = {2021},
author = {Tuda, M and Iwase, SI and Kébé, K and Haran, J and Skuhrovec, J and Sanaei, E and Tsuji, N and Podlussány, A and Merkl, O and El-Heneidy, AH and Morimoto, K},
title = {Diversification, selective sweep, and body size in the invasive Palearctic alfalfa weevil infected with Wolbachia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {9664},
pmid = {33958611},
issn = {2045-2322},
mesh = {Animals ; Asia ; Body Size ; Europe ; Female ; Genetic Variation/genetics ; Haplotypes/genetics ; Introduced Species ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Weevils/genetics/*microbiology ; *Wolbachia ; },
abstract = {The alfalfa weevil Hypera postica, native to the Western Palearctic, is an invasive legume pest with two divergent mitochondrial clades in its invading regions, the Western clade and the Eastern/Egyptian clade. However, knowledge regarding the native populations is limited. The Western clade is infected with the endosymbiotic bacteria Wolbachia that cause cytoplasmic incompatibility in host weevils. Our aim was to elucidate the spatial genetic structure of this insect and the effect of Wolbachia on its population diversity. We analyzed two mitochondrial and two nuclear genes of the weevil from its native ranges. The Western clade was distributed in western/central Europe, whereas the Eastern/Egyptian clade was distributed from the Mediterranean basin to central Asia. Intermediate mitotypes were found from the Balkans to central Asia. Most Western clade individuals in western Europe were infected with an identical Wolbachia strain. Mitochondrial genetic diversity of the infected individuals was minimal. The infected clades demonstrated a higher nonsynonymous/synonymous substitution rate ratio than the uninfected clades, suggesting a higher fixation of nonsynonymous mutations due to a selective sweep by Wolbachia. Trans-Mediterranean and within-European dispersal routes were supported. We suggest that the ancestral populations diversified by geographic isolation due to glaciations and that the diversity was reduced in the west by a recent Wolbachia-driven sweep(s). The intermediate clade exhibited a body size and host plant that differed from the other clades. Pros and cons of the possible use of infected-clade males to control uninfected populations are discussed.},
}
@article {pmid33965538,
year = {2021},
author = {Neiber, MT and Chueca, LJ and Caro, A and Teixeira, D and Schlegel, KA and Gómez-Moliner, BJ and Walther, F and Glaubrecht, M and Hausdorf, B},
title = {Incorporating palaeogeography into ancestral area estimation can explain the disjunct distribution of land snails in Macaronesia and the Balearic Islands (Helicidae: Allognathini).},
journal = {Molecular phylogenetics and evolution},
volume = {162},
number = {},
pages = {107196},
doi = {10.1016/j.ympev.2021.107196},
pmid = {33965538},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/genetics ; *Islands ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Snails/*genetics ; Spain ; },
abstract = {The systematics and biogeographical history of the Eastern Mediterranean and Macaronesian land snail tribe Allognathini (Helicidae: Helicinae) is investigated based on mitochondrial and nuclear DNA sequence data. Our molecular phylogenetic analyses indicate that the genus-group systematics of the tribe needs to be revised. We show for the first time that the narrow-range endemics Lampadia and Idiomela from the Madeira Archipelago belong to Allognathini and represent together the sister group of the diverse Canary Island Hemicycla radiation. We therefore suggest synonymising Lampadiini with Allognathini. Sister to these Macaronesian genera was the Balearic Island Allognathus radiation. Pseudotachea was not recovered as a monophyletic group and the two currently recognised species clustered in Iberus. Similarly, Adiverticula was not recovered as a monophyletic group and clustered in Hemicycla. We therefore suggest synonymising Pseudotachea with Iberus and Adiverticula with Hemicycla. The six genera in Allognathini, which we distinguish here (Cepaea, Iberus, Allognathus, Hemicycla, Idiomela and Lampadia), originated in Western to South-western Europe according to our ancestral area estimation and the fossil record. The disjunct distribution of the Balearic Islands and Macaronesian sister clades and the mainly Iberian Iberus clade that separated earlier can be explained by the separation of the Betic-Rif System from the Iberian Peninsula during the late Oligocene to early Miocene, along with independent Miocene dispersals to the Balearic Islands and Macaronesia from the Iberian Peninsula, where the ancestral lineage became extinct.},
}
@article {pmid33975946,
year = {2021},
author = {Takusagawa, M and Kobayashi, Y and Fukao, Y and Hidaka, K and Endo, M and Sugiyama, H and Hamaji, T and Kato, Y and Miyakawa, I and Misumi, O and Shikanai, T and Nishimura, Y},
title = {HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {20},
pages = {},
pmid = {33975946},
issn = {1091-6490},
mesh = {Chlamydomonas reinhardtii/*genetics/metabolism ; Chloroplast Proteins/classification/*genetics/metabolism ; DNA, Chloroplast/*genetics/metabolism ; Gene Expression Regulation ; Genome, Chloroplast/*genetics ; HMG-Box Domains/*genetics ; Mass Spectrometry/methods ; Mutation ; Phylogeny ; Protein Binding ; Proteomics/methods ; Tandem Repeat Sequences/*genetics ; },
abstract = {Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA-protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9-mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.},
}
@article {pmid33984441,
year = {2021},
author = {Lim, LWK and Chung, HH and Lau, MML and Aziz, F and Gan, HM},
title = {Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.},
journal = {Gene},
volume = {791},
number = {},
pages = {145708},
doi = {10.1016/j.gene.2021.145708},
pmid = {33984441},
issn = {1879-0038},
mesh = {Animals ; Base Sequence/genetics ; Biomarkers ; Cyprinidae/*classification/*genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Indonesia ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.},
}
@article {pmid34009087,
year = {2022},
author = {Ma, ZJ and Li, GZ and Chen, SM and Han, JL and Hanif, Q},
title = {Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus).},
journal = {Animal biotechnology},
volume = {33},
number = {6},
pages = {1318-1321},
doi = {10.1080/10495398.2021.1895187},
pmid = {34009087},
issn = {1532-2378},
mesh = {Cattle/genetics ; Animals ; Phylogeny ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Genetic Variation/genetics ; },
abstract = {Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai-Tibetan Plateau. So far, most studies on the molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on the small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) and four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. The present study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.},
}
@article {pmid34031453,
year = {2021},
author = {Kloss-Brandstätter, A and Summerer, M and Horst, D and Horst, B and Streiter, G and Raschenberger, J and Kronenberg, F and Sanguansermsri, T and Horst, J and Weissensteiner, H},
title = {An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {10816},
pmid = {34031453},
issn = {2045-2322},
mesh = {Asian People/ethnology/*genetics ; Cambodia/ethnology ; Female ; Genome, Mitochondrial ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Maternal Inheritance ; Mitochondria/*classification/genetics ; Phylogeny ; Refugees/*classification ; Whole Genome Sequencing/*methods ; },
abstract = {Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.},
}
@article {pmid34070437,
year = {2021},
author = {Ai, D and Peng, L and Qin, D and Zhang, Y},
title = {Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers' Mitochondrial Phylogenomics.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34070437},
issn = {1422-0067},
support = {31420103911//National Natural Science Foundation of China/ ; 2015FY210300//Ministry of Science and Technology of the People's Republic of China/ ; 2005DKA21402//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Animals ; Base Composition ; Codon Usage ; Gene Order ; *Genome, Mitochondrial ; Hemiptera/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Tandem Repeat Sequences/genetics ; },
abstract = {Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers' phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.},
}
@article {pmid34072215,
year = {2021},
author = {Dür, A and Huber, N and Parson, W},
title = {Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences.},
journal = {International journal of molecular sciences},
volume = {22},
number = {11},
pages = {},
pmid = {34072215},
issn = {1422-0067},
mesh = {Algorithms ; Computational Biology/methods ; DNA, Mitochondrial/chemistry/*genetics ; Genome, Mitochondrial ; Genomics/methods ; *Haplotypes ; Humans ; Mitochondria/genetics ; *Phylogeny ; Regulatory Sequences, Nucleic Acid ; },
abstract = {In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.},
}
@article {pmid34082186,
year = {2021},
author = {Singh, L and Atilano, SR and Jager, MJ and Kenney, MC},
title = {Mitochondrial DNA polymorphisms and biogenesis genes in primary and metastatic uveal melanoma cell lines.},
journal = {Cancer genetics},
volume = {256-257},
number = {},
pages = {91-99},
doi = {10.1016/j.cancergen.2021.05.002},
pmid = {34082186},
issn = {2210-7762},
mesh = {Cell Line, Tumor ; DNA, Mitochondrial/*genetics ; Gene Dosage ; *Genes, Neoplasm ; Genome, Human ; Haplotypes/genetics ; Heteroplasmy/genetics ; Humans ; Melanoma/*genetics/*pathology ; Neoplasm Metastasis ; *Organelle Biogenesis ; Phylogeny ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide/genetics ; Uveal Neoplasms/*genetics/*pathology ; Uveal Melanoma ; },
abstract = {PURPOSE: This study was designed to identify mitochondrial (mt) DNA variations in primary and metastatic uveal melanoma (UM) cell lines and their relation with cell metabolism to gain insight into metastatic progression.<br><br>METHOD: The entire mtDNA genomes were sequenced using Sanger sequencing from two primary UM cell lines (92.1 and MEL270) and two cell lines (OMM2.3 and OMM2.5) derived from liver metastases of the MEL270 patient. The mtDNA copy numbers determined by the ratio of nDNA versus mtDNA. qRT-PCR was used to evaluate expression levels of mitochondrial biogenesis genes.<br><br>RESULTS: Sequencing showed that cell line MEL270 and metastases-derived OMM2.3 and OMM2.5 cell lines had homoplasmic single nucleotide polymorphisms (SNPs) representing J1c7a haplogroup, whereas 92.1 cells had mtDNA H31a haplogroup. mtDNA copy numbers were significantly higher in primary cell lines. The metastatic UM cells showed down-regulation of POLG, TFAM, NRF-1 and SIRT1 compared to their primary MEL270 cells. PGC-1&#x3b1; was downregulated in 92.1 and upregulated in MEL270, OMM2.3 and OMM2.5.<br><br>CONCLUSIONS: Our finding suggests that within metastatic cells, the heteroplasmic SNPs, copy numbers and mitochondrial biogenesis genes are modulated differentially compared to their primary UM cells. Therefore, investigating pathogenic mtDNA variants associated with cancer metabolic susceptibility may provide future therapeutic strategies in metastatic UM.},
}
@article {pmid34083683,
year = {2021},
author = {Feng, JT and Xia, LP and Yan, CR and Miao, J and Ye, YY and Li, JJ and Guo, BY and Lü, ZM},
title = {Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11748},
pmid = {34083683},
issn = {2045-2322},
mesh = {Animals ; Base Composition ; Codon ; Computational Biology/methods ; Gastropoda/*classification/*genetics ; Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Mitochondria/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Selection, Genetic ; },
abstract = {Neritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.},
}
@article {pmid34087289,
year = {2021},
author = {Lu, Z and Tang, M and Zhang, M and Li, Y and Shi, F and Zhan, F and Zhao, L and Li, J and Lin, L and Qin, Z},
title = {Expression and functional analysis of the BCL2-Associated agonist of cell death (BAD) gene in grass carp (Ctenopharyngodon idella) during bacterial infection.},
journal = {Developmental and comparative immunology},
volume = {123},
number = {},
pages = {104160},
doi = {10.1016/j.dci.2021.104160},
pmid = {34087289},
issn = {1879-0089},
mesh = {Aeromonas hydrophila/*physiology ; Amino Acid Sequence ; Animals ; Apoptosis ; Carps/*immunology ; Cell Line ; Cloning, Molecular ; Fish Proteins/genetics/*metabolism ; Gram-Negative Bacterial Infections/*immunology ; Immunity, Innate ; Lipopolysaccharides/immunology ; Phylogeny ; Spleen ; Staphylococcal Infections/*immunology ; Staphylococcus aureus/*physiology ; Transcriptome ; Up-Regulation ; bcl-Associated Death Protein/genetics/*metabolism ; },
abstract = {The BCL2-associated agonist of cell death protein is a key participant in apoptosis dependent on mitochondria and in disease progression that involves the regulation of cell death, such as tumorigenesis, diabetes, sepsis shock, and epilepsy. Nevertheless, the mechanisms underlying the immune responses to teleost BAD bacterial infection and mitochondrial-dependent apoptosis remains unclear. In order to elucidate the mechanisms involved, in this study, a Ctenopharyngodon idella (grass carp) BAD gene named GcBAD1 was firstly cloned and characterized. The results indicated that the ORF (open reading frame) of GcBAD1 was 438 bp in length, encoding a 145-amino acid putative protein of 16.66 kDa. This deduced amino acid sequence has a better identity than another teleost species according to a phylogenetic analysis, and contains a Bcl2-BAD-1 domain. In healthy grass carp fish, the mRNA transcripts of GcBAD1 were widely present in the studied tissues, which could be ranked as follows; spleen > brain > middle-kidney > head-kidney > liver > gills > intestines > heart and muscle. In addition, during infection by Aeromonas hydrophila and Staphylococcus aureus, the mRNA transcription and protein levels expression of GcBAD1 in the head-kidney, spleen, and liver tissues of the fish were significantly up-regulated. Moreover, when the C. idellus kidney cell line (CIK) cells were incubated with Lipopolysaccharide (LPS) and lipoteichoic acid (LTA), the GcBAD1 expression transcripts were also significantly up-regulated. Additionally, overexpression of GcBAD1 in CIK cells was able to activate apoptosis-related genes, including those encoding p53, Cytochrome C (CytoC), caspase-3, and caspase-9. Besides, in the TUNEL assays, when pEGFP-BAD1 was over-expressed, the number of red signals associated with apoptosis were significantly increased in the CIK cells infected with LPS or LTA at 12 h. This study demonstrates that GcBAD1 has a significant role in the mitochondrial apoptosis pathway of grass carp's innate immunity. Our findings provide new insight into the potential mechanisms of teleost antibacterial immunity.},
}
@article {pmid34089318,
year = {2021},
author = {Vrzoňová, R and Tóth, R and Siváková, B and Moťovská, A and Gaplovská-Kyselá, K and Baráth, P and Tomáška, &#x13d; and Gácser, A and Gabaldón, T and Nosek, J and Neboháčová, M},
title = {OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway.},
journal = {FEMS yeast research},
volume = {21},
number = {5},
pages = {},
doi = {10.1093/femsyr/foab034},
pmid = {34089318},
issn = {1567-1364},
mesh = {Acetyl-CoA C-Acetyltransferase/genetics ; Acetyl-CoA C-Acyltransferase/genetics ; Animals ; Chromatography, Liquid ; Mitochondria ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; *Tandem Mass Spectrometry ; },
abstract = {The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.},
}
@article {pmid34099752,
year = {2021},
author = {Machkour-M'Rabet, S and Hanes, MM and Martínez-Noguez, JJ and Cruz-Medina, J and García-De León, FJ},
title = {The queen conch mitogenome: intra- and interspecific mitogenomic variability in Strombidae and phylogenetic considerations within the Hypsogastropoda.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11972},
pmid = {34099752},
issn = {2045-2322},
mesh = {Animals ; Base Sequence ; Caribbean Region ; Cell Extracts/genetics ; Gastropoda/*classification/*genetics ; Mitochondria/genetics/metabolism ; NAD/metabolism ; Phylogeny ; RNA, Ribosomal/metabolism ; RNA, Transfer/metabolism ; },
abstract = {Aliger gigas is an economically important and vulnerable marine species. We present a new mitogenome of A. gigas from the Mexican Caribbean and use the eight publicly available Strombidae mitogenomes to analyze intra- and interspecific variation. We present the most complete phylogenomic understanding of Hypsogastropoda to date (17 superfamilies, 39 families, 85 genera, 109 species) to revisit the phylogenetic position of the Stromboidea and evaluate divergence times throughout the phylogeny. The A. gigas mitogenome comprises 15,460 bp including 13 PCGs, 22 tRNAs, and two rRNAs. Nucleotide diversity suggested divergence between the Mexican and Colombian lineages of A. gigas. Interspecific divergence showed high differentiation among Strombidae species and demonstrated a close relationship between A. gigas and Strombus pugilis, between Lambis lambis and Harpago chiragra, and among Tridentarius dentatus/Laevistrombus canarium/Ministrombus variabilis. At the intraspecific level, the gene showing the highest differentiation is ATP8 and the lowest is NAD4L, whereas at the interspecific level the NAD genes show the highest variation and the COX genes the lowest. Phylogenomic analyses confirm that Stromboidea belongs in the non-Latrogastropoda clade and includes Xenophoridea. The phylogenomic position of other superfamilies, including those of previously uncertain affiliation, is also discussed. Finally, our data indicated that Stromboidea diverged into two principal clades in the early Cretaceous while Strombidae diversified in the Paleocene, and lineage diversification within A. gigas took place in the Pleistocene.},
}
@article {pmid34109499,
year = {2021},
author = {Riyaz, M and Shah, RA and Savarimuthu, I and Kuppusamy, S},
title = {Comparative mitochondrial genome analysis of Eudocima salaminia (Cramer, 1777) (Lepidoptera: Noctuoidea), novel gene rearrangement and phylogenetic relationship within the superfamily Noctuoidea.},
journal = {Molecular biology reports},
volume = {48},
number = {5},
pages = {4449-4463},
pmid = {34109499},
issn = {1573-4978},
support = {EMR/2017/000566//DST/ ; },
mesh = {Animals ; Base Pairing/genetics ; Gene Order ; *Gene Rearrangement ; *Genes, Insect ; *Genome, Mitochondrial ; India ; Insect Proteins/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Moths/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {The species Eudocima salaminia (Cramer, 1777) commonly known as the fruit-piercing moth belongs to family Erebidae. Its distribution varies from India and across South-east Asia, pacific islands and parts of Australia. The insect is a devastating pest of citrus, longans and lychees. In the present study, complete mitochondrial genome of Eudocima salaminia was sequenced and analyzed using Illumina sequencer. The phylogenetic tree was reconstructed based on nucleotide sequences of 13 PCGs using Maximum likelihood method-General Reversible mitochondrial (mtREV) model. The mitogenome has 15,597 base pairs (bp) in length, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A + T-rich region. All protein-coding genes (PCGs) initiate with canonical start codon ATN. The gene order (trnQ-trnI-trnM) of tRNA shows a different rearrangement compared to ancestral insect gene order (trnI-trnQ-trnM). Almost all tRNAs have a typical cloverleaf secondary structure except for trnS1 (AGN) which lacks the dihydrouridine arm. At the beginning of the control region, we observed a conserved polyT", motif "ATTTA" and microsatellite (TA)n element. There are 21 intergenic regions and five overlapping regions ranging from 1 to 73 bp and 1 to 8 bp, respectively. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Maximum likelihood method showed the family level relationships as (Notodontidae + (Euteliidae + Noctuidae + (Erebidae + Nolidae))). The present study represents the similarity to phylogenetic analysis of Noctuoidea mitogenome. Moreover, the family Erebidae is the sister to the families of (Euteliidae + Noctuidae + Nolidae).},
}
@article {pmid34111145,
year = {2021},
author = {Horoiwa, M and Mandagi, IF and Sutra, N and Montenegro, J and Tantu, FY and Masengi, KWA and Nagano, AJ and Kusumi, J and Yasuda, N and Yamahira, K},
title = {Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0245316},
pmid = {34111145},
issn = {1932-6203},
mesh = {Animals ; *Haplotypes ; *DNA, Mitochondrial/genetics ; Islands ; Phylogeny ; Polymorphism, Single Nucleotide ; Genetic Introgression ; Mitochondria/genetics ; Genetics, Population ; Fishes/genetics/classification ; Ecosystem ; },
abstract = {Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.},
}
@article {pmid34154402,
year = {2021},
author = {Comandatore, F and Radaelli, G and Montante, S and Sacchi, L and Clementi, E and Epis, S and Cafiso, A and Serra, V and Pajoro, M and Di Carlo, D and Floriano, AM and Stavru, F and Bandi, C and Sassera, D},
title = {Modeling the Life Cycle of the Intramitochondrial Bacterium "Candidatus Midichloria mitochondrii" Using Electron Microscopy Data.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0057421},
pmid = {34154402},
issn = {2150-7511},
mesh = {Alphaproteobacteria/*growth &amp; development/*ultrastructure ; Animals ; DNA, Bacterial ; Ixodes/*microbiology ; *Life Cycle Stages ; Microscopy, Electron/*methods ; Mitochondria/microbiology ; Phylogeny ; Symbiosis ; },
abstract = {"Candidatus Midichloria mitochondrii" is a Gram-negative bacterium that lives in strict intracellular symbiosis with the hard tick Ixodes ricinus, forming one of the most intriguing endosymbiosis described to date. The bacterium is capable of durably colonizing the host mitochondria, a peculiar tropism that makes "Ca. Midichloria mitochondrii" a very interesting tool to study the physiology of these cellular organelles. The interaction between the symbiont and the organelle has, however, been difficult to characterize. A parallelism with the predatory bacterium Bdellovibrio bacteriovorus has been drawn, suggesting the hypothesis that "Ca. Midichloria mitochondrii" could prey on mitochondria and consume them to multiply. We studied the life cycle of the bacterium within the host oocytes using a multidisciplinary approach, including electron microscopy, molecular biology, statistics, and systems biology. Our results were not coherent with a predatory-like behavior by "Ca. Midichloria mitochondrii" leading us to propose a novel hypothesis for its life cycle. Based on our results, we here present a novel model called the "mitochondrion-to-mitochondrion hypothesis." Under this model, the bacterium would be able to move from mitochondrion to mitochondrion, possibly within a mitochondrial network. We show that this model presents a good fit with quantitative electron microscopy data. IMPORTANCE Our results suggest that "Candidatus Midichloria mitochondrii," the intramitochondrial bacterium, does not invade mitochondria like predatory bacteria do but instead moves from mitochondrion to mitochondrion within the oocytes of Ixodes ricinus. A better understanding of the lifestyle of "Ca. Midichloria mitochondrii" will allow us to better define the role of this bacterial symbiont in the host physiology.},
}
@article {pmid34175310,
year = {2021},
author = {Parrot, C and Moulinier, L and Bernard, F and Hashem, Y and Dupuy, D and Sissler, M},
title = {Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids.},
journal = {The Journal of biological chemistry},
volume = {297},
number = {2},
pages = {100913},
pmid = {34175310},
issn = {1083-351X},
mesh = {Amino Acid Sequence ; Amino Acids/*metabolism ; Amino Acyl-tRNA Synthetases/chemistry/genetics/*metabolism ; Animals ; Cytosol/metabolism ; Humans ; Leishmania/*enzymology/isolation &amp; purification ; Leishmaniasis/enzymology/parasitology/*pathology ; Mitochondria/metabolism ; Phylogeny ; RNA, Transfer/*genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Trypanosomatid parasites are responsible for various human diseases, such as sleeping sickness, animal trypanosomiasis, or cutaneous and visceral leishmaniases. The few available drugs to fight related parasitic infections are often toxic and present poor efficiency and specificity, and thus, finding new molecular targets is imperative. Aminoacyl-tRNA synthetases (aaRSs) are essential components of the translational machinery as they catalyze the specific attachment of an amino acid onto cognate tRNA(s). In trypanosomatids, one gene encodes both cytosolic- and mitochondrial-targeted aaRSs, with only three exceptions. We identify here a unique specific feature of aaRSs from trypanosomatids, which is that most of them harbor distinct insertion and/or extension sequences. Among the 26 identified aaRSs in the trypanosome Leishmania tarentolae, 14 contain an additional domain or a terminal extension, confirmed in mature mRNAs by direct cDNA nanopore sequencing. Moreover, these RNA-Seq data led us to address the question of aaRS dual localization and to determine splice-site locations and the 5'-UTR lengths for each mature aaRS-encoding mRNA. Altogether, our results provided evidence for at least one specific mechanism responsible for mitochondrial addressing of some L. tarentolae aaRSs. We propose that these newly identified features of trypanosomatid aaRSs could be developed as relevant drug targets to combat the diseases caused by these parasites.},
}
@article {pmid34175396,
year = {2021},
author = {Lin, C and Tang, D and Gao, X and Jiang, H and Du, C and Zhu, J},
title = {Molecular characterization, dynamic transcription, and potential function of KIF3A/KIF3B during spermiogenesis in Opsariichthys bidens.},
journal = {Gene},
volume = {798},
number = {},
pages = {145795},
doi = {10.1016/j.gene.2021.145795},
pmid = {34175396},
issn = {1879-0038},
mesh = {Animals ; Cyprinidae/genetics/*physiology ; Kinesins/chemistry/genetics/*physiology ; Male ; Microtubules/metabolism ; Mitochondria/metabolism ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sperm Tail/physiology ; Spermatids/physiology/ultrastructure ; Spermatogenesis/genetics/*physiology ; Testis/metabolism ; Transcription, Genetic ; },
abstract = {Spermiogenesis is the final phase of spermatogenesis, wherein the spermatids differentiate into mature spermatozoa via complex morphological transformation. In this process, kinesin plays an important role. Here, we observed the morphological transformation of spermatids and analyzed the characterization, dynamic transcription, and potential function of kinesin KIF3A/KIF3B during spermiogenesis in Chinese hook snout carp (Opsariichthys bidens). We found that the full-length cDNAs of O. bidens kif3a and kif3b were 2544 and 2806 bp in length comprising 119 bp and 259 bp 5' untranslated region (UTR), 313 bp and 222 bp 3' UTR, and 2112 bp and 2325 bp open reading frame encoding 703 and 774 amino acids, respectively. Ob-KIF3A/KIF3B proteins have three domains, namely N-terminal head, coiled-coil stalk, and C-terminal tail, and exhibit high similarity with homologous proteins in vertebrates and invertebrates. Ob-kif3a/kif3b mRNAs were ubiquitously expressed in all tissues examined, with the highest expression in the brain and stage-IV testis. Immunofluorescence results showed that Ob-KIF3A was co-localized with tubulin and the mitochondria. Particularly, in early spermatids, Ob-KIF3A, tubulin, and the mitochondrial signals were evenly distributed in the cytoplasm, whereas in middle spermatids, they were distributed around the nucleus. In the late stage, the signals were concentrated on one side of the nucleus, where the tail is formed, whereas in mature sperms, they were detected in the midpiece and flagellum. These results indicate that Ob-KIF3A/KIF3B may participate in nuclear reshaping, flagellum formation, and mitochondrial aggregation in the midpiece during spermiogenesis.},
}
@article {pmid34211040,
year = {2021},
author = {Sarkar, BK and Sharma, AR and Bhattacharya, M and Sharma, G and Lee, SS and Chakraborty, C},
title = {Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13701},
pmid = {34211040},
issn = {2045-2322},
mesh = {*Algorithms ; Animals ; Base Sequence ; Cluster Analysis ; DNA/genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial ; Humans ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA/*methods ; beta-Globins/genetics ; },
abstract = {We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.},
}
@article {pmid34222053,
year = {2021},
author = {Li, T and Fang, Z and He, Q and Wang, C and Meng, X and Yu, B and Zhou, Z},
title = {Characterizing the Xenoma of Vairimorpha necatrix Provides Insights Into the Most Efficient Mode of Microsporidian Proliferation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {699239},
pmid = {34222053},
issn = {2235-2988},
mesh = {Animals ; Cell Proliferation ; Humans ; In Situ Hybridization, Fluorescence ; *Microsporidia/genetics ; Phylogeny ; },
abstract = {Microsporidia are a group of obligated intracellular parasites that can infect nearly all vertebrates and invertebrates, including humans and economic animals. Microsporidian Vairimorpha necatrix is a natural pathogen of multiple insects and can massively proliferate by making tumor-like xenoma in host tissue. However, little is known about the subcellular structures of this xenoma and the proliferation features of the pathogens inside. Here, we characterized the V. necatrix xenoma produced in muscle cells of silkworm midgut. In result, the whitish xenoma was initially observed on the 12[th] day post infection on the outer surface of the midgut and later became larger and numerous. The observation by scanning electronic microscopy showed that the xenoma is mostly elliptical and spindle with dense pathogen-containing protrusions and spores on the surface, which were likely shedding off the xenoma through exocytosis and could be an infection source of other tissues. Demonstrated with transmission electron microscopy and fluorescent staining, the xenoma was enveloped by a monolayer membrane, and full of vesicle structures, mitochondria, and endoplasmic reticulum around parasites in development, suggesting that high level of energy and nutrients were produced to support the massive proliferation of the parasites. Multiple hypertrophic nuclei were found in one single xenoma, indicating that the cyst was probably formed by fusion of multiple muscle cells. Observed by fluorescence in situ hybridization, pathogens in the xenoma were in merongony, sporogony, and octosporogony, and mature stages. And mature spores were pushed to the center while vegetative pathogens were in the surface layer of the xenoma. The V. necatrix meront usually contained two to three nuclei, and sporont contained two nuclei and was wrapped by a thick membrane with high electron density. The V. necatrix sporogony produces two types of spores, the ordinary dikaryotic spore and unicellular octospores, the latter of which were smaller in size and packed in a sporophorous vesicle. In summary, V. necatrix xenoma is a specialized cyst likely formed by fusion of multiple muscle cells and provides high concentration of energy and nutrients with increased number of mitochondria and endoplasmic reticulum for the massive proliferation of pathogens inside.},
}
@article {pmid34274481,
year = {2021},
author = {Kimball, RT and Guido, M and Hosner, PA and Braun, EL},
title = {When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes).},
journal = {Gene},
volume = {801},
number = {},
pages = {145841},
doi = {10.1016/j.gene.2021.145841},
pmid = {34274481},
issn = {1879-0038},
mesh = {Animals ; Cell Nucleus/genetics ; Galliformes/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; },
abstract = {Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is "genuine" and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the "inaccurate estimation" hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.},
}
@article {pmid34287642,
year = {2021},
author = {Vendramin, R and Katopodi, V and Cinque, S and Konnova, A and Knezevic, Z and Adnane, S and Verheyden, Y and Karras, P and Demesmaeker, E and Bosisio, FM and Kucera, L and Rozman, J and Gladwyn-Ng, I and Rizzotto, L and Dassi, E and Millevoi, S and Bechter, O and Marine, JC and Leucci, E},
title = {Activation of the integrated stress response confers vulnerability to mitoribosome-targeting antibiotics in melanoma.},
journal = {The Journal of experimental medicine},
volume = {218},
number = {9},
pages = {},
pmid = {34287642},
issn = {1540-9538},
mesh = {Aged ; Animals ; Antibiotics, Antineoplastic/*pharmacology ; Cell Line, Tumor ; Doxycycline/pharmacology ; Drug Resistance, Neoplasm/drug effects ; Female ; Humans ; Male ; Melanoma/*drug therapy/genetics/mortality/*pathology ; Mice, Inbred C57BL ; Mice, Nude ; Mitochondrial Ribosomes/*drug effects ; Protein Kinase Inhibitors/pharmacology ; Stress, Physiological/drug effects ; Tigecycline/pharmacology ; Uveal Neoplasms/drug therapy/pathology ; Xenograft Model Antitumor Assays ; Mice ; Uveal Melanoma ; },
abstract = {The ability to adapt to environmental stress, including therapeutic insult, contributes to tumor evolution and drug resistance. In suboptimal conditions, the integrated stress response (ISR) promotes survival by dampening cytosolic translation. We show that ISR-dependent survival also relies on a concomitant up-regulation of mitochondrial protein synthesis, a vulnerability that can be exploited using mitoribosome-targeting antibiotics. Accordingly, such agents sensitized to MAPK inhibition, thus preventing the development of resistance in BRAFV600E melanoma models. Additionally, this treatment compromised the growth of melanomas that exhibited elevated ISR activity and resistance to both immunotherapy and targeted therapy. In keeping with this, pharmacological inactivation of ISR, or silencing of ATF4, rescued the antitumoral response to the tetracyclines. Moreover, a melanoma patient exposed to doxycycline experienced complete and long-lasting response of a treatment-resistant lesion. Our study indicates that the repurposing of mitoribosome-targeting antibiotics offers a rational salvage strategy for targeted therapy in BRAF mutant melanoma and a therapeutic option for NRAS-driven and immunotherapy-resistant tumors.},
}
@article {pmid34344905,
year = {2021},
author = {Collado, GA and Torres-Díaz, C and Valladares, MA},
title = {Phylogeography and molecular species delimitation reveal cryptic diversity in Potamolithus (Caenogastropoda: Tateidae) of the southwest basin of the Andes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15735},
pmid = {34344905},
issn = {2045-2322},
mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Chile ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics/*metabolism ; Gastropoda/classification/*physiology ; *Genetic Speciation ; *Genetic Variation ; Mitochondria/enzymology/genetics ; *Phylogeography ; },
abstract = {The species of the genus Potamolithus inhabiting the southwestern basin of the Andes are difficult to distinguish due to small size and similar shell morphology. Only Potamolithus australis and Potamolithus santiagensis have been traditionally recognized in this region, but the occurrence of several morphologically similar undescribed populations could increase the regional richness. Here we delimit described and potentially undescribed cryptic species of the genus using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis and diversity indices inferred six highly differentiated haplogroups, many of them sympatric and widespread in the study area. Phylogeographic analyses suggest a scenario of recent diversification and the occurrence of multiple refuges during the successive Pleistocene glaciations. Phylogenetic analysis also recovered six major clades that showed no relationship with physiography. Species delimitation analyses consistently recognized three or four candidate species apart from P. australis and P. santiagensis. Divergence times indicate that speciation of Chilean Potamolithus began at the end of the Pliocene, probably driven by climatic rather than geographic events. Considering the high inter- and intra-basin genetic diversity, conservation efforts should be focused on protecting sympatric taxa in the basins with the highest species richness.},
}
@article {pmid34378290,
year = {2021},
author = {Liu, X and Xu, L and Hu, K and Ren, S and Weng, M and Yu, J and Li, D and Zhang, J},
title = {New isolate of Loma psittaca (Microsporidia: Glugeidae) infecting the stomach wall of cultured hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀) in South China.},
journal = {The Journal of eukaryotic microbiology},
volume = {68},
number = {6},
pages = {e12868},
doi = {10.1111/jeu.12868},
pmid = {34378290},
issn = {1550-7408},
mesh = {Animals ; *Bass ; *Fish Diseases ; *Loma ; *Microsporidia ; *Microsporidiosis/veterinary ; Phylogeny ; Stomach ; },
abstract = {Loma psittaca, previously described as inhabiting the intestinal mucosa of an anadromous fish, Colomesus pisttacus, from the Amazon Basin, is reported as being found for the first time in a marine fish, the hybrid grouper (Epinephelus lanceolatus♂×Epinephelus fuscoguttatus♀), from Lingshui city, Hainan Province, China, expanding the geographical distribution and host range of this parasite. Numerous whitish xenomas (0.5-0.7 mm in diameter) of this new isolate of L. psittaca were found distinctly in the muscle layer of the host stomach wall. Electron microscopic observations showed a monokaryotic nucleus in all developmental stages. Round or elongated multinucleate merogonial plasmodia surrounded by numerous mitochondria were observed initially, subsequently transforming into uninucleate sporonts through multiple fissions. Sporonts, each with a large centrally positioned nucleus, further developed into sporoblasts. Each sporoblast mother cell gave rise to two uninucleate sporoblasts by binary fission. Mature spores were ellipsoidal, measuring 4.0 ± 0.3 (3.7-4.3) μm in length and 2.2 ± 0.2 (2.1-2.5) μm in width. Spores possessed a mushroom-like anchoring disk, a bipartite polarplast, isofilar polar filaments arranged in 12-14 turns in one row, and a trilaminar spore wall. The obtained partial SSU rRNA gene sequence of the new isolate was 1330 bp in length and showed 99.4% sequence similarity with an estuary isolate of L. psittaca previously reported in South America. SSU rRNA gene-based phylogenetic analyses demonstrated that the two L. psittaca isolates first clustered together and then formed a dichotomy that included the digestive-tract-infecting Loma species, L. acerinae, with high support values within group I.},
}
@article {pmid34384346,
year = {2021},
author = {Schäffer, AA and McVeigh, R and Robbertse, B and Schoch, CL and Johnston, A and Underwood, BA and Karsch-Mizrachi, I and Nawrocki, EP},
title = {Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {400},
pmid = {34384346},
issn = {1471-2105},
mesh = {DNA, Ribosomal ; *Databases, Nucleic Acid ; Phylogeny ; *RNA, Ribosomal ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, RNA ; },
abstract = {BACKGROUND: The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron.<br><br>RESULTS: To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa.<br><br>CONCLUSION: Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.},
}
@article {pmid34388165,
year = {2021},
author = {Gul, S and Shah, KN and Rana, RM and Khan, MA and El-Shehawi, AM and Elseehy, MM},
title = {Phylogenetic and expression dynamics of tomato ClpB/Hsp100 gene under heat stress.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0255847},
pmid = {34388165},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Chloroplasts/metabolism ; Cluster Analysis ; Endopeptidase Clp/classification/*metabolism ; Hot Temperature ; Solanum lycopersicum/*metabolism ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/classification/*metabolism ; Seedlings/metabolism ; Sequence Alignment ; },
abstract = {Heat shock proteins (Hsps) are stress-responsive molecular chaperones, which uphold proper protein folding in response to external and internal stresses. The Hsp100 gene family plays a substantial role in thermos-tolerance of plants. This study investigated evolutionary relationship and expression of ClpB/Hsp100 gene family in tomato under heat stress. Six SlHsp100 genes were identified using bioinformatics tools. In silico sub-cellular localization indicated that of these 6 ClpB/Hsp100 members, 4 are found in chloroplast, 1 in mitochondria and 1 in the cytoplasm. For evolutionary study, 36 SlHsp100 genes were included in the phylogenetic tree showing a hierarchical clustering shared by the members of the kingdoms Plantae, Archaea, Chromista, Fungi and Bacteria. A total 4 pairs of orthologous and 5 pairs of paralogous genes were identified. Functional divergence between different Hsp100 clusters showed considerable functional homology. Thermo-tolerance measured in terms of cell viability, cell membrane stability and pollen viability indicated that it was paralleled by thermal resistance of Hsps. Reverse transcriptase polymerase chain reaction was used to analyze gene expression in leaves of five-week-old tomato seedlings following exposure to heat stress (45°C) and control (25°C). Chloroplastic LeHSP110/ClpB gene was upregulated in all tomato genotypes after exposure to heat stress highlighting the crucial role of this gene family in acquired thermo-tolerance.},
}
@article {pmid34397079,
year = {2021},
author = {Wang, T and He, T and Ding, X and Zhang, Q and Yang, L and Nie, Z and Zhao, T and Gai, J and Yang, S},
title = {Confirmation of GmPPR576 as a fertility restorer gene of cytoplasmic male sterility in soybean.},
journal = {Journal of experimental botany},
volume = {72},
number = {22},
pages = {7729-7742},
doi = {10.1093/jxb/erab382},
pmid = {34397079},
issn = {1460-2431},
mesh = {Cytoplasm ; Fertility/genetics ; Phylogeny ; *Plant Infertility/genetics ; *Glycine max/genetics ; },
abstract = {In soybean, heterosis achieved through the three-line system has been gradually applied in breeding to increase yield, but the underlying molecular mechanism remains unknown. We conducted a genetic analysis using the pollen fertility of offspring of the cross NJCMS1A×NJCMS1C. All the pollen of F1 plants was semi-sterile; in F2, the ratio of pollen-fertile plants to pollen-semi-sterile plants was 208:189. This result indicates that NJCMS1A is gametophyte sterile, and the fertility restoration of NJCMS1C to NJCMS1A is a quality trait controlled by a single gene locus. Using bulked segregant analysis, the fertility restorer gene Rf in NJCMS1C was located on chromosome 16 between the markers BARCSOYSSR_16_1067 and BARCSOYSSR_16_1078. Sequence analysis of genes in that region showed that GmPPR576 was non-functional in rf cultivars. GmPPR576 has one functional allele in Rf cultivars but three non-functional alleles in rf cultivars. Phylogenetic analysis showed that the GmPPR576 locus evolved rapidly with the presence of male-sterile cytoplasm. GmPPR576 belongs to the RFL fertility restorer gene family and is targeted to the mitochondria. GmPPR576 was knocked out in soybean N8855 using CRISPR/Cas9. The T1 plants showed sterile pollen, and T2 plants produced few pods at maturity. The results indicate that GmPPR576 is the fertility restorer gene of NJCMS1A.},
}
@article {pmid34410224,
year = {2021},
author = {Bandini, G and Damerow, S and Sempaio Guther, ML and Guo, H and Mehlert, A and Paredes Franco, JC and Beverley, S and Ferguson, MA},
title = {An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34410224},
issn = {2050-084X},
support = {101842/WT_/Wellcome Trust/United Kingdom ; R01 AI031078/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Cloning, Molecular ; Fucosyltransferases/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Humans ; Mitochondria/*enzymology ; Phylogeny ; Trypanosoma brucei brucei/enzymology/*metabolism ; Galactoside 2-alpha-L-fucosyltransferase ; },
abstract = {Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential in Trypanosoma brucei. Here we show that the single identifiable T. brucei fucosyltransferase (TbFUT1) is a GDP-Fuc: β-D-galactose α-1,2-fucosyltransferase with an apparent preference for a Galβ1,3GlcNAcβ1-O-R acceptor motif. Conditional null mutants of TbFUT1 demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion of T. brucei and found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, the TbFUT1 gene was able to complement a Leishmania major mutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids.},
}
@article {pmid34492093,
year = {2021},
author = {Phadungsaksawasdi, K and Sunantaraporn, S and Seatamanoch, N and Kongdachalert, S and Phumee, A and Kraivichian, K and Sawaswong, V and Payungporn, S and Brownell, N and Siriyasatien, P},
title = {Molecular analysis of mitochrondrial cytb of Pediculus humanus capitis in Thailand revealed potential historical connection with South Asia.},
journal = {PloS one},
volume = {16},
number = {9},
pages = {e0257024},
pmid = {34492093},
issn = {1932-6203},
mesh = {Animals ; Child ; Cytochromes b/*genetics ; Ectoparasitic Infestations/epidemiology/*genetics/parasitology ; Female ; Genetic Variation/genetics ; Haplotypes/genetics ; Human Migration ; Humans ; Lice Infestations/epidemiology/*genetics/parasitology ; Male ; Mitochondria/genetics ; Pediculus/classification/*genetics/pathogenicity ; Phylogeny ; Thailand/epidemiology ; },
abstract = {BACKGROUND: Pediculus humanus capitis or head louse is an obligate ectoparasite and its infestation remains a major public health issue worldwide. Molecular analysis divides head lice into six clades and intra-clade genetic differences have been identified. Several hypotheses have been formulated to elucidate the discrepancies of the variety of head lice among different regions of the world. It is currently concluded that head lice distribution might be associated with human migration history. This study aims to investigate genetic data of human head lice in Thailand. We believe that the analysis could help establish the correlation between local and global head lice populations.<br><br>METHOD: We investigated mitochondrial cytochrome b (cytb) gene of the collected 214 head lice to evaluate genetic diversity from 15 provinces among 6 regions of Thailand. The head lice genes were added to the global pool for the phylogenetic tree, Bayesian tree, Skyline plot, and median joining network construction. The biodiversity, neutrality tests, and population genetic differentiation among the 6 Thailand geographic regions were analyzed by DNAsp version 6.<br><br>RESULTS: The phylogenetic tree analysis of 214 collected head lice are of clade A and clade C accounting for roughly 65% and 35% respectively. The Bayesian tree revealed a correlation of clade diversification and ancient human dispersal timeline. In Thailand, clade A is widespread in the country. Clade C is confined to only the Central, Southern, and Northeastern regions. We identified 50 novel haplotypes. Statistical analysis showed congruent results between genetic differentiation and population migration especially with South Asia.<br><br>CONCLUSIONS: Pediculosis remains problematic among children in the rural areas in Thailand. Cytb gene analysis of human head lice illustrated clade distribution and intra-clade diversity of different areas. Our study reported novel haplotypes of head lice in Thailand. Moreover, the statistic calculation provided a better understanding of their relationship with human, as an obligate human parasite and might help provide a better insight into the history of human population migration. Determination of the correlation between phylogenetic data and pediculicide resistance gene as well as residing bacteria are of interest for future studies.},
}
@article {pmid34530136,
year = {2021},
author = {Duncan, WP and Machado, RN and Fernandes, MN},
title = {Environmentally-induced osmoregulation in Neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) after controlling for phylogeny.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {262},
number = {},
pages = {111076},
doi = {10.1016/j.cbpa.2021.111076},
pmid = {34530136},
issn = {1531-4332},
mesh = {Animals ; Electrolytes/blood/*metabolism ; Fish Proteins/genetics/metabolism ; Fresh Water ; Gills/metabolism ; Kidney/metabolism ; Mitochondria/genetics/*metabolism ; *Osmoregulation ; Osmosis ; Phylogeny ; Renal Reabsorption ; Skates, Fish/blood/genetics/*metabolism ; Sodium-Potassium-Exchanging ATPase/genetics/metabolism ; *Tropical Climate ; },
abstract = {The osmotic physiology of freshwater stingrays was investigated in fifteen species from white (WW), black (BW), and clearwater (CW) rivers of Brazilian hydrographic basins. Regardless of phylogeny, potamotrygonids collected in the BW (Negro, Jutai, Nhamunda, and Manacapuru rivers), and CW (Tapajos, Parana, Mutum, Demeni, and Branco rivers) exhibited lower levels of osmolytes and plasma osmolality than those from WW (Amazon estuary, Solimoes, and Tarauaca rivers). However, the gill and kidney Na[+]/K[+]-ATPase activities were higher in the potamotrygonid species from BW and CW than those from WW. These results may be related to the ability of the potamotrygonids to achieve high ion uptake from ion-poor waters, such as those of BW and/or CW. Additionally, the high kidney Na[+]/K[+]-ATPase activity may help to minimize ion loss and generate diluted urine. Thus, diffusional losses of salts are balanced by uptake of ions in the gill, and reabsorption by the kidney. The physiological traits showed a weak phylogenetic signal, which indicates a strong evolutionary convergence. Multivariate analyses revealed that variations in physiological traits has a significant association with the type of water, as well as its physical and chemical characteristics such as electric conductivity and pH. Therefore, the South American Neotropical freshwater stingrays adjust their osmoregulatory mechanisms according to the environment in which they live.},
}
@article {pmid34545138,
year = {2021},
author = {Ruíz-Rivero, O and Garcia-Lor, A and Rojas-Panadero, B and Franco, JC and Khamis, FM and Kruger, K and Cifuentes, D and Bielza, P and Tena, A and Urbaneja, A and Pérez-Hedo, M},
title = {Insights into the origin of the invasive populations of Trioza erytreae in Europe using microsatellite markers and mtDNA barcoding approaches.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18651},
pmid = {34545138},
issn = {2045-2322},
mesh = {Animals ; Citrus/chemistry ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Europe ; Hemiptera/*genetics ; Insect Vectors ; Introduced Species/trends ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Plant Diseases ; },
abstract = {The African citrus psyllid Trioza erytreae is one of the major threats to citrus industry as the vector of the incurable disease known as huanglongbing (HLB) or citrus greening. The psyllid invaded the northwest of the Iberian Peninsula 6 years ago. The invasion alarmed citrus growers in the Mediterranean basin, the largest citrus producing area in Europe, which is still free of HLB. Before our study, no research had been carried out on the genetic diversity of T. erytreae populations that have invaded the Iberian Peninsula and the archipelagos of the Macaronesia (Madeira and the Canary Islands). In this study, combining microsatellites markers and mtDNA barcoding analysis, we characterize the genetic diversity, structure and maternal relationship of these new invasive populations of T. erytreae and those from Africa. Our results suggest that the outbreaks of T. erytreae in the Iberian Peninsula may have derived from the Canary Islands. The populations of T. erytreae that invaded Macaronesia and the Iberian Peninsula are likely to have originated from southern Africa. We anticipate our results to be a starting point for tracking the spread of this invasive pest outside of Africa and to be important for optimizing contingency and eradication plans in newly invaded and free areas.},
}
@article {pmid34565456,
year = {2021},
author = {Bunmee, K and Thaenkham, U and Saralamba, N and Ponlawat, A and Zhong, D and Cui, L and Sattabongkot, J and Sriwichai, P},
title = {Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {496},
pmid = {34565456},
issn = {1756-3305},
support = {U19AI089672/NH/NIH HHS/United States ; D43 TW006571/TW/FIC NIH HHS/United States ; D43TW006571/NH/NIH HHS/United States ; U19 AI089672/AI/NIAID NIH HHS/United States ; P0108_19_AF_06.01//Armed Forces Health Surveillance Branch/ ; },
mesh = {Animals ; Anopheles/classification/*genetics/physiology ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics/metabolism ; Gene Flow ; Genetic Markers ; Insect Proteins/*genetics ; Malaria/*transmission ; Mitochondria/*genetics ; Mosquito Vectors/classification/*genetics/physiology ; Phylogeny ; Thailand ; },
abstract = {BACKGROUND: The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand.<br><br>METHODS: Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20&#xa0;years ago.<br><br>RESULTS: The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection.<br><br>CONCLUSIONS: This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers.},
}
@article {pmid34592348,
year = {2022},
author = {Li, Y and Wang, S and Zhou, J and Li, T and Jiang, K and Zhang, Y and Zheng, C and Liang, J and Bu, W},
title = {The phylogenic position of aschiphasmatidae in euphasmatodea based on mitochondrial genomic evidence.},
journal = {Gene},
volume = {808},
number = {},
pages = {145974},
doi = {10.1016/j.gene.2021.145974},
pmid = {34592348},
issn = {1879-0038},
mesh = {Animals ; Base Sequence/genetics ; Gene Order/genetics ; Gene Rearrangement/genetics ; Genome, Mitochondrial/*genetics ; Genomics/methods ; Mitochondria/*genetics ; Nematoda/*genetics ; Neoptera/genetics ; Phylogeny ; },
abstract = {The mitochondrial genome (mitogenome) has been regarded as significant source of data to better understand the phylogenetic relationships within the Euphasmatodea, but no mitogenome in Aschiphasmatoidea has been sequenced to date. In this study, two mitogenomes of Orthomeria smaragdinum and Nanhuaphasma hamicercum of Aschiphasmatidae were sequenced and annotated for the first time. The same mitochondrial gene rearrangement structure was present in the two mitogenomes sequenced, showing as the translocation of tRNA-Arg and tRNA-Asn, which conformed to the tandem duplication-random loss and could be used as a possible synapomorphy for Aschiphasmatidae. The phylogenetic results based on the maximum likelihood (ML) and bayesian inference (BI) methods both showed that Aschiphasmatidae and Neophasmatodea in Euphasmatodea are sister taxa. Although the monophyly of Oriophasmata, Occidophasmata, Diapheromeridae, Phasmatidae, Lonchodidae and Bacilloidea has not been solved, the monophyly of Neophasmatodea and Phyllioidea was well supported.},
}
@article {pmid34600050,
year = {2022},
author = {Yu, X and Yang, H and Liu, J and Qi, Y and Sun, L and Tian, X},
title = {A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis.},
journal = {Gene},
volume = {808},
number = {},
pages = {145986},
doi = {10.1016/j.gene.2021.145986},
pmid = {34600050},
issn = {1879-0038},
mesh = {Animals ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Genome, Insect/genetics ; Genome, Mitochondrial/genetics ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Insecta/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Next-generation sequencing has dramatically fostered insect mitogenomic research in recent years. However, studies on the insect mitochondrial genome (mitogenome) assembly mainly rely on the sequencing data from total DNA, which is not cost-effective as a huge data from nuclear DNA are wasted. Besides, many mitogenomic studies require genomic information from individual organisms, whereas the DNA yield from small individual insects is too low to meet the sequencing requirements. Here, we describe a strategy for a high enrichment of insect mitochondrial DNA (mtDNA) using rolling circle amplification (RCA) technique. This strategy consists of standard DNA extraction, RCA enrichment, next-generation sequencing and mitogenome assembly. We have evaluated the performance of this strategy on nine insect species representing eight families of insecta, three other invertebrates, and even two vertebrate specimens. Results show that our strategy is especially suitable for insects, which allows almost all tested insect mtDNA contents to reach 80% and above. A further examination of enrichment efficiency of our strategy among different taxa shows that it is also applicable to other invertebrates and even some vertebrates such as Rhacophorus and ptyas species, although its enrichment efficiency in these groups is lower than that of insects. After treatment with our strategy, small flux sequencing data can realize the assembly of mitogenome with deep coverage, providing a solid base for subsequent mitogenome-based studies.},
}
@article {pmid34614167,
year = {2021},
author = {Sanchez-Contreras, M and Sweetwyne, MT and Kohrn, BF and Tsantilas, KA and Hipp, MJ and Schmidt, EK and Fredrickson, J and Whitson, JA and Campbell, MD and Rabinovitch, PS and Marcinek, DJ and Kennedy, SR},
title = {A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA.},
journal = {Nucleic acids research},
volume = {49},
number = {19},
pages = {11103-11118},
pmid = {34614167},
issn = {1362-4962},
support = {T32 AG066574/AG/NIA NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; R21 HG011229/HG/NHGRI NIH HHS/United States ; R21 DK128540/DK/NIDDK NIH HHS/United States ; K01 AG062757/AG/NIA NIH HHS/United States ; R21 CA259780/CA/NCI NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; },
mesh = {Aging/*genetics/metabolism ; Animals ; Chromosome Mapping ; DNA Polymerase gamma/deficiency/genetics ; *DNA Replication ; DNA, Mitochondrial/*genetics/metabolism ; Genetic Speciation ; *Genome, Mitochondrial ; *Germ-Line Mutation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*genetics/metabolism ; *Mutation Accumulation ; Mutation Rate ; Polymorphism, Single Nucleotide ; },
abstract = {Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational 'hot-spots' or 'cold-spots'. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.},
}
@article {pmid34626646,
year = {2021},
author = {Latimer, S and Keene, SA and Stutts, LR and Berger, A and Bernert, AC and Soubeyrand, E and Wright, J and Clarke, CF and Block, AK and Colquhoun, TA and Elowsky, C and Christensen, A and Wilson, MA and Basset, GJ},
title = {A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis.},
journal = {The Journal of biological chemistry},
volume = {297},
number = {5},
pages = {101283},
pmid = {34626646},
issn = {1083-351X},
support = {R01 GM139978/GM/NIGMS NIH HHS/United States ; RF1 AG061566/AG/NIA NIH HHS/United States ; },
mesh = {*Arabidopsis/enzymology/genetics ; *Arabidopsis Proteins/genetics/metabolism ; *Mitochondria/enzymology/genetics ; *Mixed Function Oxygenases/genetics/metabolism ; *Phylogeny ; *Ubiquinone/genetics/metabolism ; },
abstract = {Ubiquinone (Coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. In plants, it is not known how the C-6 hydroxylation of demethoxyubiquinone, the penultimate step in ubiquinone biosynthesis, is catalyzed. The combination of cross-species gene network modeling along with mining of embryo-defective mutant databases of Arabidopsis thaliana identified the embryo lethal locus EMB2421 (At1g24340) as a top candidate for the missing plant demethoxyubiquinone hydroxylase. In marked contrast with prototypical eukaryotic demethoxyubiquinone hydroxylases, the catalytic mechanism of which depends on a carboxylate-bridged di-iron domain, At1g24340 is homologous to FAD-dependent oxidoreductases that instead use NAD(P)H as an electron donor. Complementation assays in Saccharomyces cerevisiae and Escherichia coli demonstrated that At1g24340 encodes a functional demethoxyubiquinone hydroxylase and that the enzyme displays strict specificity for the C-6 position of the benzoquinone ring. Laser-scanning confocal microscopy also showed that GFP-tagged At1g24340 is targeted to mitochondria. Silencing of At1g24340 resulted in 40 to 74% decrease in ubiquinone content and de novo ubiquinone biosynthesis. Consistent with the role of At1g24340 as a benzenoid ring modification enzyme, this metabolic blockage could not be bypassed by supplementation with 4-hydroxybenzoate, the immediate precursor of ubiquinone's ring. Unlike in yeast, in Arabidopsis overexpression of demethoxyubiquinone hydroxylase did not boost ubiquinone content. Phylogenetic reconstructions indicated that plant demethoxyubiquinone hydroxylase is most closely related to prokaryotic monooxygenases that act on halogenated aromatics and likely descends from an event of horizontal gene transfer between a green alga and a bacterium.},
}
@article {pmid34643951,
year = {2022},
author = {Adriano, EA and Zatti, SA and Okamura, B},
title = {How to build single-celled cnidarians with worm-like motility: Lessons from Myxozoa.},
journal = {Journal of anatomy},
volume = {240},
number = {3},
pages = {475-488},
pmid = {34643951},
issn = {1469-7580},
mesh = {Animals ; *Cnidaria ; *Fish Diseases/parasitology ; Gallbladder ; *Myxozoa/physiology/ultrastructure ; Phylogeny ; },
abstract = {Metazoans with worm-like morphologies across diverse and disparate groups typically demonstrate motility generated by hydrostatic skeletons involving tissue layers (muscles and epithelia). Here we present representative morphological, behavioural and molecular data for parasitic cnidarians (myxozoans) that demonstrate unprecedented variation in form and function, developing as cellular hydrostats. Motile elongate plasmodia characterise a remarkable radiation of species in the genus Ceratomyxa. The vermiform plasmodia inhabit gall bladders of a range of South American freshwater fish and exhibit undulatory motility reminiscent of nematodes but achieved at the cellular level. Collective insights from ultrastructure, confocal and light microscopy along with videos depicting movements highlight key features that we propose explain the unique motility of the plasmodia. These features include cytoskeletal elements (net forming microfilaments and microtubules), a large internal vacuole, a relatively rigid outer glycocalyx and peripherally arranged mitochondria. These constituents provide collective evidence for repurposing of the cnidarian epitheliomuscular cell to support worm-like motility at the cellular level. The apparent restriction of vermiform ceratomyxids to South American freshwaters suggests an origination via Cretaceous or Miocene marine transgressions and subsequent radiation.},
}
@article {pmid34662686,
year = {2022},
author = {Omeka, WKM and Liyanage, DS and Jeong, T and Lee, S and Lee, J},
title = {Molecular characterization, immune responses, and functional activities of manganese superoxide dismutase in disk abalone (Haliotis discus discus).},
journal = {Developmental and comparative immunology},
volume = {127},
number = {},
pages = {104299},
doi = {10.1016/j.dci.2021.104299},
pmid = {34662686},
issn = {1879-0089},
mesh = {Animals ; *Gastropoda ; Gene Expression Regulation ; Hydrogen Peroxide ; Immunity, Innate ; Mammals ; Phylogeny ; Superoxide Dismutase/genetics ; *Vibrio parahaemolyticus ; },
abstract = {Superoxide dismutases (SODs) are metalloenzymes that convert superoxide radicals to H2O2 and O2. Although SODs have been extensively studied in mammals and other species, comparative studies in invertebrates, such as abalones, are lacking. Here, we aimed to characterize manganese superoxide dismutase in disk abalone (Haliotis discus discus) (AbMnSOD) by assessing its transcriptional levels at different embryonic developmental stages. Additionally, the temporal expression of AbMnSOD in different abalone tissues in response to bacterial, viral, and pathogen-associated molecular pattern (PAMP) stimuli was investigated. SOD activity was measured at various recombinant protein concentrations via the xanthine oxidase/WST-1 system. Cell viability upon exposure to H2O2, wound healing ability, and subcellular localization were determined in AbMnSOD-transfected cells. AbMnSOD was 681 bp long and contained the SOD-A domain. AbMnSOD expression was higher at the trochophore stage than at the other stages. When challenged with immune stimulants, AbMnSOD showed the highest expression at 6 h post-injection (p.i.) for all stimulants except lipopolysaccharides. In the gills, the highest AbMnSOD expression was observed at 6 h p.i., except for the Vibrio parahaemolyticus challenge. Recombinant AbMnSOD showed concentration-dependent xanthine oxidase activity. Furthermore, AbMnSOD-transfected cells survived H2O2-induced apoptosis and exhibited significant wound gap closure. As expected, AbMnSOD was localized in the mitochondria of the cells. Our findings suggest that AbMnSOD is an essential antioxidant enzyme that participates in regulating developmental processes and defense mechanisms against oxidative stress in hosts.},
}
@article {pmid34678134,
year = {2023},
author = {Satyanarayana, DS and Ahlawat, S and Sharma, R and Arora, R and Sharma, A and Tantia, MS and Vijh, RK},
title = {Genetic differentiation of Indian dromedary and Bactrian camel populations based on mitochondrial ATP8 and ATP6 genes.},
journal = {Animal biotechnology},
volume = {34},
number = {3},
pages = {756-760},
doi = {10.1080/10495398.2021.1990079},
pmid = {34678134},
issn = {1532-2378},
mesh = {Animals ; *Camelus/genetics ; Phylogeny ; *Mitochondria/genetics ; Genetic Drift ; DNA, Mitochondrial/genetics ; },
abstract = {Camelids are acknowledged worldwide to endure hostile conditions prevalent in the hot as well cold deserts across the globe. Adaptations to climatic extremes have been associated with mitochondrial protein variants such as ATP8 and ATP6 in different species. The camel genetic resources of India are represented by 9 breeds of dromedary camels which inhabit hot arid and semi-arid zones of the country and a small population of Bactrian camels found in the cold desert of Ladakh. In this study, within and between breed genetic diversity in Indian dromedaries and their divergence from Bactrian camels was investigated based on ATP8/6 genes. Sequence analysis of a mitochondrial DNA fragment encompassing ATP8 and ATP6 genes identified 15 haplotypes in the dromedaries of India and 3 haplotypes in Bactrian camels. The values of haplotype diversity and nucleotide diversity were 0.647 and 0.00187 in the former and 0.679 and 0.00098, respectively in the latter. AMOVA analysis revealed 97.81% variance between the two species. Median-Joining network delineated three distinct mitochondrial haplogroups for Camelus dromedarius, Camelus ferus and Camelus bactrianus. Clear demarcation of the old world (Dromedary and Bactrian camels) and new world camelids (Alpaca, llama, guanaco and vicugna) was evident through the phylogenetic analysis.},
}
@article {pmid34678428,
year = {2022},
author = {Yu, M and Yu, Y and Song, T and Zhang, Y and Wei, F and Cheng, J and Zhang, B and Zhang, X},
title = {Characterization of the voltage-dependent anion channel (VDAC) gene family in wheat (Triticum aestivum L.) and its potential mechanism in response to drought and salinity stresses.},
journal = {Gene},
volume = {809},
number = {},
pages = {146031},
doi = {10.1016/j.gene.2021.146031},
pmid = {34678428},
issn = {1879-0038},
mesh = {Amino Acid Motifs ; Arabidopsis/genetics ; Chromosomes, Plant ; Droughts ; Gene Expression Regulation, Plant ; Multigene Family ; Oxidoreductases/genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Salinity ; Stress, Physiological/*genetics ; Triticum/*genetics/physiology ; Voltage-Dependent Anion Channels/chemistry/*genetics/metabolism ; },
abstract = {Voltage-dependent anion channels (VDACs) are major transport proteins localized in the outer membrane of mitochondria and play critical roles in regulating plant growth and responding to stress. In this study, a total of 26 VDAC genes in common wheat (Triticum aestivum L.) were identified. TaVDACs that contained β-barrel structures were classified into three groups with phylogenetic and sequence alignment. Additionally, the gene structure and protein conserved motif composition varied among diverse subfamilies but were relatively conserved within the same subfamily. The basic elements that were stress- and hormone-related, including TATA-box, CAAT-box, MBS, LTR, TC-rich repeats, ABRE, P-box and TATC-box, were predicted within the promoter region of TaVDAC genes. TaVDAC expression patterns differed among tissues, organs and abiotic stress conditions. Overexpression (OE) of TaVDAC1-B conferred high tolerance to salinity and less resistance to drought stress in Arabidopsis thaliana. TaVDAC1-B interacted with Nucleoredoxin-D1 (TaNRX-D1) protein. Furthermore, compared with WT lines, salinity stress further upregulated the level of AtNRX1 (homologous gene of TaNRX-D1 in Arabidopsis) expression and the activity of superoxide dismutase in TaVDAC1-B OE lines, which led to a decrease in superoxide radical accumulation; drought stress further downregulated AtNRX1 expression and superoxide dismutase activity in TaVDAC1-B OE lines, resulting in the accumulation of superoxide radicals. Our study not only presents comprehensive information for understanding the VDAC gene family in wheat but also proposes a potential mechanism in response to drought and salinity stress.},
}
@article {pmid34678674,
year = {2021},
author = {Rothmann-Meyer, W and Naidoo, K and de Waal, PJ},
title = {Comparative mitogenomics of Spirocerca lupi from South Africa and China: Variation and possible heteroplasmy.},
journal = {Veterinary parasitology},
volume = {300},
number = {},
pages = {109595},
doi = {10.1016/j.vetpar.2021.109595},
pmid = {34678674},
issn = {1873-2550},
mesh = {Animals ; *Dog Diseases/epidemiology ; Dogs ; Heteroplasmy ; Phylogeny ; South Africa/epidemiology ; *Spirurida Infections/veterinary ; *Thelazioidea/genetics ; },
abstract = {The complete mitochondrial genome of Spirocerca lupi isolated from a dog in South Africa was sequenced using next generation sequencing (NGS) technology and the 12 protein coding genes along with the two rRNA genes were compared to 18 other nematode species as well as S. lupi from China. The mitochondrial genome of S. lupi South Africa had a mean genetic diversity of 6.1 % compared to S. lupi China with some variation in nucleotide composition, gene positioning and size. Pairwise distance results indicated slightly higher variation when compared to the pairwise distances of other closely related species, however, this variation was not high enough for it to be considered a cryptic species. Phylogenetic analysis indicated that S. lupi from the two continents are very similar. In addition, single nucleotide polymorphisms were detected in the nad2 gene with ten sequence variants identified from 10 clones from a single nematode, suggesting possible heteroplasmy. The origin of the heteroplasmy is currently unknown but it is speculated to have arisen from accumulated mutations in the mitochondria during somatic replication.},
}
@article {pmid34724985,
year = {2021},
author = {Wu, Y and Wang, XH and Li, XH and Song, LY and Yu, SL and Fang, ZC and Liu, YQ and Yuan, LY and Peng, CY and Zhang, SY and Cheng, W and Ma, HC and Wang, LF and Tang, JM and Wang, YF and Ji, FY},
title = {Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China.},
journal = {Military Medical Research},
volume = {8},
number = {1},
pages = {57},
pmid = {34724985},
issn = {2054-9369},
support = {&#x2116;:2020XGFYZR11//the Special Project of Contingency Research for COVID-19 at Hubei University of Medicine/ ; &#x2116;:2020XGFYZR03//the Special Project of Contingency Research for COVID-19 at Hubei University of Medicine/ ; &#x2116;: 2018QDJZR01//the Cultivating Project for Young Scholar at Hubei University of Medicine/ ; },
mesh = {*COVID-19/genetics ; Case-Control Studies ; China ; *DNA, Mitochondrial/genetics ; Humans ; Mitochondria/genetics ; Phylogeny ; Risk Factors ; },
abstract = {BACKGROUND: Mitochondria have been shown to play vital roles during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) development. Currently, it is unclear whether mitochondrial DNA (mtDNA) variants, which define mtDNA haplogroups and determine oxidative phosphorylation performance and reactive oxygen species production, are associated with COVID-19 risk.<br><br>METHODS: A population-based case-control study was conducted to compare the distribution of mtDNA variations defining mtDNA haplogroups between healthy controls (n&#x2009;=&#x2009;615) and COVID-19 patients (n&#x2009;=&#x2009;536). COVID-19 patients were diagnosed based on molecular diagnostics of the viral genome by qPCR and chest X-ray or computed tomography scanning. The exclusion criteria for the healthy controls were any history of disease in the month preceding the study assessment. MtDNA variants defining mtDNA haplogroups were identified by PCR-RFLPs and HVS-I sequencing and determined based on mtDNA phylogenetic analysis using Mitomap Phylogeny. Student's t-test was used for continuous variables, and Pearson's chi-squared test or Fisher's exact test was used for categorical variables. To assess the independent effect of each mtDNA variant defining mtDNA haplogroups, multivariate logistic regression analyses were performed to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) with adjustments for possible confounding factors of age, sex, smoking and diseases (including cardiopulmonary diseases, diabetes, obesity and hypertension) as determined through clinical and radiographic examinations.<br><br>RESULTS: Multivariate logistic regression analyses revealed that the most common investigated mtDNA variations (>&#x2009;10% in the control population) at C5178a (in NADH dehydrogenase subunit 2 gene, ND2) and A249d (in the displacement loop region, D-loop)/T6392C (in cytochrome c oxidase I gene, CO1)/G10310A (in ND3) were associated with a reduced risk of severe COVID-19 (OR&#x2009;=&#x2009;0.590, 95% CI 0.428-0.814, P&#x2009;=&#x2009;0.001; and OR&#x2009;=&#x2009;0.654, 95% CI 0.457-0.936, P&#x2009;=&#x2009;0.020, respectively), while A4833G (ND2), A4715G (ND2), T3394C (ND1) and G5417A (ND2)/C16257a (D-loop)/C16261T (D-loop) were related to an increased risk of severe COVID-19 (OR&#x2009;=&#x2009;2.336, 95% CI 1.179-4.608, P&#x2009;=&#x2009;0.015; OR&#x2009;=&#x2009;2.033, 95% CI 1.242-3.322, P&#x2009;=&#x2009;0.005; OR&#x2009;=&#x2009;3.040, 95% CI 1.522-6.061, P&#x2009;=&#x2009;0.002; and OR&#x2009;=&#x2009;2.890, 95% CI 1.199-6.993, P&#x2009;=&#x2009;0.018, respectively).<br><br>CONCLUSIONS: This is the first study to explore the association of mtDNA variants with individual's risk of developing severe COVID-19. Based on the case-control study, we concluded that the common mtDNA variants at C5178a and A249d/T6392C/G10310A might contribute to an individual's resistance to developing severe COVID-19, whereas A4833G, A4715G, T3394C and G5417A/C16257a/C16261T might increase an individual's risk of developing severe COVID-19.},
}
@article {pmid34727288,
year = {2022},
author = {Liu, K and Xie, N and Ma, HJ},
title = {Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855).},
journal = {Molecular biology reports},
volume = {49},
number = {2},
pages = {943-950},
pmid = {34727288},
issn = {1573-4978},
support = {20162012A03//Hangzhou Agricultural &amp; Social Development Research Program/ ; 2019HNCT-01//Science &amp; Technology Innovation Program of Hangzhou Academy of Agricultural Sciences/ ; },
mesh = {Animals ; China ; Cyprinidae/*genetics ; Cypriniformes/genetics ; DNA, Mitochondrial/*genetics ; Fish Proteins/genetics ; Heteroplasmy/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitogens/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known.<br><br>METHODS AND RESULTS: This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent.<br><br>CONCLUSIONS: This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.},
}
@article {pmid34728739,
year = {2021},
author = {Wang, X and Li, LL and Xiao, Y and Chen, XY and Chen, JH and Hu, XS},
title = {A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {21452},
pmid = {34728739},
issn = {2045-2322},
support = {2018-GDTK-08//Central Finance Forestry Reform and Development Fund/ ; 4400-K16013//South China Agricultural University/ ; },
mesh = {DNA, Mitochondrial/analysis/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Rubiaceae/*genetics/growth &amp; development ; *Transcriptome ; },
abstract = {Neolamarckia cadamba is an important tropical and subtropical tree for timber industry in southern China and is also a medicinal plant because of the secondary product cadambine. N. cadamba belongs to Rubiaceae family and its taxonomic relationships with other species are not fully evaluated based on genome sequences. Here, we report the complete sequences of mitochondrial genome of N. cadamba, which is 414,980 bp in length and successfully assembled in two genome circles (109,836 bp and 305,144 bp). The mtDNA harbors 83 genes in total, including 40 protein-coding genes (PCGs), 31 transfer RNA genes, 6 ribosomal RNA genes, and 6 other genes. The base composition of the whole genome is estimated as 27.26% for base A, 22.63% for C, 22.53% for G, and 27.56% for T, with the A + T content of 54.82% (54.45% in the small circle and 54.79% in the large circle). Repetitive sequences account for ~ 0.14% of the whole genome. A maximum likelihood (ML) tree based on DNA sequences of 24 PCGs supports that N. cadamba belongs to order Gentianales. A ML tree based on rps3 gene of 60 species in family Rubiaceae shows that N. cadamba is more related to Cephalanthus accidentalis and Hymenodictyon parvifolium and belongs to the Cinchonoideae subfamily. The result indicates that N. cadamba is genetically distant from the species and genera of Rubiaceae in systematic position. As the first sequence of mitochondrial genome of N. cadamba, it will provide a useful resource to investigate genetic variation and develop molecular markers for genetic breeding in the future.},
}
@article {pmid34773616,
year = {2022},
author = {Skuza, L},
title = {Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2392},
number = {},
pages = {83-91},
pmid = {34773616},
issn = {1940-6029},
mesh = {Chloroplasts/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Phylogeny ; Plants/genetics ; Secale/genetics ; },
abstract = {Noncoding regions of the chloroplast (cpDNA) and mitochondrial (mtDNA) genomes are commonly used in plant phylogenetic and population studies. Consensus primers, which are homologous to most coding regions, but amplify variable noncoding regions, are very useful for this purpose. However, high genetic diversity of plants poses a problem in developing molecular methods that require conserved DNA sequences between species.This chapter describes the protocol for designing PCR primers suitable for analysis of closely related plant species. As an example, we used PCR primer design for cpDNA noncoding regions of the rye (Secale).},
}
@article {pmid34773990,
year = {2021},
author = {Liu, Y and Qu, J and Shi, Z and Zhang, P and Ren, M},
title = {Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {821},
pmid = {34773990},
issn = {1471-2164},
mesh = {Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; *Solanum tuberosum/genetics ; Vegetables ; },
abstract = {BACKGROUND: The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported.<br><br>RESULTS: In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-&#x3b2;-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm.<br><br>CONCLUSIONS: This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.},
}
@article {pmid34783988,
year = {2022},
author = {López-Cuamatzi, IL and Ortega, J and Baeza, JA},
title = {The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico.},
journal = {Molecular biology reports},
volume = {49},
number = {2},
pages = {1141-1149},
pmid = {34783988},
issn = {1573-4978},
mesh = {Animals ; Conservation of Natural Resources/methods ; Endangered Species ; Gene Order ; Genome, Mitochondrial/*genetics ; Lagomorpha/*genetics ; Mexico ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Rabbits/genetics ; },
abstract = {BACKGROUND: The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species.<br><br>METHODS AND RESULTS: This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150&#xa0;bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400&#xa0;bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs.<br><br>CONCLUSIONS: This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.},
}
@article {pmid34797494,
year = {2022},
author = {Yamazaki, D and Chiba, S},
title = {Comparing the genetic diversity and population structure of sister marine snails having contrasting habitat specificity.},
journal = {Molecular biology reports},
volume = {49},
number = {1},
pages = {393-401},
pmid = {34797494},
issn = {1573-4978},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene Flow ; Genetic Variation ; Genetics, Population ; Japan ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Snails/*classification/genetics ; Species Specificity ; },
abstract = {BACKGROUND: To grasp the processes of spatial genetic structuring in open and connectable marine environments is the principal study goal in molecular biological studies. Comparative seascape genetics using multiple species are a powerful approach to understand the physical geographic and oceanographic effects on genetic variation. Besides, species-specific ecological traits such as dispersal abilities and habitat specificity are important factors for spatial genetic structuring.<br><br>METHODS AND RESULTS: We focused on the sister marine snail species Tegula kusairo and T. xanthostigma around the Japanese mainland, which have contrasting habitat specificities for wave strength. Tegula kusairo only inhabits sheltered coastal environments, while T. xanthostigma is found mainly on wave-exposed rocky shores facing the open sea. We estimated their genetic diversity indices and levels of population differentiation based on mtDNA. We found that the genetic diversity of T. kusairo was lower than that of T. xanthostigma, while their level of population genetic differentiation was higher than that of T. xanthostigma. Namely, the species specific to weak wave environments had a higher level of population genetic differentiation than the species specific to strong wave action.<br><br>CONCLUSION: Ecological traits linked not only to dispersal abilities but also to habitat specificity can influence genetic variation in a pair of closely related sister species distributed in the same seascape.},
}
@article {pmid34798191,
year = {2021},
author = {Lin, Y and Xiao, Q and Hao, Q and Qian, Z and Li, X and Li, P and Li, H and Chen, L},
title = {Genome-wide identification and functional analysis of the glutathione S-transferase (GST) family in Pomacea canaliculata.},
journal = {International journal of biological macromolecules},
volume = {193},
number = {Pt B},
pages = {2062-2069},
doi = {10.1016/j.ijbiomac.2021.11.038},
pmid = {34798191},
issn = {1879-0003},
mesh = {Animals ; Cold-Shock Response/genetics ; Gastropoda/*genetics ; Genome/*genetics ; Glutathione Transferase/*genetics ; Oxidative Stress/genetics ; Phylogeny ; Reactive Oxygen Species/metabolism ; },
abstract = {Cold causes oxidative stress in living organisms, mainly caused by the accumulation of reactive oxygen species (ROS). In the antioxidant defense systems, Glutathione S-transferases (GSTs) play a vital role in the regulation of detoxification and redox balance of ROS. In this study, the P. canaliculata GST gene family were characterized using a genome-wide search of the conserved domain. Phylogenetic tree and domain composition analysis revealed that 30 PcGSTs belong to seven classes, including five in MAPEG, two in Mu, nine in Omega, 11 in Sigma, one in Rho, Theta and Alpha class, respectively. RNA-seq analysis revealed that most PcGSTs localized in mitochondria highly expressed in hepatopancreas, and most PcGSTs localized in cytoplasm highly expressed in kidney. A total of 12 PcGST genes were significantly up-regulated and PcGST12 was significantly down-regulated after cold acclimation. Ten PcGSTs were identified as DEGs under cold stress after cold acclimation. qRT-PCR revealed that the expression level of five PcGST genes were significantly varied during the cold acclimation. The present study investigated the characterization of the P. canaliculata GST gene family, extending our understanding of GST mediated cold acclimation and cold stress-response mechanisms in this invasive snail.},
}
@article {pmid34811145,
year = {2021},
author = {Parrinha, D and Marques, MP and Heinicke, MP and Khalid, F and Parker, KL and Tolley, KA and Childers, JL and Conradie, W and Bauer, AM and Ceraco, LMP},
title = {A revision of Angolan species in the genus Pedioplanis Fitzinger (Squamata: Lacertidae), with the description of a new species.},
journal = {Zootaxa},
volume = {5032},
number = {1},
pages = {1-46},
doi = {10.11646/zootaxa.5032.1.1},
pmid = {34811145},
issn = {1175-5334},
mesh = {Animals ; Cell Nucleus ; *Lizards/genetics ; Mitochondria ; Phylogeny ; },
abstract = {The genus Pedioplanis reaches its northernmost limit in western Angola, where it is represented by three species, Pedioplanis benguelensis, P. haackei and P. huntleyi. The taxonomic status of P. benguelensis remains problematic, mainly due to the vague original description and the loss of the original type material. Here we provide a revision of the Angolan representatives of the genus, with the description of a new species, Pedioplanis serodioi sp. nov., from the lowlands of southwestern Angola. Phylogenetic analyses using a combination of mitochondrial (16S and ND2) and nuclear (RAG-1) markers, as well as morphological data, support the recognition of the new species. For purposes of nomenclatural stability, we designate a neotype for P. benguelensis and provide motivation to correct the spelling of the specific epithet to benguelensis. The clarification of the status of P. benguelensis and the description of a new species contribute to a better understanding of the taxonomy and biogeography of the genus Pedioplanis, as well as the general biogeographic context of southwestern Angola, adding to the growing evidence in favor of the recognition of this region as a hotspot of lizard diversity and endemism. An updated key to the genus is also provided.},
}
@article {pmid34818432,
year = {2022},
author = {Jiang, Y and Yue, L and Yang, F and Gillung, JP and Winterton, SL and Price, BW and Contreras-Ramos, A and Hayashi, F and Aspöck, U and Aspöck, H and Yeates, DK and Yang, D and Liu, X},
title = {Similar pattern, different paths: tracing the biogeographical history of Megaloptera (Insecta: Neuropterida) using mitochondrial phylogenomics.},
journal = {Cladistics : the international journal of the Willi Hennig Society},
volume = {38},
number = {3},
pages = {374-391},
doi = {10.1111/cla.12494},
pmid = {34818432},
issn = {1096-0031},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Holometabola/genetics ; Insecta/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {The sequential breakup of the supercontinent Pangaea since the Middle Jurassic is one of the crucial factors that has driven the biogeographical patterns of terrestrial biotas. Despite decades of effort searching for concordant patterns between diversification and continental fragmentation among taxonomic groups, increasing evidence has revealed more complex and idiosyncratic scenarios resulting from a mixture of vicariance, dispersal and extinction. Aquatic insects with discreet ecological requirements, low vagility and disjunct distributions represent a valuable model for testing biogeographical hypotheses by reconstructing their distribution patterns and temporal divergences. Insects of the order Megaloptera have exclusively aquatic larvae, their adults have low vagility, and the group has a highly disjunct geographical distribution. Here we present a comprehensive phylogeny of Megaloptera based on a large-scale mitochondrial genome sequencing of 99 species representing >90% of the world genera from all major biogeographical regions. Molecular dating suggests that the deep divergence within Megaloptera pre-dates the breakup of Pangaea. Subsequently, the intergeneric divergences within Corydalinae (dobsonflies), Chauliodinae (fishflies) and Sialidae (alderflies) might have been driven by both vicariance and dispersal correlated with the shifting continent during the Cretaceous, but with strikingly different and incongruent biogeographical signals. The austral distribution of many corydalids appears to be a result of colonization from Eurasia through southward dispersal across Europe and Africa during the Cretaceous, whereas a nearly contemporaneous dispersal via northward rafting of Gondwanan landmasses may account for the colonization of extant Eurasian alderflies from the south.},
}
@article {pmid34880150,
year = {2022},
author = {Hussain, M and Liaqat, I and Mubin, M and Nisar, B and Shahzad, K and Durrani, AI and Zafar, U and Afzaal, M and Ehsan, A and Rubab, S},
title = {DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan.},
journal = {Journal of oleo science},
volume = {71},
number = {1},
pages = {83-93},
doi = {10.5650/jos.ess21246},
pmid = {34880150},
issn = {1347-3352},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Oligochaeta/anatomy &amp; histology/classification/*genetics ; Pakistan ; *Phylogeny ; Species Specificity ; },
abstract = {The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.},
}
@article {pmid34887330,
year = {2022},
author = {Zandi, M},
title = {ORF8/ORF8a: a difference between SARS-CoV-2 and SARS-CoV.},
journal = {The European respiratory journal},
volume = {59},
number = {2},
pages = {},
pmid = {34887330},
issn = {1399-3003},
mesh = {Biomarkers ; *COVID-19 ; Humans ; Phylogeny ; *SARS-CoV-2 ; },
abstract = {ORF8 as an accessory protein of SARS-CoV-2 https://bit.ly/3Gr3OTK},
}
@article {pmid34890311,
year = {2021},
author = {Zaccaron, AZ and Stergiopoulos, I},
title = {Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition.},
journal = {Microbial genomics},
volume = {7},
number = {12},
pages = {},
pmid = {34890311},
issn = {2057-5858},
mesh = {Ascomycota/*genetics ; Base Composition ; Cytochromes b/genetics ; Erysiphe/*genetics ; Genome Size ; Genome, Fungal ; *Genome, Mitochondrial ; Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Powdery mildews comprise a large group of economically important phytopathogenic fungi. However, limited information exists on their mitochondrial genomes. Here, we assembled and compared the mitochondrial genomes of the powdery mildew pathogens Blumeria graminis f. sp. tritici, Erysiphe pisi, and Golovinomyces cichoracearum. Included in the comparative analysis was also the mitochondrial genome of Erysiphe necator that was previously analysed. The mitochondrial genomes of the four Erysiphales exhibit a similar gene content and organization but a large variation in size, with sizes ranging from 109800 bp in B. graminis f. sp. tritici to 332165 bp in G. cichoracearum, which is the largest mitochondrial genome of a fungal pathogen reported to date. Further comparative analysis revealed an unusual bimodal GC distribution in the mitochondrial genomes of B. graminis f. sp. tritici and G. cichoracearum that was not previously observed in fungi. The cytochrome b (cob) genes of E. necator, E. pisi, and G. cichoracearum were also exceptionally rich in introns, which in turn harboured rare open reading frames encoding reverse transcriptases that were likely acquired horizontally. Golovinomyces cichoracearum had also the longest cob gene (45 kb) among 703 fungal cob genes analysed. Collectively, these results provide novel insights into the organization of mitochondrial genomes of powdery mildew pathogens and represent valuable resources for population genetics and evolutionary studies.},
}
@article {pmid34941991,
year = {2022},
author = {Song, MH and Yan, C and Li, JT},
title = {MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data.},
journal = {Briefings in bioinformatics},
volume = {23},
number = {1},
pages = {},
doi = {10.1093/bib/bbab538},
pmid = {34941991},
issn = {1477-4054},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Software ; Whole Genome Sequencing/*methods ; },
abstract = {Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.},
}
@article {pmid34993838,
year = {2022},
author = {Jiang, Z and Cai, X and Kong, J and Zhang, R and Ding, Y},
title = {Maternally transmitted diabetes mellitus may be associated with mitochondrial ND5 T12338C and tRNA[Ala] T5587C variants.},
journal = {Irish journal of medical science},
volume = {191},
number = {6},
pages = {2625-2633},
pmid = {34993838},
issn = {1863-4362},
mesh = {Humans ; *RNA, Transfer, Ala ; *Diabetes Mellitus, Type 2/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria ; Pedigree ; Mutation ; },
abstract = {INTRODUCTION: Mutations/variants in mitochondrial genomes are found to be associated with type 2 diabetes mellitus (T2DM), but the pathophysiology of this disease remains largely unknown.<br><br>AIM: The aim of this study is to investigate the relationship between mitochondrial DNA (mtDNA) variants and T2DM.<br><br>METHODOLOGY: A maternally inherited T2DM pedigree is underwent clinical, genetic, and molecular assessment. Moreover, the complete mitochondrial genomes of the matrilineal relatives of this family are PCR amplified and sequenced. We also utilize the phylogenetic conservation analysis, haplogroup classification, and the pathogenicity scoring system to determine the T2DM-associated potential pathogenic mtDNA variants.<br><br>RESULT: Four of seven matrilineal relatives of this pedigree suffered from T2DM with variable ages of onset. Screening for the entire mtDNA genes of matrilineal members reveals co-existence of ND5 T12338C and tRNA[Ala] T5587C variants, as well as 21 genetic polymorphisms which belong to East Asian haplogroup F2. Interestingly, the T12338C variant causes the alternation of first amino acid Met to Thr, shortened two amino acids of ND5 protein. Furthermore, T5587C variant is located at position 73 in the 3'end of mt-tRNA[Ala] and may have structural and functional consequences.<br><br>CONCLUSIONS: The co-occurrence of ND5 T12338C and tRNA[Ala] T5587C variants may impair the mitochondrial function, which are associated with the development of T2DM in this family.},
}
@article {pmid34997986,
year = {2022},
author = {Ereskovsky, A and Tokina, D},
title = {Ultrastructural research of spermiogenesis in two sponges, Crellomima imparidens and Hymedesmia irregularis (Demospongiae): New evidence of sperms with acrosome in sponges.},
journal = {Journal of morphology},
volume = {283},
number = {3},
pages = {333-345},
doi = {10.1002/jmor.21446},
pmid = {34997986},
issn = {1097-4687},
mesh = {*Acrosome/ultrastructure ; Animals ; Male ; Phylogeny ; *Porifera ; Spermatids/ultrastructure ; Spermatogenesis ; Spermatozoa ; },
abstract = {Details of spermatogenesis and sperm organization are often useful for reconstructing the phylogeny of closely related taxa of invertebrates. Here, the spermiogenesis and the ultrastructure of sperm were studied in two marine demosponges, Crellomima imparidens and Hymedesmia irregularis (order Poecilosclerida). In C. imparidens and H. irregularis, we found bundles of microtubules arranged along the nucleus during spermiogenesis. These bundles derived from the basal body of axoneme, reaching the apical pole of the cell. In C. imparidens, the microtubules surround the nucleus, forming the manchette. In H. irregularis, the microtubules pass along only one side of the cell periphery. During spermiogenesis, the nucleus stretches and elongates. In both species, the nucleus is twisted into a spiral structure. We suppose that the manchette of microtubules could be responsible for controlling the elongation and shaping of the sperm nucleus to a helical form and for the twisting and/or condensation of chromatin in these sponges. The spermatozoon of both species has an elongated shape. Its apical part has an acrosome, which is dome-shaped in C. imparidens and flattened and lenticular in H. irregularis. The cytoplasm of the spermatozoa contains some small mitochondria, and proximal and distal centrioles arranged at an angle to each other. There is a small volume of residual cytoplasm with dark glycogen-like granules. The axoneme of the spermatid and the flagellum of the sperm of both sponges is located in the deep tunnel-like cytoplasmic depression. The comparison of spermatozoa morphology of different species of the order Poecilosclerida demonstrates that the knowledge of variation within genera and families can give valuable insights into the significance of many characters proposed for phylogenetic studies of this order.},
}
@article {pmid35007655,
year = {2022},
author = {Liu, T and Lin, S and Du, Y and Gong, Y and Li, S},
title = {SpBAG3 assisted WSSV infection in mud crab (Scylla paramamosain) by inhibiting apoptosis.},
journal = {Developmental and comparative immunology},
volume = {129},
number = {},
pages = {104349},
doi = {10.1016/j.dci.2022.104349},
pmid = {35007655},
issn = {1879-0089},
mesh = {Animals ; Apoptosis ; Apoptosis Regulatory Proteins/genetics ; Arthropod Proteins/genetics ; Brachyura/*immunology ; Gene Expression Profiling ; Hemocytes/immunology ; Immunity, Innate/genetics ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism ; Phylogeny ; White spot syndrome virus 1/physiology ; },
abstract = {The function of B-cell lymphoma-2 (Bcl-2) family proteins can be divided into two categories: anti-apoptotic and pro-apoptotic. As an anti-apoptotic protein, Bcl2-associated athanogene 3 (BAG3) plays a key role in regulating apoptosis, development, cell movement, and autophagy, and mediating the adaptability of cells to stimulation. However, SpBAG3 has not been reported in mud crab (Scylla paramamosain), and the regulatory effect of SpBAG3 on apoptosis in mud crab and its function in antiviral immunity is still unknown. In this study, SpBAG3 was found, and characterized, which encoded a total of 175 amino acid (molecular mass 19.3 kDa), including a specific conserved domain of the BAG family. SpBAG3 was significantly down-regulated at 0-48 h post-infection with WSSV in vivo. The antiviral effect of SpBAG3 was investigated using RNA interference. The results indicated that SpBAG3 might be involved in assisting the replication of WSSV in the host. SpBAG3 could change the mitochondrial membrane potential (△ψm), and affect cell apoptosis through mitochondrial apoptotic pathways. Therefore, the results of this study suggested that SpBAG3 could assist WSSV infection by inhibiting the apoptosis of the hemocytes in mud crab.},
}
@article {pmid35017538,
year = {2022},
author = {Li, CH and Haider, S and Boutros, PC},
title = {Age influences on the molecular presentation of tumours.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {208},
pmid = {35017538},
issn = {2041-1723},
support = {P30 CA016042/CA/NCI NIH HHS/United States ; U01 CA214194/CA/NCI NIH HHS/United States ; SVB-145586//CIHR/Canada ; },
mesh = {Age Factors ; Aging/*genetics/metabolism ; CREB-Binding Protein/*genetics/metabolism ; Carcinogenesis/genetics/metabolism/pathology ; Cell Line, Tumor ; Cell Nucleus/metabolism ; Cyclin-Dependent Kinase Inhibitor p16/*genetics/metabolism ; *DNA Repair ; DNA, Neoplasm/*genetics/metabolism ; Datasets as Topic ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mitochondria/metabolism ; Mutation Rate ; Neoplasm Proteins/*genetics/metabolism ; Neoplasms/classification/*genetics/metabolism/pathology ; Repressor Proteins/deficiency/genetics ; Smoking/genetics/metabolism ; Transcriptome ; X-linked Nuclear Protein/genetics/metabolism ; },
abstract = {Cancer is often called a disease of aging. There are numerous ways in which cancer epidemiology and behaviour change with the age of the patient. The molecular bases for these relationships remain largely underexplored. To characterise them, we analyse age-associations in the nuclear and mitochondrial somatic mutational landscape of 20,033 tumours across 35 tumour-types. Age influences both the number of mutations in a tumour (0.077 mutations per megabase per year) and their evolutionary timing. Specific mutational signatures are associated with age, reflecting differences in exogenous and endogenous oncogenic processes such as a greater influence of tobacco use in the tumours of younger patients, but higher activity of DNA damage repair signatures in those of older patients. We find that known cancer driver genes such as CDKN2A and CREBBP are mutated in age-associated frequencies, and these alter the transcriptome and predict for clinical outcomes. These effects are most striking in brain cancers where alterations like SUFU loss and ATRX mutation are age-dependent prognostic biomarkers. Using three cancer datasets, we show that age shapes the somatic mutational landscape of cancer, with clinical implications.},
}
@article {pmid35022483,
year = {2022},
author = {Dash, A and Ghag, SB},
title = {Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {625},
pmid = {35022483},
issn = {2045-2322},
mesh = {*Musa/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; *Phylogeny ; Multigene Family ; Genome, Plant ; Computer Simulation ; Gene Expression Profiling ; },
abstract = {Programmed cell death (PCD) is a genetically controlled process for the selective removal of damaged cells. Though understanding about plant PCD has improved over years, the mechanisms are yet to be fully deciphered. Among the several molecular players of PCD in plants, B cell lymphoma 2 (Bcl-2)-associated athanogene (BAG) family of co-chaperones are evolutionary conserved and regulate cell death, growth and development. In this study, we performed a genome-wide in silico analysis of the MusaBAG gene family in a globally important fruit crop banana. Thirteen MusaBAG genes were identified, out of which MusaBAG1, 7 and 8 genes were found to have multiple copies. MusaBAG genes were distributed on seven out of 11 chromosomes in banana. Except for one paralog of MusaBAG8 all the other 12 proteins have characteristic BAG domain. MusaBAG1, 2 and 4 have an additional ubiquitin-like domain whereas MusaBAG5-8 have a calmodulin binding motif. Most of the MusaBAG proteins were predicted to be localized in the nucleus and mitochondria or chloroplast. The in silico cis-regulatory element analysis suggested regulation associated with photoperiodic control, abiotic and biotic stress. The phylogenetic analysis revealed 2 major clusters. Digital gene expression analysis and quantitative real-time RT-PCR depicted the differential expression pattern of MusaBAG genes under abiotic and biotic stress conditions. Further studies are warranted to uncover the role of each of these proteins in growth, PCD and stress responses so as to explore them as candidate genes for engineering transgenic banana plants with improved agronomic traits.},
}
@article {pmid35025030,
year = {2022},
author = {Liu, S and Liu, Y and He, J and Lin, Z and Xue, Q},
title = {The complete mitochondrial genome of Crassostrea hongkongensis from East China Sea indicates species' range may extend northward.},
journal = {Molecular biology reports},
volume = {49},
number = {2},
pages = {1631-1635},
pmid = {35025030},
issn = {1573-4978},
support = {2021S009//Science and Technology Planning Project of Ningbo City/ ; },
mesh = {Animals ; China ; Conservation of Natural Resources/methods ; Crassostrea/*genetics ; Ecosystem ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Crassostrea hongkongensis is an important mariculture shellfish with a relatively narrow distribution range. Recently, larger wild oysters were identified as C. hongkongensis from Sanmen bay in East China Sea. No natural distribution had been reported for this species here, and its origin remains unknown.<br><br>METHODS AND RESULTS: We assembled the complete 18,617&#xa0;bp circular mitochondrial genome of C. hongkongensis from Sanmen bay by next generation sequencing. It included 12 protein-coding genes, 23 tRNAs, and two rRNAs. The A/T content of the mitogenome was higher than its G/C content. Similar values and features were previously found for five other specimens of C. hongkongensis, and were comparable to those of other congeneric species. A phylogenetic analysis based on the 12 protein-coding genes and complete mitochondrial sequence indicated that the six specimens of C. hongkongensis formed a monophyletic group and shared a sister group relationship with C. ariakensis, C. nippona, C. sikamea, C. angulata, C. gigas, and C. iredalei, whereas specimens from the Sanmen bay area clustered later with the five other C. hongkongensis individuals, sharing a sub-clade. The newly sequenced mitogenome had more singleton sites than previously published C. hongkongensis mitogenomes.<br><br>CONCLUSIONS: Crassostrea hongkongensis may be a native species, and the species' range extends further to the north than previously known. Our data may therefore contribute to a better understanding of the species diversity and conservation of Crassostrea oysters.},
}
@article {pmid35078356,
year = {2022},
author = {Munasinghe, M and Haller, BC and Clark, AG},
title = {Migration restores hybrid incompatibility driven by mitochondrial-nuclear sexual conflict.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1967},
pages = {20212561},
pmid = {35078356},
issn = {1471-2954},
mesh = {Cell Nucleus/genetics ; Female ; *Genome, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mutation ; Reproductive Isolation ; },
abstract = {In the mitochondrial genome, sexual asymmetry in transmission allows the accumulation of male-harming mutations since selection acts only on the effect of the mutation in females. Called the 'Mother's Curse', this phenomenon induces a selective pressure for nuclear variants that compensate for this reduction in male fitness. Previous work has demonstrated the existence of these interactions and their potential to act as Dobzhansky-Muller incompatibilities, contributing to reproductive isolation between populations. However, it is not clear how readily they would give rise to and sustain hybrid incompatibilities. Here, we use computer simulations in SLiM 3 to investigate the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population. We consider distinct migration schemes and vary the chromosomal location, and consequently the transmission pattern, of nuclear restorers. Disrupting these co-evolved interactions results in less-fit males, skewing the sex ratio toward females. Restoration of male fitness depends on both the chromosomal location of nuclear restorer loci and the migration scheme. Our results show that these interactions may act as Dobzhansky-Muller incompatibilities, but their strength is not enough to drive population isolation. Overall, this model shows the varied ways in which populations can respond to migration's disruption of co-evolved mitochondrial-nuclear interactions.},
}
@article {pmid35104579,
year = {2022},
author = {Gowri, P and Sathish, P and Mahesh Kumar, S and Sundaresan, P},
title = {Mutation profile of neurodegenerative mitochondriopathy - LHON in Southern India.},
journal = {Gene},
volume = {819},
number = {},
pages = {146202},
doi = {10.1016/j.gene.2022.146202},
pmid = {35104579},
issn = {1879-0038},
mesh = {Adolescent ; Adult ; Asian People/genetics ; Child ; Child, Preschool ; DNA, Mitochondrial/metabolism ; Female ; Genes, Mitochondrial ; Genetic Predisposition to Disease ; Genome, Mitochondrial ; Humans ; India ; Male ; Methylation ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Neurodegenerative Diseases/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Phylogeny ; Young Adult ; },
abstract = {BACKGROUND: Leber's Hereditary Optic Neuropathy (LHON) is a rare mitochondriopathy causing retinal ganglion cell degeneration resulting in central vision loss. It is caused by mitochondrial DNA (mtDNA) mutations and thus follows maternal inheritance pattern.<br><br>METHODS: We analysed the whole mitochondrial genome in 100 South Indian LHON patients by utilizing Sanger and Next Generation Sequencing approaches. Haplogroup analysis was performed using HaploGrep2 to predict the risk group. Methylation changes in the mtDNA D-loop region were investigated by performing methylation-specific polymerase chain reaction (MSP).<br><br>RESULTS: LHON associated mutations were detected in 55% of the patients of which 42% harboured the primary mutations and 13% harboured potentially pathogenic variants that were previously reported to cause LHON. The candidate mutations identified with confirmed pathogenicity are: m.11778G&#xa0;>&#xa0;A (38%), m.14484&#xa0;T&#xa0;>&#xa0;C (3%), m.4171C&#xa0;>&#xa0;A (1%) and m.11696G&#xa0;>&#xa0;A (1%). MSP results demonstrated that the D-loop region was unmethylated in all the study subjects including mutation-positive patients, mutation-negative patients, asymptomatic carriers, and controls. Haplogroup-M was prevalent (69%) in the study cohort followed by R (14%), U (9%), N (3%), HV (2%), G (2%), and W (1%). The frequency of the predominant mutation m.11778G&#xa0;>&#xa0;A was found lower (&#x334; 11%) in haplogroup-U.<br><br>CONCLUSIONS: South Indian LHON cohort shows a unique profile of mtDNA mutations and haplogroup association presumably with no role of D-loop methylation. MT-ND4, MT-ND5, and MT-ND1 serve as the hotspot genes in this cohort. The presence of LHON associated mutations in patients lacking the common primary mutations insists on the necessity of mitochondrial genome sequencing in individuals suspected with LHON.},
}
@article {pmid35111395,
year = {2022},
author = {Yuan, Z and Jiang, W and Sha, Z},
title = {A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12735},
pmid = {35111395},
issn = {2167-8359},
mesh = {Animals ; Male ; *Brachyura/anatomy &amp; histology ; Phylogeny ; Oceans and Seas ; Mitochondria ; China ; },
abstract = {Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda &amp; Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species.},
}
@article {pmid35129136,
year = {2022},
author = {Balasubramaniam, S and Soman, M and Katneni, VK and Tomy, S and Gopalapillay, G and Vijayan, KK},
title = {Mitochondrial DNA based diversity studies reveal distinct and substructured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters.},
journal = {Journal of genetics},
volume = {101},
number = {},
pages = {},
pmid = {35129136},
issn = {0973-7731},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; India ; *Mitochondria/genetics ; Phylogeny ; },
abstract = {Pearlspot (Etroplus suratensis) is one of the most commercially important brackish water fish species widely found along the coastal regions of peninsular India and Sri Lanka. Pearlspot is known for its tender flesh, delectable taste, culinary tourism and highyielding market value. Information on the genetic makeup of stocks/populations is extremely vital as it forms the basis for future genetic studies. For this, we utilized ATPase6/8 genes of mtDNA of pearlspot populations collected from nine different locations ranging from Ratnagiri in Maharashtra state on the west coast to Chilika in Odisha on the east coast. Sequence analyses of these genes revealed 33 polymorphic sites, which include 17 singleton and 16 parsimony informative sites. Pair-wise genetic differentiation study (FST = 0.75) indicated significant (P<0.001) differences among all the pairs of stocks except those from Chilika and Nagayalanka. The spatial analysis of molecular variance (SAMOVA) significantly delineated the population into four groups (FCT = 0.69, P = 0.0001), namely northwest (Ratnagiri and Goa); southwest (Mangalore and lakes at Vembanad, Ashtamudi and Vellayani in Kerala); southeast (Pulicat in Tamil Nadu) and northeast (Chilika in Odisha and Nagayalanka in Andhra Pradesh). The above delineation is supported by clades of the phylogenetic tree and also the clusters of median joining haplotype network. The high haplotype diversity (0.84), low nucleotide diversity (0.003), and negative values of Tajima's D (-1.47) and Fu's Fs statistic (-14.89) are characteristic of populations having recently undergone demographic expansion. Mantel test revealed significant isolation by distance. The study identifies highly delineated structured populations with restricted gene flow. If such a stock is overfished, it is highly unlikely that it would recover through migration. For any future breeding programme in this species, it would be desirable to form a base population which incorporates the genetic material from all the locations so that we get a wide gene pool to select from.},
}
@article {pmid35133488,
year = {2022},
author = {Shumenko, PG and Tatonova, YV},
title = {Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers.},
journal = {Parasitology research},
volume = {121},
number = {3},
pages = {915-923},
pmid = {35133488},
issn = {1432-1955},
mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Asia, Eastern ; Genetic Variation ; *Heterophyidae/genetics ; Mitochondria/genetics ; Phylogeny ; Russia ; },
abstract = {In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.},
}
@article {pmid35135343,
year = {2022},
author = {Horrell, HD and Lindeque, A and Farrell, AP and Seymour, RS and White, CR and Kruger, KM and Snelling, EP},
title = {Relationship between capillaries, mitochondria and maximum power of the heart: a meta-study from shrew to elephant.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1968},
pages = {20212461},
pmid = {35135343},
issn = {1471-2954},
mesh = {Animals ; *Capillaries ; *Elephants ; Humans ; Mitochondria ; Oxygen ; Oxygen Consumption ; Phylogeny ; Shrews ; },
abstract = {This meta-study uses phylogenetic scaling models across more than 30 species, spanning five orders of magnitude in body mass, to show that cardiac capillary numerical density and mitochondrial volume density decrease with body mass raised to the -0.07 ± 0.03 and -0.04 ± 0.01 exponents, respectively. Thus, while an average 10 g mammal has a cardiac capillary density of approximately 4150 mm[-2] and a mitochondrial density of 33%, a 1 t mammal has considerably lower corresponding values of 1850 mm[-2] and 21%. These similar scaling trajectories suggest quantitative matching for the primary oxygen supply and oxygen consuming structures of the heart, supporting economic design at the cellular level of the oxygen cascade in this aerobic organ. These scaling trajectories are nonetheless somewhat shallower than the exponent of -0.11 calculated for the maximum external mechanical power of the cardiac tissue, under conditions of heavy exercise, when oxygen flow between capillaries and mitochondria is probably fully exploited. This mismatch, if substantiated, implies a declining external mechanical efficiency of the heart with increasing body mass, whereby larger individuals put more energy in but get less energy out, a scenario with implications for cardiovascular design, aerobic capacity and limits of body size.},
}
@article {pmid35143947,
year = {2022},
author = {Sai Satyanarayana, D and Ahlawat, S and Sharma, R and Arora, R and Sharma, A and Tantia, MS and Vijh, RK},
title = {Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels.},
journal = {Gene},
volume = {820},
number = {},
pages = {146279},
doi = {10.1016/j.gene.2022.146279},
pmid = {35143947},
issn = {1879-0038},
mesh = {Animals ; Biodiversity ; Camelus/*genetics ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Haplotypes ; India ; Male ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNA[Thr], tRNA[Pro] and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.},
}
@article {pmid35163839,
year = {2022},
author = {Davoudi, M and Chen, J and Lou, Q},
title = {Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (HSP70) Gene Family in Pumpkin (Cucurbita moschata) Rootstock under Drought Stress Suggested the Potential Role of these Chaperones in Stress Tolerance.},
journal = {International journal of molecular sciences},
volume = {23},
number = {3},
pages = {},
pmid = {35163839},
issn = {1422-0067},
support = {BE2021357 and 2021YFD1200201-04//the Key Research and Development Program/ ; },
mesh = {Cucurbita/genetics/*physiology ; *Down-Regulation ; Droughts ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Genomics/*methods ; HSP70 Heat-Shock Proteins/*genetics ; Multigene Family ; Phylogeny ; Plant Proteins/genetics ; Promoter Regions, Genetic ; Selection, Genetic ; Stress, Physiological ; },
abstract = {Heat shock protein 70s (HSP70s) are highly conserved proteins that are involved in stress responses. These chaperones play pivotal roles in protein folding, removing the extra amounts of oxidized proteins, preventing protein denaturation, and improving the antioxidant system activities. This conserved family has been characterized in several crops under drought stress conditions. However, there is no study on HSP70s in pumpkin (Cucurbita moschata). Therefore, we performed a comprehensive analysis of this gene family, including phylogenetic relationship, motif and gene structure analysis, gene duplication, collinearity, and promoter analysis. In this research, we found 21 HSP70s that were classified into five groups (from A to E). These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). We could observe more similarity in closely linked subfamilies in terms of motifs, the number of introns/exons, and the corresponding cellular compartments. According to the collinearity analysis, gene duplication had occurred as a result of purifying selection. The results showed that the occurrence of gene duplication for all nine gene pairs was due to segmental duplication (SD). Synteny analysis revealed a closer relationship between pumpkin and cucumber than pumpkin and Arabidopsis. Promoter analysis showed the presence of various cis-regulatory elements in the up-stream region of the HSP70 genes, such as hormones and stress-responsive elements, indicating a potential role of this gene family in stress tolerance. We furtherly performed the gene expression analysis of the HSP70s in pumpkin under progressive drought stress. Pumpkin is widely used as a rootstock to improve stress tolerance, as well as fruit quality of cucumber scion. Since stress-responsive mobile molecules translocate through vascular tissue from roots to the whole plant body, we used the xylem of grafted materials to study the expression patterns of the HSP70 (potentially mobile) gene family. The results indicated that all CmoHSP70s had very low expression levels at 4 days after stress (DAS). However, the genes showed different expression patterns by progressing he drought period. For example, the expression of CmoHSP70-4 (in subgroup E) and CmoHSP70-14 (in subgroup C) sharply increased at 6 and 11 DAS, respectively. However, the expression of all genes belonging to subgroup A did not change significantly in response to drought stress. These findings indicated the diverse roles of this gene family under drought stress and provided valuable information for further investigation on the function of this gene family, especially under stressful conditions.},
}
@article {pmid35187492,
year = {2022},
author = {Juhaszova, M and Kobrinsky, E and Zorov, DB and Nuss, HB and Yaniv, Y and Fishbein, KW and de Cabo, R and Montoliu, L and Gabelli, SB and Aon, MA and Cortassa, S and Sollott, SJ},
title = {ATP Synthase K[+]- and H[+]-fluxes Drive ATP Synthesis and Enable Mitochondrial K[+]-"Uniporter" Function: II. Ion and ATP Synthase Flux Regulation.},
journal = {Function (Oxford, England)},
volume = {3},
number = {2},
pages = {zqac001},
pmid = {35187492},
issn = {2633-8823},
mesh = {Bayes Theorem ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Phylogeny ; *Mitochondrial Proton-Translocating ATPases/genetics ; *Mitochondria/metabolism ; Adenosine Triphosphate/metabolism ; },
abstract = {We demonstrated that ATP synthase serves the functions of a primary mitochondrial K[+] "uniporter," i.e., the primary way for K[+] to enter mitochondria. This K[+] entry is proportional to ATP synthesis, regulating matrix volume and energy supply-vs-demand matching. We show that ATP synthase can be upregulated by endogenous survival-related proteins via IF1. We identified a conserved BH3-like domain of IF1 which overlaps its "minimal inhibitory domain" that binds to the β-subunit of F1. Bcl-xL and Mcl-1 possess a BH3-binding-groove that can engage IF1 and exert effects, requiring this interaction, comparable to diazoxide to augment ATP synthase's H[+] and K[+] flux and ATP synthesis. Bcl-xL and Mcl-1, but not Bcl-2, serve as endogenous regulatory ligands of ATP synthase via interaction with IF1 at this BH3-like domain, to increase its chemo-mechanical efficiency, enabling its function as the recruitable mitochondrial KATP-channel that can limit ischemia-reperfusion injury. Using Bayesian phylogenetic analysis to examine potential bacterial IF1-progenitors, we found that IF1 is likely an ancient (∼2 Gya) Bcl-family member that evolved from primordial bacteria resident in eukaryotes, corresponding to their putative emergence as symbiotic mitochondria, and functioning to prevent their parasitic ATP consumption inside the host cell.},
}
@article {pmid35189365,
year = {2022},
author = {Hawlitschek, O and Ortiz, EM and Noori, S and Webster, KC and Husemann, M and Pereira, RJ},
title = {Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae).},
journal = {Molecular phylogenetics and evolution},
volume = {170},
number = {},
pages = {107439},
doi = {10.1016/j.ympev.2022.107439},
pmid = {35189365},
issn = {1095-9513},
mesh = {Animals ; *Grasshoppers/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Orthoptera/genetics ; Phylogeny ; Transcriptome ; },
abstract = {The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. Resolving the phylogeny of the Chorthippus biguttulus species complex is important because many morphologically cryptic species occupy overlapping ranges across Eurasia and serve important ecological functions. We investigated whether multispecies coalescent analysis of 540 genes generated by transcriptome sequencing could resolve the phylogeny of the C. biguttulus complex and related Gomphocerinae species. Our divergence time estimates confirm that Gomphocerinae is a very young radiation, with an age estimated at 1.38 (2.35-0.77) mya for the C. biguttulus complex. Our estimated topology based on complete mitogenomes recovered some species as para- or polyphyletic. In contrast, the multispecies coalescent based on nuclear genes retrieved all species as monophyletic clusters, corroborating most taxonomic hypotheses. Our results underline the importance of using nuclear multispecies coalescent methods for studying young radiations and highlight the need of further taxonomic revision in Gomphocerinae grasshoppers.},
}
@article {pmid35205291,
year = {2022},
author = {Zhang, BQ and Song, XP and Zhang, XQ and Huang, YX and Liang, YJ and Zhou, S and Yang, CF and Yang, LT and Huang, X and Li, YR},
title = {Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress.},
journal = {Genes},
volume = {13},
number = {2},
pages = {},
pmid = {35205291},
issn = {2073-4425},
mesh = {Calcineurin/genetics ; Cold-Shock Response/genetics ; Gene Expression ; Phylogeny ; *Saccharum/genetics ; },
abstract = {Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter's low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.},
}
@article {pmid35247316,
year = {2022},
author = {Moorthy, BT and Jiang, C and Patel, DM and Ban, Y and O'Shea, CR and Kumar, A and Yuan, T and Birnbaum, MD and Gomes, AV and Chen, X and Fontanesi, F and Lampidis, TJ and Barrientos, A and Zhang, F},
title = {The evolutionarily conserved arginyltransferase 1 mediates a pVHL-independent oxygen-sensing pathway in mammalian cells.},
journal = {Developmental cell},
volume = {57},
number = {5},
pages = {654-669.e9},
pmid = {35247316},
issn = {1878-1551},
support = {R01 GM138557/GM/NIGMS NIH HHS/United States ; R35 GM118141/GM/NIGMS NIH HHS/United States ; },
mesh = {*Aminoacyltransferases/genetics/metabolism ; Animals ; Humans ; Mammals/metabolism ; *Oxygen ; Phylogeny ; Proteolysis ; },
abstract = {The response to oxygen availability is a fundamental process concerning metabolism and survival/death in all mitochondria-containing eukaryotes. However, the known oxygen-sensing mechanism in mammalian cells depends on pVHL, which is only found among metazoans but not in other species. Here, we present an alternative oxygen-sensing pathway regulated by ATE1, an enzyme ubiquitously conserved in eukaryotes that influences protein degradation by posttranslational arginylation. We report that ATE1 centrally controls the hypoxic response and glycolysis in mammalian cells by preferentially arginylating HIF1α that is hydroxylated by PHD in the presence of oxygen. Furthermore, the degradation of arginylated HIF1α is independent of pVHL E3 ubiquitin ligase but dependent on the UBR family proteins. Bioinformatic analysis of human tumor data reveals that the ATE1/UBR and pVHL pathways jointly regulate oxygen sensing in a transcription-independent manner with different tissue specificities. Phylogenetic analysis suggests that eukaryotic ATE1 likely evolved during mitochondrial domestication, much earlier than pVHL.},
}
@article {pmid35391113,
year = {2022},
author = {Lobon-Rovira, J and Conradie, W and Pinto, PV and Keates, C and Edwards, S and Plessis, AD and Branch, WR},
title = {Systematic revision of Afrogecko ansorgii (Boulenger, 1907) (Sauria: Gekkonidae) from western Angola.},
journal = {Zootaxa},
volume = {5124},
number = {4},
pages = {401-430},
doi = {10.11646/zootaxa.5124.4.1},
pmid = {35391113},
issn = {1175-5334},
mesh = {Angola ; Animals ; Cell Nucleus/genetics ; *Lizards/genetics ; Male ; Mitochondria ; Phylogeny ; },
abstract = {Here we provide the first phylogenetic analysis that include Afrogecko ansorgii and a detailed morphological comparison with other species of leaf-toed geckos. For this purpose, we used two mitochondrial (16S, ND2) and four nuclear (RAG1, RAG2, CMOS, PDC) genes to produce a robust phylogenetic reconstruction. This allowed us to show that A. ansorgii is not related as previously believed to circum-Indian Ocean leaf-toed geckos and is rather more closely related to other Malagasy leaf-toed geckos. Additionally, we explore and compare osteological variation in A. ansorgii skulls through High Resolution X-ray Computed Tomography with previously published material. This allowed us to describe herein a new genus, Bauerius gen. nov., and additionally provide a detailed redescription of the species (including the first description of male material), supplementing the limited original description and type series, which consisted of only two females.},
}
@article {pmid35409414,
year = {2022},
author = {Tsai, HC and Hsieh, CH and Hsu, CW and Hsu, YH and Chien, LF},
title = {Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae.},
journal = {International journal of molecular sciences},
volume = {23},
number = {7},
pages = {},
pmid = {35409414},
issn = {1422-0067},
support = {NSC96-2313-B-005-030-MY2, NSC96-2752-B-005-013-PAE, MOST110-2221-E-005-078//Ministry of Science and Technology of Taiwan/ ; },
mesh = {Cloning, Molecular ; DNA, Mitochondrial/genetics ; *Electron Transport Complex I/genetics ; Mitochondria/genetics ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; },
abstract = {Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H[+]) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5'-terminal and 3'-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K[+], Na[+], or H[+].},
}
@article {pmid35435757,
year = {2022},
author = {Nakabachi, A and Moran, NA},
title = {Extreme Polyploidy of Carsonella, an Organelle-Like Bacterium with a Drastically Reduced Genome.},
journal = {Microbiology spectrum},
volume = {10},
number = {3},
pages = {e0035022},
pmid = {35435757},
issn = {2165-0497},
mesh = {Animals ; Bacteria/genetics ; *Gammaproteobacteria ; Genome, Bacterial ; *Hemiptera/genetics/microbiology ; Organelles ; Phylogeny ; Polyploidy ; Symbiosis ; },
abstract = {Polyploidy is the state of having multiple copies of the genome within a nucleus or a cell, which has repeatedly evolved across the domains of life. Whereas most bacteria are monoploid, some bacterial species and endosymbiotic organelles that are derived from bacteria are stably polyploid. In the present study, using absolute quantitative PCR, we assessed the ploidy of Candidatus Carsonella ruddii (Gammaproteobacteria, Oceanospirillales), the obligate symbiont of the hackberry petiole gall psyllid, Pachypsylla venusta (Hemiptera, Psylloidea). The genome of this symbiont is one of the smallest known for cellular organisms, at 160 kb. The analysis revealed that Carsonella within a single bacteriocyte has ∼6 × 10[4] copies of the genome, indicating that some Carsonella cells can contain thousands or even tens of thousands of genomic copies per cell. The basis of polyploidy of Carsonella is unknown, but it potentially plays a role in the repair of DNA damage through homologous recombination. IMPORTANCE Mitochondria and plastids are endosymbiotic organelles in eukaryotic cells and are derived from free-living bacteria. They have many highly reduced genomes from which numerous genes have been transferred to the host nucleus. Similar, but more recently established, symbiotic systems are observed in some insect lineages. Although the genomic sequence data of such bacterial symbionts are rapidly accumulating, little is known about their ploidy. The present study revealed that a bacterium with a drastically reduced genome is an extreme polyploid, which is reminiscent of the case of organelles.},
}
@article {pmid35451706,
year = {2022},
author = {Vella, A and Vella, N and Acosta-Díaz, C},
title = {The first complete mitochondrial genomes for Serranus papilionaceus and Serranus scriba, and their phylogenetic position within Serranidae.},
journal = {Molecular biology reports},
volume = {49},
number = {7},
pages = {6295-6302},
pmid = {35451706},
issn = {1573-4978},
support = {BioCon_Innovate Research Excellence Grant//University of Malta/ ; FINS//Ministry of Education/ ; },
mesh = {Animals ; *Bass/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {BACKGROUND: Butterfly-winged comber, Serranus papilionaceus Valenciennes, 1832, was recently resurrected and so it is no longer considered as a junior synonym of the Painted comber, Serranus scriba (Linneus, 1758). This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationship and delineate these two species.<br><br>METHODS AND RESULTS: Next-generation Sequencing was applied to sequence the genome of these two Serranus species. The data generated was then used to construct the mitochondrial genome of these two species. This produced the first complete mitochondrial genomes for the genus Serranus here represented by Serranus papilionaceus and Serranus scriba. These two mitochondrial genomes are 16,514&#xa0;bp and 16,512&#xa0;bp respectively, and both contained the typical 37 genes found in vertebrates (13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs), together with the OL and the control region.<br><br>CONCLUSIONS: These mitochondrial genomes provide a new insight into the phylogenetic and evolutionary connections between the various subfamilies within Serranidae, while providing new molecular data that can be applied to discriminate between the studied species.},
}
@article {pmid35452707,
year = {2022},
author = {Chen, Q and Chen, L and Liao, CQ and Wang, X and Wang, M and Huang, GH},
title = {Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species.},
journal = {Gene},
volume = {830},
number = {},
pages = {146516},
doi = {10.1016/j.gene.2022.146516},
pmid = {35452707},
issn = {1879-0038},
mesh = {Animals ; *Butterflies/genetics ; *Genome, Mitochondrial ; *Lepidoptera/genetics ; Mitochondria/genetics ; *Moths/genetics ; Phylogeny ; RNA, Transfer/genetics ; },
abstract = {Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).},
}
@article {pmid35457201,
year = {2022},
author = {Juskeviciene, R and Fritz, AK and Brilkova, M and Akbergenov, R and Schmitt, K and Rehrauer, H and Laczko, E and Isnard-Petit, P and Thiam, K and Eckert, A and Schacht, J and Wolfer, DP and Böttger, EC and Shcherbakov, D},
title = {Phenotype of Mrps5-Associated Phylogenetic Polymorphisms Is Intimately Linked to Mitoribosomal Misreading.},
journal = {International journal of molecular sciences},
volume = {23},
number = {8},
pages = {},
pmid = {35457201},
issn = {1422-0067},
mesh = {Animals ; Mice ; *Mitochondrial Proteins/genetics ; Mutation ; Phenotype ; Phylogeny ; Protein Biosynthesis ; *Ribosomal Proteins/genetics ; },
abstract = {We have recently identified point mutation V336Y in mitoribosomal protein Mrps5 (uS5m) as a mitoribosomal ram (ribosomal ambiguity) mutation conferring error-prone mitochondrial protein synthesis. In vivo in transgenic knock-in animals, homologous mutation V338Y was associated with a discrete phenotype including impaired mitochondrial function, anxiety-related behavioral alterations, enhanced susceptibility to noise-induced hearing damage, and accelerated metabolic aging in muscle. To challenge the postulated link between Mrps5 V338Y-mediated misreading and the in vivo phenotype, we introduced mutation G315R into the mouse Mrps5 gene as Mrps5 G315R is homologous to the established bacterial ram mutation RpsE (uS5) G104R. However, in contrast to bacterial translation, the homologous G → R mutation in mitoribosomal Mrps5 did not affect the accuracy of mitochondrial protein synthesis. Importantly, in the absence of mitochondrial misreading, homozygous mutant MrpS5[G315R/G315R] mice did not show a phenotype distinct from wild-type animals.},
}
@article {pmid35460877,
year = {2022},
author = {Kodagoda, YK and Liyanage, DS and Omeka, WKM and Kwon, H and Hwang, SD and Lee, J},
title = {Molecular characterization, expression, and functional analysis of cystatin B in the big-belly seahorse (Hippocampus abdominalis).},
journal = {Fish &amp; shellfish immunology},
volume = {124},
number = {},
pages = {442-453},
doi = {10.1016/j.fsi.2022.04.020},
pmid = {35460877},
issn = {1095-9947},
mesh = {Animals ; *Cyprinidae/genetics ; Cystatin B/genetics ; *Cystatins/genetics ; *Fish Diseases ; Fish Proteins/chemistry ; Male ; Phylogeny ; Poly I-C/pharmacology ; Sequence Alignment ; *Smegmamorpha ; },
abstract = {Cystatins are a diverse group of cysteine protease inhibitors widely present among various organisms. Beyond their protease inhibitor function, cystatins play a crucial role in diverse pathophysiological conditions in animals, including neurodegenerative disorders, tumor progression, inflammatory diseases, and immune response. However, the role of cystatins in immunity against viral and bacterial infections in fish remains to be elucidated. In this study, the cystatin B from big-belly seahorse, Hippocampus abdominalis, designated as HaCSTB, was identified and characterized. HaCSTB shared the highest homology with type 1 cystatin family members of teleosts and had three cystatin catalytic domains with no signal peptides or disulfide bonds. HaCSTB transcripts were mainly expressed in peripheral blood cells (PBCs), followed by the testis and pouch of healthy big-belly seahorses. Immune challenge with lipopolysaccharides (LPS), polyinosinic:polycytidylic acid (Poly I:C), and Streptococcus iniae induced upregulation of relative HaCSTB mRNA expression in PBCs. Subcellular localization analysis revealed the distribution of HaCSTB in the cytosol, mitochondria, and nuclei of fathead minnow cells (FHM). Recombinant HaCSTB (rHaCSTB) exhibited potent in vitro inhibitory activity against papain, a cysteine protease, in a concentration-, pH-, and temperature-dependent manner. Overexpression of HaCSTB in viral hemorrhagic septicemia virus (VHSV)-susceptible FHM cells increased cell viability and reduced VHSV-induced apoptosis. Collectively, these results suggest that HaCSTB might engage in the teleostean immune protection against bacteria and viruses.},
}
@article {pmid35497189,
year = {2022},
author = {Chen, Z and Schrödl, M},
title = {How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13285},
pmid = {35497189},
issn = {2167-8359},
mesh = {Animals ; *Gastropoda/genetics ; Phylogeny ; Mollusca ; Genome/genetics ; Transcriptome ; },
abstract = {The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.},
}
@article {pmid35508562,
year = {2022},
author = {Kidd, KK and Evsanaa, B and Togtokh, A and Brissenden, JE and Roscoe, JM and Dogan, M and Neophytou, PI and Gurkan, C and Bulbul, O and Cherni, L and Speed, WC and Murtha, M and Kidd, JR and Pakstis, AJ},
title = {North Asian population relationships in a global context.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7214},
pmid = {35508562},
issn = {2045-2322},
mesh = {*Asian People/genetics ; Ethnicity/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; Phylogeny ; Principal Component Analysis ; },
abstract = {Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.},
}
@article {pmid35575078,
year = {2022},
author = {Lee, J and Willett, CS},
title = {Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids.},
journal = {The Journal of heredity},
volume = {113},
number = {2},
pages = {171-183},
doi = {10.1093/jhered/esab068},
pmid = {35575078},
issn = {1465-7333},
support = {IOS-1155325//National Science Foundation/ ; //University of North Carolina at Chapel Hill/ ; },
mesh = {Animals ; *Copepoda/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.},
}
@article {pmid35580797,
year = {2022},
author = {Sandamalika, WMG and Udayantha, HMV and Liyanage, DS and Lim, C and Kim, G and Kwon, H and Lee, J},
title = {Identification of reactive oxygen species modulator 1 (Romo 1) from black rockfish (Sebastes schlegelii) and deciphering its molecular characteristics, immune responses, oxidative stress modulation, and wound healing properties.},
journal = {Fish &amp; shellfish immunology},
volume = {125},
number = {},
pages = {266-275},
doi = {10.1016/j.fsi.2022.05.026},
pmid = {35580797},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; *Bass ; DNA, Complementary/genetics ; Female ; Fish Proteins/chemistry ; Immunity, Innate/genetics ; Lipopolysaccharides/metabolism/pharmacology ; Male ; Mammals/genetics/metabolism ; Oxidative Stress ; *Perciformes ; Phylogeny ; Reactive Oxygen Species ; Sequence Alignment ; Wound Healing ; },
abstract = {Reactive oxygen species modulator 1 (Romo1) is a mitochondrial inner membrane protein that induces mitochondrial reactive oxygen species (ROS) generation. In this study, we identified the Romo1 homolog from the black rockfish (Sebastes schlegelii), named it as SsRomo1, and characterized it at the molecular as well as functional levels. An open reading frame consisting of 240 bp was identified in the SsRomo1 complementary DNA (cDNA) sequence that encodes a 79 amino acid-long polypeptide with a molecular weight of 8,293 Da and a theoretical isoelectric point (pI) of 9.89. The in silico analysis revealed the characteristic features of SsRomo1, namely the presence of a transmembrane domain and the lack of a signal peptide. Homology analysis revealed that SsRomo1 exhibits the highest sequence identity with its fish counterparts (>93%) and shares a similar percentage of sequence identity with mammals (>92%). Additionally, it is closely clustered together with the fish clade in the constructed phylogenetic tree. The subcellular localization analysis confirmed its mitochondrial localization within the fathead minnow (FHM) cells. Under normal physiological conditions, the SsRomo1 mRNA is highly expressed in the rockfish ovary, followed by the blood and testis, indicating the abundance of mitochondria in these tissues. Furthermore, the significant upregulation of SsRomo1 in cells treated with lipopolysachharide (LPS), polyinosinic:polycytidylic acid, and Streptococcus iniae suggest that the increased ROS production is induced by SsRomo1 to eliminate pathogens during infections. Incidentally, we believe that this study is the first to determine the involvement of SsRomo1 in LPS-mediated nitric oxide (NO) production in RAW267.4 cells, based on their higher NO production as compared to that in the control. Moreover, overexpression of SsRomo1 enhanced the wound healing ability of FHM cells, indicating its high invasion and migration properties. We also determined the hydrogen peroxide-mediated cell viability of SsRomo1-overexpressed FHM cells and observed a significant reduction in viability, which is possibly due to increased ROS production. Collectively, our observations suggest that SsRomo1 plays an important role in oxidative stress modulation upon immune stimulation and in maintenance of tissue homeostasis in black rockfish.},
}
@article {pmid35584780,
year = {2022},
author = {da Silva E Silva, LH and da Silva, FS and Medeiros, DBA and Cruz, ACR and da Silva, SP and Aragão, AO and Dias, DD and Sena do Nascimento, BL and Júnior, JWR and Vieira, DBR and Monteiro, HAO and Neto, JPN},
title = {Description of the mitogenome and phylogeny of Aedes spp. (Diptera: Culicidae) from the Amazon region.},
journal = {Acta tropica},
volume = {232},
number = {},
pages = {106500},
doi = {10.1016/j.actatropica.2022.106500},
pmid = {35584780},
issn = {1873-6254},
mesh = {*Aedes ; Animals ; *Culicidae/genetics ; *Genome, Mitochondrial/genetics ; Mosquito Vectors/genetics ; Phylogeny ; *Zika Virus/genetics ; *Zika Virus Infection ; },
abstract = {The genus Aedes (Diptera: Culicidae) includes species of great epidemiological relevance, particularly involved in transmission cycles of leading arboviruses in the Brazilian Amazon region, such as the Zika virus (ZIKV), Dengue virus (DENV), Yellow fever virus (YFV), and Chikungunya virus (CHIKV). We report here the first putatively complete sequencing of the mitochondrial genomes of Brazilian populations of the species Aedes albopictus, Aedes scapularis and Aedes serratus. The sequences obtained showed an average length of 14,947 bp, comprising 37 functional subunits, typical in animal mitochondria (13 PCGs, 22 tRNA, and 2 rRNA). The phylogeny reconstructed by Maximum likelihood method, based on the concatenated sequences of all 13 PCGs produced at least two non-directly related groupings, composed of representatives of the subgenus Ochlerotatus and Stegomyia of the genus Aedes. The data and information produced here may be useful for future taxonomic and evolutionary studies of the genus Aedes, as well as the Culicidae family.},
}
@article {pmid35585601,
year = {2022},
author = {Vujovic, F and Hunter, N and Farahani, RM},
title = {Notch ankyrin domain: evolutionary rise of a thermodynamic sensor.},
journal = {Cell communication and signaling : CCS},
volume = {20},
number = {1},
pages = {66},
pmid = {35585601},
issn = {1478-811X},
mesh = {Animals ; *Ankyrins/chemistry/metabolism ; Mice ; *Neural Stem Cells/chemistry/metabolism ; Phylogeny ; Protein Domains ; *Receptors, Notch/chemistry/metabolism ; Signal Transduction ; Thermodynamics ; },
abstract = {Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notch[on] to Notch[off] state, characterised by dissociation of Notch intracellular domain (NICD) from DNA-bound RBPJ. Here we provide evidence that transitioning to the Notch[off] state is regulated by heat flux, a phenomenon that aligns resolution of fate dichotomies to mitochondrial activity. A combination of phylogenetic analysis and computational biochemistry was utilised to disclose structural adaptations of Notch1 ankyrin domain that enabled function as a sensor of heat flux. We then employed DNA-based micro-thermography to measure heat flux during brain development, followed by analysis in vitro of the temperature-dependent behaviour of Notch1 in mouse neural progenitor cells. The structural capacity of NICD to operate as a thermodynamic sensor in metazoans stems from characteristic enrichment of charged acidic amino acids in β-hairpins of the ankyrin domain that amplify destabilising inter-residue electrostatic interactions and render the domain thermolabile. The instability emerges upon mitochondrial activity which raises the perinuclear and nuclear temperatures to 50 °C and 39 °C, respectively, leading to destabilization of Notch1 transcriptional complex and transitioning to the Notch[off] state. Notch1 functions a metazoan thermodynamic sensor that is switched on by intercellular contacts, inputs heat flux as a proxy for mitochondrial activity in the Notch[on] state via the ankyrin domain and is eventually switched off in a temperature-dependent manner. Video abstract.},
}
@article {pmid35630799,
year = {2022},
author = {Xie, DM and Zhang, Q and Xin, LK and Wang, GK and Liu, CB and Qin, MJ},
title = {Cloning and Functional Characterization of Two Germacrene A Oxidases Isolated from Xanthium sibiricum.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {10},
pages = {},
pmid = {35630799},
issn = {1420-3049},
support = {81503190//Dongmei Xie/ ; 2021hxts22//Dongmei Xie/ ; },
mesh = {Cloning, Molecular ; Oxidoreductases/metabolism ; Phylogeny ; Plant Proteins/metabolism ; Sesquiterpenes, Germacrane ; *Xanthium/genetics ; },
abstract = {Sesquiterpene lactones (STLs) from the cocklebur Xanthium sibiricum exhibit significant anti-tumor activity. Although germacrene A oxidase (GAO), which catalyzes the production of Germacrene A acid (GAA) from germacrene A, an important precursor of germacrene-type STLs, has been reported, the remaining GAOs corresponding to various STLs' biosynthesis pathways remain unidentified. In this study, 68,199 unigenes were studied in a de novo transcriptome assembly of X. sibiricum fruits. By comparison with previously published GAO sequences, two candidate X. sibiricum GAO gene sequences, XsGAO1 (1467 bp) and XsGAO2 (1527 bp), were identified, cloned, and predicted to encode 488 and 508 amino acids, respectively. Their protein structure, motifs, sequence similarity, and phylogenetic position were similar to those of other GAO proteins. They were most strongly expressed in fruits, according to a quantitative real-time polymerase chain reaction (qRT-PCR), and both XsGAO proteins were localized in the mitochondria of tobacco leaf epidermal cells. The two XsGAO genes were cloned into the expression vector for eukaryotic expression in Saccharomyces cerevisiae, and the enzyme reaction products were detected by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) methods. The results indicated that both XsGAO1 and XsGAO2 catalyzed the two-step conversion of germacrene A (GA) to GAA, meaning they are unlike classical GAO enzymes, which catalyze a three-step conversion of GA to GAA. This cloning and functional study of two GAO genes from X. sibiricum provides a useful basis for further elucidation of the STL biosynthesis pathway in X. sibiricum.},
}
@article {pmid35695456,
year = {2022},
author = {Jiang, X and Coroian, D and Barahona, E and Echavarri-Erasun, C and Castellanos-Rueda, R and Eseverri, &#xc1; and Aznar-Moreno, JA and Burén, S and Rubio, LM},
title = {Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana.},
journal = {mBio},
volume = {13},
number = {3},
pages = {e0026822},
pmid = {35695456},
issn = {2150-7511},
mesh = {*Archaeal Proteins/genetics ; *Azotobacter vinelandii/genetics ; Bacterial Proteins/metabolism ; Chloroplasts/genetics/metabolism ; Fertilizers ; Iron Compounds/*metabolism ; Mitochondria/metabolism ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Nitrogenase/genetics/metabolism ; Phylogeny ; Nicotiana/genetics/metabolism ; },
abstract = {Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This technology can be achieved by expressing prokaryotic nitrogen fixation gene products for the assembly of a functional nitrogenase in plants. NifB is a critical nitrogenase component since it catalyzes the first committed step in the biosynthesis of all types of nitrogenase active-site cofactors. Here, we used a library of 30 distinct nifB sequences originating from different phyla and ecological niches to restore diazotrophic growth of an Azotobacter vinelandii nifB mutant. Twenty of these variants rescued the nifB mutant phenotype despite their phylogenetic distance to A. vinelandii. Because multiple protein interactions are required in the iron-molybdenum cofactor (FeMo-co) biosynthetic pathway, the maturation of nitrogenase in a heterologous host can be divided in independent modules containing interacting proteins that function together to produce a specific intermediate. Therefore, nifB functional modules composed of a nifB variant, together with the A. vinelandii NifS and NifU proteins (for biosynthesis of NifB [Fe4S4] clusters) and the FdxN ferredoxin (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to accept [Fe4S4] clusters from NifU and were functional in FeMo-co synthesis in vitro. The accumulation of significant levels of soluble and functional NifB proteins in chloroplasts and mitochondria is critical to engineering biological nitrogen fixation in plants. IMPORTANCE Biological nitrogen fixation is the conversion of inert atmospheric dinitrogen gas into nitrogen-reactive ammonia, a reaction catalyzed by the nitrogenase enzyme of diazotrophic bacteria and archaea. Because plants cannot fix their own nitrogen, introducing functional nitrogenase in cereals and other crop plants would reduce our strong dependency on N fertilizers. NifB is required for the biosynthesis of the active site cofactors of all nitrogenases, which arguably makes it the most important protein in global nitrogen fixation. NifB functionality is therefore a requisite to engineer a plant nitrogenase. The expression of nifB genes from a wide range of prokaryotes into the model diazotroph Azotobacter vinelandii shows a surprising level of genetic complementation suggestive of plasticity in the nitrogenase biosynthetic pathway. In addition, we obtained NifB proteins from both mitochondria and chloroplasts of tobacco that are functional in vitro after reconstitution by providing [Fe4S4] clusters from NifU, paving the way to nitrogenase cofactor biosynthesis in plants.},
}
@article {pmid35701688,
year = {2022},
author = {Zheng, J and Zhao, L and Zhao, X and Gao, T and Song, N},
title = {High Genetic Connectivity Inferred from Whole-Genome Resequencing Provides Insight into the Phylogeographic Pattern of Larimichthys polyactis.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {24},
number = {4},
pages = {671-680},
pmid = {35701688},
issn = {1436-2236},
support = {2018YFD0900905//Key Technologies Research and Development Program/ ; 41806180//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Fishes/genetics ; Gene Flow ; Microsatellite Repeats ; *Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Compared with terrestrial biota, marine fishes usually present lower genetic differentiation among different geographical populations because of high-level gene flow and lack of physical barriers. Understanding the genetic structure of marine fishes is essential for dividing management unit and making reasonable protection measures. The small yellow croaker (Larimichthys polyactis) belongs to the family Sciaenidae, which is an economic fish and widely distributed in the Western Pacific. To delineate genetic diversity and phylogeographic pattern, whole-genome resequencing was used to evaluate genetic connectivity, genetic diversity, and spatial pattern of L. polyactis for the first time. We obtained 6,645,711 high-quality single nucleotide polymorphisms (SNPs) markers from 40 L. polyactis individuals. The phylogenetic analysis, STRUCTURE, principal component analysis, and Fst results all indicated that no genetic structure consistent with the distribution pattern was found. This result revealed high genetic connectivity of L. polyactis in different sampling sites. High genetic diversity was also detected, indicating that there was sufficient evolutionary potential to maintain its effective population size. Besides, a similar result of high genetic connectivity and genetic diversity was also detected by mitochondria DNA marker. Our study demonstrated the persistence of high levels of genetic connectivity and a lack of population structure across L. polyactis in different sea areas. This study aimed to analyze the division of population structure and the reason for the decline and not exhaustion of L. polyactis resource on a genetic level.},
}
@article {pmid35741703,
year = {2022},
author = {Orlova, VF and Solovyeva, EN and Dunayev, EA and Ananjeva, NB},
title = {Integrative Taxonomy within Eremias multiocellata Complex (Sauria, Lacertidae) from the Western Part of Range: Evidence from Historical DNA.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
pmid = {35741703},
issn = {2073-4425},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Lizards/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The Kokshaal racerunner, Eremias kokshaaliensis Eremchenko et Panfilov, 1999, together with other central Asian racerunner species, is included in the Eremias multiocellata complex. In the present work, for the first time, the results of the analysis of historical mitochondrial DNA (barcode) are presented and the taxonomic status and preliminary phylogenetic relationships within the complex are specified. We present, for the first time, the results of the molecular analysis using historical DNA recovered from specimens of several species of this complex (paratypes of the Kokshaal racerunner and historical collections of the Kashgar racerunner E. buechneri from Kashgaria) using DNA barcoding.},
}
@article {pmid35741788,
year = {2022},
author = {Hawkins, MTR and Bailey, CA and Brown, AM and Tinsman, J and Hagenson, RA and Culligan, RR and Barela, AG and Randriamanana, JC and Ranaivoarisoa, JF and Zaonarivelo, JR and Louis, EE},
title = {Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
pmid = {35741788},
issn = {2073-4425},
mesh = {Animals ; Ecosystem ; Humans ; *Indriidae/classification ; Mitochondria ; Phylogeny ; Sea Urchins ; },
abstract = {The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken’s (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier’s (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.},
}
@article {pmid35741832,
year = {2022},
author = {Solana, JC and Chicharro, C and García, E and Aguado, B and Moreno, J and Requena, JM},
title = {Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing.},
journal = {Genes},
volume = {13},
number = {6},
pages = {},
pmid = {35741832},
issn = {2073-4425},
mesh = {*Genome, Mitochondrial ; Humans ; *Leishmania infantum/genetics ; *Leishmaniasis ; Phylogeny ; *Trypanosoma ; },
abstract = {Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been proposed as a promising phylogenetic marker. Using whole-DNA sequencing data, it is also possible to assemble maxicircle sequences as shown here and in previous works. In this study, based on data available in public databases and using a bioinformatics workflow previously reported by our group, we assembled the complete coding region of the maxicircles for 26 prototypical strains of trypanosomatid species. Phylogenetic analysis based on this dataset resulted in a robust tree showing an accurate taxonomy of kinetoplastids, which was also able to discern between closely related Leishmania species that are usually difficult to discriminate by classical methodologies. In addition, we provide a dataset of the maxicircle sequences of 60 Leishmania infantum field isolates from America, Western Europe, North Africa, and Eastern Europe. In agreement with previous studies, our data indicate that L. infantum parasites from Brazil are highly homogeneous and closely related to European strains, which were transferred there during the discovery of America. However, this study showed the existence of different L. infantum populations/clades within the Mediterranean region. A maxicircle signature for each clade has been established. Interestingly, two L. infantum clades were found coexisting in the same region of Spain, one similar to the American strains, represented by the Spanish JPCM5 reference strain, and the other, named "non-JPC like", may be related to an important leishmaniasis outbreak that occurred in Madrid a few years ago. In conclusion, the maxicircle sequence emerges as a robust molecular marker for phylogenetic analysis and species typing within the kinetoplastids, which also has the potential to discriminate intraspecific variability.},
}
@article {pmid35764672,
year = {2022},
author = {Jenkins, HL and Graham, R and Porter, JS and Vieira, LM and de Almeida, ACS and Hall, A and O'Dea, A and Coppard, SE and Waeschenbach, A},
title = {Unprecedented frequency of mitochondrial introns in colonial bilaterians.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {10889},
pmid = {35764672},
issn = {2045-2322},
mesh = {Animals ; *Gene Transfer, Horizontal ; Introns/genetics ; *Mitochondria/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; },
abstract = {Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.},
}
@article {pmid35764832,
year = {2022},
author = {Kurt, F and Kurt, B and Filiz, E and Yildiz, K and Akbudak, MA},
title = {Mitochondrial iron transporter (MIT) gene in potato (Solanum tuberosum): comparative bioinformatics, physiological and expression analyses in response to drought and salinity.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {35},
number = {5},
pages = {875-887},
pmid = {35764832},
issn = {1572-8773},
mesh = {*Arabidopsis/genetics ; Computational Biology ; Droughts ; Gene Expression Regulation, Plant ; Iron/metabolism ; Membrane Transport Proteins/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants/metabolism ; Salinity ; *Solanum tuberosum/genetics/metabolism ; Stress, Physiological/genetics ; },
abstract = {Mitochondrial iron transporter (MIT) genes are essential for mitochondrial acquisition/import of iron and vital to proper functioning of mitochondria. Unlike other organisms, research on the MITs in plants is limited. The present study provides comparative bioinformatics assays for the potato MIT gene (StMIT) as well as gene expression analyses. The phylogenetic analyses revealed monocots-dicot divergence in MIT proteins and it was also found clade specific motif diversity. In addition, docking analyses indicated that Asp172 and Gly100 residues to be identified as the closest residues binding to ferrous iron. The percentage of structure overlap of the StMIT 3D protein model with Arabidopsis, maize and rice MIT proteins was found between 80.18% and 85.71%. The transcript analyses exhibited that the expression of StMIT was triggered under drought and salinity stresses. The findings of the present study would provide valuable leads for further studies targeting specifically the MIT gene and generally the plant iron metabolism.},
}
@article {pmid35808858,
year = {2023},
author = {Cassidy-Hanley, DM and Doerder, FP and Hossain, M and Devine, C and Clark, T},
title = {Molecular identification of Tetrahymena species.},
journal = {The Journal of eukaryotic microbiology},
volume = {70},
number = {1},
pages = {e12936},
pmid = {35808858},
issn = {1550-7408},
support = {P40 OD010964/OD/NIH HHS/United States ; P40 RR019688/RR/NCRR NIH HHS/United States ; },
mesh = {*Tetrahymena/genetics ; Mitochondria/genetics ; DNA, Intergenic/genetics ; Phylogeny ; },
abstract = {Mitochondrial cox1 689 bp barcodes are routinely used for identification of Tetrahymena species. Here, we examine whether two shorter nuclear sequences, the 5.8S rRNA gene region and the intergenic region between H3 and H4 histone genes, might also be useful either singly or in combination with each other or cox1. We obtained sequences from ~300 wild isolates deposited at the Tetrahymena Stock Center and analyzed additional sequences obtained from GenBank. The 5.8S rRNA gene and portions of its transcribed flanks identify isolates as to their major clade and uniquely identify some, but not all, species. The ~330 bp H3/H4 intergenic region possesses low intraspecific variability and is unique for most species. However, it fails to distinguish between two pairs of common species and their rarer counterparts, and its use is complicated by the presence of duplicate genes in some species. The results show that while the cox1 sequence is the best single marker for Tetrahymena species identification, 5.8S rRNA, and the H3/H4 intergenic regions sequences are useful, singly or in combination, to confirm cox1 species assignments or as part of a preliminary survey of newly collected Tetrahymena. From our newly collected isolates, the results extend the biogeographical range of T. shanghaiensis and T. malaccensis and identify a new species, Tetrahymena arleneae n. sp. herein described.},
}
@article {pmid35842180,
year = {2022},
author = {Biró, B and Gál, Z and Schiavo, G and Ribari, A and Joe Utzeri, V and Brookman, M and Fontanesi, L and Hoffmann, OI},
title = {Nuclear mitochondrial DNA sequences in the rabbit genome.},
journal = {Mitochondrion},
volume = {66},
number = {},
pages = {1-6},
doi = {10.1016/j.mito.2022.07.003},
pmid = {35842180},
issn = {1872-8278},
mesh = {Animals ; Cell Nucleus/genetics ; *DNA, Mitochondrial/chemistry/genetics ; Genome ; *Genome, Mitochondrial ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Rabbits ; Sequence Analysis, DNA ; },
abstract = {Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.},
}
@article {pmid35860045,
year = {2022},
author = {Jamaludin, NA and Jamaluddin, JAF and Rahim, MA and Mohammed Akib, NA and Ratmuangkhwang, S and Mohd Arshaad, W and Mohd Nor, SA},
title = {Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13706},
pmid = {35860045},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Fisheries ; *Conservation of Natural Resources ; Mitochondria/genetics ; Fishes/genetics ; China ; },
abstract = {The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.},
}
@article {pmid35879672,
year = {2022},
author = {Ge, H and Xu, J and Hua, M and An, W and Wu, J and Wang, B and Li, P and Fang, H},
title = {Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {538},
pmid = {35879672},
issn = {1471-2164},
support = {32101730//National Natural Science Foundation of China/ ; MS22020033//the Social Livelihood Science and Technology Project of Nantong City,china/ ; 135420609055//Nantong University Scientific Research Start-up project for Introducing Talents/ ; 202110304081Y//the Practice Innovation Training Program Projects for College Students in 2021/ ; },
mesh = {Acyl Carrier Protein/genetics/metabolism ; Droughts ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics/metabolism ; *Sorghum/metabolism ; Stress, Physiological/genetics ; Zea mays/genetics/metabolism ; },
abstract = {BACKGROUND: Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.<br><br>RESULTS: Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four &#x3b1; helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.<br><br>CONCLUSIONS: In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.},
}
@article {pmid35891364,
year = {2022},
author = {Tao, J and Li, B and Cheng, J and Shi, Y and Qiao, C and Lin, Z and Liu, H},
title = {Genomic Divergence Characterization and Quantitative Proteomics Exploration of Type 4 Porcine Astrovirus.},
journal = {Viruses},
volume = {14},
number = {7},
pages = {},
pmid = {35891364},
issn = {1999-4915},
mesh = {Animals ; Antiviral Agents ; *Astroviridae Infections/veterinary ; China ; Genomics ; Humans ; Mamastrovirus ; Mitochondrial Proteins ; Phylogeny ; Proteomics ; Swine ; *Swine Diseases ; },
abstract = {Porcine astrovirus (PAstV) has been identified as an important diarrheic pathogen with a broad global distribution. The PAstV is a potential pathogen to human beings and plays a role in public health. Until now, the divergence characteristics and pathogenesis of the PAstV are still not well known. In this study, the PAstV-4 strain PAstV/CH/2022/CM1 was isolated from the diarrheal feces of a piglet in Shanghai, which was identified to be a recombination of PAstV4/JPN (LC201612) and PAstV4/CHN (JX060808). A time tree based on the ORF2 protein of the astrovirus demonstrated that type 2-5 PAstV (PAstV-2 to 5) diverged from type 1 PAstV (PAstV-1) at a point from 1992 to 2000. To better understand the molecular basis of the virus, we sought to explore the host cell response to the PAstV/CH/2022/CM1 infection using proteomics. The results demonstrate that viral infection elicits global protein changes, and that the mitochondria seems to be a primary and an important target in viral infection. Importantly, there was crosstalk between autophagy and apoptosis, in which ATG7 might be the key mediator. In addition, the NOD-like receptor X1 (NLRX1) in the mitochondria was activated and participated in several important antiviral signaling pathways after the PAstV/CH/2022/CM1 infection, which was closely related to mitophagy. The NLRX1 may be a crucial protein for antagonizing a viral infection through autophagy, but this has yet to be validated. In conclusion, the data in this study provides more information for understanding the virus genomic characterization and the potential antiviral targets in a PAstV infection.},
}
@article {pmid35973607,
year = {2022},
author = {Holt, AG and Davies, AM},
title = {A comparison of mtDNA deletion mutant proliferation mechanisms.},
journal = {Journal of theoretical biology},
volume = {551-552},
number = {},
pages = {111244},
doi = {10.1016/j.jtbi.2022.111244},
pmid = {35973607},
issn = {1095-8541},
mesh = {Cell Proliferation/genetics ; Clone Cells ; *DNA, Mitochondrial/genetics ; Humans ; *Mitochondria/genetics ; Mutation ; Mutation Rate ; },
abstract = {In this paper we use simulation methods to investigate the proliferation of deletion mutations of mitochondrial DNA in neurons. We simulate three mtDNA proliferation mechanisms, namely, random drift, replicative advantage and vicious cycle. For each mechanism, we investigated the effect mutation rates have on neuron loss within a human host. We also compare heteroplasmy of each mechanism at mutation rates that yield the levels neuron loss that would be associated with dementia. Both random drift and vicious cycle predicted high levels of heteroplasmy, while replicative advantage showed a small number of dominant clones with a low background of heteroplasmy.},
}
@article {pmid35998817,
year = {2022},
author = {Franzolin, GN and Araújo, BL and Zatti, SA and Naldoni, J and Adriano, EA},
title = {Occurrence of the host-parasite system Rhaphiodon vulpinus and Ceratomyxa barbata n. sp. in the two largest watersheds in South America.},
journal = {Parasitology international},
volume = {91},
number = {},
pages = {102651},
doi = {10.1016/j.parint.2022.102651},
pmid = {35998817},
issn = {1873-0329},
mesh = {Animals ; DNA, Ribosomal/genetics ; *Fish Diseases/epidemiology/parasitology ; Fishes ; Gallbladder/parasitology ; *Myxozoa ; *Parasites/genetics ; *Parasitic Diseases, Animal/parasitology ; Phylogeny ; },
abstract = {While around world, species of the genus Ceratomyxa parasite majority marine hosts, growing diversity has been reported in South American freshwater fish. The present study reports Ceratomyxa barbata n. sp. parasitizing the gallbladder of the Rhaphiodon vulpinus fish from the Amazon and La Plata basins. Morphological (light and transmission electron microscopy), molecular (sequencing of small subunit ribosomal DNA - SSU rDNA), and phylogenetic analyses were used to characterize the new species. Worm-like plasmodia endowed with motility were found swimming freely in the bile. The myxospores were elongated, lightly arcuate, with rounded ends and had polar tubules with 3 coils in the polar capsules. Ultrastructural analysis revealed plasmodia composed of an outer cytoplasmic region, where elongated tubular mitochondria, a rough endoplasmic reticulum, sporogonic stages, and a large vacuole occupying the internal area were observed. Phylogenetic analysis, based on SSU rDNA, found that among all South America freshwater Ceratomyxa species, C. barbata n. sp. arises as an earlier divergent species. The present study reveals the occurrence of this host-parasite system (R. vulpinus/C. barbata n. sp.) in the two largest watersheds on the continent.},
}
@article {pmid36071602,
year = {2022},
author = {Zhang, M and Zhang, C and Hu, P and Shi, L and Ju, M and Zhang, B and Li, X and Han, X and Wang, K and Li, X and Qiao, R},
title = {Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds.},
journal = {Animal genetics},
volume = {53},
number = {6},
pages = {803-813},
doi = {10.1111/age.13261},
pmid = {36071602},
issn = {1365-2052},
support = {U1904115//National Natural Science Foundation of China/ ; 202300410195//Outstanding Youth Foundation of Henan Province/ ; },
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Phylogeny ; Swine/genetics ; },
abstract = {Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.},
}
@article {pmid36085554,
year = {2022},
author = {Jacquat, AG and Ulla, SB and Debat, HJ and Muñoz-Adalia, EJ and Theumer, MG and Pedrajas, MDG and Dambolena, JS},
title = {An in silico analysis revealed a novel evolutionary lineage of putative mitoviruses.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {6463-6475},
doi = {10.1111/1462-2920.16202},
pmid = {36085554},
issn = {1462-2920},
mesh = {Genome, Viral ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; *RNA Viruses/genetics ; RNA, Viral ; },
abstract = {Mitoviruses (family Mitoviridae) are small capsid-less RNA viruses that replicate in the mitochondria of fungi and plants. However, to date, the only authentic animal mitovirus infecting an insect was identified as Lutzomyia longipalpis mitovirus 1 (LulMV1). Public databases of transcriptomic studies from several animals may be a good source for identifying the often missed mitoviruses. Consequently, a search of mitovirus-like transcripts at the NCBI transcriptome shotgun assembly (TSA) library, and a search for the mitoviruses previously recorded at the NCBI non-redundant (nr) protein sequences library, were performed in order to identify new mitovirus-like sequences associated with animals. In total, 10 new putative mitoviruses were identified in the TSA database and 8 putative mitoviruses in the nr protein database. To our knowledge, these results represent the first evidence of putative mitoviruses associated with poriferan, cnidarians, echinoderms, crustaceans, myriapods and arachnids. According to different phylogenetic inferences using the maximum likelihood method, these 18 putative mitoviruses form a robust monophyletic lineage with LulMV1, the only known animal-infecting mitovirus. These findings based on in silico procedures provide strong evidence for the existence of a clade of putative mitoviruses associated with animals, which has been provisionally named 'kvinmitovirus'.},
}
@article {pmid36097126,
year = {2022},
author = {Joshi, BD and Kumar, V and De, R and Sharma, R and Bhattacharya, A and Dolker, S and Pal, R and Kumar, VP and Sathyakumar, S and Adhikari, BS and Habib, B and Goyal, SP},
title = {Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications.},
journal = {Molecular biology reports},
volume = {49},
number = {11},
pages = {11177-11186},
pmid = {36097126},
issn = {1573-4978},
mesh = {Animals ; *Cytochromes b/genetics ; *Genetics, Population ; Haplotypes/genetics ; Phylogeny ; Phylogeography ; Sheep/genetics ; *Mitochondria/metabolism ; },
abstract = {BACKGROUND: Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species.<br><br>METHODS AND RESULTS: Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220&#xa0;bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH.<br><br>CONCLUSION: We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.},
}
@article {pmid36180833,
year = {2022},
author = {Xiao, S and Xing, J and Nie, T and Su, A and Zhang, R and Zhao, Y and Song, W and Zhao, J},
title = {Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {469},
pmid = {36180833},
issn = {1471-2229},
mesh = {*Genome, Mitochondrial/genetics ; Humans ; *Infertility, Male/genetics ; Male ; NADH Dehydrogenase/genetics ; Phylogeny ; Plant Infertility/genetics ; Zea mays/genetics ; },
abstract = {BACKGROUND: Cytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome. However, the relationship between mitochondrial function and sterility stability is largely unknown.<br><br>RESULTS: In this study, we determined the ratio of plants carrying exerted anthers in the population of two CMS-S subtypes. The subtype with a high ratio of exerted anthers was designated as CMS-Sa, and the other with low ratio was designated as CMS-Sb. Through next-generation sequencing, we assembled and compared mitochondrial genomes of two CMS-S subtypes. Phylogenetic analyses revealed strong similarities between the two mitochondrial genomes. The sterility-associated regions, S plasmids, and terminal inverted repeats (TIRs) were intact in both genomes. The two subtypes maintained high transcript levels of the sterility gene orf355 in anther tissue. Most of the functional genes/proteins were identical at the nucleotide sequence and amino acid sequence levels in the two subtypes, except for NADH dehydrogenase subunit 1 (nad1). In the mitochondrial genome of CMS-Sb, a 3.3-kilobase sequence containing nad1-exon1 was absent from the second copy of the 17-kb repeat region. Consequently, we detected two copies of nad1-exon1 in CMS-Sa, but only one copy in CMS-Sb. During pollen development, nad1 transcription and mitochondrial biogenesis were induced in anthers of CMS-Sa, but not in those of CMS-Sb. We suggest that the impaired mitochondrial function in the anthers of CMS-Sb is associated with its more stable sterility.<br><br>CONCLUSIONS: Comprehensive analyses revealed diversity in terms of the copy number of the mitochondrial gene nad1-exon1 between two subtypes of CMS-S maize. This difference in copy number affected the transcript levels of nad1 and mitochondrial biogenesis in anther tissue, and affected the reversion rate of CMS-S maize. The results of this study suggest the involvement of mitochondrial robustness in modulation of sterility stability in CMS-S maize.},
}
@article {pmid36198798,
year = {2022},
author = {Wei, W and Schon, KR and Elgar, G and Orioli, A and Tanguy, M and Giess, A and Tischkowitz, M and Caulfield, MJ and Chinnery, PF},
title = {Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes.},
journal = {Nature},
volume = {611},
number = {7934},
pages = {105-114},
pmid = {36198798},
issn = {1476-4687},
support = {212219/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; //Medical Research Council UK/ ; MR/S005021/1/MRC_/Medical Research Council/United Kingdom ; RPG-2018-408/WT_/Wellcome Trust/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/9/MRC_/Medical Research Council/United Kingdom ; MC_UU_00028/7/MRC_/Medical Research Council/United Kingdom ; MR/M008886/1/MRC_/Medical Research Council/United Kingdom ; MC_PC_13047/MRC_/Medical Research Council/United Kingdom ; MR/S035699/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Cell Nucleus/genetics/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; *Genome, Human/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Mutation ; Liposarcoma, Myxoid/genetics ; Neoplasms/genetics ; Germ-Line Mutation ; DNA Breaks, Double-Stranded ; DNA Repair ; Histone-Lysine N-Methyltransferase ; },
abstract = {DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation[1-3]. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 10[4] births and once in every 10[3] cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.},
}
@article {pmid36205366,
year = {2022},
author = {Nofrianto, AB and Lawelle, SA and Mokodongan, DF and Masengi, KWA and Inomata, N and Hashiguchi, Y and Kitano, J and Sumarto, BKA and Kakioka, R and Yamahira, K},
title = {Ancient Admixture in Freshwater Halfbeaks of the Genus Nomorhamphus in Southeast Sulawesi.},
journal = {Zoological science},
volume = {39},
number = {5},
pages = {453-458},
doi = {10.2108/zs220023},
pmid = {36205366},
issn = {0289-0003},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Fresh Water ; Indonesia ; *Mitochondria/genetics ; Phylogeny ; Water ; },
abstract = {Freshwater halfbeaks of the genus Nomorhamphus (Zenarchopteridae) uniquely diversified on Sulawesi Island, where tectonic movements have been very active since the Pliocene. Most species of this genus have quite limited distributions, which indicates that geographic isolations have contributed to their diversification. In this study, we demonstrated that secondary contacts and resultant admixtures between long-isolated species/populations may have also been important. We found that the mitochondrial phylogeny of a group of Nomorhamphus in Southeast Sulawesi was discordant with the nuclear phylogeny. Most notably, individuals in the upper and lower streams of the Moramo River, a small river in this region, clustered with each other in the mitochondrial phylogeny but not in the nuclear phylogeny; in the latter, the lower-stream individuals formed a clade with individuals in the Anduna River, a different river with no present water connection to the Moramo River. Phylogenetic network and population structure analyses using genomic data obtained from RNA-seq revealed that the lower-stream Moramo population admixed with the upper-stream Moramo lineage in ancient times. These findings indicate that the observed mito-nuclear discordance was caused by mitochondrial introgression and not incomplete lineage sorting. The phylogenetic network also revealed several other admixtures between ancient lineages. Repeated admixtures were also evidenced by topological incongruence in population trees estimated using the RNA-seq data. We propose that activities of many fault systems dissecting Southeast Sulawesi caused repeated secondary contact.},
}
@article {pmid36225907,
year = {2022},
author = {Zhang, A and Xu, J and Xu, X and Wu, J and Li, P and Wang, B and Fang, H},
title = {Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench).},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e14156},
pmid = {36225907},
issn = {2167-8359},
mesh = {*Sorghum/genetics ; Plant Proteins/genetics ; Phylogeny ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic ; },
abstract = {The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0-1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of KCS family in sorghum and in response to abiotic stress.},
}
@article {pmid36255631,
year = {2023},
author = {Marx, C and Marx-Blümel, L and Sonnemann, J and Wang, ZQ},
title = {Assessment of Mitochondrial Dysfunctions After Sirtuin Inhibition.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2589},
number = {},
pages = {269-291},
pmid = {36255631},
issn = {1940-6029},
mesh = {*Sirtuins/metabolism ; Lysine/metabolism ; Phylogeny ; Acetylation ; Histone Deacetylases/metabolism ; Histone Acetyltransferases/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Histone Deacetylase Inhibitors/pharmacology ; },
abstract = {Posttranslational modifications are important for protein functions and cellular signaling pathways. The acetylation of lysine residues is catalyzed by histone acetyltransferases (HATs) and removed by histone deacetylases (HDACs), with the latter being grouped into four phylogenetic classes. The class III of the HDAC family, the sirtuins (SIRTs), contributes to gene expression, genomic stability, cell metabolism, and tumorigenesis. Thus, several specific SIRT inhibitors (SIRTi) have been developed to target cancer cell proliferation. Here we provide an overview of methods to study SIRT-dependent cell metabolism and mitochondrial functionality. The chapter describes metabolic flux analysis using Seahorse analyzers, methods for normalization of Seahorse data, flow cytometry and fluorescence microscopy to determine the mitochondrial membrane potential, mitochondrial content per cell and mitochondrial network structures, and Western blot analysis to measure mitochondrial proteins.},
}
@article {pmid36271979,
year = {2022},
author = {Hajibarat, Z and Saidi, A and Gorji, AM and Zeinalabedini, M and Ghaffari, MR and Hajibarat, Z and Nasrollahi, A},
title = {Identification of myosin genes and their expression in response to biotic (PVY, PVX, PVS, and PVA) and abiotic (Drought, Heat, Cold, and High-light) stress conditions in potato.},
journal = {Molecular biology reports},
volume = {49},
number = {12},
pages = {11983-11996},
pmid = {36271979},
issn = {1573-4978},
mesh = {*Solanum tuberosum/genetics/metabolism ; Droughts ; Phylogeny ; Plant Proteins/metabolism ; Hot Temperature ; Plant Breeding ; Stress, Physiological/genetics ; Plants/metabolism ; Myosins/genetics/metabolism ; Gene Expression Regulation, Plant/genetics ; },
abstract = {BACKGROUND: Plant organelles are highly motile where their movement is significant for fast distribution of material around the cell, facilitation of the plant's ability to respond to abiotic and biotic signals, and for appropriate growth. Abiotic and biotic stresses are among the major factors limiting crop yields, and biological membranes are the first target of these stresses. Plants utilize adaptive mechanisms namely myosin to repair injured membranes following exposure to abiotic and biotic stresses.<br><br>OBJECTIVE: Due to the economic importance and cultivation of potato grown under abiotic and biotic stress prone areas, identification and characterization of myosin family members in potato were performed in the present research.<br><br>METHODS: To identify the myosin genes in potato, we performed genome-wide analysis of myosin genes in the S. tuberosum genome using the phytozome. All putative sequences were approved with the interproscan. Bioinformatics analysis was conducted using phylogenetic tree, gene structure, cis-regulatory elements, protein-protein interaction, and gene expression.<br><br>RESULT: The majority of the cell machinery contain actin cytoskeleton and myosins, where motility of organelles are dependent on them. Homology-based analysis was applied to determine seven myosin genes in the potato genome. The members of myosin could be categorized into two groups (XI and VIII). Some of myosin proteins were sub-cellularly located in the nucleus containing 71.5% of myosin proteins and other myosin proteins were localized in the mitochondria, plasma-membrane, and cytoplasm. Determination of co-expressed network, promoter analysis, and gene structure were also performed and gene expression pattern of each gene was surveyed. Number of introns in the gene family members varied from 1 to 39. Gene expression analysis demonstrated that StMyoXI-B and StMyoVIII-2 had the highest transcripts, induced by biotic and abiotic stresses in all three tissues of stem, root, and leaves, respectively. Overall, different cis-elements including abiotic and biotic responsive, hormonal responsive, light responsive, defense responsive elements were found in the myosin promoter sequences. Among the cis-elements, the MYB, G-box, ABRE, JA, and SA contributed the most in the plant growth and development, and in response to abiotic and biotic stress conditions.<br><br>CONCLUSION: Our results showed that myosin genes can be utilized in breeding programs and genetic engineering of plants with the aim of increasing tolerance to abiotic and biotic stresses, especially to viral stresses such as PVY, PVX, PVA, PVS, high light, drought, cold and heat.},
}
@article {pmid36280780,
year = {2022},
author = {Martijn, J and Vosseberg, J and Guy, L and Offre, P and Ettema, TJG},
title = {Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact.},
journal = {Nature ecology &amp; evolution},
volume = {6},
number = {12},
pages = {1829-1831},
pmid = {36280780},
issn = {2397-334X},
mesh = {*Rickettsiales ; Phylogeny ; *Artifacts ; Mitochondria ; },
}
@article {pmid36282276,
year = {2023},
author = {Wang, D and Teng, J and Ning, C and Wang, W and Liu, S and Zhang, Q and Tang, H},
title = {Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens.},
journal = {Animal biotechnology},
volume = {34},
number = {7},
pages = {3154-3161},
doi = {10.1080/10495398.2022.2137035},
pmid = {36282276},
issn = {1532-2378},
mesh = {Animals ; *Chickens/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; Phenotype ; Haplotypes/genetics ; Polymorphism, Single Nucleotide/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.},
}
@article {pmid36326769,
year = {2023},
author = {Kierepka, EM and Preckler-Quisquater, S and Reding, DM and Piaggio, AJ and Riley, SPD and Sacks, BN},
title = {Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains.},
journal = {The Journal of heredity},
volume = {114},
number = {2},
pages = {110-119},
doi = {10.1093/jhered/esac060},
pmid = {36326769},
issn = {1465-7333},
mesh = {Humans ; Animals ; *Foxes/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genomics ; },
abstract = {The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying <10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g. post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages.},
}
@article {pmid36327950,
year = {2023},
author = {Filimonova, S},
title = {Fine structure of the posterior midgut in the mite Anystis baccarum (L.).},
journal = {Arthropod structure &amp; development},
volume = {72},
number = {},
pages = {101218},
doi = {10.1016/j.asd.2022.101218},
pmid = {36327950},
issn = {1873-5495},
mesh = {Animals ; *Mites/ultrastructure ; Phylogeny ; Digestive System/ultrastructure ; *Arachnida ; Epithelial Cells ; },
abstract = {Homology of the posterior midgut regions (PMG) in different phylogenetic lineages of acariform mites (superorder Acariformes) remains unresolved. In the order Trombidiformes, the ultrastructure of the PMG is known primarily in derived groups; thus this study focuses on species belonging to a relatively basal trombidiform family. PMG of Anystis baccarum consists of the colon and postcolon separated by a small intercolon. The fine structure of the colon and postcolon is close to that of the corresponding organs of sarcoptiform mites with the epithelium showing absorptive and endocytotic activity. The epithelial cells produce a variety of excretory vacuoles and a peritrophic matrix around the feces. Morover, the epithelium of the postcolon is characterized by the highest apical brush border and especially numerous mitochondria suggesting involvement in water and ion absorption. The intercolon functions as a sphincter lined with an epithelium capable of producing excretory granules. A pair of short blind extensions arises assimmetrically from the intercolon into the body cavity. Ultrastructurally, these extensions are similar to the arachnid Malpighian tubules and may be their reduced version. Rare endocrine-like cells have been observed in the colon and postcolon.},
}
@article {pmid36330786,
year = {2022},
author = {De, AK and Bhattacharya, D and Sawhney, S and Bala, P and Sunder, J and Sujatha, T and Ponraj, P and Chakurkar, EB},
title = {Molecular characterization of Rhipicephalus microplus in Andaman and Nicobar Islands, India: an insight into genetic assemblages.},
journal = {Journal of genetics},
volume = {101},
number = {},
pages = {},
pmid = {36330786},
issn = {0973-7731},
mesh = {Animals ; *Rhipicephalus/genetics ; Phylogeny ; Haplotypes ; Geography ; Mitochondria/genetics ; India ; Islands ; },
abstract = {The tick, Rhipicephalus microplus is considered as the most notorious ectoparasite of veterinary importance in tropical and sub-tropical regions of the world. The present study deals with the molecular characterization of R. microplus in different regions of Andaman and Nicobar Islands using sequence information of mitochondrial cytochrome C oxidase subunit I (COX1) and their phylogenetic relationship with other Indian R. microplus genotypes. DNA polymorphism study identified a total of eight haplotypes with haplotype diversity of 0.909 ± 0.065 and nucleotide diversity of 0.01911 ± 0.00493. Currently, R. microplus complex consists of five taxa; R. microplus clade A sensu Burger et al. (2014), R. microplus clade B sensu Burger et al. (2014), R. microplus clade C sensu Low et al. (2015), R. australis and R. annulatus. Phylogenetic analysis revealed the presence of two clades (clade A and clade C) of R. microplus in Andaman and Nicobar isolates; Nicobar isolates belonged to clade A whereas Andaman isolates belonged to clade C of R. microplus complex. All the other Indian sequences retrieved from GenBank belonged to clade C of R. microplus complex. Andaman isolates under clade C of R. microplus were phylogenetically distinct from Indian isolates, which indicates independent speciation under isolated island milieu. In Indian isolates, no host-specific or geographical location-specific sub-clustering was observed which indicates the species jumping potential of the R. microplus tick. Therefore, this study indicated the presence of two different genetic makeup of R. microplus complex in two areas of the Andaman and Nicobar archipelago separated by a natural geographical barrier. This indicates presence of two different founding populations of ticks, one in the south and north-middle Andaman and the other in Nicobar Island.},
}
@article {pmid36331499,
year = {2023},
author = {Lestari, SM and Khatun, MF and Acharya, R and Sharma, SR and Shrestha, YK and Jahan, SMH and Aye, TT and Lynn, OM and Win, NKK and Hoat, TX and Thi Dao, H and Tsai, CW and Lee, J and Hwang, HS and Kil, EJ and Lee, S and Kim, SM and Lee, KY},
title = {Genetic diversity of cryptic species of Bemisia tabaci in Asia.},
journal = {Archives of insect biochemistry and physiology},
volume = {112},
number = {2},
pages = {e21981},
doi = {10.1002/arch.21981},
pmid = {36331499},
issn = {1520-6327},
support = {I-1543086-2017-21-01//Exportation Support of Agricultural Products at Animal and Plant Quarantine Agency/ ; Z-1543086-2017-21-01//Exportation Support of Agricultural Products at Animal and Plant Quarantine Agency/ ; },
mesh = {Animals ; Phylogeny ; Asia ; China ; *Mitochondria ; *Hemiptera/genetics ; Genetic Variation ; },
abstract = {Bemisia tabaci is a species complex consisting of various genetically different cryptic species worldwide. To understand the genetic characteristics and geographic distribution of cryptic species of B. tabaci in Asia, we conducted an extensive collection of B. tabaci samples in ten Asian countries (Bangladesh, Indonesia, Japan, Korea, Myanmar, Nepal, Philippines, Singapore, Taiwan, and Vietnam) from 2013 to 2020 and determined 56 different partial sequences of mitochondrial cytochrome oxidase subunit I (COI) DNA. In addition, information on 129 COI sequences of B. tabaci identified from 16 Asian countries was downloaded from the GenBank database. Among the total 185 COI sequences of B. tabaci, the sequence variation reached to 19.68%. In addition, there were 31 cryptic species updated from 16 countries in Asia, that is, Asia I, Asia I India, Asia II (1-13), Asia III, Asia IV, Asia V, China 1-6, MEAM (1, 2, K), MED, Australia/Indonesia, Japan (1 and 2). Further, MED cryptic species consisted of 2 clades, Q1 and Q2. This study provides updated information to understand the genetic variation and geographic diversity of B. tabaci in Asia.},
}
@article {pmid36360198,
year = {2022},
author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A},
title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.},
journal = {Genes},
volume = {13},
number = {11},
pages = {},
pmid = {36360198},
issn = {2073-4425},
mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.},
}
@article {pmid36362255,
year = {2022},
author = {Zhao, W and Bu, X and Zou, H and Li, W and Wu, S and Li, M and Wang, G},
title = {The Genome of the Mitochondrion-Related Organelle in Cepedea longa, a Large Endosymbiotic Opalinid Inhabiting the Recta of Frogs.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
pmid = {36362255},
issn = {1422-0067},
support = {32170437//National Natural Science Foundation of China/ ; 2021M703435//China Postdoctoral Science Foundation/ ; 2019QZKK0304//Second Tibetan Plateau Scienti&#xfb01;c Expedition and Research Program/ ; CARS-45//earmarked fund for CARS/ ; },
mesh = {Animals ; Phylogeny ; *Anura/genetics ; *Stramenopiles/genetics ; Organelles/metabolism ; Mitochondria/genetics ; },
abstract = {Mitochondrion-related organelles (MROs) are loosely defined as degenerated mitochondria in anaerobic and microaerophilic lineages. Opalinids are commonly regarded as commensals in the guts of cold-blooded amphibians. It may represent an intermediate adaptation stage between the conventional aerobic mitochondria and derived anaerobic MROs. In the present study, we sequenced and analyzed the MRO genome of Cepedea longa. It has a linear MRO genome with large inverted repeat gene regions at both ends. Compared to Blastocystis and Proteromonas lacertae, the MRO genome of C. longa has a higher G + C content and repeat sequences near the central region. Although three Opalinata species have different morphological characteristics, phylogenetic analyses based on eight concatenated nad genes indicate that they are close relatives. The phylogenetic analysis showed that C. longa clustered with P. lacertae with strong support. The 18S rRNA gene-based phylogeny resolved the Opalinea clade as a sister clade to Karotomorpha, which then further grouped with Proteromonas. The paraphyly of Proteromonadea needs to be verified due to the lack of MRO genomes for key species, such as Karotomorpha, Opalina and Protoopalina. Besides, our dataset and analyses offered slight support for the paraphyly of Bigyra.},
}
@article {pmid36463372,
year = {2023},
author = {Nikelski, E and Rubtsov, AS and Irwin, D},
title = {High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression.},
journal = {Heredity},
volume = {130},
number = {1},
pages = {1-13},
pmid = {36463372},
issn = {1365-2540},
mesh = {Animals ; *Songbirds/genetics ; Genome ; Genomics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.},
}
@article {pmid36463410,
year = {2023},
author = {Krynická, V and Skotnicová, P and Jackson, PJ and Barnett, S and Yu, J and Wysocka, A and Kaňa, R and Dickman, MJ and Nixon, PJ and Hunter, CN and Komenda, J},
title = {FtsH4 protease controls biogenesis of the PSII complex by dual regulation of high light-inducible proteins.},
journal = {Plant communications},
volume = {4},
number = {1},
pages = {100502},
pmid = {36463410},
issn = {2590-3462},
support = {BB/M000265/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M012166/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Peptide Hydrolases ; Photosystem II Protein Complex/genetics/metabolism ; Phylogeny ; Thylakoids/metabolism ; Chloroplasts/metabolism ; *Arabidopsis/genetics/metabolism ; *Synechocystis/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Metalloproteases/genetics/metabolism ; },
abstract = {FtsH proteases are membrane-embedded proteolytic complexes important for protein quality control and regulation of various physiological processes in bacteria, mitochondria, and chloroplasts. Like most cyanobacteria, the model species Synechocystis sp. PCC 6803 contains four FtsH homologs, FtsH1-FtsH4. FtsH1-FtsH3 form two hetero-oligomeric complexes, FtsH1/3 and FtsH2/3, which play a pivotal role in acclimation to nutrient deficiency and photosystem II quality control, respectively. FtsH4 differs from the other three homologs by the formation of a homo-oligomeric complex, and together with Arabidopsis thaliana AtFtsH7/9 orthologs, it has been assigned to another phylogenetic group of unknown function. Our results exclude the possibility that Synechocystis FtsH4 structurally or functionally substitutes for the missing or non-functional FtsH2 subunit in the FtsH2/3 complex. Instead, we demonstrate that FtsH4 is involved in the biogenesis of photosystem II by dual regulation of high light-inducible proteins (Hlips). FtsH4 positively regulates expression of Hlips shortly after high light exposure but is also responsible for Hlip removal under conditions when their elevated levels are no longer needed. We provide experimental support for Hlips as proteolytic substrates of FtsH4. Fluorescent labeling of FtsH4 enabled us to assess its localization using advanced microscopic techniques. Results show that FtsH4 complexes are concentrated in well-defined membrane regions at the inner and outer periphery of the thylakoid system. Based on the identification of proteins that co-purified with the tagged FtsH4, we speculate that FtsH4 concentrates in special compartments in which the biogenesis of photosynthetic complexes takes place.},
}
@article {pmid36497015,
year = {2022},
author = {Kozhukhar, N and Alexeyev, MF},
title = {TFAM's Contributions to mtDNA Replication and OXPHOS Biogenesis Are Genetically Separable.},
journal = {Cells},
volume = {11},
number = {23},
pages = {},
pmid = {36497015},
issn = {2073-4409},
support = {S10 OD025089/OD/NIH HHS/United States ; R01 OD010944/OD/NIH HHS/United States ; P01 HL066299/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Chickens/genetics ; *DNA Replication ; DNA, Mitochondrial/genetics/metabolism ; *DNA-Binding Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Phylogeny ; *Transcription Factors/genetics/metabolism ; },
abstract = {The ability of animal orthologs of human mitochondrial transcription factor A (hTFAM) to support the replication of human mitochondrial DNA (hmtDNA) does not follow a simple pattern of phylogenetic closeness or sequence similarity. In particular, TFAM from chickens (Gallus gallus, chTFAM), unlike TFAM from the "living fossil" fish coelacanth (Latimeria chalumnae), cannot support hmtDNA replication. Here, we implemented the recently developed GeneSwap approach for reverse genetic analysis of chTFAM to obtain insights into this apparent contradiction. By implementing limited "humanization" of chTFAM focused either on amino acid residues that make DNA contacts, or the ones with significant variances in side chains, we isolated two variants, Ch13 and Ch22. The former has a low mtDNA copy number (mtCN) but robust respiration. The converse is true of Ch22. Ch13 and Ch22 complement each other's deficiencies. Opposite directionalities of changes in mtCN and respiration were also observed in cells expressing frog TFAM. This led us to conclude that TFAM's contributions to mtDNA replication and respiratory chain biogenesis are genetically separable. We also present evidence that TFAM residues that make DNA contacts play the leading role in mtDNA replication. Finally, we present evidence for a novel mode of regulation of the respiratory chain biogenesis by regulating the supply of rRNA subunits.},
}
@article {pmid36498828,
year = {2022},
author = {Ge, Q and Peng, P and Cheng, M and Meng, Y and Cao, Y and Zhang, S and Long, Y and Li, G and Kang, G},
title = {Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat (Triticum asetivum).},
journal = {International journal of molecular sciences},
volume = {23},
number = {23},
pages = {},
pmid = {36498828},
issn = {1422-0067},
mesh = {*Triticum/metabolism ; Genome, Plant ; Phylogeny ; Gene Expression Regulation, Plant ; Tacrolimus Binding Proteins/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; *Arabidopsis/genetics ; Multigene Family ; },
abstract = {FK506-binding protein (FKBP) genes have been found to play vital roles in plant development and abiotic stress responses. However, limited information is available about this gene family in wheat (Triticum aestivum L.). In this study, a total of 64 FKBP genes were identified in wheat via a genome-wide analysis involving a homologous search of the latest wheat genome data, which was unevenly distributed in 21 chromosomes, encoded 152 to 649 amino acids with molecular weights ranging from 16 kDa to 72 kDa, and was localized in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum. Based on sequence alignment and phylogenetic analysis, 64 TaFKBPs were divided into four different groups or subfamilies, providing evidence of an evolutionary relationship with Aegilops tauschii, Brachypodium distachyon, Triticum dicoccoides, Arabidopsis thaliana and Oryza sativa. Hormone-related, abiotic stress-related and development-related cis-elements were preferentially presented in promoters of TaFKBPs. The expression levels of TaFKBP genes were investigated using transcriptome data from the WheatExp database, which exhibited tissue-specific expression patterns. Moreover, TaFKBPs responded to drought and heat stress, and nine of them were randomly selected for validation by qRT-PCR. Yeast cells expressing TaFKBP19-2B-2 or TaFKBP18-6B showed increased influence on drought stress, indicating their negative roles in drought tolerance. Collectively, our results provide valuable information about the FKBP gene family in wheat and contribute to further characterization of FKBPs during plant development and abiotic stress responses, especially in drought stress.},
}
@article {pmid36512580,
year = {2022},
author = {Guo, S and Lin, X and Song, N},
title = {Mitochondrial phylogenomics reveals deep relationships of scarab beetles (Coleoptera, Scarabaeidae).},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0278820},
pmid = {36512580},
issn = {1932-6203},
mesh = {Animals ; Phylogeny ; *Coleoptera/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Base Sequence ; },
abstract = {In this study, we newly sequenced the complete mitochondrial genomes (mitogenomes) of two phytophagous scarab beetles, and investigated the deep level relationships within Scarabaeidae combined with other published beetle mitogenome sequences. The complete mitogenomes of Dicronocephalus adamsi Pascoe (Cetoniinae) and Amphimallon sp. (Melolonthinae) are 15,563 bp and 17,433 bp in size, respectively. Both mitogenomes have the typical set of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) and an A+T-rich region, with the same gene arrangement found in the majority of beetles. The secondary structures for ribosomal RNA genes (rrnL and rrnS) were inferred by comparative analysis method. Results from phylogenetic analyses provide support for major lineages and current classification of Scarabaeidae. Amino acid data recovered Scarabaeidae as monophyletic. The Scarabaeidae was split into two clades. One clade contained the subfamilies Scarabaeinae and Aphodiinae. The other major clade contained the subfamilies Dynastinae, Rutelinae, Cetoniinae, Melolonthinae and Sericini. The monophyly of Scarabaeinae, Aphodiinae, Dynastinae, Cetoniinae and Sericini were strongly supported. The Scarabaeinae was the sister group of Aphodiinae. The Cetoniinae was sister to the Dynastinae + Rutelinae clade. The Melolonthinae was a non-monophyletic group. The removal of fast-evolving sites from nucleotide dataset using a pattern sorting method (OV-sorting) supported the family Scarabaeidae as a monophyletic group. At the tribe level, the Onthophagini was non-monophyletic with respect to Oniticellini. Ateuchini was sister to a large clade comprising the tribes Onthophagini, Oniticellini and Onitini. Eurysternini was a sister group of the Phanaeini + Ateuchini clade.},
}
@article {pmid36543798,
year = {2022},
author = {Zawal, A and Skuza, L and Michoński, G and Bańkowska, A and Szućko-Kociuba, I and Gastineau, R},
title = {Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen &amp; Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22063},
pmid = {36543798},
issn = {2045-2322},
mesh = {Animals ; Female ; Male ; *Acari/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Codon, Initiator ; RNA, Ribosomal/genetics ; Phylogeny ; Sequence Analysis, DNA ; RNA, Transfer/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen &amp; Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56'41.4''N, 24°48'44.6''E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński &amp; Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.},
}
@article {pmid36543927,
year = {2022},
author = {Cunha, RL and Faleh, AB and Francisco, S and Šanda, R and Vukić, J and Corona, L and Dia, M and Glavičić, I and Kassar, A and Castilho, R and Robalo, JI},
title = {Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distribution.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {22124},
pmid = {36543927},
issn = {2045-2322},
mesh = {Humans ; Animals ; Phylogeny ; Phylogeography ; Azores ; Portugal ; *Mitochondria ; *Perciformes/genetics ; Atlantic Ocean ; Genetic Variation ; Mediterranean Sea ; },
abstract = {Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cádiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almería-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.},
}
@article {pmid36543969,
year = {2023},
author = {Zhu, X and Zhao, Y and Zheng, X and Sun, X},
title = {Genetic Diversity of Four Populations of Silver Carp (Hypophthalmichthys molitrix) Based on Mitochondrial Sequences.},
journal = {Biochemical genetics},
volume = {61},
number = {4},
pages = {1231-1241},
pmid = {36543969},
issn = {1573-4927},
support = {HSY2020K1//Open Project of the National and Local Joint Engineering Laboratory for Freshwater Fish Breeding/ ; },
mesh = {Animals ; *Carps/genetics ; Phylogeny ; Genetic Variation ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Haplotypes ; China ; },
abstract = {Three mitochondrial DNA sequences (COI, ATP 8&amp;6, and D-loop) were employed to assess the genetic diversity of four populations of silver carp from three main drainages in China, including the Yangtze River, the Amur River, and the Pearl River. As a result, 98 haplotypes were identified in combined sequences of COI, ATP8&amp;6, and D-loop. A total of 196 variable sites and 116 parsimony-informative sites were observed. AMOVA based on assembled sequences indicated that 12.12% of the variation was among populations, while 87.88% of the variation was within populations. Additionally, the phylogenetic relationships of populations were depicted in a phylogenetic tree based on assembled sequences. Mismatch distribution analysis and the negative significant Fu's Fs values supported population expansion in all populations. Despite the high level of genetic diversity, the establishment of a state-level original breeding farm in the Amur River basin and the Pearl River basin may be an effective conservation strategy for the protection of local unique haplotypes.},
}
@article {pmid36553495,
year = {2022},
author = {Kunerth, HD and Tapisso, JT and Valente, R and Mathias, MDL and Alves, PC and Searle, JB and Vega, R and Paupério, J},
title = {Characterising Mitochondrial Capture in an Iberian Shrew.},
journal = {Genes},
volume = {13},
number = {12},
pages = {},
pmid = {36553495},
issn = {2073-4425},
mesh = {Animals ; Phylogeny ; *Shrews/genetics ; *Chromosomes ; Mitochondria/genetics ; Spain ; },
abstract = {Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.},
}
@article {pmid36602189,
year = {2023},
author = {Delling, B and Thörn, F and Norén, M and Irestedt, M},
title = {Museomics reveals the phylogenetic position of the extinct Moroccan trout Salmo pallaryi.},
journal = {Journal of fish biology},
volume = {102},
number = {3},
pages = {619-627},
doi = {10.1111/jfb.15299},
pmid = {36602189},
issn = {1095-8649},
mesh = {Animals ; Phylogeny ; *Trout/genetics ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses, including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes, place S. pallaryi among other North African trouts. mtDNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure. They suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20th century.},
}
@article {pmid36634115,
year = {2023},
author = {Rossitto De Marchi, B and Gama, AB and Smith, HA},
title = {Evidence of the association between the Q2 mitochondrial group of Bemisia tabaci MED species (Hemiptera: Aleyrodidae) and low competitive displacement capability.},
journal = {PloS one},
volume = {18},
number = {1},
pages = {e0280002},
pmid = {36634115},
issn = {1932-6203},
mesh = {Animals ; Phylogeny ; *Hemiptera/genetics ; Mitochondria/genetics ; Food ; Florida ; },
abstract = {The whitefly, Bemisia tabaci (Gennadius), is one of the most serious agricultural pests worldwide. Bemisia tabaci is a cryptic species complex of more than 40 species among which the invasive MEAM1 and MED species are the most widespread and economically important. Both MEAM1 and MED present intraspecific genetic variability and some haplotypes are reported to be more invasive than others. MED can be further deconstructed into different genetic groups, including MED-Q1 and MED-Q2. However, distinct biological phenotypes discerning the different MED mitochondrial haplotypes are yet to be characterized. Competitive displacement and life-history trials were carried out between MED-Q2 and MEAM1 populations collected in Florida, USA. In addition, a phylogenetic analysis was carried out including populations from previous whitefly competitive displacement studies for identification and comparison of the MED mitochondrial groups. In contrast to other studies with MED-Q1, the MED-Q2 population from Florida is less likely to displace MEAM1 on pepper. In addition, both pepper and watermelon were a more favorable host to MEAM1 compared to MED-Q2 according to the life history trials.},
}
@article {pmid36636864,
year = {2023},
author = {Achatz, TJ and Von Holten, ZS and Kipp, JW and Fecchio, A and LaFond, LR and Greiman, SE and Martens, JR and Tkach, VV},
title = {Phylogenetic relationships and further unknown diversity of diplostomids (Diplostomida: Diplostomidae) parasitic in kingfishers.},
journal = {Journal of helminthology},
volume = {97},
number = {},
pages = {e8},
doi = {10.1017/S0022149X22000852},
pmid = {36636864},
issn = {1475-2697},
support = {P20GM103442/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Phylogeny ; *Trematoda ; Fishes/parasitology ; Mitochondria ; Brazil ; },
abstract = {Kingfishers (Alcedinidae Rafinesque) are common inhabitants of wetlands and are known to be definitive hosts to a wide range of digeneans that parasitize fish as second intermediate hosts. Among these digeneans, members of the Diplostomidae Poirier, 1886 (diplostomids) are particularly common. Recent studies of diplostomids collected from kingfishers have revealed that they are probably more diverse than currently known. This particularly concerns the genera Crassiphiala Van Haitsma, 1925 and Uvulifer Yamaguti, 1934. In the present work, we studied seven diplostomid taxa from kingfishers in Brazil, the USA and the Philippines. Partial DNA sequences of the nuclear large ribosomal subunit (28S) and mitochondrial cytochrome c oxidase I (cox1) genes were obtained, and 28S sequences were used to study the phylogenetic interrelationships of these diplostomids. We provide the first DNA sequences from Uvulifer semicircumcisus Dubois et Rausch, 1950 and a member of Subuvulifer Dubois, 1952. Pseudocrassiphiala n. gen. is erected for a previously recognized species-level lineage of Crassiphiala and a new generic diagnosis of Crassiphiala is provided. Crassiphiala jeffreybelli n. sp., Crassiphiala wecksteini n. sp. and Pseudocrassiphiala tulipifera n. sp. are described, and a description of newly collected, high-quality specimens of Crassiphiala bulboglossa Van Haitsma, 1925 (the type-species of the genus) is provided.},
}
@article {pmid36642905,
year = {2022},
author = {Zhou, XQ and Ma, J and Wang, RY and Wang, RH and Wu, YQ and Yang, XY and Chen, YJ and Tang, XN and Sun, ET},
title = {[Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {34},
number = {6},
pages = {630-634},
doi = {10.16250/j.32.1374.2022105},
pmid = {36642905},
issn = {1005-6661},
support = {31870352//National Natural Science Foundation of China/ ; S202110368010//Anhui Provincial University Students' Innovation and Entrepreneurship Training Program/ ; },
mesh = {Humans ; Animals ; *Dermatophagoides farinae/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; },
abstract = {OBJECTIVE: To investigate the bacterial community diversity in Dermatophagoides farinae.<br><br>METHODS: Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software.<br><br>RESULTS: A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus.<br><br>CONCLUSIONS: A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.},
}
@article {pmid36672951,
year = {2023},
author = {Zhang, T and Wang, Y and Song, H},
title = {The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei.},
journal = {Genes},
volume = {14},
number = {1},
pages = {},
pmid = {36672951},
issn = {2073-4425},
mesh = {Animals ; *Genome, Mitochondrial ; Phylogeny ; Gene Order ; Mollusca/genetics ; Mitochondria/genetics ; },
abstract = {The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.},
}
@article {pmid36695030,
year = {2023},
author = {Röhricht, H and Przybyla-Toscano, J and Forner, J and Boussardon, C and Keech, O and Rouhier, N and Meyer, EH},
title = {Mitochondrial ferredoxin-like is essential for forming complex I-containing supercomplexes in Arabidopsis.},
journal = {Plant physiology},
volume = {191},
number = {4},
pages = {2170-2184},
pmid = {36695030},
issn = {1532-2548},
mesh = {*Ferredoxins/genetics/metabolism ; *Arabidopsis/genetics/metabolism ; Phylogeny ; Electron Transport Complex I/genetics/metabolism ; Mitochondria/metabolism ; },
abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I-V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.},
}
@article {pmid36717086,
year = {2023},
author = {Nishita, Y and Amaike, Y and Spassov, N and Hristova, L and Kostov, D and Vladova, D and Peeva, S and Raichev, E and Vlaeva, R and Masuda, R},
title = {Diversity of mitochondrial D-loop haplotypes from ancient Thracian horses in Bulgaria.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {94},
number = {1},
pages = {e13810},
doi = {10.1111/asj.13810},
pmid = {36717086},
issn = {1740-0929},
support = {Joint Research Project Grant//Japan Society for the Promotion of Science/ ; The Thracians: Genesis and Development of the Ethn//Bulgarian Academy of Sciences/ ; },
mesh = {Horses/genetics ; Animals ; Bulgaria ; Haplotypes/genetics ; Phylogeny ; *Mitochondria/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; },
abstract = {The domestication of the horse began possibly more than 5000 years ago in the western part of the Eurasian steppe, and according to the leading hypothesis, horses first spread from the Steppe toward the region of the Thracian culture, starting in the second half of the 2nd millennium BCE and flourished from the fifth to first centuries BCE, mainly located in present-day Bulgaria. We analyzed 17 horse bone remains excavated from Thracian archaeological sites (fourth to first centuries BCE) in Bulgaria and successfully identified 17 sequences representing 14 different haplotypes of the mitochondrial D-loop. Compared with the mtDNA haplotypes of modern horses around the world, ancient Thracian horses in Bulgaria are thought to be more closely related to modern horses of Southern Europe and less related to those of Central Asia. In addition, the haplotypes we obtained represented 11 previously reported modern horse mtDNA haplogroups: A, B, D, E, G, H, I, L, N, P, and Q. All the haplogroups contain modern and regionally predominant haplotypes occurring in Europe, the Middle East, and Central Asia. Our results indicate that Thracian horses in Bulgaria have had relatively high genetic diversity and are closely related to modern horse breeds.},
}
@article {pmid36724679,
year = {2023},
author = {Rivero, J and Cutillas, C and Callejón, R},
title = {New genetic lineage of whipworm present in Bactrian camel (Camelus bactrianus).},
journal = {Veterinary parasitology},
volume = {315},
number = {},
pages = {109886},
doi = {10.1016/j.vetpar.2023.109886},
pmid = {36724679},
issn = {1873-2550},
mesh = {Animals ; *Camelus/parasitology ; Trichuris/genetics ; Bayes Theorem ; Phylogeny ; Mitochondria ; *Parasites ; },
abstract = {With a global population of around 35 million in 47 countries, camels play a crucial role in the economy of many marginal and desert areas of the world where they survive in harsh conditions. Nonetheless, there is insufficient knowledge regarding camels' parasite fauna which can reduce their milk and meat production. A molecular study for the Trichuris population of Camelus bactrianus from Spain is presented based on sequences of mitochondrial (cox1, cob, rrnL) and ribosomal (ITS1 and ITS2) DNA regions. Bayesian Inference and Maximum Likelihood methods were used to infer phylogenies for (i) each gene separately, (ii) the combined mitochondrial data, and (iii) the combined mitochondrial and ribosomal dataset. Molecular analyses revealed the existence of two different genetic lineages in the Trichuris parasites populations of C. bactrianus. Future studies should focus on whether there is a coevolution process corresponding to the wild or domestic character of C. bactrianus and Camelus dromedarius. Furthermore, it is necessary to increase integrative taxonomic studies on Trichuris spp. based on morphological, biometric, and molecular data, which will inevitably contribute to our knowledge of the etiology of trichuriasis.},
}
@article {pmid36726084,
year = {2023},
author = {Li, Y and Gu, M and Liu, X and Lin, J and Jiang, H and Song, H and Xiao, X and Zhou, W},
title = {Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {58},
pmid = {36726084},
issn = {1471-2164},
support = {2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; },
mesh = {Toona/genetics ; Phylogeny ; *Genome, Mitochondrial ; Plant Breeding ; *Meliaceae/genetics ; },
abstract = {BACKGROUND: Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives.<br><br>RESULTS: (1)&#xa0;T. sinensis and T.ciliata are both circular structures with lengths of 683482&#xa0;bp and 68300&#xa0;bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other.<br><br>CONCLUSIONS: This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.},
}
@article {pmid36736695,
year = {2023},
author = {Fähnrich, A and Stephan, I and Hirose, M and Haarich, F and Awadelkareem, MA and Ibrahim, S and Busch, H and Wohlers, I},
title = {North and East African mitochondrial genetic variation needs further characterization towards precision medicine.},
journal = {Journal of advanced research},
volume = {54},
number = {},
pages = {59-76},
pmid = {36736695},
issn = {2090-1224},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *East African People/genetics ; Genetic Variation/genetics ; Haplotypes ; Phylogeny ; Precision Medicine ; Sequence Analysis, DNA ; *North African People/genetics ; },
abstract = {INTRODUCTION: Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied.<br><br>OBJECTIVES: To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region.<br><br>METHODS: We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n&#xa0;=&#xa0;2504) and the Human Genome Diversity Project (n&#xa0;=&#xa0;828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples.<br><br>RESULTS: Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1.<br><br>CONCLUSION: Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.},
}
@article {pmid36740932,
year = {2023},
author = {Becher, H and Nichols, RA},
title = {Assembly-free quantification of vagrant DNA inserts.},
journal = {Molecular ecology resources},
volume = {23},
number = {5},
pages = {1002-1013},
pmid = {36740932},
issn = {1755-0998},
support = {MC_UU_00007/16/MRC_/Medical Research Council/United Kingdom ; PhD studentship awarded to HB//Queen Mary University of London, School of Biological and Chemical Sciences/ ; },
mesh = {Humans ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Eukaryota/genetics ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; Phylogeny ; },
abstract = {Inserts of DNA from extranuclear sources, such as organelles and microbes, are common in eukaryote nuclear genomes. However, sequence similarity between the nuclear and extranuclear DNA, and a history of multiple insertions, make the assembly of these regions challenging. Consequently, the number, sequence and location of these vagrant DNAs cannot be reliably inferred from the genome assemblies of most organisms. We introduce two statistical methods to estimate the abundance of nuclear inserts even in the absence of a nuclear genome assembly. The first (intercept method) only requires low-coverage (<1×) sequencing data, as commonly generated for population studies of organellar and ribosomal DNAs. The second method additionally requires that a subset of the individuals carry extranuclear DNA with diverged genotypes. We validated our intercept method using simulations and by re-estimating the frequency of human NUMTs (nuclear mitochondrial inserts). We then applied it to the grasshopper Podisma pedestris, exceptional for both its large genome size and reports of numerous NUMT inserts, estimating that NUMTs make up 0.056% of the nuclear genome, equivalent to >500 times the mitochondrial genome size. We also re-analysed a museomics data set of the parrot Psephotellus varius, obtaining an estimate of only 0.0043%, in line with reports from other species of bird. Our study demonstrates the utility of low-coverage high-throughput sequencing data for the quantification of nuclear vagrant DNAs. Beyond quantifying organellar inserts, these methods could also be used on endosymbiont-derived sequences. We provide an R implementation of our methods called "vagrantDNA" and code to simulate test data sets.},
}
@article {pmid36759539,
year = {2023},
author = {Kise, H and Iguchi, A and Ikegami, T and Onishi, Y and Goto, K and Tanaka, Y and Washburn, TW and Nishijima, M and Kunishima, T and Okamoto, N and Suzuki, A},
title = {Genetic population structures of common scavenging species near hydrothermal vents in the Okinawa Trough.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {2348},
pmid = {36759539},
issn = {2045-2322},
mesh = {Animals ; *Hydrothermal Vents ; Phylogeny ; Genetics, Population ; *Decapoda ; Mitochondria/genetics ; Ecosystem ; },
abstract = {Deep-sea mining of hydrothermal deposits off the coast of Japan is currently under consideration, and environmental baseline studies of the area are required to understand possible impacts. The aim of this study is to clarify population structures of dominant benthic megafaunal species near hydrothermal vent fields in the Okinawa Trough, using a population genetics approach. We examined dominant deep-sea scavenging species including eels, several amphipods, and a decapod and performed population genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region. Several sites were sampled within Okinawa Trough to examine intra-population diversity while two other locations 1400-2400 km away were chosen for inter-population comparisons. For synaphobranchid eels Simenchelys parasitica and Synaphobranchus kaupii, our results showed significant intra-population diversity but no inter-population genetic differentiation, suggesting strong genetic connectivity and/or large population sizes. In addition, single nucleotide polymorphism analysis also confirmed strong genetic connectivity for Simenchelys parasitica. Among scavenging amphipods, we detected seven putative species using molecular phylogenetic analysis. We evaluated population structures of the most abundant species of amphipods and a decapod species (Nematocarcinus lanceopes). Our results provide basic information on the genetic population structures of benthic megafaunal species near hydrothermal vent fields, which can be used to select candidate species for future connectivity analysis with high-resolution genetic markers and aid understanding of the potential population impacts of environmental disturbances.},
}
@article {pmid36795453,
year = {2023},
author = {Dong, LF and Rohlena, J and Zobalova, R and Nahacka, Z and Rodriguez, AM and Berridge, MV and Neuzil, J},
title = {Mitochondria on the move: Horizontal mitochondrial transfer in disease and health.},
journal = {The Journal of cell biology},
volume = {222},
number = {3},
pages = {},
pmid = {36795453},
issn = {1540-8140},
mesh = {Animals ; Phylogeny ; *Mitochondria/metabolism ; *Neoplasms/genetics/metabolism ; Energy Metabolism ; Mammals ; },
abstract = {Mammalian genes were long thought to be constrained within somatic cells in most cell types. This concept was challenged recently when cellular organelles including mitochondria were shown to move between mammalian cells in culture via cytoplasmic bridges. Recent research in animals indicates transfer of mitochondria in cancer and during lung injury in vivo, with considerable functional consequences. Since these pioneering discoveries, many studies have confirmed horizontal mitochondrial transfer (HMT) in vivo, and its functional characteristics and consequences have been described. Additional support for this phenomenon has come from phylogenetic studies. Apparently, mitochondrial trafficking between cells occurs more frequently than previously thought and contributes to diverse processes including bioenergetic crosstalk and homeostasis, disease treatment and recovery, and development of resistance to cancer therapy. Here we highlight current knowledge of HMT between cells, focusing primarily on in vivo systems, and contend that this process is not only (patho)physiologically relevant, but also can be exploited for the design of novel therapeutic approaches.},
}
@article {pmid36841519,
year = {2023},
author = {Tomita, K and Indo, HP and Sato, T and Tangpong, J and Majima, HJ},
title = {Development of a sensitive double TaqMan Probe-based qPCR Angle-Degree method to detect mutation frequencies.},
journal = {Mitochondrion},
volume = {70},
number = {},
pages = {1-7},
doi = {10.1016/j.mito.2023.02.010},
pmid = {36841519},
issn = {1872-8278},
mesh = {Humans ; Mutation Rate ; *MELAS Syndrome/genetics ; Mutation ; DNA, Mitochondrial/genetics ; *Stroke ; },
abstract = {We designed a method to examine the mutation frequencies of the A3243G mutation of mitochondrial DNA (mtDNA) in patients with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome. We performed a qPCR assay using the FAM and VIC TaqMan probes, which detect the 3243G (mutated) and 3243A (wild-type) sequences of mtDNA, respectively. The results obtained by "degree" in a series of differential mutation frequencies were used to plot a standard curve of the mutation frequency. The standard curve was then applied for qPCR assays of the desired samples. The standard deviation (%) of the samples calculated using the standard curve for the TaqMan probe was 2.4 ± 1.5%. This method could be used to examine mutation frequencies in the context of diabetes, aging, cancer, and neurodegenerative diseases.},
}
@article {pmid36877343,
year = {2023},
author = {Palacios-Barreto, P and Mar-Silva, AF and Bayona-Vasquez, NJ and Adams, DH and Díaz-Jaimes, P},
title = {Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications.},
journal = {Molecular biology reports},
volume = {50},
number = {5},
pages = {4083-4095},
pmid = {36877343},
issn = {1573-4978},
support = {IN207621//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT)/ ; 341//LANCAD UNAM-DGTIC/ ; },
mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; Brazil ; DNA, Mitochondrial/genetics ; *Skates, Fish/genetics ; Codon, Terminator ; RNA, Transfer/genetics ; },
abstract = {BACKGROUND: The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species.<br><br>METHODS AND RESULTS: The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759&#xa0;bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica.<br><br>CONCLUSION: The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.},
}
@article {pmid36882771,
year = {2023},
author = {Bu, XL and Zhao, WS and Li, WX and Zou, H and Wu, SG and Li, M and Wang, GT},
title = {Mitochondrial metabolism of the facultative parasite Chilodonella uncinata (Alveolata, Ciliophora).},
journal = {Parasites &amp; vectors},
volume = {16},
number = {1},
pages = {92},
pmid = {36882771},
issn = {1756-3305},
support = {No. 32170437//National Natural Science Foundation of China/ ; No. 2019QZKK0304//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; No. CARS-45//the earmarked fund for CARS/ ; },
mesh = {Animals ; *Alveolata ; *Parasites ; Phylogeny ; *Ciliophora/genetics ; Mitochondria ; },
abstract = {BACKGROUND: Chilodonella uncinata is an aerobic ciliate capable of switching between being free-living and parasitic on fish fins and gills, causing tissue damage and host mortality. It is widely used as a model organism for genetic studies, but its mitochondrial metabolism has never been studied. Therefore, we aimed to describe the morphological features and metabolic characteristics of its mitochondria.<br><br>METHODS: Fluorescence&#xa0;staining and transmission electron microscopy (TEM) were used to observe the morphology of mitochondria. Single-cell transcriptome data of C. uncinata were annotated by the Clusters of Orthologous Genes (COG) database. Meanwhile, the metabolic pathways were constructed based on the transcriptomes. The phylogenetic analysis was also made based on the sequenced cytochrome c oxidase subunit 1 (COX1) gene.<br><br>RESULTS: Mitochondria were stained red using Mito-tracker Red staining and were stained slightly blue by DAPI dye. The cristae and double membrane structures of the mitochondria were observed by TEM. Besides, many lipid droplets were evenly distributed around the macronucleus. A total of 2594 unigenes were assigned to 23 functional classifications of COG. Mitochondrial metabolic pathways were depicted. The mitochondria contained enzymes for the complete tricarboxylic acid (TCA) cycle, fatty acid metabolism, amino acid metabolism, and cytochrome-based electron transport chain (ETC), but only partial enzymes involved in the iron-sulfur clusters (ISCs).<br><br>CONCLUSIONS: Our results showed that C. uncinata possess typical mitochondria. Stored lipid droplets inside mitochondria may be the energy storage of C. uncinata that helps its transmission from a free-living to a parasitic lifestyle. These findings also have improved our knowledge of the mitochondrial metabolism of C. uncinata and increased the volume of molecular data for future studies of this facultative parasite.},
}
@article {pmid36889655,
year = {2023},
author = {Zhu, X and Liu, T and He, A and Zhang, L and Li, J and Li, T and Miao, X and You, M and You, S},
title = {Diversity of Wolbachia infection and its influence on mitochondrial DNA variation in the diamondback moth, Plutella xylostella.},
journal = {Molecular phylogenetics and evolution},
volume = {182},
number = {},
pages = {107751},
doi = {10.1016/j.ympev.2023.107751},
pmid = {36889655},
issn = {1095-9513},
mesh = {Animals ; *Moths/genetics ; *Wolbachia/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Plutella xylostella is a pest that severely damages cruciferous vegetables worldwide and has been shown to be infected with the maternally inherited bacteria Wolbachia, with the main infected strain was plutWB1. In this study, we performed a large-scale global sampling of P. xylostella and amplified 3 mtDNA genes of P. xylostella and 6 Wolbachia genes to analyze the infection status, diversity of Wolbachia in P. xylostella, and its effect on mtDNA variation in P. xylostella. This study provides a conservative estimate of Wolbachia infection rates in P. xylostella, which was found to be 7% (104/1440). The ST 108 (plutWB1) was shared among butterfly species and the moth species P. xylostella, revealing that Wolbachia strain plutWB1 acquisition in P. xylostella may be through horizontal transmission. The Parafit analyses indicated a significant association between Wolbachia and Wolbachia-infected P. xylostella individuals, and individuals infected with plutWB1 tended to cluster in the basal positions of the phylogenetic tree based on the mtDNA data. Additionally, Wolbachia infections were associated with increased mtDNA polymorphism in the infected P. xylostella population. These data suggest that Wolbachia endosymbionts may have a potential effect on mtDNA variation of P. xylostella.},
}
@article {pmid36893930,
year = {2023},
author = {Jesus, PB and Lyra, GM and Zhang, H and Fujii, MT and Nauer, F and Nunes, JMC and Davis, CC and Oliveira, MC},
title = {Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta).},
journal = {Molecular phylogenetics and evolution},
volume = {183},
number = {},
pages = {107752},
doi = {10.1016/j.ympev.2023.107752},
pmid = {36893930},
issn = {1095-9513},
mesh = {Phylogeny ; *Rhodophyta/genetics ; Organelles ; Mitochondria ; Chloroplasts ; },
abstract = {Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantiae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.},
}
@article {pmid36921565,
year = {2023},
author = {Huang, L and Zhang, L and Shi, S and Zhou, X and Yuan, H and Song, X and Hu, Y and Pang, W and Yang, G and Gao, L and Chu, G},
title = {Mitochondrial function and E2 synthesis are impaired following alteration of CLOCK gene expression in porcine ovarian granulosa cells.},
journal = {Theriogenology},
volume = {202},
number = {},
pages = {51-60},
doi = {10.1016/j.theriogenology.2023.03.004},
pmid = {36921565},
issn = {1879-3231},
mesh = {Female ; Swine ; Animals ; *Gene Expression Regulation ; Phylogeny ; *Granulosa Cells/physiology ; Estradiol/metabolism ; Mitochondria/metabolism ; Gene Expression ; Mammals ; },
abstract = {Circadian locomotor output cycles kaput (CLOCK) is a critical component of the mammalian circadian clock system and regulates ovarian physiology. However, the functions and mechanisms of CLOCK in porcine granulosa cells (GCs) are poorly understood. The present study focused on CLOCK's effects on estradiol synthesis. Similarity analysis showed that CLOCK is highly conserved between pigs and other species. The phylogenetic tree analysis indicated that porcine CLOCK was most closely related to that in Arabian camels. CLOCK significantly reduced E2 synthesis in GCs. CLOCK reduced the expression of steroidogenesis-related genes at the mRNA and protein levels, including CYP19A1, CYP11A1, and StAR. CYP17A1 levels were significantly downregulated. We demonstrated that CLOCK dramatically decreased ATP content, mitochondrial copy number, and mitochondrial membrane potential (MMP) and increased reactive oxygen species levels in GCs. We observed that mitochondria were severely damaged with fuzzy and fractured cristae and swollen matrix. These findings suggest that mitochondrial function and E2 synthesis are impaired following the alteration of CLOCK gene expression in porcine ovarian GCs.},
}
@article {pmid36944856,
year = {2023},
author = {Niedziałkowska, M and Tarnowska, E and Babik, W and Konczal, M and Gharbi, K and Cezard, T and Jędrzejewska, B},
title = {Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland.},
journal = {Heredity},
volume = {130},
number = {5},
pages = {269-277},
pmid = {36944856},
issn = {1365-2540},
mesh = {Humans ; Animals ; Poland ; Phylogeny ; *DNA, Mitochondrial/genetics ; *Genomics ; Arvicolinae/genetics ; Genetic Variation ; },
abstract = {Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.},
}
@article {pmid36972795,
year = {2023},
author = {Benites, P and Zaldívar-Riverón, A and Meza-Lázaro, RN and Samacá-Sáenz, E and Gutiérrez-Rodríguez, J and Hernández-López, A},
title = {Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).},
journal = {Molecular phylogenetics and evolution},
volume = {183},
number = {},
pages = {107774},
doi = {10.1016/j.ympev.2023.107774},
pmid = {36972795},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Grasshoppers/genetics ; Mexico ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; },
abstract = {Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.},
}
@article {pmid36981035,
year = {2023},
author = {Kundu, S and Kamalakannan, M and Mukherjee, T and Banerjee, D and Kim, HW},
title = {Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication.},
journal = {Genes},
volume = {14},
number = {3},
pages = {},
pmid = {36981035},
issn = {2073-4425},
mesh = {Animals ; *Chiroptera/genetics ; Phylogeny ; Bayes Theorem ; Mammals ; Mitochondria ; },
abstract = {The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km[2]), of which the majority (171 km[2]) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.},
}
@article {pmid37009644,
year = {2023},
author = {Cheng, B and Zhou, M and Tang, T and Hassan, MJ and Zhou, J and Tan, M and Li, Z and Peng, Y},
title = {A Trifolium repens flavodoxin-like quinone reductase 1 (TrFQR1) improves plant adaptability to high temperature associated with oxidative homeostasis and lipids remodeling.},
journal = {The Plant journal : for cell and molecular biology},
volume = {115},
number = {2},
pages = {369-385},
doi = {10.1111/tpj.16230},
pmid = {37009644},
issn = {1365-313X},
support = {sccxtd-2020-16//Sichuan Forage Innovation Team Program/ ; 2022YFH0059//Sichuan Science and Technology Program/ ; },
mesh = {*Trifolium/genetics/metabolism ; Flavodoxin/genetics/metabolism ; Diglycerides/metabolism ; Phylogeny ; Temperature ; Plant Proteins/genetics/metabolism ; Oxidative Stress ; *Arabidopsis/genetics/metabolism ; Homeostasis ; Gene Expression Regulation, Plant ; Plants, Genetically Modified/metabolism ; },
abstract = {Maintenance of stable mitochondrial respiratory chains could enhance adaptability to high temperature, but the potential mechanism was not elucidated clearly in plants. In this study, we identified and isolated a TrFQR1 gene encoding the flavodoxin-like quinone reductase 1 (TrFQR1) located in mitochondria of leguminous white clover (Trifolium repens). Phylogenetic analysis indicated that amino acid sequences of FQR1 in various plant species showed a high degree of similarities. Ectopic expression of TrFQR1 protected yeast (Saccharomyces cerevisiae) from heat damage and toxic levels of benzoquinone, phenanthraquinone and hydroquinone. Transgenic Arabidopsis thaliana and white clover overexpressing TrFQR1 exhibited significantly lower oxidative damage and better photosynthetic capacity and growth than wild-type in response to high-temperature stress, whereas AtFQR1-RNAi A. thaliana showed more severe oxidative damage and growth retardation under heat stress. TrFQR1-transgenic white clover also maintained better respiratory electron transport chain than wild-type plants, as manifested by significantly higher mitochondrial complex II and III activities, alternative oxidase activity, NAD(P)H content, and coenzyme Q10 content in response to heat stress. In addition, overexpression of TrFQR1 enhanced the accumulation of lipids including phosphatidylglycerol, monogalactosyl diacylglycerol, sulfoquinovosyl diacylglycerol and cardiolipin as important compositions of bilayers involved in dynamic membrane assembly in mitochondria or chloroplasts positively associated with heat tolerance. TrFQR1-transgenic white clover also exhibited higher lipids saturation level and phosphatidylcholine:phosphatidylethanolamine ratio, which could be beneficial to membrane stability and integrity during a prolonged period of heat stress. The current study proves that TrFQR1 is essential for heat tolerance associated with mitochondrial respiratory chain, cellular reactive oxygen species homeostasis, and lipids remodeling in plants. TrFQR1 could be selected as a key candidate marker gene to screen heat-tolerant genotypes or develop heat-tolerant crops via molecular-based breeding.},
}
@article {pmid37017198,
year = {2023},
author = {Parida, M and Gouda, G and Chidambaranathan, P and Umakanta, N and Katara, JL and Sai, CB and Samantaray, S and Patra, BC and Mohapatra, T},
title = {Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight.},
journal = {Journal of genetics},
volume = {102},
number = {},
pages = {},
pmid = {37017198},
issn = {0973-7731},
mesh = {Phylogeny ; *Oryza/genetics ; India ; },
abstract = {The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives (O. rufipogon and O. nivara) along with IR64 (indica) and Nipponbare (japonica) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.},
}
@article {pmid37045317,
year = {2022},
author = {Opler, PA and Stout, TL and Back, W and Zhang, J and Cong, Q and Shen, J and Grishin, NV},
title = {DNA barcodes reveal different speciation scenarios in the four North American Anthocharis Boisduval, Rambur, [Duménil] &amp; Graslin, [1833] (Lepidoptera: Pieridae: Pierinae: Anthocharidini) species groups.},
journal = {Zootaxa},
volume = {5194},
number = {4},
pages = {519-539},
doi = {10.11646/zootaxa.5194.4.3},
pmid = {37045317},
issn = {1175-5334},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics ; DNA, Mitochondrial/genetics ; Mitochondria ; Phylogeny ; },
abstract = {The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.7% barcode difference separates the two species: A. lanceolata Lucas, 1852 including A. lanceolata australis (F. Grinnell, 1908), from A. desertolimbus J. Emmel, T. Emmel &amp; Mattoon, 1998. The sara group consists of three species distinctly defined by more than 2% sequence divergence: A. sara Lucas, 1852, A. julia W. H. Edwards, 1872, and A. thoosa (Scudder, 1878). Our treatment is fully consistent with morphological evidence largely based on the characters of fifth instar larvae and pupal cone curvature (Stout, 2005, 2018). In barcodes, it is not possible to see evidence of introgression or hybridization between the three species, and identification by morphology of immature stages always agrees with DNA barcode identification. Interestingly, A. thoosa exhibited the largest intraspecific divergence in DNA barcodes, and several of its metapopulations are identifiable by haplotypes. The cethura group is characterized by the smallest divergence and is best considered as a single species variable in expression of yellow coloration: A cethura C. Felder &amp; R. Felder, 1865. Notably, the most sexually dimorphic subspecies A. cethura morrisoni W. H. Edwards, 1881 is the most distinct by the barcodes. Finally, the midea group barcodes do not always separate A. midea (Hübner, [1809]) and A. limonea (A. Butler, 1871) and we observe gradual accumulation of differences from north (northeastern USA) to south (Hidalgo, Mexico). This barcode gradient suggests a recent origin of the two midea group species and provides another example of vicariant sister species well defined by morphology, ecology and geography, but not necessarily by DNA barcodes.},
}
@article {pmid37087094,
year = {2023},
author = {Carella, F and De Vico, G},
title = {Pathology, epidemiology, and phylogeny of mussel egg disease due to the microsporidian Steinhausia mytilovum (Field, 1924) in the Mediterranean mussel (Mytilus galloprovincialis).},
journal = {Journal of invertebrate pathology},
volume = {198},
number = {},
pages = {107927},
doi = {10.1016/j.jip.2023.107927},
pmid = {37087094},
issn = {1096-0805},
mesh = {Female ; Animals ; *Mytilus/microbiology ; *Microsporidia/genetics ; Phylogeny ; Italy ; Seafood ; },
abstract = {Microsporidia are well known fungal pathogens of aquatic animals. However, the taxonomy of microsporidia is generally poorly resolved, which has consequently constrained our understanding of their pathology and epidemiology in marine animals. To date, microsporidia have been reported in both bivalves and gastropods, and microsporidia from mollusks have been classified in different genera. Despite ongoing work to better describe these genera, including detailed microscopic and ultrastructural images, so far we lack information on microsporidian phylogeny and pathogenicity of species within these genera. Here we investigate the microsporidian parasite Steinhausia mytilovum associated with the mussel, Mytilus galloprovincialis, in natural beds and farms along coast of southern Italy. A survey of M. galloprovincialis was conducted in 13 mussel farms and one natural bed between 2009 and 2020. We found the presence of S. mytilovum in 10 of the investigated farms, with a prevalence ranging between 14 and 100% of female mussels, depending on the population and season in which they were sampled. The parasite developed in the oocytes within a sporophorous vesicle (SV) where it produced 1-3 spores per cell, both in the cytoplasm and in the nucleus. Stenhausia mytilovum elicited an infiltrative (24.8%) or a strong capsular inflammatory response (43.4%) at gonadal follicles and surrounding vesicular connective tissue, in some cases accompanied by gonadal atresia (24.8%), leading to loss of gonadal architecture. In 7% of cases no reaction was observed. Ultrastructural observations revealed a mitochondrial re-organization to interact with all the phases of parasite development; the mitochondria were arranged outside the parasitophorous vesicle (PV) or directly interacting with the spore inside vesicle. There are five taxonomic clades of microsporidians as identified by SSU ribosomal gene sequence data. Maximum likelihood analysis assigned S. mytilovum within the Clade IV, defined as the Class Terresporidia, with closest genetic relationship (83.6% identity) to an undetermined invertebrate ovarian microsporidian. The constant presence, prevalence, and severity of S. mytilovum in coastline populations of M. galloprovincialis populations in southern Italy may indirectly reflect immunocompetence at both individual and population levels.},
}
@article {pmid37107542,
year = {2023},
author = {De, AK and Sawhney, S and Sunder, J and Muthiyan, R and Ponraj, P and Sujatha, T and Malakar, D and Mondal, S and Bera, AK and Kumar, A and Chakurkar, EB and Bhattacharya, D},
title = {Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling.},
journal = {Genes},
volume = {14},
number = {4},
pages = {},
pmid = {37107542},
issn = {2073-4425},
mesh = {Animals ; Cattle ; Swine ; *Goats/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; Mitochondria/genetics ; },
abstract = {Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.},
}
@article {pmid37156858,
year = {2023},
author = {Smirnova, J and Loerke, J and Kleinau, G and Schmidt, A and Bürger, J and Meyer, EH and Mielke, T and Scheerer, P and Bock, R and Spahn, CMT and Zoschke, R},
title = {Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.},
journal = {Nature plants},
volume = {9},
number = {6},
pages = {987-1000},
pmid = {37156858},
issn = {2055-0278},
support = {416210002//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 221545957//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 394046635//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 421152132//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ZO 302/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TRR 175 (A4)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 956314//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Cytosol ; *RNA, Ribosomal/chemistry ; Cryoelectron Microscopy ; Phylogeny ; Models, Molecular ; *Ribosomes/chemistry ; Plants/genetics ; Nicotiana/genetics ; },
abstract = {In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.},
}
@article {pmid37221210,
year = {2023},
author = {Paukszto, &#x141; and Górski, P and Krawczyk, K and Maździarz, M and Szczecińska, M and Ślipiko, M and Sawicki, J},
title = {The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8303},
pmid = {37221210},
issn = {2045-2322},
mesh = {*Hepatophyta ; *Genome, Mitochondrial ; Phylogeny ; Mitochondria ; *Genome, Plastid ; *Anemone ; },
abstract = {Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts-109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.},
}
@article {pmid37221926,
year = {2023},
author = {Dong, X and Zhang, H and Zhu, X and Wang, K and Xue, H and Ye, Z and Zheng, C and Bu, W},
title = {Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae).},
journal = {Molecular phylogenetics and evolution},
volume = {184},
number = {},
pages = {107802},
doi = {10.1016/j.ympev.2023.107802},
pmid = {37221926},
issn = {1095-9513},
mesh = {Animals ; *Heteroptera ; Phylogeny ; China ; *Genome, Mitochondrial ; Mitochondria ; Mitomycin ; },
abstract = {Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.},
}
@article {pmid37239358,
year = {2023},
author = {Ran, B and Zhu, W and Zhao, X and Li, L and Yi, Z and Li, M and Wang, T and Li, D},
title = {Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239358},
issn = {2073-4425},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chickens/genetics ; Genetic Variation/genetics ; Phylogeny ; Mitochondria/genetics ; },
abstract = {The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.},
}
@article {pmid37289794,
year = {2023},
author = {Hebert, PDN and Bock, DG and Prosser, SWJ},
title = {Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.},
journal = {PloS one},
volume = {18},
number = {6},
pages = {e0286620},
pmid = {37289794},
issn = {1932-6203},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genome, Insect ; Mitochondria/genetics ; Insecta/genetics ; Risk Assessment ; Cell Nucleus/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.},
}
@article {pmid37330026,
year = {2023},
author = {Nguyen, TP and Nguyen, BT and Dao, TNL and Ho, TH and Lee, PT},
title = {Investigation of the functional role of UNC93B1 in Nile tilapia (Oreochromis niloticus): mRNA expression, subcellular localization, and physical interaction with fish-specific TLRs.},
journal = {Fish &amp; shellfish immunology},
volume = {139},
number = {},
pages = {108902},
doi = {10.1016/j.fsi.2023.108902},
pmid = {37330026},
issn = {1095-9947},
mesh = {Humans ; Animals ; Mice ; *Cichlids ; Phylogeny ; Fish Proteins/chemistry ; Toll-Like Receptors/genetics/metabolism ; Phagocytosis ; Streptococcus agalactiae/physiology ; *Fish Diseases ; *Streptococcal Infections/veterinary ; Gene Expression Regulation ; Immunity, Innate/genetics ; Membrane Transport Proteins/genetics ; },
abstract = {Nile tilapia (Oreochromis niloticus) is one of the major food fish worldwide. The farming business, on the other hand, has faced considerable obstacles, such as disease infestations. Toll-like receptors (TLRs) play an important function in the activation of the innate immune system in response to infections. Unc-93 homolog B1 (UNC93B1) is a key regulator of nucleic acid (NA)-sensing TLRs. Here the UNC93B1 gene, which was cloned from Nile tilapia tissue for this investigation, had the same genetic structure as a homologous gene in humans and mice. Phylogenetic analysis revealed that Nile tilapia UNC93B1 clustered with UNC93B1 from other species and separately from the UNC93A clade. The gene structure of the Nile tilapia UNC93B1 was found to be identical to that of human UNC93B1. Our gene expression studies revealed that Nile tilapia UNC93B1 was highly expressed in the spleen, followed by other immune-related tissues such as the head kidney, gills, and intestine. Moreover, Nile tilapia UNC93B1 mRNA transcripts were up-regulated in vivo in the head kidney and spleen tissues from poly I:C and Streptococcus agalactiae injected Nile tilapia, as well as in vitro in LPS stimulated Tilapia head kidney (THK) cells. The Nile tilapia UNC93B1-GFP protein signal was detected in the cytosol of THK cells and was co-localized with endoplasmic reticulum and lysosome but not with mitochondria. Moreover, the results of a co-immunoprecipitation and immunostaining analysis showed that Nile tilapia UNC93B1 can be pulled down with fish-specific TLRs such as TLR18 and TLR25 from Nile tilapia, and was found to be co-localized with these fish-specific TLRs in the THK cells. Overall, our findings highlight the potential role of UNC93B1 as an accessory protein in fish-specific TLR signaling.},
}
@article {pmid37364695,
year = {2023},
author = {Barrera, CA and Ortega, J and Gutierrez-Guerrero, YT and Baeza, JA},
title = {Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae.},
journal = {Gene},
volume = {879},
number = {},
pages = {147588},
doi = {10.1016/j.gene.2023.147588},
pmid = {37364695},
issn = {1879-0038},
mesh = {Animals ; Phylogeny ; *Chiroptera/genetics ; Plant Nectar ; Genomics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; },
abstract = {Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.},
}
@article {pmid37381996,
year = {2023},
author = {Zhao, JH and Chen, YC and Hua, ZY and Liu, TR and Zhao, YY and Huang, LQ and Yuan, Y},
title = {[Cloning and gene function of dicarboxylate-tricarboxylate carrier protein in Gastrodia elata].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {48},
number = {12},
pages = {3140-3148},
doi = {10.19540/j.cnki.cjcmm.20230310.102},
pmid = {37381996},
issn = {1001-5302},
mesh = {*Gastrodia/genetics ; Phylogeny ; Amino Acids ; Cloning, Molecular ; Carrier Proteins ; },
abstract = {The gene GeDTC encoding the dicarboxylate-tricarboxylate carrier protein in Gastrodia elata was cloned by specific primers which were designed based on the transcriptome data of G. elata. Bioinformatics analysis on GeDTC gene was carried out by using ExPASY, ClustalW, MEGA, etc. Positive transgenic plants and potato minituber were obtained by virtue of the potato genetic transformation system. Agronomic characters, such as size, weight, organic acid content, and starch content, of potato minituber were tested and analyzed and GeDTC gene function was preliminarily investigated. The results showed that the open reading frame of GeDTC gene was 981 bp in length and 326 amino acid residues were encoded, with a relative molecular weight of 35.01 kDa. It was predicted that the theoretical isoelectric point of GeDTC protein was 9.83, the instability coefficient was 27.88, and the average index of hydrophilicity was 0.104, which was indicative of a stable hydrophilic protein. GeDTC protein had a transmembrane structure and no signal peptide and was located in the inner membrane of mitochondria. The phylogenetic tree showed that GeDTC was highly homologous with DTC proteins of other plant species, among which GeDTC had the highest homology with DcDTC(XP＿020675804.1) in Dendrobium candidum, reaching 85.89%. GeDTC overexpression vector pCambia1300-35Spro-GeDTC was constructed by double digests, and transgenic potato plants were obtained by Agrobacterium-mediated gene transformation. Compared with the wild-type plants, transgenic potato minituber harvested by transplanting had smaller size, lighter weight, lower organic acid content, and no significant difference in starch content. It is preliminarily induced that GeDTC is the efflux channel of tricarboxylate and related to the tuber development, which lays a foundation for further elucidating the molecular mechanism of G. elata tuber development.},
}
@article {pmid37424790,
year = {2023},
author = {Margenat, M and Betancour, G and Irving, V and Costábile, A and García-Cedrés, T and Portela, MM and Carrión, F and Herrera, FE and Villarino, A},
title = {Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1095060},
pmid = {37424790},
issn = {2235-2988},
mesh = {Humans ; Lipid Metabolism ; *Mycobacterium tuberculosis ; Phylogeny ; Ubiquitins ; *Mitochondrial Trifunctional Protein/metabolism ; *Bacterial Proteins/metabolism ; },
abstract = {During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.},
}
@article {pmid37429369,
year = {2023},
author = {Ahlawat, S and Sharma, U and Arora, R and Sharma, R and Chhabra, P and Veer Singh, K and Vijh, RK},
title = {Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys.},
journal = {Gene},
volume = {880},
number = {},
pages = {147627},
doi = {10.1016/j.gene.2023.147627},
pmid = {37429369},
issn = {1879-0038},
mesh = {Animals ; Humans ; *Equidae/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Africa ; Domestication ; Haplotypes ; Genetic Variation ; },
abstract = {To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.},
}
@article {pmid37481145,
year = {2023},
author = {DeCicco, LH and DeRaad, DA and Ostrow, EN and Moyle, RG},
title = {A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae).},
journal = {Molecular phylogenetics and evolution},
volume = {187},
number = {},
pages = {107883},
doi = {10.1016/j.ympev.2023.107883},
pmid = {37481145},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Passeriformes/genetics ; DNA ; Genes, Mitochondrial ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; },
abstract = {Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.},
}
@article {pmid37489100,
year = {2023},
author = {Yordanov, G and Palova, N and Mehandjyiski, I and Hristov, P},
title = {Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius.},
journal = {Animal biotechnology},
volume = {34},
number = {8},
pages = {3897-3907},
pmid = {37489100},
issn = {1532-2378},
mesh = {Animals ; Horses/genetics ; Female ; *DNA, Mitochondrial/genetics ; Serbia ; *Genetic Variation/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; Haplotypes/genetics ; Phylogeny ; },
abstract = {From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.},
}
@article {pmid37518286,
year = {2023},
author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ},
title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.},
journal = {Zootaxa},
volume = {5278},
number = {2},
pages = {201-238},
doi = {10.11646/zootaxa.5278.2.1},
pmid = {37518286},
issn = {1175-5334},
mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; },
abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.},
}
@article {pmid37518493,
year = {2023},
author = {Tomimori, Y and Matsui, M and Okawa, H and Nishikawa, K and Tanabe, S and Kamasaka, R},
title = {Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae).},
journal = {Zootaxa},
volume = {5293},
number = {1},
pages = {145-160},
doi = {10.11646/zootaxa.5293.1.6},
pmid = {37518493},
issn = {1175-5334},
mesh = {Animals ; *Caudata/genetics ; Phylogeny ; Japan ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.},
}
@article {pmid37518527,
year = {2023},
author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X},
title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.},
journal = {Zootaxa},
volume = {5306},
number = {2},
pages = {215-231},
doi = {10.11646/zootaxa.5306.2.3},
pmid = {37518527},
issn = {1175-5334},
mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; },
abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.},
}
@article {pmid37518710,
year = {2023},
author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA},
title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).},
journal = {Zootaxa},
volume = {5285},
number = {1},
pages = {187-195},
doi = {10.11646/zootaxa.5285.1.9},
pmid = {37518710},
issn = {1175-5334},
mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; },
abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.},
}
@article {pmid37522604,
year = {2023},
author = {Chukaew, T and Isomura, N and Mezaki, T and Matsumoto, H and Kitano, YF and Nozawa, Y and Tachikawa, H and Fukami, H},
title = {Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.},
journal = {Zoological science},
volume = {40},
number = {4},
pages = {326-340},
doi = {10.2108/zs230009},
pmid = {37522604},
issn = {0289-0003},
mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Japan ; DNA, Ribosomal/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; },
abstract = {The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.},
}
@article {pmid37569876,
year = {2023},
author = {Antos-Krzeminska, N and Kicinska, A and Nowak, W and Jarmuszkiewicz, W},
title = {Acanthamoeba castellanii Uncoupling Protein: A Complete Sequence, Activity, and Role in Response to Oxidative Stress.},
journal = {International journal of molecular sciences},
volume = {24},
number = {15},
pages = {},
pmid = {37569876},
issn = {1422-0067},
support = {OPUS 2020/37/B/NZ1/01188//National Science Centre/ ; },
mesh = {*Oxidative Stress ; *Acanthamoeba castellanii/metabolism/genetics ; Phylogeny ; *Mitochondrial Uncoupling Proteins/genetics/metabolism/chemistry ; Saccharomyces cerevisiae/genetics/metabolism ; Reactive Oxygen Species/metabolism ; *Protozoan Proteins/genetics/metabolism/chemistry ; Mitochondria/metabolism ; Membrane Potential, Mitochondrial ; Amino Acid Sequence ; },
abstract = {Uncoupling proteins (UCPs) are mitochondrial inner membrane transporters that mediate free-fatty-acid-induced, purine-nucleotide-inhibited proton leak into the mitochondrial matrix, thereby uncoupling respiratory substrate oxidation from ATP synthesis. The aim of this study was to provide functional evidence that the putative Acucp gene of the free-living protozoan amoeba, A. castellanii, encodes the mitochondrial protein with uncoupling activity characteristic of UCPs and to investigate its role during oxidative stress. We report the sequencing and cloning of a complete Acucp coding sequence, its phylogenetic analysis, and the heterologous expression of AcUCP in the S. cerevisiae strain InvSc1. Measurements of mitochondrial respiratory activity and membrane potential indicate that the heterologous expression of AcUCP causes AcUCP-mediated uncoupling activity. In addition, in a model of oxidative stress with increased reactive oxygen species levels (superoxide dismutase 1 knockout yeasts), AcUCP expression strongly promotes cell survival and growth. The level of superoxide anion radicals is greatly reduced in the ΔSOD1 strain expressing AcUCP. These results suggest that AcUCP targeted to yeast mitochondria causes uncoupling and may act as an antioxidant system. Phylogenetic analysis shows that the A. castellanii UCP diverges very early from other UCPs, but clearly locates within the UCP subfamily rather than among other mitochondrial anion carrier proteins.},
}
@article {pmid37604791,
year = {2023},
author = {Fernández-Álvarez, F&#xc1; and Sanchez, G and Deville, D and Taite, M and Villanueva, R and Allcock, AL},
title = {Atlantic Oceanic Squids in the "Grey Speciation Zone".},
journal = {Integrative and comparative biology},
volume = {63},
number = {6},
pages = {1214-1225},
pmid = {37604791},
issn = {1557-7023},
support = {IJC2020-043170-I//Generalitat de Catalunya/ ; GOIPD/2019/460//Irish Research Council/ ; 22K15085//Grant-in-Aid for Early-Career Scientists/ ; //Ministerio de Ciencia e Innovaci&#xf3;n/ ; //European Union/ ; CEX2019-000928-S//Spanish Government/ ; CTM2016-78853-R//FEDER/ ; },
mesh = {Animals ; Phylogeny ; *Decapodiformes ; Oceans and Seas ; *Biodiversity ; Mitochondria ; },
abstract = {Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.},
}
@article {pmid37628665,
year = {2023},
author = {Havaš Auguštin, D and Šarac, J and Reidla, M and Tamm, E and Grahovac, B and Kapović, M and Novokmet, N and Rudan, P and Missoni, S and Marjanović, D and Korolija, M},
title = {Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates.},
journal = {Genes},
volume = {14},
number = {8},
pages = {},
pmid = {37628665},
issn = {2073-4425},
mesh = {Humans ; Phylogeny ; Croatia ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.},
}
@article {pmid37667092,
year = {2023},
author = {Kar, C and Mariyambi, PC and Raghavan, R and Sureshkumar, S},
title = {Mitochondrial phylogeny of fusilier fishes (family Caesionidae) from the Laccadive archipelago reveals a new species and two new records from the Central Indian Ocean.},
journal = {Journal of fish biology},
volume = {103},
number = {6},
pages = {1445-1451},
doi = {10.1111/jfb.15553},
pmid = {37667092},
issn = {1095-8649},
support = {CRG/2020/004498//Department of Science and Technology, Government of India/ ; 200510341520//University Grants Commission/ ; },
mesh = {Animals ; Phylogeny ; Indian Ocean ; *Fishes/genetics ; *Mitochondria/genetics ; Genes, Mitochondrial ; Pacific Ocean ; },
abstract = {Fusiliers of the family Caesionidae comprise a group of Indo-Pacific reef fishes important in the live bait and artisanal fisheries in many parts of its range, particularly in the Indian Ocean region. Using newly generated mitochondrial COI sequences of 10 species of caesionid fishes from the Laccadive archipelago, we carried out a molecular phylogenetic analysis, which has helped improve our understanding of the diversity, distribution, and systematics of this poorly known group of fishes. The two speciose genera within Caesionidae, Caesio and Pterocaesio, were revealed to be paraphyletic, and as a result, four names earlier considered as subgenera within Caesionidae (Flavicaesio, Odontonectes, Pisinnicaesio, and Squamosicaesio) were elevated to the status of distinct genera. We also discovered the presence of a new lineage in the Central Indian Ocean, sister to Caesio caerulaurea and Caesio xanthalytos, but distinct from both in several morphological characters and a genetic distance of between 2% and 3% in the mitochondrial COI gene. We describe this lineage as Caesio idreesi, a new species, with a distribution spanning the Laccadive Sea and the Bay of Bengal. Our genetic data also helped confirm the first confirmed records of two species, Pisinnicaesio digramma and Squamosicaesio randalli, from the Central Indian Ocean, and a new distribution record for C. xanthalytos in the Laccadive Sea. Combined, these results have helped bridge key biodiversity knowledge gaps of the family Caesionidae and form an excellent baseline for further investigations on their taxonomy, systematics, and life history.},
}
@article {pmid37717227,
year = {2024},
author = {Chen, S and Tran, TTT and Yeh, AY and Yang, H and Chen, J and Yang, Y and Wang, X},
title = {The Globodera rostochiensis Gr29D09 Effector with a Role in Defense Suppression Targets the Potato Hexokinase 1 Protein.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {37},
number = {1},
pages = {25-35},
doi = {10.1094/MPMI-07-23-0095-R},
pmid = {37717227},
issn = {0894-0282},
mesh = {Animals ; *Solanum tuberosum ; Hexokinase/genetics ; Reactive Oxygen Species ; Phylogeny ; Proteins/genetics ; *Nematoda ; *Tylenchoidea/physiology ; },
abstract = {The potato cyst nematode (Globodera rostochiensis) is an obligate root pathogen of potatoes. G. rostochiensis encodes several highly expanded effector gene families, including the Gr4D06 family; however, little is known about the function of this effector family. We cloned four 29D09 genes from G. rostochiensis (named Gr29D09v1/v2/v3/v4) that share high sequence similarity and are homologous to the Hg29D09 and Hg4D06 effector genes from the soybean cyst nematode (Heterodera glycines). Phylogenetic analysis revealed that Gr29D09 genes belong to a subgroup of the Gr4D06 family. We showed that Gr29D09 genes are expressed exclusively within the nematode's dorsal gland cell and are dramatically upregulated in parasitic stages, indicating involvement of Gr29D09 effectors in nematode parasitism. Transgenic potato lines overexpressing Gr29D09 variants showed increased susceptibility to G. rostochiensis. Transient expression assays in Nicotiana benthamiana demonstrated that Gr29D09v3 could suppress reactive oxygen species (ROS) production and defense gene expression induced by flg22 and cell death mediated by immune receptors. These results suggest a critical role of Gr29D09 effectors in defense suppression. The use of affinity purification coupled with nanoliquid chromatography-tandem mass spectrometry identified potato hexokinase 1 (StHXK1) as a candidate target of Gr29D09. The Gr29D09-StHXK1 interaction was further confirmed using in planta protein-protein interaction assays. Plant HXKs have been implicated in defense regulation against pathogen infection. Interestingly, we found that StHXK1 could enhance flg22-induced ROS production, consistent with a positive role of plant HXKs in defense. Altogether, our results suggest that targeting StHXK1 by Gr29D09 effectors may impair the positive function of StHXK1 in plant immunity, thereby aiding nematode parasitism. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.},
}
@article {pmid37758449,
year = {2023},
author = {Claramunt, S and Haddrath, O},
title = {No Signs of Adaptations for High Flight Intensity in the Mitochondrial Genome of Birds.},
journal = {Genome biology and evolution},
volume = {15},
number = {10},
pages = {},
pmid = {37758449},
issn = {1759-6653},
mesh = {Animals ; *Genome, Mitochondrial ; *Flight, Animal ; *Birds/genetics/physiology ; *Adaptation, Physiological/genetics ; Phylogeny ; },
abstract = {Mitochondrial genomes are expected to show adaptations for optimizing aerobic respiration in birds that make intense use of flight. However, there is limited empirical evidence of such a relationship. We here examine correlates of several mitochondrial genome characteristics and flight use across a diverse sample of 597 bird species. We developed an index of flight use intensity that ranged from 0 in flightless species to 9 in migratory hummingbirds and examined its association with nucleobase composition, amino acid class composition, and amino acid site allelic variation using phylogenetic comparative methods. We found no evidence of mitochondrial genome adaptations to flight intensity. Neither nucleotide composition nor amino acid properties showed consistent patterns related to flight use. While specific sites in mitochondrial genes exhibited variation associated with flight intensity, there was limited association between specific amino acid residues and flight intensity levels. Our findings suggest a complex genetic architecture for aerobic performance traits, where multiple genes in both mitochondria and the nucleus may contribute to overall performance. Other factors, such as gene expression regulation and anatomical adaptations, may play a more significant role in influencing flight performance than changes in mitochondrial genes. These findings highlight the need for comprehensive genomic analyses to unravel the intricate relationship between genetic variants and aerobic performance in birds.},
}
@article {pmid37759714,
year = {2023},
author = {Byrne, KL and Szeligowski, RV and Shen, H},
title = {Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.},
journal = {Biomolecules},
volume = {13},
number = {9},
pages = {},
pmid = {37759714},
issn = {2218-273X},
support = {R35 GM150619/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Caenorhabditis elegans/genetics/metabolism ; Drosophila melanogaster/metabolism/genetics ; Mitochondria/metabolism/genetics ; Mitochondrial Membrane Transport Proteins/genetics/metabolism ; *Mitochondrial Proteins/chemistry/genetics/metabolism ; *Organic Anion Transporters/chemistry/genetics/metabolism ; Phylogeny ; Saccharomyces cerevisiae/metabolism/genetics ; },
abstract = {Homology search and phylogenetic analysis have commonly been used to annotate gene function, although they are prone to error. We hypothesize that the power of homology search in functional annotation depends on the coupling of sequence variation to functional diversification, and we herein focus on the SoLute Carrier (SLC25) family of mitochondrial metabolite transporters to survey this coupling in a family-wide manner. The SLC25 family is the largest family of mitochondrial metabolite transporters in eukaryotes that translocate ligands of different chemical properties, ranging from nucleotides, amino acids, carboxylic acids and cofactors, presenting adequate experimentally validated functional diversification in ligand transport. Here, we combine phylogenetic analysis to profile SLC25 transporters across common eukaryotic model organisms, from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, to Homo sapiens, and assess their sequence adaptations to the transported ligands within individual subfamilies. Using several recently studied and poorly characterized SLC25 transporters, we discuss the potentials and limitations of phylogenetic analysis in guiding functional characterization.},
}
@article {pmid37761841,
year = {2023},
author = {Koshkina, O and Deniskova, T and Dotsev, A and Kunz, E and Selionova, M and Medugorac, I and Zinovieva, N},
title = {Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761841},
issn = {2073-4425},
mesh = {Sheep/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; *Mitochondria/genetics ; Animals, Domestic/genetics ; Russia ; },
abstract = {Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.},
}
@article {pmid37761909,
year = {2023},
author = {Mendivil, A and Ramírez, R and Morin, J and Ramirez, JL and Siccha-Ramirez, R and Britzke, R and Rivera, F and Ampuero, A and Oliveros, N and Congrains, C},
title = {Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon.},
journal = {Genes},
volume = {14},
number = {9},
pages = {},
pmid = {37761909},
issn = {2073-4425},
mesh = {Animals ; Peru ; Phylogeny ; *Genome, Mitochondrial/genetics ; Snails/genetics ; Mitochondria/genetics ; },
abstract = {Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero &amp; Ramírez, 2023 and Pomacea aulanieri (Deville &amp; Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.},
}
@article {pmid37810794,
year = {2023},
author = {Rodriguez, D and Harding, SF and Sirsi, S and McNichols-O'Rourke, K and Morris, T and Forstner, MRJ and Schwalb, AN},
title = {Mitochondrial sequence data reveal population structure within Pustulosa pustulosa.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e15974},
pmid = {37810794},
issn = {2167-8359},
mesh = {Humans ; Animals ; Phylogeny ; Mitochondria ; *Bivalvia ; *Unionidae/genetics ; Texas ; Ontario ; },
abstract = {Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.},
}
@article {pmid37815994,
year = {2023},
author = {Chen, YH and Miller, WB and Hay, A},
title = {Postharvest bacterial succession on cut flowers and vase water.},
journal = {PloS one},
volume = {18},
number = {10},
pages = {e0292537},
pmid = {37815994},
issn = {1932-6203},
mesh = {*Water ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; *Asteraceae ; Flowers ; Bacteria/genetics ; },
abstract = {In cut flowers, xylem occlusion or blockage by bacteria negatively affects water balance and postharvest quality. Many studies have used culture-based methods to examine bacterial populations in vase water and their effects on flower longevity. It is still unclear if and how bacterial communities at the 16S rRNA gene (16S) level change during the vase period and how such change might correlate with postharvest longevity. This study compared the sequences of 16S amplicons from 4 different types of flowers and their vase water over the course of 7 days (Rosa spp., Gerbera jamesonii, and two Lilium varieties). The relative abundance of plant chloroplast and mitochondria 16S decreased significantly over the course 7 days in all 4 flowers as bacterial diversity increased. Richness and evenness of the bacterial communities increased over time, as did the number of rare taxa and phylogenetic diversity. Bacterial communities varied with time, as well as by flower source, types, and sample location (water, stem surface, whole stem). Some taxa, such as Enterobacteriacea and Bradyhizobiaceae decreased significantly over time while others such as Pseudomonas spp. increased. For example, Pseudomonas veronii, implicated in soft rot of calla lily, increased in both whole stem samples and water samples from Gerbera jamesonii. Erwinia spp., which includes plant pathogenic species, also increased in water samples. This work highlights the dynamic and complex nature of bacterial succession in the flower vase ecosystem. More work is needed to understand if and how bacterial community structure can be managed to improve cut flower vase life.},
}
@article {pmid37818890,
year = {2023},
author = {Chen, H and Shi, BY and Du, LN and Sun, HY},
title = {Description of a New Species of Hua (Gastropoda: Semisulcospiridae) from Guizhou, China, Based on Morphology and Molecular Evidence.},
journal = {Zoological science},
volume = {40},
number = {5},
pages = {414-421},
doi = {10.2108/zs230025},
pmid = {37818890},
issn = {0289-0003},
mesh = {Female ; Animals ; *Gastropoda/anatomy &amp; histology ; Phylogeny ; China ; Mitochondria ; },
abstract = {A new species of Hua, Hua qiannanensis sp. nov., is described from Guizhou Province, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: the smooth shell, only three smaller cusps of lateral teeth on the inner side, outer marginal teeth with eight flattened and rounded denticles, an ovipositor pore in females, and BW/H ≥ 80%, B/H = 76.8-82.3%. Molecular analysis based on partial mitochondrial COI and 16S rDNA also supports the systematic position of the new taxon.},
}
@article {pmid37847106,
year = {2023},
author = {Sharma, A and Ahlawat, S and Sharma, R and Arora, R and Singh, KV and Malik, D and Banik, S and Singh, TR and Tantia, MS},
title = {Tracing the genetic footprints: India's role as a gateway for pig migration and domestication across continents.},
journal = {Animal biotechnology},
volume = {34},
number = {9},
pages = {5173-5179},
doi = {10.1080/10495398.2023.2268683},
pmid = {37847106},
issn = {1532-2378},
mesh = {Swine/genetics ; Animals ; *Domestication ; *Sus scrofa/genetics ; India ; Mitochondria/genetics ; Haplotypes/genetics ; Phylogeny ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India's contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.},
}
@article {pmid37877347,
year = {2024},
author = {Choi, SW and Yu, HJ and Kim, JK},
title = {Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly.},
journal = {Journal of fish biology},
volume = {104},
number = {1},
pages = {284-303},
doi = {10.1111/jfb.15595},
pmid = {37877347},
issn = {1095-8649},
support = {R2023001//the National Institute of Fisheries Science/ ; 2023//the National Marine Biodiversity Institute of Korea/ ; },
mesh = {Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Fishes/anatomy &amp; histology ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Larva ; },
abstract = {Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.},
}
@article {pmid37929337,
year = {2023},
author = {Ibrahim, MK and Haria, A and Mehta, NV and Degani, MS},
title = {Antimicrobial potential of quaternary phosphonium salt compounds: a review.},
journal = {Future medicinal chemistry},
volume = {15},
number = {22},
pages = {2113-2141},
doi = {10.4155/fmc-2023-0188},
pmid = {37929337},
issn = {1756-8927},
mesh = {Phylogeny ; Microbial Sensitivity Tests ; *Anti-Infective Agents/pharmacology/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Mitochondria ; Quaternary Ammonium Compounds/chemistry ; },
abstract = {Given that mitochondrial dysregulation is a biomarker of many cancers, cationic quaternary phosphonium salt (QPS) conjugation is a widely utilized strategy for anticancer drug design. QPS-conjugated compounds exhibit greater cell permeation and accumulation in negatively charged mitochondria, and thus, show enhanced activity. Phylogenetic similarities between mitochondria and bacteria have provided a rationale for exploring the antibacterial properties of mitochondria-targeted compounds. Additionally, due to the importance of mitochondria in the survival of pathogenic microbes, including fungi and parasites, this strategy can be extended to these organisms as well. This review examines recent literature on the antimicrobial activities of various QPS-conjugated compounds and provides future directions for exploring the medicinal chemistry of these compounds.},
}
@article {pmid37930986,
year = {2023},
author = {Diaz-Recio Lorenzo, C and Patel, T and Arsenault-Pernet, EJ and Poitrimol, C and Jollivet, D and Martinez Arbizu, P and Gollner, S},
title = {Highly structured populations of deep-sea copepods associated with hydrothermal vents across the Southwest Pacific, despite contrasting life history traits.},
journal = {PloS one},
volume = {18},
number = {11},
pages = {e0292525},
pmid = {37930986},
issn = {1932-6203},
mesh = {Animals ; *Copepoda/genetics ; *Hydrothermal Vents ; *Life History Traits ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Ecosystem ; },
abstract = {Hydrothermal vents are extreme environments, where abundant communities of copepods with contrasting life history traits co-exist along hydrothermal gradients. Here, we discuss how these traits may contribute to the observed differences in molecular diversity and population genetic structure. Samples were collected from vent locations across the globe including active ridges and back-arc basins and compared to existing deep-sea hydrothermal vent and shallow water data, covering a total of 22 vents and 3 non-vent sites. A total of 806 sequences of mtDNA from the Cox1 gene were used to reconstruct the phylogeny, haplotypic relationship and demography within vent endemic copepods (Dirivultidae, Stygiopontius spp.) and non-vent-endemic copepods (Ameiridae, Miraciidae and Laophontidae). A species complex within Stygiopontius lauensis was studied across five pacific back-arc basins at eight hydrothermal vent fields, with cryptic species being restricted to the basins they were sampled from. Copepod populations from the Lau, North Fiji and Woodlark basins are undergoing demographic expansion, possibly linked to an increase in hydrothermal activity in the last 10 kya. Highly structured populations of Amphiascus aff. varians 2 were also observed from the Lau to the Woodlark basins with populations also undergoing expansion. Less abundant harpacticoids exhibit little to no population structure and stable populations. This study suggests that similarities in genetic structure and demography may arise in vent-associated copepods despite having different life history traits. As structured meta-populations may be at risk of local extinction should major anthropogenic impacts, such as deep-sea mining, occur, we highlight the importance of incorporating a trait-based approach to investigate patterns of genetic connectivity and demography, particularly regarding area-based management tools and environmental management plans.},
}
@article {pmid37940011,
year = {2023},
author = {Lopez-Jimenez, J and Herrera, J and Alzate, JF},
title = {Expanding the knowledge frontier of mitoviruses in Cannabis sativa.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {116},
number = {},
pages = {105523},
doi = {10.1016/j.meegid.2023.105523},
pmid = {37940011},
issn = {1567-7257},
mesh = {*Cannabis/genetics ; Phylogeny ; *RNA Viruses/genetics ; Mitochondria/genetics ; Fungi ; },
abstract = {Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.},
}
@article {pmid38047014,
year = {2023},
author = {Kobayashi, G},
title = {Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16446},
pmid = {38047014},
issn = {2167-8359},
mesh = {Humans ; Animals ; Genes, Mitochondrial ; Phylogeny ; *Annelida ; DNA, Mitochondrial/genetics ; *Polychaeta/genetics ; },
abstract = {BACKGROUND: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.<br><br>METHODS: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.<br><br>RESULTS AND DISCUSSION: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.},
}
@article {pmid38062387,
year = {2023},
author = {Ouyang, L and Liu, Y and Yao, R and He, D and Yan, L and Chen, Y and Huai, D and Wang, Z and Yu, B and Kang, Y and Jiang, H and Lei, Y and Liao, B and Wang, X},
title = {Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.).},
journal = {BMC plant biology},
volume = {23},
number = {1},
pages = {626},
pmid = {38062387},
issn = {1471-2229},
support = {CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; 32170278//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Arachis/genetics ; Glycosyltransferases/genetics ; Phylogeny ; Flavonoids ; Plant Breeding ; Stress, Physiological/genetics ; *Arabidopsis ; Uridine Diphosphate ; },
abstract = {BACKGROUND: Glycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut.<br><br>RESULTS: In present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging.<br><br>CONCLUSIONS: Our research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.},
}
@article {pmid38070787,
year = {2024},
author = {Das, PJ and Kumar, S and Choudhury, M and Banik, S and Pegu, SR and Kumar, S and Deb, R and Gupta, VK},
title = {Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig.},
journal = {Gene},
volume = {897},
number = {},
pages = {148070},
doi = {10.1016/j.gene.2023.148070},
pmid = {38070787},
issn = {1879-0038},
mesh = {Animals ; *Genome, Mitochondrial/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genomics ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090[th] to 1099[th] position, deletion of a 10 bp sequence at the 755[th] position, insertion of (CA) at the 137[th] position, and substitution of AT to GA at the 638[th] position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.},
}
@article {pmid38077409,
year = {2023},
author = {Santamaria, CA and Griffiths, CL},
title = {Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16529},
pmid = {38077409},
issn = {2167-8359},
mesh = {Humans ; Animals ; *Isopoda/genetics ; Phylogeny ; Phylogeography ; Africa, Southern ; Mitochondria ; },
abstract = {Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.},
}
@article {pmid38093186,
year = {2023},
author = {Hamza, H and Villa, S and Torre, S and Marchesini, A and Benabderrahim, MA and Rejili, M and Sebastiani, F},
title = {Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {772},
pmid = {38093186},
issn = {1471-2164},
support = {GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; },
mesh = {*Phoeniceae/genetics ; *Genome, Chloroplast ; Phylogeny ; Plant Breeding ; Chloroplasts/genetics ; Mitochondria/genetics ; },
abstract = {BACKGROUND: Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail.<br><br>RESULTS: Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico.<br><br>CONCLUSIONS: The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.},
}
@article {pmid38095728,
year = {2023},
author = {Chen, W and Zhang, H and Meng, R and Zhang, X and Duo, H and Guo, Z and Shen, X and Chen, C and Li, Z and Fu, Y},
title = {Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau.},
journal = {Parasitology research},
volume = {123},
number = {1},
pages = {43},
pmid = {38095728},
issn = {1432-1955},
mesh = {Animals ; Cattle ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Tibet ; *Diptera ; Mitochondria/genetics ; Mammals ; },
abstract = {Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.},
}
@article {pmid38097150,
year = {2024},
author = {Hew, YX and Ya'cob, Z and Chen, CD and Lau, KW and Sofian-Azirun, M and Muhammad-Rasul, AH and Putt, QY and Tan, TK and Hadi, UK and Suana, IW and Takaoka, H and Low, VL},
title = {Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line.},
journal = {Acta tropica},
volume = {250},
number = {},
pages = {107097},
doi = {10.1016/j.actatropica.2023.107097},
pmid = {38097150},
issn = {1873-6254},
mesh = {Animals ; Indonesia ; *Simuliidae/genetics ; Mitochondria ; Phylogeny ; Genetic Variation ; },
abstract = {Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.},
}
@article {pmid38100746,
year = {2024},
author = {Araujo, TQ and King-Trudeau, S and VanDyke, J and Hochberg, R},
title = {First ultrastructural description of an apomictic opsiblastic egg in freshwater Gastrotricha.},
journal = {Journal of morphology},
volume = {285},
number = {1},
pages = {e21659},
doi = {10.1002/jmor.21659},
pmid = {38100746},
issn = {1097-4687},
support = {//National Science Foundation/ ; },
mesh = {Animals ; Phylogeny ; *Oocytes/ultrastructure ; *Oogenesis ; Endoplasmic Reticulum ; Fresh Water ; },
abstract = {Freshwater gastrotrichs have a biphasic lifecycle that reputedly involves the production of three types of eggs: apomictic and fast hatching (tachyblastic ova), apomictic and delayed hatching (opsiblastic ova), and plaque-bearing eggs (potentially derived from mixis). While some details of oogenesis and eggshell structure are known for tachyblastic ova, there are few details on other egg types. Here, we provide the first ultrastructural description of the oviposited opsiblastic eggs of the freshwater gastrotrich, Lepidodermella squamata. Scanning electron microscopy revealed the eggshell surface to be ornamented with long flattened pillar-like structures centered on polygonal plates that are pitted along their periphery. Transmission electron microscopy showed the pits to lead to a vast labyrinth of tubular spaces and larger cavities throughout the thick apical layer of the shell. The basal layer of the shell is amorphous and connected to a network of fine fibers that traverse an extra-oocyte space and forms a protective sheet around the uncleaved oocyte. The uncleaved oocyte has a dense layer of peripheral ooplasm surrounding a core of organelles including mitochondria, membrane-bound secretion granules, endoplasmic reticulum, and a single nucleus in a granular, ribosome-rich cytoplasm. Secretion granules are the most abundant organelles and presumably contain lipid-rich yolk that will be used as energy for delayed cleavage, thus functioning in temporal dispersal. These data are compared to the fine structure of invertebrate resting eggs across the phylogenetic spectrum to determine the novelty of opsiblastic egg structure in L. squamata.},
}
@article {pmid38135240,
year = {2024},
author = {Bľandová, G and Janoštiaková, N and Kodada, D and Pastorek, M and Lipták, R and Hodosy, J and Šebeková, K and Celec, P and Krasňanská, G and Eliaš, V and Wachsmannová, L and Konečný, M and Repiská, V and Baldovič, M},
title = {Mitochondrial DNA variability and Covid-19 in the Slovak population.},
journal = {Mitochondrion},
volume = {75},
number = {},
pages = {101827},
doi = {10.1016/j.mito.2023.101827},
pmid = {38135240},
issn = {1872-8278},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; Phylogeny ; Slovakia/epidemiology ; Haplotypes ; *COVID-19/genetics ; Mitochondria/genetics ; },
abstract = {Recent studies have shown that mitochondria are involved in the pathogenesis of Covid-19. Mitochondria play a role in production of reactive oxygen species and induction of an innate immune response, both important during infections. Common variability of mitochondrial DNA (mtDNA) can affect oxidative phosphorylation and the risk or lethality of cardiovascular, neurodegenerative diseases and sepsis. However, it is unclear whether susceptibility of severe Covid-19 might be affected by mtDNA variation. Thus, we have analyzed mtDNA in a sample of 446 Slovak patients hospitalized due to Covid-19 and a control population group consisting of 1874 individuals. MtDNA variants in the HVRI region have been analyzed and classified into haplogroups at various phylogenetic levels. Binary logistic regression was used to assess the risk of Covid-19. Haplogroups T1, H11, K and variants 16256C > T, 16265A > C, 16293A > G, 16311 T > C and 16399A > G were associated with an increased Covid-19 risk. On contrary, Haplogroup J1, haplogroup clusters H + U5b and T2b + U5b, and the mtDNA variant 16189 T > C were associated with decreased risk of Covid-19. Following the application of the Bonferroni correction, statistical significance was observed exclusively for the cluster of haplogroups H + U5b. Unsurprisingly, the most significant factor contributing to the mortality of patients with Covid-19 is the age of patients. Our findings suggest that mtDNA haplogroups can play a role in Covid-19 pathogenesis, thus potentially useful in identifying susceptibility to its severe form. To confirm these associations, further studies taking into account the nuclear genome or other non-biological influences are needed.},
}
@article {pmid38142270,
year = {2024},
author = {Khan, MM and Suhail, SM and Majid, HA and Ahmad, I and Sadique, U and Khan, R and Ahmad, I and Ijaz, A and Khan, K and Ali, F and Khan, MS and El-Mansi, AA},
title = {Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat.},
journal = {Animal biotechnology},
volume = {35},
number = {1},
pages = {2290528},
pmid = {38142270},
issn = {1532-2378},
mesh = {Animals ; *Goats/genetics ; Phylogeny ; Base Sequence ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; },
abstract = {The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.},
}
@article {pmid38157080,
year = {2023},
author = {Kuprina, K and Smorkatcheva, A and Rudyk, A and Galkina, S},
title = {Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {36},
pmid = {38157080},
issn = {1573-4978},
mesh = {Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; Genome ; Mitochondria/genetics ; Arvicolinae/genetics ; Sequence Analysis, DNA ; *Genome, Mitochondrial/genetics ; },
abstract = {BACKGROUND: Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.<br><br>METHODS AND RESULTS: PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.<br><br>CONCLUSIONS: Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.},
}
@article {pmid38177203,
year = {2024},
author = {Yonezawa, T and Mannen, H and Honma, K and Matsunaga, M and Rakotondraparany, F and Ratsoavina, FM and Wu, J and Nishibori, M and Yamamoto, Y},
title = {Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {569},
pmid = {38177203},
issn = {2045-2322},
support = {21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; },
mesh = {Animals ; Africa ; *Chickens/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Madagascar ; Mitochondria/genetics ; Phylogeny ; },
abstract = {Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.},
}
@article {pmid38185291,
year = {2024},
author = {Bian, C and Ji, S and Xue, R and Zhou, L and Sun, J and Ji, H},
title = {Molecular cloning and characterization of BNIP3 and NIX1/2 and their role in DHA-induced mitophagy and apoptosis in grass carp (Ctenopharyngodon idellus) adipocytes.},
journal = {Gene},
volume = {899},
number = {},
pages = {148140},
doi = {10.1016/j.gene.2024.148140},
pmid = {38185291},
issn = {1879-0038},
mesh = {Animals ; *Mitophagy/genetics ; *Carps/genetics ; Phylogeny ; Apoptosis/genetics ; Adipocytes/metabolism ; Cloning, Molecular ; Mammals/genetics ; },
abstract = {B-cell lymphoma-2 and adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) and BNIP3 like (BNIP3L or NIX) play a vital role in regulating mitophagy and the intrinsic apoptosis in mammals, but their gene characterizations remain unclear in fish. Herein, bnip3, nix1 and nix2 were isolated and characterized from grass carp (Ctenopharyngodon idellus), which encode peptides of 194, 233 and 222 amino acids, respectively. As typical BH3-only proteins, grass carp BNIP3, NIX1 and NIX2 proteins contain BH3 and C-terminal transmembrane domains for inducing apoptosis. Moreover, the LC3-interacting region motif of BNIP3, NIX1 and NIX2 is also conserved in grass carp. Phylogenetic analyses also demonstrated that nix1 and nix2 may have originated from the genome duplication event. Expression pattern analysis indicated that bnip3, nix1 and nix2 were highest expressed in brain, followed by eye (bnip3) and liver (nix1 and nix2). BNIP3, NIX1 and NIX2 localized to the nucleus and the cytoplasm, with a predominant localization to mitochondria within the cytoplasm. In the present study, we found that 200 μM DHA impaired the mitochondrial function, manifested as the decreased antioxidant ability, cellular ATP content and mitochondrial membrane potential in grass carp adipocytes. In addition, the gene expression and enzyme activities of caspase family were significantly increased in 200 μM DHA group, indicating that adipocyte apoptosis was induced. Meanwhile, DHA increased the gene expression of bnip3, nix1 and nix2 in a dose-dependent manner in grass carp adipocytes. The colocalization of mitochondria and lysosomes was promoted by 200 μM DHA treatment, implying that BNIP3/NIX-related mitophagy was activated in adipocytes. Based on these findings, it can be inferred that BNIP3/NIX-related mitophagy may be involved in the adipocyte apoptosis induced by DHA in grass carp.},
}
@article {pmid38221354,
year = {2023},
author = {Hoare, RJB and Patrick, BH and Buckley, TR and Brav-Cubitt, T},
title = {Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.},
journal = {Zootaxa},
volume = {5346},
number = {1},
pages = {1-27},
doi = {10.11646/zootaxa.5346.1.1},
pmid = {38221354},
issn = {1175-5334},
mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; New Zealand ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Moths/genetics/anatomy &amp; histology ; Phylogeny ; },
abstract = {The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.},
}
@article {pmid38231368,
year = {2024},
author = {Nevarez-Lopez, CA and Muhlia-Almazan, A and Gamero-Mora, E and Sanchez-Paz, A and Sastre-Velasquez, CD and Lopez-Martinez, J},
title = {The branched mitochondrial respiratory chain from the jellyfish Stomolophus sp2 as a probable adaptive response to environmental changes.},
journal = {Journal of bioenergetics and biomembranes},
volume = {56},
number = {2},
pages = {101-115},
pmid = {38231368},
issn = {1573-6881},
support = {171862//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; },
mesh = {Animals ; Electron Transport ; Phylogeny ; *Mitochondrial Membranes/metabolism ; *Scyphozoa/chemistry/metabolism ; Mitochondria/metabolism ; Electron Transport Complex IV ; },
abstract = {During their long evolutionary history, jellyfish have faced changes in multiple environmental factors, to which they may selectively fix adaptations, allowing some species to survive and inhabit diverse environments. Previous findings have confirmed the jellyfish's ability to synthesize large ATP amounts, mainly produced by mitochondria, in response to environmental challenges. This study characterized the respiratory chain from the mitochondria of the jellyfish Stomolophus sp2 (previously misidentified as Stomolophus meleagris). The in-gel activity from isolated jellyfish mitochondria confirmed that the mitochondrial respiratory chain contains the four canonical complexes I to IV and F0F1-ATP synthase. Specific additional activity bands, immunodetection, and mass spectrometry identification confirmed the occurrence of four alternative enzymes integrated into a branched mitochondrial respiratory chain of Stomolophus sp2: an alternative oxidase and three dehydrogenases (two NADH type II enzymes and a mitochondrial glycerol-3-phosphate dehydrogenase). The analysis of each transcript sequence, their phylogenetic relationships, and each protein's predicted models confirmed the mitochondrial alternative enzymes' identity and specific characteristics. Although no statistical differences were found among the mean values of transcript abundance of each enzyme in the transcriptomes of jellyfish exposed to three different temperatures, it was confirmed that each gene was expressed at all tested conditions. These first-time reported enzymes in cnidarians suggest the adaptative ability of jellyfish's mitochondria to display rapid metabolic responses, as previously described, to maintain energetic homeostasis and face temperature variations due to climate change.},
}
@article {pmid38243053,
year = {2024},
author = {Seesamut, T and Oba, Y and Jirapatrasilp, P and Martinsson, S and Lindström, M and Erséus, C and Panha, S},
title = {Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {1753},
pmid = {38243053},
issn = {2045-2322},
support = {TRF-DPG628001//Thailand Research Fund/ ; BDC-PG2-161002//Center of Excellence on Biodiversity/ ; N35E660138//National Research Council of Thailand/ ; },
mesh = {Animals ; Phylogeny ; *Oligochaeta/genetics ; Mitochondria ; Asia ; Australia ; },
abstract = {The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.},
}
@article {pmid38243701,
year = {2024},
author = {Gangavarapu, K and Ji, X and Baele, G and Fourment, M and Lemey, P and Matsen, FA and Suchard, MA},
title = {Many-core algorithms for high-dimensional gradients on phylogenetic trees.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {2},
pages = {},
pmid = {38243701},
issn = {1367-4811},
support = {R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/NH/NIH HHS/United States ; },
mesh = {Phylogeny ; *Software ; Bayes Theorem ; *Algorithms ; Codon ; Nucleotides ; },
abstract = {MOTIVATION: Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations.<br><br>RESULTS: We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable.<br><br>We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).},
}
@article {pmid38258637,
year = {2024},
author = {Li, X and Li, W and Huo, J and Li, L and Chen, B and Guo, Z and Ma, Z},
title = {[Identification and expression analysis of citrate synthase 3 gene family members in apple].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {40},
number = {1},
pages = {137-149},
doi = {10.13345/j.cjb.230166},
pmid = {38258637},
issn = {1872-2075},
mesh = {*Citric Acid ; *Malus/genetics ; Citrate (si)-Synthase ; Phylogeny ; Citrates ; },
abstract = {As one of the key enzymes in cell metabolism, the activity of citrate synthase 3 (CS3) regulates the substance and energy metabolism of organisms. The protein members of CS3 family were identified from the whole genome of apple, and bioinformatics analysis was performed and expression patterns were analyzed to provide a theoretical basis for studying the potential function of CS3 gene in apple. BLASTp was used to identify members of the apple CS3 family based on the GDR database, and the basic information of CS3 protein sequence, subcellular localization, domain composition, phylogenetic relationship and chromosome localization were analyzed by Pfam, SMART, MEGA5.0, clustalx.exe, ExPASy Proteomics Server, MEGAX, SOPMA, MEME, WoLF PSORT and other software. The tissue expression and inducible expression characteristics of 6 CS3 genes in apple were determined by acid content and real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). Apple CS3 gene family contains 6 members, and these CS3 proteins contain 473-608 amino acid residues, with isoelectric point distribution between 7.21 and 8.82. Subcellular localization results showed that CS3 protein was located in mitochondria and chloroplasts, respectively. Phylogenetic analysis divided them into 3 categories, and the number of genes in each subfamily was 2. Chromosome localization analysis showed that CS3 gene was distributed on different chromosomes of apple. The secondary structure of protein is mainly α-helix, followed by random curling, and the proportion of β-angle is the smallest. The 6 members were all expressed in different apple tissues. The overall expression trend from high to low was the highest relative expression content of MdCS3.4, followed by MdCS3.6, and the relative expression level of other members was in the order of MdCS3.3 > MdCS3.2 > MdCS3.1 > MdCS3.5. qRT-PCR results showed that MdCS3.1 and MdCS3.3 genes had the highest relative expression in the pulp of 'Chengji No. 1' with low acid content, and MdCS3.2 and MdCS3.3 genes in the pulp of 'Asda' with higher acid content had the highest relative expression. Therefore, in this study, the relative expression of CS3 gene in apple cultivars with different acid content in different apple varieties was detected, and its role in apple fruit acid synthesis was analyzed. The experimental results showed that the relative expression of CS3 gene in different apple varieties was different, which provided a reference for the subsequent study of the quality formation mechanism of apple.},
}
@article {pmid38275595,
year = {2023},
author = {Li, K and Yu, SW and Hu, H and Feng, YF and Storey, KB and Ma, Y and Zhang, JY and Yu, DN},
title = {The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes.},
journal = {Genes},
volume = {15},
number = {1},
pages = {},
pmid = {38275595},
issn = {2073-4425},
support = {LY23C040002//the Natural Science Foundation of Zhejiang Province/ ; },
mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Coleoptera/genetics ; Bayes Theorem ; Mitochondria/genetics ; },
abstract = {Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.},
}
@article {pmid38309455,
year = {2024},
author = {Miyakawa, Y and Otsuka, M and Shibata, C and Seimiya, T and Yamamoto, K and Ishibashi, R and Kishikawa, T and Tanaka, E and Isagawa, T and Takeda, N and Kamio, N and Imai, K and Fujishiro, M},
title = {Gut Bacteria-derived Membrane Vesicles Induce Colonic Dysplasia by Inducing DNA Damage in Colon Epithelial Cells.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {17},
number = {5},
pages = {745-767},
pmid = {38309455},
issn = {2352-345X},
mesh = {Mice ; Animals ; Humans ; *Colon/microbiology ; Reactive Oxygen Species ; Base Composition ; Phylogeny ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Induced Pluripotent Stem Cells ; Epithelial Cells ; Bacteria/genetics ; },
abstract = {BACKGROUND &amp; AIMS: Colorectal cancer (CRC) is the third most common cancer in the world. Gut microbiota has recently been implicated in the development of CRC. Actinomyces odontolyticus is one of the most abundant bacteria in the gut of patients with very early stages of CRC. A odontolyticus is an anaerobic bacterium existing principally in the oral cavity, similar to Fusobacterium nucleatum, which is known as a colon carcinogenic bacterium. Here we newly determined the biological functions of A odontolyticus on colonic oncogenesis.<br><br>METHODS: We examined the induction of intracellular signaling by A odontolyticus in human colonic epithelial cells (CECs). DNA damage levels in CECs were confirmed using the human induced pluripotent stem cell-derived gut organoid model and mouse colon tissues in&#xa0;vivo.<br><br>RESULTS: A odontolyticus secretes membrane vesicles (MVs), which induce nuclear factor kappa B signaling and also produce excessive reactive oxygen species (ROS) in colon epithelial cells. We found that A odontolyticus secretes lipoteichoic acid-rich MVs, promoting inflammatory signaling via TLR2. Simultaneously, those MVs are internalized into the colon epithelial cells, co-localize with the mitochondria, and cause mitochondrial dysfunction, resulting in excessive ROS production and DNA damage. Induction of excessive DNA damage in colonic cells by A odontolyticus-derived MVs was confirmed in the gut organoid model and also in mouse colon tissues.<br><br>CONCLUSIONS: A odontolyticus secretes MVs, which cause&#xa0;chronic inflammation and ROS production in colonic epithelial cells, leading to the initiation of CRC.},
}
@article {pmid38316513,
year = {2024},
author = {Liu, X and You, Q and Liu, M and Bo, C and Zhu, Y and Duan, Y and Xue, J and Wang, D and Xue, T},
title = {Assembly and comparative analysis of the complete mitochondrial genome of Pinellia ternata.},
journal = {Functional plant biology : FPB},
volume = {51},
number = {},
pages = {},
doi = {10.1071/FP23256},
pmid = {38316513},
issn = {1445-4416},
mesh = {*Pinellia/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plants, Medicinal/genetics ; Plant Tubers ; },
abstract = {Pinellia ternata is an important natural medicinal herb in China. However, it is susceptible to withering when exposed to high temperatures during growth, which limits its tuber production. Mitochondria usually function in stress response. The P . ternata mitochondrial (mt) genome has yet to be explored. Therefore, we integrated PacBio and Illumina sequencing reads to assemble and annotate the mt genome of P . ternata . The circular mt genome of P . ternata is 876 608bp in length and contains 38 protein-coding genes (PCGs), 20 tRNA genes and three rRNA genes. Codon usage, sequence repeats, RNA editing and gene migration from chloroplast (cp) to mt were also examined. Phylogenetic analysis based on the mt genomes of P . ternata and 36 other taxa revealed the taxonomic and evolutionary status of P . ternata . Furthermore, we investigated the mt genome size and GC content by comparing P . ternata with the other 35 species. An evaluation of non-synonymous substitutions and synonymous substitutions indicated that most PCGs in the mt genome underwent negative selection. Our results provide comprehensive information on the P . ternata mt genome, which may facilitate future research on the high-temperature response of P . ternata and provide new molecular insights on the Araceae family.},
}
@article {pmid38325701,
year = {2024},
author = {Wang, C and Yu, X and Wang, J and Zhao, Z and Wan, J},
title = {Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {51},
number = {6},
pages = {583-593},
doi = {10.1016/j.jgg.2024.01.007},
pmid = {38325701},
issn = {1673-8527},
mesh = {*Oryza/genetics ; *Hybrid Vigor/genetics ; *Reproductive Isolation ; *Plant Breeding/methods ; *Hybridization, Genetic ; Mitochondria/genetics ; },
abstract = {Heterosis, also known as hybrid vigor, is commonly observed in rice crosses. The hybridization of rice species or subspecies exhibits robust hybrid vigor, however, the direct harnessing of this vigor is hindered by reproductive isolation. Here, we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific hybrids. This review encompasses the genetic model of reproductive isolation within and among Oryza sativa species, emphasizing the essential role of mitochondria in this process. Additionally, we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes, elucidating their significant contribution to reproductive isolation. Furthermore, our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in rice. Building on these advances, we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.},
}
@article {pmid38349189,
year = {2024},
author = {Lanza, A and Kimura, S and Hirono, I and Yoshitake, K and Kinoshita, S and Asakawa, S},
title = {Transcriptome analysis of Edwardsiella piscicida during intracellular infection reveals excludons are involved with the activation of a mitochondrion-like energy generation program.},
journal = {mBio},
volume = {15},
number = {3},
pages = {e0352623},
pmid = {38349189},
issn = {2150-7511},
support = {20H00429//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //Toagosei (Toagosei Co., Ltd.)/ ; },
mesh = {Animals ; Zebrafish ; Phylogeny ; *Edwardsiella/genetics ; Gene Expression Profiling ; *Enterobacteriaceae Infections/microbiology ; *Fish Diseases/microbiology ; },
abstract = {Phylogenetic evidence suggests a shared ancestry between mitochondria and modern Proteobacteria, a phylum including several genera of intracellular pathogens. Studying these diverse pathogens, particularly during intracellular infection of their hosts, can reveal characteristics potentially representative of the mitochondrial-Proteobacterial ancestor by identifying traits shared with mitochondria. While transcriptomic approaches can provide global insights into intracellular acclimatization by pathogens, they are often limited by excess host RNAs in extracts. Here, we developed a method employing magnetic nanoparticles to enrich RNA from an intracellular Gammaproteobacterium, Edwardsiella piscicida, within zebrafish, Danio rerio, fin fibroblasts, enabling comprehensive exploration of the bacterial transcriptome. Our findings revealed that the intracellular E. piscicida transcriptome reflects a mitochondrion-like energy generation program characterized by the suppression of glycolysis and sugar transport, coupled with upregulation of the tricarboxylic acid (TCA) cycle and alternative import of simple organic acids that directly flux into TCA cycle intermediates or electron transport chain donors. Additionally, genes predicted to be members of excludons, loci of gene pairs antagonistically co-regulated by overlapping antisense transcription, are significantly enriched in the set of all genes with perturbed sense and antisense transcription, suggesting a general but important involvement of excludons with intracellular acclimatization. Notably, genes involved with the activation of the mitochondrion-like energy generation program, specifically with metabolite import and glycolysis, are also members of predicted excludons. Other intracellular Proteobacterial pathogens appear to employ a similar mitochondrion-like energy generation program, suggesting a potentially conserved mechanism for optimized energy acquisition from hosts centered around the TCA cycle.IMPORTANCEPhylogenetic evidence suggests that mitochondria and Proteobacteria, a phylum encompassing various intracellular pathogens, share a common ancestral lineage. In this study, we developed a novel method employing magnetic nanoparticles to explore the transcriptome of an aquatic Gammaproteobacterium, Edwardsiella piscicida, during intracellular infection of host cells. We show that the strategy E. piscicida uses to generate energy strikingly mirrors the function of mitochondria-energy generators devoid of glycolytic processes. Notably, several implicated genes are members of excludons-gene pairs antagonistically co-regulated by overlapping antisense transcription. Other intracellular Proteobacterial pathogens appear to adopt a similar mitochondrion-like energy generation program, indicating a possibly conserved strategy for optimized energy acquisition from hosts centered around the tricarboxylic acid cycle.},
}
@article {pmid38402284,
year = {2024},
author = {Li, G and Zhang, H and Lin, Z and Li, H and Xu, G and Xu, Y and Ji, R and Luo, W and Qiu, Y and Qiu, S and Tang, H},
title = {Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {4547},
pmid = {38402284},
issn = {2045-2322},
mesh = {*Ipomoea batatas/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Ipomoea/genetics ; *Genome, Chloroplast/genetics ; Chloroplasts/genetics ; Amino Acids/genetics ; RNA, Transfer/genetics ; },
abstract = {The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.},
}
@article {pmid38422090,
year = {2024},
author = {Yu, TS and Park, K and Han, KH and Kwak, IS},
title = {Morphological and genetic analysis for the diversity conservation of rare species, Thamnaconus multilineatus (Tetraodontiformes: Monacanthidae).},
journal = {PloS one},
volume = {19},
number = {2},
pages = {e0292916},
pmid = {38422090},
issn = {1932-6203},
mesh = {Animals ; *Tetraodontiformes ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; Endangered Species ; },
abstract = {Climate changes have altered biodiversity and ultimately induced community changes that have threatened the survival of certain aquatic organisms such as fish species. Obtaining biological and genetic information on endangered fish species is critical for ecological population management. Thamnaconus multilineatus, registered as an endangered species by the IUCN in 2019, is a Data Deficient (DD) species with a remarkably small number of habitats worldwide and no known information other than its habitat and external form. In this study, we characterized the external and osteological morphology of a T. multilineatus specimen collected from eastern Jeju Island, South Korea, in 2020. We also investigated the phylogenetic relationships among related fish species through complete mitochondrial DNA (mtDNA) analysis of the T. multilineatus specimen. The external and skeletal characteristics of T. multilineatus were similar to those of previous reports describing other fish of the genus Thamnaconus, making it difficult to classify T. multilineatus as a similar species based only on morphological characteristics. As a result of analyzing the complete mtDNA of T. multilineatus, the length of the mtDNA was determined to be 16,435 bp, and the mitochondrial genome was found to have 37 CDCs, including 13 PCGs, 22 tRNAs, and 2 rRNAs. In the phylogenetic analysis within the suborder Balistoidei, T. multilineatus mtDNA formed a cluster with fish of the genus Thamnaconus. This study is the first to report on the skeletal structure and complete mtDNA of T. multilineatus. Since the current research on T. multilineatus has only been reported on morphology, the results of this study will be utilized as important information for the management and restoration of T. multilineatus as an endangered species and significant fishery resource.},
}
@article {pmid38480132,
year = {2024},
author = {Methou, P and Chen, C and Komai, T},
title = {Revision of the alvinocaridid shrimp genus Rimicaris Williams &amp; Rona, 1986 (Decapoda: Caridea) with description of a new species from the Mariana Arc hydrothermal vents.},
journal = {Zootaxa},
volume = {5406},
number = {4},
pages = {501-518},
doi = {10.11646/zootaxa.5406.4.1},
pmid = {38480132},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; *Hydrothermal Vents ; *Decapoda ; Mitochondria ; },
abstract = {A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 16191667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Williams &amp; Rona, 1986 with four other generaAlvinocaridinides, Manuscaris, Opaepele, and Shinkaicarisnested within it. We re-examine material of these four problematic genera, and synonymise them under Rimicaris whose diagnosis has been amended, in order to maintain a monophyletic Rimicaris. Our new species, Rimicaris cambonae sp. nov. is genetically close to Rimicaris loihi (Williams &amp; Dobbs, 1995) comb. nov. (previously Opaepele loihi) with which it co-occurs, but can be morphologically distinguished by the less elevated dorsal surface of the rostrum, this being devoid of a median carina, a stronger pterygostomial tooth on the carapace, and a blunt rather than acuminate proximolateral process on the antennular stylocerite. Species previously assigned to the above listed, synonymized genera are also discussed, with new material examined for three key species: R. loihi, R. acuminata, and R. leurokolos. Further, Alvinocaridinides formosa Komai &amp; Chan, 2010 and Manuscaris liui Wang &amp; Sha, 2016 are synonymized under Rimicaris leurokolos (Kikuchi &amp; Hashimoto, 2000) comb. nov. and R. acuminata (Komai &amp; Tsuchida, 2015) comb. nov., respectively. Revised diagnoses are presented for R. loihi, R. acuminata, and R. leurokolos. After the present revision revision, Rimicaris now consists of 15 species.},
}
@article {pmid38480282,
year = {2024},
author = {Gordon, DP and Quek, ZBR and Huang, D},
title = {Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa.},
journal = {Zootaxa},
volume = {5424},
number = {3},
pages = {323-357},
doi = {10.11646/zootaxa.5424.3.3},
pmid = {38480282},
issn = {1175-5334},
mesh = {Animals ; Phylogeny ; New Zealand ; RNA, Ribosomal, 18S/genetics ; Base Sequence ; *Mitochondria/genetics ; },
abstract = {All eight extant species ofRhabdopleuradescribed between 1869 and 2018 are provisionally accepted as valid based on a review of the literature and new data on two little-known species from the Azores. Additionally, four new species are described from the New Zealand region, increasing global diversity by 50%, and a dichotomous key to all 12 described species is provided based on morphological criteria. The distinction between colony morphologies based on erect-tube inception is regarded as particularly helpful in initial characterization of species. Erect ringed tubes are either produced directly from the surface of creeping-tubes or indirectly, i.e. a short adherent side branch from a creeping tube is interpolated between the creeping tube and an erect tube; such side branches are blind-ending. These two modes of erect-tube origination are here respectively termeddirectandindirect. Species with indirect erect-tube budding are predominant in the North Atlantic whereas species with direct erect-tube budding dominate in New Zealand waters. The only indirect-erect species from New Zealand, Rhabdopleura chathamica n. sp., was discovered on deepwater coral from 10081075 m, constituting the deepest record of the genus to date. Rhabdopleura emancipata n. sp., collected only in a detached state, constitutes a three-dimensional tangled growth that grew freely into the water columna unique morphology hitherto unknown among extant species. Owing to this growth mode, it provided a substratum for epibionts from several phyla. Rhabdopleura francesca n. sp. and Rhabdopleura decipula n. sp. are morphologically very similar but are distinguishable by their distinct placements in a phylogeny based on 16S mitochondrial and 18S nuclear rRNA genes. Phylogenetic reconstructions based on rRNA and mitochondrial genome data contribute to an updated phylogeny of all Rhabdopleura species sequenced thus far, some of which require more molecular sequences and morphological analyses for taxonomic determination.},
}
@article {pmid38488948,
year = {2024},
author = {Ren, P and Zhang, J and Vijg, J},
title = {Somatic mutations in aging and disease.},
journal = {GeroScience},
volume = {46},
number = {5},
pages = {5171-5189},
pmid = {38488948},
issn = {2509-2723},
support = {AG038072/GF/NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; AG047200/GF/NIH HHS/United States ; 82172461//National Natural Science Foundation of China/ ; U19 AG056278/AG/NIA NIH HHS/United States ; P01 AG017242/AG/NIA NIH HHS/United States ; ES029519/GF/NIH HHS/United States ; AG056278/GF/NIH HHS/United States ; BC180689P1//DOD grant/ ; AG017242/GF/NIH HHS/United States ; HL145560/GF/NIH HHS/United States ; },
mesh = {*Aging/genetics ; Humans ; Animals ; *Mutation ; Mice ; Mutation Rate ; DNA Repair/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.},
}
@article {pmid38503345,
year = {2024},
author = {Nuryadi, H and Mandagi, IF and Masengi, KWA and Kusumi, J and Inomata, N and Yamahira, K},
title = {Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake.},
journal = {Biology letters},
volume = {20},
number = {3},
pages = {20230385},
pmid = {38503345},
issn = {1744-957X},
mesh = {Humans ; Animals ; *Heteroplasmy ; Lakes ; Phylogeny ; *Oryzias/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.},
}
@article {pmid38503840,
year = {2024},
author = {Duran, DP and Laroche, RA and Roman, SJ and Godwin, W and Herrmann, DP and Bull, E and Egan, SP},
title = {Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {6617},
pmid = {38503840},
issn = {2045-2322},
mesh = {Animals ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; *Coleoptera/genetics ; Species Specificity ; },
abstract = {In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.},
}
@article {pmid38531492,
year = {2024},
author = {López-Hervas, K and Santos, JC and Ron, SR and Betancourth-Cundar, M and Cannatella, DC and Tarvin, RD},
title = {Deep divergences among inconspicuously colored clades of Epipedobates poison frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {195},
number = {},
pages = {108065},
doi = {10.1016/j.ympev.2024.108065},
pmid = {38531492},
issn = {1095-9513},
mesh = {Animals ; Phylogeny ; *Poison Frogs ; *Anura/genetics ; Mitochondria ; Ecuador ; },
abstract = {Poison frogs (Dendrobatidae) are famous for their aposematic species, having a combination of diverse color patterns and defensive skin toxins, yet most species in this family are inconspicuously colored and considered non-aposematic. Epipedobates is among the youngest genus-level clades of Dendrobatidae that includes both aposematic and inconspicuous species. Using Sanger-sequenced mitochondrial and nuclear markers, we demonstrate deep genetic divergences among inconspicuous species of Epipedobates but relatively shallow genetic divergences among conspicuous species. Our phylogenetic analysis includes broad geographic sampling of the inconspicuous lineages typically identified as E. boulengeri and E. espinosai, which reveals two putative new species, one in west-central Colombia (E. sp. 1) and the other in north-central Ecuador (E. aff. espinosai). We conclude that E. darwinwallacei is a junior subjective synonym of E. espinosai. We also clarify the geographic distributions of inconspicuous Epipedobates species including the widespread E. boulengeri. We provide a qualitative assessment of the phenotypic diversity in each nominal species, with a focus on the color and pattern of inconspicuous species. We conclude that Epipedobates contains eight known valid species, six of which are inconspicuous. A relaxed molecular clock analysis suggests that the most recent common ancestor of Epipedobates is ∼11.1 million years old, which nearly doubles previous estimates. Last, genetic information points to a center of species diversity in the Chocó at the southwestern border of Colombia with Ecuador. A Spanish translation of this text is available in the supplementary materials.},
}
@article {pmid38540407,
year = {2024},
author = {Zhang, G and Jiao, Y and Zhao, Z and Chen, Q and Wang, Z and Zhu, J and Lv, N and Sun, G},
title = {Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum.},
journal = {Genes},
volume = {15},
number = {3},
pages = {},
pmid = {38540407},
issn = {2073-4425},
mesh = {*Gossypium/metabolism ; *Verticillium/genetics ; Phylogeny ; Disease Resistance/genetics ; Chromosome Mapping ; },
abstract = {Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.},
}
@article {pmid38543688,
year = {2024},
author = {Ramos-González, PL and Alexandre, MAV and Potsclam-Barro, M and Duarte, LML and Michea Gonzalez, GL and Chabi-Jesus, C and Ramos, AF and Harakava, R and Lorenzi, H and Freitas-Astúa, J and Kitajima, EW},
title = {Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii.},
journal = {Viruses},
volume = {16},
number = {3},
pages = {},
pmid = {38543688},
issn = {1999-4915},
support = {PNPD20132154 - 33141010001P4 - PNPD - IBSP, 88882.157041/2017-01//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 17/50334-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/25078-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/02179-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; },
mesh = {*Aristolochia/genetics ; *Mirabilis/genetics ; Genome, Viral ; *Rhabdoviridae ; Plants/genetics ; Phylogeny ; Plant Diseases ; },
abstract = {Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.},
}
@article {pmid38568891,
year = {2024},
author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN},
title = {A genetic atlas for the butterflies of continental Canada and United States.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0300811},
pmid = {38568891},
issn = {1932-6203},
mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; },
abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.},
}
@article {pmid38630841,
year = {2024},
author = {Gonzalez, RC and Bezerra de Lima, LC and Passos, P and Silva, MJJ},
title = {The good, the bad and the boa: An unexpected new species of a true boa revealed by morphological and molecular evidence.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298159},
pmid = {38630841},
issn = {1932-6203},
mesh = {Animals ; Male ; Phylogeny ; *Boidae/genetics ; Mitochondria/genetics ; Brazil ; *Lepidoptera ; },
abstract = {Snakes of the genus Boa are outstanding elements of the New World biota with a broad sociological influence on pop culture. Historically, several taxa have been recognized in the past 300 years, being mostly described in the early days of binomial nomenclature. As a rule, these taxa were recognized based on a suite of phenotypic characters mainly those from the external morphology. However, there is a huge disagreement with respect to the current taxonomy and available molecular phylogenies. In order to reconcile both lines of evidence, we investigate the phylogenetic reconstruction (using mitochondrial and nuclear genes) of the genus in parallel to the detailed study of some phenotypic systems from a geographically representative sample of the cis-Andean mainland Boa constrictor. We used cyt-b only (744bp) from 73 samples, and cyt-b, ND4, NTF3, and ODC partial sequences (in a total of 2305 bp) from 35 samples, comprising nine currently recognized taxa (species or subspecies), to infer phylogenetic relationships of boas. Topologies recovered along all the analyses and genetic distances obtained allied to a unique combination of morphological traits (colouration, pholidosis, meristic, morphometric, and male genitalia features) allowed us to recognize B. constrictor lato sensu, B. nebulosa, B. occidentalis, B. orophias and a distinct lineage from the eastern coast of Brazil, which we describe here as a new species, diagnosing it from the previously recognized taxa. Finally, we discuss the minimally necessary changes in the taxonomy of Boa constrictor complex; the value of some usually disregarded phenotypic character system; and we highlight the urgency of continuing environmental policy to preserve one of the most impacted Brazilian hotspots, the Atlantic Forest, which represents an ecoregion full of endemism.},
}
@article {pmid38652016,
year = {2024},
author = {Kwok van der Giezen, FM and Viljoen, A and Campbell-Clause, L and Dao, NT and Colas des Francs-Small, C and Small, I},
title = {Insights into U-to-C RNA editing from the lycophyte Phylloglossum drummondii.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {1},
pages = {445-459},
doi = {10.1111/tpj.16775},
pmid = {38652016},
issn = {1365-313X},
support = {DP200102981//Australian Research Council/ ; },
mesh = {*RNA Editing/genetics ; *RNA, Plant/genetics ; Genome, Mitochondrial/genetics ; Transcriptome ; Uridine/metabolism/genetics ; Genome, Chloroplast ; Phylogeny ; Mitochondria/genetics/metabolism ; },
abstract = {The lycophyte Phylloglossum drummondii is the sole inhabitant of its genus in the Huperzioideae group and one of a small minority of plants which perform uridine to cytidine RNA editing. We assembled the P. drummondii chloroplast and mitochondrial genomes and used RNA sequence data to build a comprehensive profile of organellar RNA editing events. In addition to many C-to-U editing events in both organelles, we found just four U-to-C editing events in the mitochondrial transcripts cob, nad1, nad5 and rpl2. These events are conserved in related lycophytes in the genera Huperzia and Phlegmariurus. De novo transcriptomes for three of these lycophytes were assembled to search for putative U-to-C RNA editing enzymes. Four putative U-to-C editing factors could be matched to the four mitochondrial U-to-C editing sites. Due to the unusually few numbers of U-to-C RNA editing sites, P. drummondii and related lycophytes are useful models for studying this poorly understood mechanism.},
}
@article {pmid38658152,
year = {2024},
author = {Fan, C and Yang, J and Chen, R and Liu, W and Xiang, X},
title = {[Identification and expression analysis of the HSP70 gene family under abiotic stresses in Litchi chinensis].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {40},
number = {4},
pages = {1102-1119},
doi = {10.13345/j.cjb.230450},
pmid = {38658152},
issn = {1872-2075},
mesh = {*Litchi/genetics/metabolism ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism/biosynthesis ; *Phylogeny ; *Droughts ; Multigene Family ; Salt Stress/genetics ; },
abstract = {HSP70 protein, as an important member of the heat shock protein (HSP) family, plays an important role in plant growth, development, and response to biotic and abiotic stresses. In order to explore the role of HSP70 gene family members in Litchi chinensis under low temperature, high temperature, drought, and salt stress, bioinformatics methods were used to identify the HSP70 gene family members within the entire L. chinensis genome. The expression of these genes under various abiotic stresses was then detected using quantitative real-time PCR (qRT-PCR). The results showed that the LcHSP70 gene family consisted of 18 members, which were unevenly distributed across ten L. chinensis chromosomes. The LcHSP70 protein contained 479-851 amino acids, with isoelectric points ranging from 5.07 to 6.95, and molecular weights from 52.44 kDa to 94.07 kDa. The predicted subcellular localization showed that LcHSP70 protein was present in the nucleus, cytoplasm, endoplasmic reticulum, mitochondria, and chloroplast. Phylogenetic analysis divided the LcHSP70 proteins into five subgroups, namely Ⅰ, Ⅱ, Ⅲ, Ⅳ, and Ⅵ. The promoter regions of the LcHSP70 genes contained various cis-acting elements related to plant growth, development, hormone response, and stress response. Moreover, the expression of LcHSP70 genes displayed distint tissue-specific expression level, categorized into universal expression and specific expression. From the selected 6 LcHSP70 genes (i.e., LcHSP70-1, LcHSP70-5, LcHSP70-10, LcHSP70-14, LcHSP70-16, and LcHSP70-18), their relative expression levels were assessed under different abiotic stresses using qRT-PCR. The results indicated that the gene family members exhibited diverse responses to low temperature, high temperature, drought, and salt stress, with significant variations in their expression levels across different time periods. These results provide a foundation for further exploration of the function of the LcHSP70 gene family.},
}
@article {pmid38735623,
year = {2024},
author = {Strücker, GK and Jaramillo, ML and de Quadros, T and Nazari, EM},
title = {UVB radiation exposure modulates mitophagy in embryonic cells of freshwater prawn Macrobrachium olfersii: Exploring a protective organelle quality control mechanism.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {295},
number = {},
pages = {111664},
doi = {10.1016/j.cbpa.2024.111664},
pmid = {38735623},
issn = {1531-4332},
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; *Mitophagy/radiation effects ; *Palaemonidae/radiation effects/embryology/genetics ; Mitochondria/metabolism/radiation effects ; Embryo, Nonmammalian/radiation effects/metabolism ; Arthropod Proteins/metabolism/genetics ; Phylogeny ; Organelles/metabolism/radiation effects ; },
abstract = {Aquatic environments are subject to ultraviolet B (UVB) radiation incidence, and its effects on organisms are dose-dependent. Besides DNA, mitochondria are an important target of this radiation that causes structural damage and impairs its functional dynamics. Here, we hypothesize that mitophagy acts as an organelle quality control mechanism to mitigate UVB impacts in embryonic cells. Then, freshwater prawn Macrobrachium olfersii embryos was used as a model to investigate the effects of UVB on genes (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) and proteins (TOM20, PINK1, p62 and LC3B) involved in mitophagy modulation. The choice of genes and proteins was based on the identification of mitochondrial membrane (Tomm20, Opa1 and TOM20), mediation of mitophagy (Pink1, Prkn and PINK1), and recognition of mitochondria by the autophagosome membrane (Sqstm1, Map1lc3, p62 and LC3B). First, the phylogeny of all genes presented bootstrap values >80 and conserved domains among crustacean species. Gene expression was inherently modulated during development, with transcripts (Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3) overexpressed in the initial and final stages of development. Moreover, UVB radiation induced upregulation of Tomm20, Opa1, Pink, Prkn, Sqstm1, and Map1lc3 genes at 6 h after exposure. Interestingly, after 12 h, the protein content of PINK1, p62, and LC3B increased, while TOM20 was not responsive. Despite UVB radiation's harmful effects on embryonic cells, the chronology of gene expression and protein content indicates rapid activation of mitophagy, serving as an organelle quality control mechanism, given the analyzed cells' integrity.},
}
@article {pmid38740227,
year = {2024},
author = {Zhang, M and Li, W and Zhang, X and Bi, M and Wang, X and Sun, F and Lu, J and Chi, Y and Han, Y and Li, Q and Li, T},
title = {Lamprey VDAC2: Suppressing hydrogen peroxide-induced 293T cell apoptosis by downregulating BAK expression.},
journal = {Fish &amp; shellfish immunology},
volume = {150},
number = {},
pages = {109622},
doi = {10.1016/j.fsi.2024.109622},
pmid = {38740227},
issn = {1095-9947},
mesh = {Animals ; Humans ; Amino Acid Sequence ; *Apoptosis ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; Down-Regulation/drug effects ; *Fish Proteins/genetics/immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation ; HEK293 Cells ; Hydrogen Peroxide ; *Lampreys/genetics/immunology ; Phylogeny ; Sequence Alignment/veterinary ; *Voltage-Dependent Anion Channel 2/metabolism ; },
abstract = {The voltage-dependent anion channel 2 (VDAC2) is the abundant protein in the outer mitochondrial membrane. Opening VDAC2 pores leads to the induction of mitochondrial energy and material transport, facilitating interaction with various mitochondrial proteins implicated in essential processes such as cell apoptosis and proliferation. To investigate the VDAC2 in lower vertebrates, we identified Lr-VDAC2, a homologue of VDAC2 found in lamprey (Lethenteron reissneri), sharing a sequence identity of greater than 50 % with its counterparts. Phylogenetic analysis revealed that the position of Lr-VDAC2 aligns with the lamprey phylogeny, indicating its evolutionary relationship within the species. The Lr-VDAC2 protein was primarily located in the mitochondria of lamprey cells. The expression of the Lr-VDAC2 protein was elevated in high energy-demanding tissues, such as the gills, muscles, and myocardial tissue in normal lampreys. Lr-VDAC2 suppressed H2O2 (hydrogen peroxide)-induced 293 T cell apoptosis by reducing the expression levels of Caspase 3, Caspase 9, and Cyt C (cytochrome c). Further research into the mechanism indicated that the Lr-VDAC2 protein inhibited the pro-apoptotic activity of BAK (Bcl-2 antagonist/killer) protein by downregulating its expression at the protein translational level, thus exerting an anti-apoptotic function similar to the role of VDAC2 in humans.},
}
@article {pmid38750421,
year = {2024},
author = {Wang, X and Pei, J and Xiong, L and Bao, P and Chu, M and Ma, X and La, Y and Liang, C and Yan, P and Guo, X},
title = {Genetic diversity, phylogeography, and maternal origin of yak (Bos grunniens).},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {481},
pmid = {38750421},
issn = {1471-2164},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; 25-LZIHPS-01//the Innovation Project of Chinese Academy of Agricultural Sciences/ ; },
mesh = {Animals ; Cattle/genetics ; *Phylogeography ; *Genetic Variation ; *Haplotypes ; *Phylogeny ; *Genome, Mitochondrial ; Maternal Inheritance ; Female ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: There is no consensus as to the origin of the domestic yak (Bos grunniens). Previous studies on yak mitochondria mainly focused on mitochondrial displacement loop (D-loop), a region with low phylogenetic resolution. Here, we analyzed the entire mitochondrial genomes of 509 yaks to obtain greater phylogenetic resolution and a comprehensive picture of geographical diversity.<br><br>RESULTS: A total of 278 haplotypes were defined in 509 yaks from 21 yak breeds. Among them, 28 haplotypes were shared by different varieties, and 250 haplotypes were unique to specific varieties. The overall haplotype diversity and nucleotide diversity of yak were 0.979&#x2009;&#xb1;&#x2009;0.0039 and 0.00237&#x2009;&#xb1;&#x2009;0.00076, respectively. Phylogenetic tree and network analysis showed that yak had three highly differentiated genetic branches with high support rate. The differentiation time of clades I and II were about 0.4328&#xa0;Ma, and the differentiation time of clades (I and II) and III were 0.5654&#xa0;Ma. Yushu yak is shared by all haplogroups. Most (94.70%) of the genetic variation occurred within populations, and only 5.30% of the genetic variation occurred between populations. The classification showed that yaks and wild yaks were first clustered together, and yaks were clustered with American bison as a whole. Altitude had the highest impact on the distribution of yaks.<br><br>CONCLUSIONS: Yaks have high genetic diversity and yak populations have experienced population expansion and lack obvious phylogeographic structure. During the glacial period, yaks had at least three or more glacial refugia.},
}
@article {pmid38750703,
year = {2024},
author = {Gong, Y and Luo, X and Zhang, T and Zhou, G and Li, J and Zhang, B and Li, P and Huang, H},
title = {Assembly and comparative analysis of the complete mitochondrial genome of white towel gourd (Luffa cylindrica).},
journal = {Genomics},
volume = {116},
number = {3},
pages = {110859},
doi = {10.1016/j.ygeno.2024.110859},
pmid = {38750703},
issn = {1089-8646},
mesh = {*Genome, Mitochondrial ; *Phylogeny ; *Luffa/genetics ; RNA, Transfer/genetics ; Genome, Plant ; Plant Proteins/genetics/metabolism ; },
abstract = {Mitochondria play an important role in the energy production of plant cells through independent genetic systems. This study has aimed to assemble and annotate the functions of the mitochondrial (mt) genome of Luffa cylindrica. The mt genome of L. cylindrica contained two chromosomes with lengths of 380,879 bp and 67,982 bp, respectively. Seventy-seven genes including 39 protein-coding genes, 34 tRNA genes, 3 rRNA genes, and 1 pseudogene, were identified. About 90.63% of the codons ended with A or U bases, and 98.63% of monomers contained A/T, which contributed to the high A/T content (55.91%) of the complete mt genome. Six genes (ATP8, CCMFC, NAD4, RPL10, RPL5 and RPS4) showed positive selection. Phylogenetic analysis indicates that L. cylindrica is closely related to L. acutangula. The present results provide the mt genome of L. cylindrica, which may facilitate possible genetic variation, evolutionary, and molecular breeding studies of L. cylindrica.},
}
@article {pmid38812151,
year = {2024},
author = {Zhang, XY and Yu, JC and Chen, WT and Zhou, DY and Yuan, Y and Liu, HG and Liang, YL},
title = {[Identification of HSP70 gene family members in Fritillaria cirrhosa and expression analysis in different tissues under high temperature stress].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {9},
pages = {2422-2433},
doi = {10.19540/j.cnki.cjcmm.20240214.101},
pmid = {38812151},
issn = {1001-5302},
mesh = {*HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry ; *Plant Proteins/genetics/metabolism/chemistry ; *Fritillaria/genetics/chemistry ; *Phylogeny ; *Gene Expression Regulation, Plant ; Hot Temperature ; Stress, Physiological/genetics ; Gene Expression Profiling ; Multigene Family ; },
abstract = {The heat shock protein 70 family contains the stress proteins ubiquitous in plants. These proteins are involved in the responses to different abiotic stress conditions and have highly conserved gene sequences. However, little is known about the molecular mechanisms of Fritillaria cirrhosa in response to high-temperature stress. Here, 26 HSP70s, FcHSP70-1 to FcHSP70-26, were identified from the transcriptome data of root, bulb, stem, leaf, and fruit samples of F. cirrhosa. The proteins encoded by FcHSP70s had the lengths ranging from 560 aa to 944 aa, with the molecular weight of 61.64-100.01 kDa and the theoretical isoelectric point between 5.00 and 6.59. The secondary structural elements of HSP70s were mainly random coils and α-helixes. Subcellular localization prediction revealed that FcHSP70s were distributed in mitochondria, chloroplasts, nuclei, endoplasmic reticulum, and cytoplasm. The phylogenetic tree showed that 7 members of the HSP70 family belonged to the Dnak subfamily and 19 members belonged to the HSP110/SSE subfamily. In addition, the qRT-PCR results showed that the expression of FcHSP70-5, FcHSP70-8, FcHSP70-17, FcHSP70-18, and FcHSP70-23 in F. cirrhosa was significantly up-regulated at 35 ℃, which indicated that these genes might play a role in the response to high temperature stress. In addition, compared with other tissues, stems and leaves were sensitive to high temperature stress, with the expression of 18 genes up-regulated by 18.18 and 8.03 folds on average, respectively. These findings provide valuable information about the molecular mechanism of HSP70s of F. cirrhosa in response to high temperature stress.},
}
@article {pmid38816808,
year = {2024},
author = {Xing, J and Zhang, Y and Song, W and Ali, NA and Su, K and Sun, X and Sun, Y and Jiang, Y and Zhao, X},
title = {Comprehensive identification, characterization, and expression analysis of the MORF gene family in Brassica napus.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {475},
pmid = {38816808},
issn = {1471-2229},
support = {32170556//National Natural Science Foundation of China/ ; the Hundred-Talent Program//Zhejiang University/ ; },
mesh = {*Brassica napus/genetics/metabolism ; *Multigene Family ; *Phylogeny ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Genes, Plant ; RNA Editing ; Gene Expression Profiling ; Chloroplasts/genetics/metabolism ; },
abstract = {BACKGROUND: RNA editing in chloroplast and mitochondrion transcripts of plants is an important type of post-transcriptional RNA modification in which members of the multiple organellar RNA editing factor gene family (MORF) play a crucial role. However, a systematic identification and characterization of MORF members in Brassica napus is still lacking.<br><br>RESULTS: In this study, a total of 43 MORF genes were identified from the genome of the Brassica napus cultivar "Zhongshuang 11". The Brassica napus MORF (BnMORF) family members were divided into three groups through phylogenetic analysis. BnMORF genes distributed on 14 chromosomes and expanded due to segmental duplication and whole genome duplication repetitions. The majority of BnMORF proteins were predicted to be localized to mitochondria and chloroplasts. The promoter cis-regulatory element analysis, spatial-temporal expression profiling, and co-expression network of BnMORF genes indicated the involvement of BnMORF genes in stress and phytohormone responses, as well as growth and development.<br><br>CONCLUSION: This study provides a comprehensive analysis of BnMORF genes and lays a foundation for further exploring their physiological functions in Brassica napus.},
}
@article {pmid38827288,
year = {2024},
author = {Liu, Y and Fu, X and Wang, Y and Liu, J and Liu, Y and Li, C and Dong, J},
title = {Exploring Barbronia species diversity and phylogenetic relationship within Suborder Erpobdelliformes (Clitellata: Annelida).},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17480},
pmid = {38827288},
issn = {2167-8359},
mesh = {Animals ; *Phylogeny ; Genome, Mitochondrial/genetics ; Leeches/genetics/classification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 28S/genetics ; },
abstract = {BACKGROUND: Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.<br><br>METHODS: Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.<br><br>RESULTS: The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.},
}
@article {pmid38835243,
year = {2024},
author = {Zwahlen, SM and Hayward, JA and Maguire, CS and Qin, AR and van Dooren, GG},
title = {A myzozoan-specific protein is an essential membrane-anchoring component of the succinate dehydrogenase complex in Toxoplasma parasites.},
journal = {Open biology},
volume = {14},
number = {6},
pages = {230463},
pmid = {38835243},
issn = {2046-2441},
support = {//National Health and Medical Research Council/ ; },
mesh = {*Toxoplasma/metabolism/genetics/enzymology ; *Succinate Dehydrogenase/metabolism/genetics ; *Protozoan Proteins/metabolism/genetics/chemistry ; Humans ; Mitochondrial Proteins/metabolism/genetics ; Mitochondria/metabolism ; Phylogeny ; Animals ; },
abstract = {Succinate dehydrogenase (SDH) is a protein complex that functions in the tricarboxylic acid cycle and the electron transport chain of mitochondria. In most eukaryotes, SDH is highly conserved and comprises the following four subunits: SdhA and SdhB form the catalytic core of the complex, while SdhC and SdhD anchor the complex in the membrane. Toxoplasma gondii is an apicomplexan parasite that infects one-third of humans worldwide. The genome of T. gondii encodes homologues of the catalytic subunits SdhA and SdhB, although the physiological role of the SDH complex in the parasite and the identity of the membrane-anchoring subunits are poorly understood. Here, we show that the SDH complex contributes to optimal proliferation and O2 consumption in the disease-causing tachyzoite stage of the T. gondii life cycle. We characterize a small membrane-bound subunit of the SDH complex called mitochondrial protein ookinete developmental defect (MPODD), which is conserved among myzozoans, a phylogenetic grouping that incorporates apicomplexan parasites and their closest free-living relatives. We demonstrate that TgMPODD is essential for SDH activity and plays a key role in attaching the TgSdhA and TgSdhB proteins to the membrane anchor of the complex. Our findings highlight a unique and important feature of mitochondrial energy metabolism in apicomplexan parasites and their relatives.},
}
@article {pmid38851187,
year = {2024},
author = {Árnadóttir, ER and Moore, KHS and Guðmundsdóttir, VB and Ebenesersdóttir, SS and Guity, K and Jónsson, H and Stefánsson, K and Helgason, A},
title = {The rate and nature of mitochondrial DNA mutations in human pedigrees.},
journal = {Cell},
volume = {187},
number = {15},
pages = {3904-3918.e8},
doi = {10.1016/j.cell.2024.05.022},
pmid = {38851187},
issn = {1097-4172},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Pedigree ; Female ; Iceland ; Male ; Mutation ; Mutation Rate ; },
abstract = {We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.},
}
@article {pmid38892163,
year = {2024},
author = {Hong, YH and Yuan, YN and Li, K and Storey, KB and Zhang, JY and Zhang, SS and Yu, DN},
title = {Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892163},
issn = {1422-0067},
support = {31801963//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Genome, Mitochondrial ; *Anura/genetics/physiology ; *Phylogeny ; Cold-Shock Response/genetics ; Cold Temperature ; Adaptation, Physiological/genetics ; Gene Expression Regulation ; },
abstract = {Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.},
}
@article {pmid38908469,
year = {2024},
author = {Lu, H and Liu, C and Yang, C and He, Z and Wang, L and Song, L},
title = {Genome-wide identification of the HSP70 genes in Pacific oyster Magallana gigas and their response to heat stress.},
journal = {Cell stress &amp; chaperones},
volume = {29},
number = {4},
pages = {589-602},
pmid = {38908469},
issn = {1466-1268},
mesh = {Animals ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; *Heat-Shock Response/genetics ; Phylogeny ; Ostreidae/genetics/metabolism ; Crassostrea/genetics/metabolism ; Multigene Family ; Genome ; },
abstract = {Heat shock protein 70 (HSP70), the most prominent and well-characterized stress protein in animals, plays an important role in assisting animals in responding to various adverse conditions. In the present study, a total of 113 HSP70 gene family members were identified in the updated genome of Magallana gigas (designated MgHSP70) (previously known as Crassostrea gigas). There were 75, 12, 11, and 8 HSP70s located in the cytoplasm, nucleus, mitochondria, and endoplasmic reticulum, respectively, and 7 HSP70s were located in both the nucleus and cytoplasm. Among 113 MgHSP70 genes, 107 were unevenly distributed in 8 chromosomes of M. gigas with the greatest number in chromosome 07 (61 genes, 57.01%). The MgHSP70 gene family members were mainly assigned into five clusters, among which the HSPa12 subfamily underwent lineage-specific expansion, consisting of 89 members. A total of 68 MgHSP70 genes (60.18%) were tandemly duplicated and formed 30 gene pairs, among which 14 gene pairs were under strong positive selection. In general, the expression of MgHSP70s was tissue-specific, with the highest expression in labial palp and gill and the lowest expression in adductor muscle and hemocytes. There were 35, 31, and 47 significantly upregulated genes at 6, 12, and 24 h after heat shock treatment (28 °C), respectively. The expression patterns of different tandemly duplicated genes exhibited distinct characteristics after shock treatment, indicating that these genes may have different functions. Nevertheless, genes within the same tandemly duplicated group exhibit similar expression patterns. Most of the tandemly duplicated HSP70 gene pairs showed the highest expression levels at 24 h. This study provides a comprehensive description of the MgHSP70 gene family in M. gigas and offers valuable insights into the functions of HSP70 in the mollusc adaptation of oysters to environmental stress.},
}
@article {pmid38944824,
year = {2024},
author = {Sepúlveda-Espinoza, F and Cofré-Serrano, A and Veloso-Valeria, T and Quesada-Calderon, S and Guillemin, ML},
title = {Characterization of the organellar genomes of Mazzaella laminarioides and Mazzaella membranacea (Gigartinaceae, Rhodophyta).},
journal = {Journal of phycology},
volume = {60},
number = {4},
pages = {797-805},
doi = {10.1111/jpy.13478},
pmid = {38944824},
issn = {1529-8817},
support = {15150003//Fondo de Financiamiento de Centros de Investigaci&#xf3;n en &#xc1;reas Prioritarias/ ; NCN2021-033//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1221477//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3210788//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {*Rhodophyta/genetics/classification ; *Genome, Mitochondrial ; *Genome, Chloroplast ; Phylogeny ; Chile ; },
abstract = {Mazzaella, a genus with no genomic resources available, has extensive distribution in the cold waters of the Pacific, where they represent ecologically and economically important species. In this study, we aimed to sequence, assemble, and annotate the complete mitochondrial and chloroplast genomes from two Mazzaella spp. and characterize the intraspecific variation among them. We report for the first time seven whole organellar genomes (mitochondria: OR915856, OR947465, OR947466, OR947467, OR947468, OR947469, OR947470; chloroplast: OR881974, OR909680, OR909681, OR909682, OR909683, OR909684, OR909685) obtained through high-throughput sequencing for six M. laminarioides sampled from three Chilean regions and one M. membranacea. Sequenced Mazzaella mitogenomes have identical gene number, gene order, and genome structure. The same results were observed for assembled plastomes. A total of 52 genes were identified in mitogenomes, and a total of 235 genes were identified in plastomes. Although the M. membranacea plastome included a full-length pbsA gene, in all M. laminarioides samples, the pbsA gene was split in three open reading frames (ORFs). Within M. laminarioides, we observed important plastome lineage-specific variations, such as the pseudogenization of the two hypothetical protein-coding genes, ycf23 and ycf45. Nonsense mutations in the ycf23 and ycf45 genes were only detected in the northern lineage. These results are consistent with phylogenetic reconstructions and divergence time estimation using concatenated coding sequences that not only support the monophyly of M. laminarioides but also underscore that the three M. laminarioides lineages are in an advanced stage of divergence. These new results open the question of the existence of still undisclosed species in M. laminarioides.},
}
@article {pmid38970720,
year = {2024},
author = {Shannan, PZT and Suganya, SG and Ramesh, M and Jemima, EA},
title = {Molecular based identification and phylogenetic relationship of the leech Hirudinaria manillensis from India by using mitochondrial cytochrome c oxidase subunit I gene.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {787},
pmid = {38970720},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; *Electron Transport Complex IV/genetics ; India ; *Leeches/genetics/enzymology/classification ; Mitochondria/genetics/enzymology ; *Phylogeny ; Sequence Analysis, DNA/methods ; Cyclooxygenase 1 ; },
abstract = {BACKGROUND: A molecular approach for the identification of unknown species by the using mitochondrial cox1 gene is an effective and reliable as compared with morphological-based identification. Hirudinaria manillensis referred to as Asian Buffalo Leech, is found in South Asia and traditionally used as medicine owing to its medicinal properties.<br><br>METHODS AND RESULTS: The study aimed to isolate and identify the leech species using cox1 gene sequencing and their phylogenetic relationships. The nucleotide sequences of cytochrome c oxidase subunit I (cox1) mitochondrial genes were analyzed for species identification and the phylogenetic relationship of crucial therapeutic leech Hirudinaria manillensis. The isolated DNA from the leech sample was amplified with cox1 gene-specific primers. BLAST results with the H. manillensis sequence showed 89.24% homology with H. manillensis and phylogenetic tree analysis revealed the genetic relationship with other GenBank submitted sequences.<br><br>CONCLUSION: The present study concluded that the cox1 gene could be an effective way to identify the leech H. manillensis and provided sufficient phylogenetic information to distinguish H. manillensis indicating a significant mtDNA-based approach to species identification.},
}
@article {pmid38980999,
year = {2024},
author = {Gammuto, L and Serra, V and Petroni, G and Todaro, MA},
title = {Molecular phylogenetic position and description of a new genus and species of freshwater Chaetonotidae (Gastrotricha: Chaetonotida: Paucitubulatina), and the annotation of its mitochondrial genome.},
journal = {Invertebrate systematics},
volume = {38},
number = {},
pages = {},
doi = {10.1071/IS23059},
pmid = {38980999},
issn = {1447-2600},
mesh = {*Phylogeny ; *Genome, Mitochondrial/genetics ; Animals ; Species Specificity ; Fresh Water ; },
abstract = {Chaetonotidae is the most diversified family of the entire phylum Gastrotricha; it comprises ~430 species distributed across 16 genera. The current classification, established mainly on morphological traits, has been challenged in recent years by phylogenetic studies, indicating that the cuticular ornamentations used to discriminate among species may be misleading when used to identify groupings, which has been the practice until now. Therefore, a consensus is developing toward implementing novel approaches to better define species identity and affiliation at a higher taxonomic ranking. Using an integrative morphological and molecular approach, including annotation of the mitogenome, we report on some freshwater gastrotrichs characterised by a mixture of two types of cuticular scales diagnostic of the genera Aspidiophorus and Heterolepidoderma . Our specimens' overall anatomical characteristics find no correspondence in the taxa of these two genera, calling for their affiliation to a new species. Phylogenetic analyses based on the sequence of the ribosomal RNA genes of 96 taxa consistently found the new species unrelated to Aspidiophorus or Heterolepidoderma but allied with Chaetonotus aff. subtilis, as a subset of a larger clade, including mostly planktonic species. Morphological uniqueness and position along the non-monophyletic Chaetonotidae branch advocate erecting a new genus to accommodate the current specimens; consequently, the name Litigonotus ghinii gen. nov., sp. nov. is proposed. The complete mitochondrial genome of the new taxon resulted in a single circular molecule 14,384 bp long, including 13 protein-coding genes, 17 tRNA genes and 2 rRNAs genes, showing a perfect synteny and collinearity with the only other gastrotrich mitogenome available, a possible hint of a high level of conservation in the mitochondria of Chaetonotidae. ZooBank: urn:lsid:zoobank.org:pub:9803F659-306F-4EC3-A73B-8C704069F24A.},
}
@article {pmid39039280,
year = {2024},
author = {An, J and Nam, CH and Kim, R and Lee, Y and Won, H and Park, S and Lee, WH and Park, H and Yoon, CJ and An, Y and Kim, JH and Jun, JK and Bae, JM and Shin, EC and Kim, B and Cha, YJ and Kwon, HW and Oh, JW and Park, JY and Kim, MJ and Ju, YS},
title = {Mitochondrial DNA mosaicism in normal human somatic cells.},
journal = {Nature genetics},
volume = {56},
number = {8},
pages = {1665-1677},
pmid = {39039280},
issn = {1546-1718},
mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Mosaicism ; *Mutation ; Heteroplasmy/genetics ; Mutation Rate ; Mitochondria/genetics ; Genome, Mitochondrial ; DNA Replication/genetics ; Female ; Male ; },
abstract = {Somatic cells accumulate genomic alterations with age; however, our understanding of mitochondrial DNA (mtDNA) mosaicism remains limited. Here we investigated the genomes of 2,096 clones derived from three cell types across 31 donors, identifying 6,451 mtDNA variants with heteroplasmy levels of ≳0.3%. While the majority of these variants were unique to individual clones, suggesting stochastic acquisition with age, 409 variants (6%) were shared across multiple embryonic lineages, indicating their origin from heteroplasmy in fertilized eggs. The mutational spectrum exhibited replication-strand bias, implicating mtDNA replication as a major mutational process. We evaluated the mtDNA mutation rate (5.0 × 10[-8] per base pair) and a turnover frequency of 10-20 per year, which are fundamental components shaping the landscape of mtDNA mosaicism over a lifetime. The expansion of mtDNA-truncating mutations toward homoplasmy was substantially suppressed. Our findings provide comprehensive insights into the origins, dynamics and functional consequences of mtDNA mosaicism in human somatic cells.},
}
@article {pmid39062606,
year = {2024},
author = {Li, S and Jiao, B and Wang, J and Zhao, P and Dong, F and Yang, F and Ma, C and Guo, P and Zhou, S},
title = {Identification of Wheat Glutamate Synthetase Gene Family and Expression Analysis under Nitrogen Stress.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062606},
issn = {2073-4425},
support = {2022KJCXZX-SSS-4//HAAFS Agriculture Science and Technology Innovation Project/ ; },
mesh = {*Triticum/genetics/metabolism ; *Nitrogen/metabolism ; *Gene Expression Regulation, Plant ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; Glutamate Synthase/genetics/metabolism ; Multigene Family ; Promoter Regions, Genetic ; Plant Roots/genetics/metabolism/growth &amp; development ; Seedlings/genetics/growth &amp; development/metabolism ; Plant Leaves/genetics/metabolism ; Phylogeny ; },
abstract = {Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE).},
}
@article {pmid39062690,
year = {2024},
author = {Zhang, Y and Peng, Y and Zhang, H and Gao, Q and Song, F and Cui, X and Mo, F},
title = {Genome-Wide Identification of APX Gene Family in Citrus maxima and Expression Analysis at Different Postharvest Preservation Times.},
journal = {Genes},
volume = {15},
number = {7},
pages = {},
pmid = {39062690},
issn = {2073-4425},
support = {202427060300564//Innovation and Entrepreneurship Training Program for College Students/ ; },
mesh = {*Citrus/genetics ; *Gene Expression Regulation, Plant ; *Ascorbate Peroxidases/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Multigene Family ; *Phylogeny ; Genome, Plant ; Fruit/genetics/metabolism ; Gene Expression Profiling/methods ; },
abstract = {Ascorbate peroxidase (APX) is a crucial enzyme involved in cellular antioxidant defense and plays a pivotal role in modulating reactive oxygen species (ROS) levels under various environmental stresses in plants. This study utilized bioinformatics methods to identify and analyze the APX gene family of pomelo, while quantitative real-time PCR (qRT-PCR) was employed to validate and analyze the expression of CmAPXs at different stages of fruit postharvest. This study identified 96 members of the CmAPX family in the entire pomelo genome, with uneven distribution across nine chromosomes and occurrences of gene fragment replication. The subcellular localization includes peroxisome, cytoplasm, chloroplasts, and mitochondria. The CmAPX family exhibits a similar gene structure, predominantly consisting of two exons. An analysis of the upstream promoter regions revealed a significant presence of cis-acting elements associated with light (Box 4, G-Box), hormones (ABRE, TCA-element), and stress-related (MBS, LTR, ARE) responses. Phylogenetic and collinearity analyses revealed that the CmAPX gene family can be classified into three subclasses, with seven collinear gene pairs. Furthermore, CmAPXs are closely related to citrus, pomelo, and lemon, followed by Arabidopsis, and exhibit low homology with rice. Additionally, the transcriptomic heat map and qPCR results revealed that the expression levels of CmAPX57, CmAPX34, CmAPX50, CmAPX4, CmAPX5, and CmAPX81 were positively correlated with granulation degree, indicating the activation of the endogenous stress resistance system in pomelo cells by these genes, thereby conferring resistance to ROS. This finding is consistent with the results of GO enrichment analysis. Furthermore, 38 miRNAs were identified as potential regulators targeting the CmAPX family for post-transcriptional regulation. Thus, this study has preliminarily characterized members of the APX gene family in pomelo and provided valuable insights for further research on their antioxidant function and molecular mechanism.},
}
@article {pmid39122691,
year = {2024},
author = {Williams, SK and Jerlström Hultqvist, J and Eglit, Y and Salas-Leiva, DE and Curtis, B and Orr, RJS and Stairs, CW and Atalay, TN and MacMillan, N and Simpson, AGB and Roger, AJ},
title = {Extreme mitochondrial reduction in a novel group of free-living metamonads.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6805},
pmid = {39122691},
issn = {2041-1723},
support = {FRN-142349//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Sant&#xe9; du Canada)/ ; },
mesh = {*Mitochondria/metabolism/genetics ; *Phylogeny ; *Proteome/metabolism/genetics ; Transcriptome ; Eukaryota/genetics/metabolism/classification ; Gene Transfer, Horizontal ; Iron-Sulfur Proteins/metabolism/genetics ; },
abstract = {Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.},
}
@article {pmid39127314,
year = {2024},
author = {Zhang, L and Liu, ZS and Dong, YZ and He, CF and Zhang, DD and Jiang, GZ and Liu, WB and Li, XF},
title = {Molecular cloning and functional characterization of mitochondrial RNA splicing 2 in fish Megalobrama amblycephala, and its potential roles in magnesium homeostasis and mitochondrial function.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {297},
number = {},
pages = {111727},
doi = {10.1016/j.cbpa.2024.111727},
pmid = {39127314},
issn = {1531-4332},
mesh = {Animals ; *Magnesium/metabolism ; *Homeostasis ; *Cloning, Molecular ; *Mitochondria/metabolism/genetics ; *Amino Acid Sequence ; Fish Proteins/genetics/metabolism ; Cyprinidae/genetics/metabolism ; Phylogeny ; Base Sequence ; RNA Splicing ; },
abstract = {Mitochondrial function can be regulated by ion channels. Mitochondrial RNA splicing 2 (Mrs2) is a magnesium ion (Mg[2+]) channel located in the inner mitochondrial membrane, thereby mediating the Mg[2+] influx into the mitochondrial matrix. However, its potential role in regulating the Mg homeostasis and mitochondrial function in aquatic species is still unclear. This study molecularly characterizes the gene encoding Mrs2 in fish M. amblycephala with its functions in maintaining the Mg homeostasis and mitochondrial function verified. The mrs2 gene is 2133 bp long incorporating a 1269 bp open reading frame, which encodes 422 amino acids. The Mrs2 protein includes two transmembrane domains and a conserved tripeptide Gly-Met-Asn, and has a high homology (65.92-97.64%) with those of most vertebrates. The transcript of mrs2 was relatively high in the white muscle, liver and kidney. The inhibition of mrs2 reduces the expressions of Mg[2+] influx/efflux-related proteins, mitochondrial Mg content, and the activities of mitochondrial complex I and V in hepatocytes. However, the over-expression of mrs2 increases the expressions of Mg[2+] influx/efflux-related proteins, mitochondrial Mg content, and the complex V activity, but decreases the activities of mitochondrial complex III and IV and citrate synthase in hepatocytes. Collectively, Mrs2 is highly conserved among different species, and is prerequisite for maintaining Mg homeostasis and mitochondrial function in fish.},
}
@article {pmid39152292,
year = {2024},
author = {Zhang, Y and Liu, S and Mostert, D and Yu, H and Zhuo, M and Li, G and Zuo, C and Haridas, S and Webster, K and Li, M and Grigoriev, IV and Yi, G and Viljoen, A and Li, C and Ma, LJ},
title = {Virulence of banana wilt-causing fungal pathogen Fusarium oxysporum tropical race 4 is mediated by nitric oxide biosynthesis and accessory genes.},
journal = {Nature microbiology},
volume = {9},
number = {9},
pages = {2232-2243},
pmid = {39152292},
issn = {2058-5276},
support = {IOS-165241//National Science Foundation (NSF)/ ; MASR-2009-04374//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; MAS00532//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; MAS00496//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; R01EY030150//U.S. Department of Health &amp; Human Services | NIH | National Eye Institute (NEI)/ ; },
mesh = {*Fusarium/genetics/pathogenicity/metabolism ; *Musa/microbiology ; *Plant Diseases/microbiology ; *Nitric Oxide/metabolism ; Virulence/genetics ; Virulence Factors/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Phylogeny ; },
abstract = {Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is one of the most damaging plant diseases known. Foc race 1 (R1) decimated the Gros Michel-based banana (Musa acuminata) trade, and now Foc tropical race 4 (TR4) threatens global production of its replacement, the Cavendish banana. Here population genomics revealed that all Cavendish banana-infecting Foc race 4 strains share an evolutionary origin distinct from that of R1 strains. Although TR4 lacks accessory chromosomes, it contains accessory genes at the ends of some core chromosomes that are enriched for virulence and mitochondria-related functions. Meta-transcriptomics revealed the unique induction of the entire mitochondrion-localized nitric oxide (NO) biosynthesis pathway upon TR4 infection. Empirically, we confirmed the unique induction of a NO burst in TR4, suggesting that nitrosative pressure may contribute to virulence. Targeted mutagenesis demonstrated the functional importance of fungal NO production and the accessory gene SIX4 as virulence factors.},
}
@article {pmid39155336,
year = {2025},
author = {Prajapati, MR and Diksha, D and Thapa, P and Sharma, SK and Gupta, N and Baranwal, VK},
title = {Identification of a novel mitovirus in grapevine through high-throughput sequencing.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {28},
number = {5},
pages = {909-916},
pmid = {39155336},
issn = {1618-1905},
support = {Ag.Edn.F.No./27/01/NP/2022-HRD//Indian Council of Agricultural Research/ ; },
mesh = {*Vitis/virology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Open Reading Frames ; *RNA Viruses/genetics/classification/isolation &amp; purification ; RNA, Viral/genetics ; Plant Diseases/virology ; RNA-Dependent RNA Polymerase/genetics ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Viral Proteins/genetics ; },
abstract = {BACKGROUND: Transcriptome data from a plant sample frequently include numerous reads originating from RNA virus genomes that were concurrently isolated during RNA preparation. These high-throughput sequencing reads from the virus can be assembled to form a new sequence for the plant RNA genome.<br><br>METHODS AND RESULTS: Here, we identify putative novel&#xa0;mitovirus, grapevine mitovirus 1 (GMV1) through high-throughput sequencing (HTS) of grapevine rootstocks (Vitis spp.), and the identified virus was confirmed using virus-specific primers in RT-PCR assay. The genomic RNA of GMV1 encodes complete open reading frame (ORF) of 2,496 nucleotides (nts) in length. RNA-dependent RNA polymerase (RdRp) encoded by the viral genome contained one RdRp conserved domain. BLASTx analysis of GMV1 genome showed sequence identity of 33.18-56.75% with the existing&#xa0;mitovirus sequences. Phylogenetic analysis based on genome sequences showed that&#xa0;GMV1 clustered in a distinct clade to other mitoviruses.<br><br>CONCLUSION: Grapevine mitovirus 1 represents a newly discovered species within the Unuamitovirus genus of the Mitoviridae family, targeting fungal mitochondria. While the majority of recognized mitoviruses typically lack a functional RdRp as per the plant mitochondrial genetic code,&#xa0;GMV1 encodes a complete RdRp in accordance with both fungal and plant mitochondrial genetic codes.},
}
@article {pmid39202396,
year = {2024},
author = {Wu, H and Qi, S and Fan, S and Li, H and Zhang, Y and Zhang, Y and Xu, Q and Chen, G},
title = {Analysis of the Mitochondrial COI Gene and Genetic Diversity of Endangered Goose Breeds.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
pmid = {39202396},
issn = {2073-4425},
support = {[2021YFD1200302]//the National Key Research and Development Program of China/ ; [JBGS [2021]023]//the Jiangsu Provincial Seed Industry Revitalization Announcement Leading Project/ ; },
mesh = {Animals ; *Geese/genetics ; *Endangered Species ; *Phylogeny ; *Haplotypes ; *Electron Transport Complex IV/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Breeding ; China ; Mitochondria/genetics ; },
abstract = {The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were -0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies.},
}
@article {pmid39226300,
year = {2024},
author = {de Ree, V and Nath, TC and Barua, P and Harbecke, D and Lee, D and Rödelsperger, C and Streit, A},
title = {Genomic analysis of Strongyloides stercoralis and Strongyloides fuelleborni in Bangladesh.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {9},
pages = {e0012440},
pmid = {39226300},
issn = {1935-2735},
support = {//Max-Planck-Society/ ; },
mesh = {Animals ; Bangladesh/epidemiology ; *Strongyloidiasis/epidemiology/veterinary/parasitology ; Humans ; Dogs ; *Strongyloides stercoralis/genetics/isolation &amp; purification/classification ; *Phylogeny ; *Strongyloides/genetics/isolation &amp; purification/classification ; Dog Diseases/parasitology/epidemiology ; Genomics ; },
abstract = {BACKGROUND: About 600 million people are estimated to be infected with Strongyloides stercoralis, the species that causes most of the human strongyloidiasis cases. S. stercoralis can also infect non-human primates (NHPs), dogs and cats, rendering these animals putative sources for zoonotic human S. stercoralis infection. S. fuelleborni is normally found in old world NHPs but occasionally also infects humans, mainly in Africa. Dogs in southeast Asia carry at least two types of Strongyloides, only one of which appears to be shared with humans ("dog only" and "human and dog" types). For S. stercoralis with molecular taxonomic information, there is a strong sampling bias towards southeast and east Asia and Australia.<br><br>In order to extend the geographic range of sampling, we collected human and dog derived Strongyloides spp. and hookworms from two locations in Bangladesh and subjected them to molecular taxonomic and genomic analysis based on nuclear and mitochondrial sequences. All hookworms found were Necator americanus. Contrary to earlier studies in Asia, we noticed a rather high incidence of S. fuelleborni in humans. Also in this study, we found the two types of S. stercoralis and no indication for genetic isolation from the southeast Asian populations. However, we found one genomically "dog only" type S. stercoralis in a human sample and we found two worms in a dog sample that had a nuclear genome of the "dog only" but a mitochondrial genome of the "human and dog" type.<br><br>CONCLUSIONS/SIGNIFICANCE: S. fuelleborni may play a more prominent role as a human parasite in certain places in Asia than previously thought. The introgression of a mitochondria haplotype into the "dog only" population suggests that rare interbreeding between the two S. stercoralis types does occur and that exchange of genetic properties, for example a drug resistance, between the two types is conceivable.},
}
@article {pmid39226612,
year = {2024},
author = {Forbes, K and Barrera, M and Nielsen-Roine, K and Hersh, E and Janes, J and Harrower, W and Gorrell, J},
title = {Stabilizing selection and mitochondrial heteroplasmy in the Canada lynx (Lynx canadensis).},
journal = {Genome},
volume = {67},
number = {12},
pages = {493-502},
doi = {10.1139/gen-2023-0094},
pmid = {39226612},
issn = {1480-3321},
mesh = {*Lynx/genetics ; Animals ; *Haplotypes ; *DNA, Mitochondrial/genetics ; Heteroplasmy/genetics ; Selection, Genetic ; Polymorphism, Single Nucleotide ; Mitochondria/genetics ; Genome, Mitochondrial ; Phylogeny ; Canada ; },
abstract = {Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change.},
}
@article {pmid39231786,
year = {2024},
author = {Duan, X and Shi, X and Zhang, P and Du, X and Chen, S and Zhang, L and Li, H and Zhang, Y and Wang, J and Ding, Y and Liu, S},
title = {Identification of concurrent infection with Jaagsiekte sheep retrovirus and maedi-visna virus in China.},
journal = {Journal of veterinary science},
volume = {25},
number = {5},
pages = {e61},
pmid = {39231786},
issn = {1976-555X},
support = {2021ZD0010//Science and Technology Major Project of Inner Mongolia/China ; 20151031//Grassland Talents Innovative Team Project of Inner Mongolia/China ; BR22-13-08//Innovation Team Project of Cattle and Sheep Disease Prevention and Development Engineering of Inner Mongolia/China ; NMGIRT2412//Veterinary Basic and Cattle and Sheep Disease Prevention and Control Technology Research and Innovation Team Project/China ; B20231072Z//Postgraduate Research Innovation Funding Program/China ; 32072819/NNSFC/National Natural Science Foundation of China/China ; 32360863/NNSFC/National Natural Science Foundation of China/China ; },
mesh = {Animals ; *Jaagsiekte sheep retrovirus ; Sheep ; China ; *Pulmonary Adenomatosis, Ovine/virology/pathology ; *Visna-maedi virus ; Male ; Coinfection/veterinary/virology ; Phylogeny ; Lung/virology/pathology ; Sheep Diseases/virology/pathology ; Visna/virology/pathology ; },
abstract = {IMPORTANCE: Ovine pulmonary adenomatosis (OPA) and maedi-visna disease (MVD) are chronic and progressive infectious diseases in sheep caused by Jaagsiekte sheep retrovirus (JSRV) and maedi-visna virus (MVV), respectively.<br><br>OBJECTIVE: To investigate the pathological changes and conduct viral gene analysis of OPA and MVD co-occurrence in Inner Mongolia, China.<br><br>METHODS: Using gross pathology, histopathology, immunohistochemistry, ultrastructural pathology, PCR, and sequence analysis, we investigated the concurrent infection of JSRV and MVV in 319 Dorper rams slaughtered in a private slaughterhouse in Inner Mongolia, in 2022.<br><br>RESULTS: Of the 319 rams included, 3 showed concurrent JSRV and MVV infection. Gross lung pathology showed diffuse enlargement, consolidation, and greyish-white miliary nodules on the lung surface; the trachea was filled with a white foamy fluid; hilar and mediastinal lymph nodes were significantly enlarged. Histopathology results revealed typical OPA and MVD lesions in the lung tissue. Immunohistochemical results were positive for JSRV envelope protein (Env) in the tumor cells and MVV CA in alveolar macrophages. Transmission electron microscopy showed several virions and autophagosomes in the lung tissue, severely damaged mitochondria, and the induced mitophagy. Nucleotide sequences obtained for JSRV env and MVV gag showed the highest homology with the Inner Mongolian strains of JSRV env (JQ837489) and MVV gag (MW248464).<br><br>CONCLUSIONS AND RELEVANCE: Our study confirmed that OPA and MVD co-occurrence and identified the pathological changes in Inner Mongolia, China, thereby providing references for the identification of concurrent JSRV and MVV infections.},
}
@article {pmid39303860,
year = {2024},
author = {Yong, Y and Hu, S and Zhong, M and Wen, Y and Zhou, Y and Ma, R and Jiang, X and Zhang, Q},
title = {Horizontal gene transfer from chloroplast to mitochondria of seagrasses in the yellow-Bohai seas.},
journal = {Genomics},
volume = {116},
number = {5},
pages = {110940},
doi = {10.1016/j.ygeno.2024.110940},
pmid = {39303860},
issn = {1089-8646},
mesh = {*Gene Transfer, Horizontal ; Genome, Mitochondrial ; Chloroplasts/genetics ; Genome, Chloroplast ; Alismatales/genetics/metabolism ; Phylogeny ; Mitochondria/genetics/metabolism ; },
abstract = {Seagrasses are ideal for studying plant adaptation to marine environments. In this study, the mitochondrial (mt) and chloroplast (cp) genomes of Ruppia sinensis were sequenced. The results showed an extensive gene loss in seagrasses, including a complete loss of cp-rpl19 genes in Zosteraceae, most cp-ndh genes in Hydrocharitaceae, and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in Phyllospadix iwatensis. Notably, most ribosomal protein genes were lost in the mt and cp genomes. The deleted cp genes were not transferred to the mt genomes through horizontal gene transfer. Additionally, a significant DNA transfer between seagrass organelles was found, with the mt genomes of Zostera containing numerous sequences from the cp genome. Rearrangement analyses revealed an unreported inversion of the cp genome in R. sinensis. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified.},
}
@article {pmid39307735,
year = {2024},
author = {Zhang, YX and Fan, X and Zhang, M and Chen, YC and Zhao, YY and Jiao, HH and Zhang, G and Yuan, Y},
title = {[Influence of Tis108 on GA content and expression of key enzyme GeCYP714A1 involved in GA deactivation of Gastrodia elata].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {15},
pages = {4007-4014},
doi = {10.19540/j.cnki.cjcmm.20240517.101},
pmid = {39307735},
issn = {1001-5302},
mesh = {*Gastrodia/genetics/chemistry ; *Gibberellins/pharmacology/metabolism ; *Plant Proteins/genetics/metabolism/chemistry ; Gene Expression Regulation, Plant/drug effects ; Lactones/pharmacology ; Phylogeny ; Amino Acid Sequence ; },
abstract = {To investigate the influence of the strigolactone inhibitor Tis108 on the growth of Gastrodia elata, this study treated G. elata tuber with Tis108 solution of 10 μmol·L~(-1) and measured the content of endogenous hormone gibberellin(GA) in the tuber. By using reverse transcription-polymerase chain reaction(RT-PCR) technology, the key enzyme GeCYP714A1 gene involved in GA deactivation was cloned. Bioinformatics analysis on the GeCYP714A1 gene was carried out by using ExPASy, SWISS-MODEL, MEGA, etc., and its expression levels in different parts of G. elata were determined. The results showed that after Tis108 treatment, GA content in G. elata tuber was significantly increased, and the transcription level of the GeCYP714A1 gene was significantly decreased. The full length of the coding region of the GeCYP714A1 gene is 1 173 bp, encoding 390 amino acids. The protein has a molecular weight of 44.85 kDa, a theoretical isoelectric point of 9.83, an instability index of 49.20, an aliphatic index of 89.03, and a grand average of hydropathicity of-0.235, classifying it as an unstable, basic, hydrophilic protein, and the GeCYP714A1 protein was localized in the mitochondria, lacking a signal peptide and a transmembrane structure. Phylogenetic tree analysis revealed that GeCYP714A1 was most closely related to the DcCYP714C2(PKU78454.1) protein from Dendrobium candidum, with a sequence identity of 67.25%. The qRT-PCR analysis of the expression patterns of the GeCYP714A1 gene indicated that GeCYP714A1 had the highest transcription level in G. elata tuber, followed by stem and inflorescence. The study represented that Tis108 inhibited the transcription level of GeCYP714A1 involved in GA deactivation in G. elata tuber, thereby increasing the accumulation of GA and affecting the growth of G. elata tuber. These results provided a basis for further studies of strigolactone regulation of GA signal and tuber development in G. elata.},
}
@article {pmid39331563,
year = {2024},
author = {Kubota, K and Oishi, M and Taniguchi, E and Akazawa, A and Matsui, K and Kitazaki, K and Toyoda, A and Toh, H and Matsuhira, H and Kuroda, Y and Kubo, T},
title = {Mitochondrial phylogeny and distribution of cytoplasmic male sterility-associated genes in Beta vulgaris.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0308551},
pmid = {39331563},
issn = {1932-6203},
mesh = {*Beta vulgaris/genetics ; *Phylogeny ; *Plant Infertility/genetics ; Mitochondria/genetics ; Polymorphism, Single Nucleotide ; Genes, Plant ; Genes, Mitochondrial ; Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; },
abstract = {Cytoplasmic male sterility (CMS) is a mitochondrial-encoded trait that confers reproductive defects in males but not in females or any vegetative function. Why CMS is so often found in plants should be investigated from the viewpoint of mitochondrial phylogeny. Beta vulgaris, including the wild subspecies maritima and cultivated subspecies vulgaris (e.g., sugar beet), is known to be mitochondrially polymorphic, from which multiple CMS mitochondria have been found, but their evolutionary relationship has been obscure. We first refined the B. vulgaris reference mitochondrial genome to conduct a more accurate phylogenetic study. We identified mitochondrial single-nucleotide polymorphic sites from 600 B. vulgaris accessions. Principal component analysis, hierarchical clustering analysis, and creation of a phylogenetic tree consistently suggested that B. vulgaris mitochondria can be classified into several groups whose geographical distribution tends to be biased toward either the Atlantic or Mediterranean coasts. We examined the distribution of CMS-associated mitochondrial genes from Owen, E- and G-type CMS mitochondria. About one-third of cultivated beets had Owen-type CMS, which reflects the prevalence of using Owen-type CMS in hybrid breeding. Occurrence frequencies for each of the three CMS genes in wild beet were less than 4%. CMS genes were tightly associated with specific mitochondrial groups that are phylogenetically distinct, suggesting their independent origin. However, homologous sequences of the Owen type CMS gene occurred in several different mitochondrial groups, for which an intricate explanation is necessary. Whereas the origin of cultivated beet had been presumed to be Greece, we found an absence of Owen-type mitochondria in Greek accessions.},
}
@article {pmid39378918,
year = {2024},
author = {Wang, Z and Wang, R and Sang, Y and Wang, T and Su, Y and Liao, W},
title = {Comparative analysis of mitochondrial genomes of invasive weed Mikania micrantha and its indigenous congener Mikania cordata.},
journal = {International journal of biological macromolecules},
volume = {281},
number = {Pt 1},
pages = {136357},
doi = {10.1016/j.ijbiomac.2024.136357},
pmid = {39378918},
issn = {1879-0003},
mesh = {*Genome, Mitochondrial/genetics ; *Plant Weeds/classification/cytology/genetics ; *Mikania/classification/cytology/genetics ; *Introduced Species ; *Mitochondria/genetics ; Codon Usage ; RNA Editing ; Repetitive Sequences, Nucleic Acid ; Hydrophobic and Hydrophilic Interactions ; Amino Acids/chemistry/genetics/metabolism ; Synteny ; Phylogeny ; Chloroplasts/genetics ; },
abstract = {Mikania micrantha and Mikania cordata are two distinct species in China. The former is notorious as one of the top 100 worst invasive species, whereas the latter is an indigenous species harmless to native plants or the environment. They form an ideal congener pair for comparative studies aimed at deeply understanding the invasion mechanisms of the exotic weed. In this study, we have assembled and annotated the mitogenomes of both species using Illumina and PacBio sequencing data and compared their characteristic differences. The complete mitogenome of M. micrantha is a double-stranded DNA with a length of 336,564 bp, while the mitogenome of M. cordata exhibits a branching structure, consisting of two small circular molecules and six linear molecules, with a combined length totaling 335,444 bp. Compared to M. cordata, M. micrantha has less SSRs, tandem repeats, dispersed repeats, mitochondrial protein coding genes (PCGs). The two plants show similar codon usage patterns. This comparative study has revealed the structure and function of the mitogenomes of the two species and laid a solid foundation for investigating the effects of gene loss and duplication on the development of invasive traits in M. micrantha.},
}
@article {pmid39408807,
year = {2024},
author = {Wang, Y and Shi, Y and Li, H and Wang, S and Wang, A},
title = {Whole Genome Identification and Biochemical Characteristics of the Tilletia horrida Cytochrome P450 Gene Family.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
pmid = {39408807},
issn = {1422-0067},
support = {32001490//National Natural Science Foundation of China/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism ; Oryza/microbiology/genetics ; Multigene Family ; Phylogeny ; Fungal Proteins/genetics/metabolism ; Genome, Fungal ; Gene Expression Regulation, Fungal ; Basidiomycota/genetics/enzymology ; Plant Diseases/microbiology/genetics ; Promoter Regions, Genetic ; },
abstract = {Rice kernel smut caused by the biotrophic basidiomycete fungus Tilletia horrida causes significant yield losses in hybrid rice-growing areas around the world. Cytochrome P450 (CYP) enzyme is a membrane-bound heme-containing monooxygenase. In fungi, CYPs play a role in cellular metabolism, adaptation, pathogenicity, decomposition, and biotransformation of hazardous chemicals. In this study, we identified 20 CYP genes based on complete sequence analysis and functional annotation from the T. horrida JY-521 genome. The subcellular localization, conserved motifs, and structures of these 20 CYP genes were further predicted. The ThCYP genes exhibit differences in gene structures and protein motifs. Subcellular localization showed that they were located in the plasma membrane, cytoplasm, nucleus, mitochondria, and extracellular space, indicating that they had multiple functions. Some cis-regulatory elements related to stress response and plant hormones were found in the promoter regions of these genes. Protein-protein interaction (PPI) analysis showed that several ThCYP proteins interact with multiple proteins involved in the ergosterol pathway. Moreover, the expression of 20 CYP genes had different responses to different infection time points and underwent dynamic changes during T. horrida JY-521 infection, indicating that these genes were involved in the interaction with rice and their potential role in the pathogenic mechanism. These results provided valuable resources for elucidating the structure of T. horrida CYP family proteins and laid an important foundation for further research of their roles in the pathogenesis.},
}
@article {pmid39417543,
year = {2025},
author = {Tu, F and Qiao, Y and Zhao, W and Wu, T},
title = {Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {35},
number = {3-4},
pages = {75-83},
doi = {10.1080/24701394.2024.2416179},
pmid = {39417543},
issn = {2470-1408},
mesh = {Animals ; *Sciuridae/genetics/classification ; Phylogeny ; Genome, Mitochondrial ; *Mitochondrial Proteins/genetics ; *Selection, Genetic ; *Genes, Mitochondrial ; },
abstract = {Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.},
}
@article {pmid39457076,
year = {2024},
author = {Zhu, K and Zhang, Y and Shen, W and Yu, L and Li, D and Zhang, H and Miao, C and Ding, X and Jiang, Y},
title = {Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.).},
journal = {International journal of molecular sciences},
volume = {25},
number = {20},
pages = {},
pmid = {39457076},
issn = {1422-0067},
support = {22ZR1460500//The Natural Science Foundation of Shanghai/ ; [2022]022//The Excellent Team Program of the Shanghai Academy of Agricultural Sciences/ ; },
mesh = {*Cucumis sativus/genetics/enzymology ; *Stress, Physiological/genetics ; *Gene Expression Regulation, Plant ; *Phylogeny ; *Lactoylglutathione Lyase/genetics/metabolism ; *Multigene Family ; Thiolester Hydrolases/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Gene Expression Profiling ; Genome-Wide Association Study ; Genome, Plant ; Hydroxyacylglutathione Hydrolase ; },
abstract = {The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein-protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.},
}
@article {pmid39462818,
year = {2025},
author = {Arce, LF and Facelli Fernández, F and Giorello, N and Butti, M and Maldonado, LL and Arrabal, JP and Natalini, MB and Kowalewski, M and Pedrassani, D and Silveira Mascarenhas, C and da Silva Rappeti, JC and Zilli, F and Beldomenico, PM and Lia, V and Franchini, GR and Kamenetzky, L},
title = {Genetic diversity of Dioctophyme renale in Southern South America.},
journal = {Parasitology},
volume = {152},
number = {8},
pages = {776-786},
pmid = {39462818},
issn = {1469-8161},
mesh = {Animals ; Animals, Wild/parasitology ; Biomarkers ; *Carnivora/parasitology ; Cyclooxygenase 1/genetics ; *Dioctophymatoidea/genetics ; *Enoplida Infections/epidemiology/transmission/veterinary ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Phylogeography ; South America ; Male ; Female ; },
abstract = {Dioctophyme renale, the giant kidney worm, is a nematode related to Trichuris sp and is distributed worldwide. These parasites locate in the kidney of their definitive hosts (mainly belonging to the order Carnivora) and have an indirect life cycle with an annelid as the main intermediate host. Humans are rarely affected, but in those that are, 1 or both kidneys are destroyed. In South America, D. renale is widespread in riparian regions where changing climatic conditions, environmental degradation, and compromised sanitation are increasing the risk of distribution of this parasite, including humans. Here, we provide the descriptions of the genetic diversity of the parasite in the region by analysing 73 adult D. renale samples collected from domestic and wild carnivores. The most common hosts were (Canis lupus familiaris) and maned wolf (Chrysocyon brachyurus Fam. Canidae) among domestic and wild carnivores, respectively. This work shows the descriptions of the genetic diversity of this parasite complementing molecular methods and classical and probabilistic phylogeography. Our results strongly suggest that this parasite has been present on the continent long enough to develop local genetic variants. Also, the phylogenies show transmission between localities and bidirectional transmission between domestic and wild species. We now have new tools to understand the ecological dynamics of this parasite such as molecular markers to study its genetic diversity as well as for identification and reporting in cryptic cases.},
}
@article {pmid39465975,
year = {2024},
author = {Cheng, YK and Zhang, Y and Zhang, ZY and Cong, PK and Feng, JY and Zhang, R and Long, SR and Zhang, X and Wang, ZQ and Cui, J},
title = {Biological characteristics and functions of a novel glutamate dehydrogenase from Trichinella spiralis.},
journal = {Parasite (Paris, France)},
volume = {31},
number = {},
pages = {65},
pmid = {39465975},
issn = {1776-1042},
support = {82172300//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Glutamate Dehydrogenase/metabolism/genetics ; *Trichinella spiralis/enzymology/genetics/growth &amp; development ; Female ; Cloning, Molecular ; Larva/enzymology/growth &amp; development/genetics ; Amino Acid Sequence ; RNA Interference ; Phylogeny ; Male ; Helminth Proteins/genetics/metabolism ; Sequence Alignment ; },
abstract = {Glutamate dehydrogenase (GDH) plays an important role in the metabolism of organisms. Its high abundance in mitochondria in particular highlights its core role in cellular physiological processes. GDH catalyzes the mutual conversion between L-glutamic acid and α-ketoglutaric acids. At the same time, this transformation is accompanied by the oxidation-reduction of NAD(H) or NADP(H). This process not only helps to link amino acid metabolism with sugar metabolism, but also helps maintain the balance of intracellular pH and nitrogen homeostasis. In this study, a novel Trichinella spiralis glutamate dehydrogenase (TsGDH) was cloned, expressed and identified. The results revealed that TsGDH was expressed at various stages of development of the nematode T. spiralis, with higher expression levels in the adult worm stage, and was mainly localized in the cuticle, muscular layer, stichosome and female intrauterine embryos. After RNAi treatment, larval natural TsGDH enzyme activity was obviously reduced, and metabolism, molting, growth and reproduction were also significantly inhibited. The results indicate that TsGDH plays an important role in the development and survival of T. spiralis, and it may be a potential molecular target of anti-Trichinella vaccines and drugs.},
}
@article {pmid39495610,
year = {2024},
author = {Tian, X and Li, F and Lin, J and Xu, Y and Tian, K and Gu, L and Zhang, Y and Xu, JR and Wang, Q},
title = {Ancient duplications, multidimensional specializations, and defense role of hexokinases in wheat.},
journal = {The Plant journal : for cell and molecular biology},
volume = {120},
number = {6},
pages = {2456-2467},
doi = {10.1111/tpj.17122},
pmid = {39495610},
issn = {1365-313X},
support = {2022YFD1400100//National Key Research and Development Program of China/ ; 32072505//National Natural Science Foundation of China/ ; 32370212//National Natural Science Foundation of China/ ; },
mesh = {*Triticum/genetics/enzymology/immunology ; *Hexokinase/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Duplication ; *Phylogeny ; Gene Expression Regulation, Plant ; Plant Diseases/genetics/immunology/microbiology ; Mitochondria/genetics/enzymology/metabolism ; },
abstract = {Hexokinases (HXKs), which sense and catalyze cellular sugar, play a critical role in the growth and development of various plants, including wheat, a primary source of human calories frequently attacked by fungal pathogens. However, the evolutionary dynamics and functional diversification of HXKs in wheat, particularly their roles in plant defense, remain unclear. Here, we discovered that the wheat hexokinase gene family originated through multiple ancient gene duplications across different plant lineages and has undergone comprehensive, multidimensional functional specialization in gene expression, subcellular localization, enzyme activity, and regulation of plant defense responses. Gene expression analysis suggests that two-thirds of the TaHXK genes are responsive to fungal infection. Subcellular analysis reveals that while six TaHXKs are localized in mitochondria, three TaHXKs from different phylogenetic branches are sorted into other cellular compartments. Notably, biochemical analysis shows that TaHXKs in mitochondria differ in their glucose-catalyzing activity, with TaHXK5 and TaHXK3 exhibiting the highest and lowest enzyme activity, respectively. Consistently, transient expression analysis suggests that TaHXK5 induces various plant defense responses, while TaHXK3 is defective in activating some plant defense responses. Furthermore, inactivation of the glucokinase activity of TaHXK5 compromised its function in defense activation, suggesting that mitochondrial TaHXKs display functional divergence in both enzyme activity and defense-inducing activity that are intrinsically connected. Overall, our findings reveal that the multidimensional specialization events following the ancient duplication events may have shaped the functional diversity of HXKs in wheat, shedding light on their evolutionary dynamics and potentially contributing to the improvement of wheat defense.},
}
@article {pmid39516195,
year = {2024},
author = {Speth, DR and Zeller, LM and Graf, JS and Overholt, WA and Küsel, K and Milucka, J},
title = {Genetic potential for aerobic respiration and denitrification in globally distributed respiratory endosymbionts.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9682},
pmid = {39516195},
issn = {2041-1723},
mesh = {*Symbiosis ; *Phylogeny ; *Denitrification ; Metagenome ; Aerobiosis ; Ciliophora/genetics/metabolism ; Groundwater/microbiology ; Gammaproteobacteria/genetics/metabolism ; Germany ; Electron Transport Complex IV/genetics/metabolism ; California ; Genome, Bacterial ; },
abstract = {The endosymbiont Candidatus Azoamicus ciliaticola was proposed to generate ATP for its eukaryotic host, an anaerobic ciliate of the Plagiopylea class, fulfilling a function analogous to mitochondria in other eukaryotic cells. The discovery of this respiratory endosymbiosis has major implications for both evolutionary history and ecology of microbial eukaryotes. However, with only a single species described, knowledge of its environmental distribution and diversity is limited. Here we report four complete, circular metagenome assembled genomes (cMAGs) representing respiratory endosymbionts inhabiting groundwater in California, Ohio, and Germany. These cMAGs form two lineages comprising a monophyletic clade within the uncharacterized gammaproteobacterial order UBA6186, enabling evolutionary analysis of their key protein complexes. Strikingly, all four cMAGs encode a cytochrome cbb3 oxidase, which indicates that these endosymbionts have the capacity for aerobic respiration. Accordingly, we detect these respiratory endosymbionts in diverse habitats worldwide, thus further expanding the ecological scope of this respiratory symbiosis.},
}
@article {pmid39518988,
year = {2024},
author = {Liu, R and Ma, T and Li, Y and Lei, X and Ji, H and Du, H and Zhang, J and Cao, SK},
title = {Genomic Identification and Expression Analysis of Regulator of Chromosome Condensation 1-Domain Protein Family in Maize.},
journal = {International journal of molecular sciences},
volume = {25},
number = {21},
pages = {},
pmid = {39518988},
issn = {1422-0067},
support = {2022CFB183, 2024AFB301, 2022CFA030//Hubei Natural Science Foundation/ ; },
mesh = {*Zea mays/genetics/metabolism ; *Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Stress, Physiological/genetics ; Phylogeny ; Multigene Family ; Chromosomes, Plant/genetics ; Promoter Regions, Genetic ; Gene Expression Profiling ; Genomics/methods ; },
abstract = {Abiotic stress affects the growth and development of maize (Zea mays). The regulator of chromosome condensation 1 (RCC1)-containing proteins (RCPs) plays crucial roles in plant growth and development and response to abiotic stresses. However, a comprehensive analysis of the maize RCP family has not been reported in detail. This study presents a systematic bioinformatics analysis of the ZmRCP family, identifying a total of 30 members distributed across nine chromosomes. The physicochemical properties and cis-acting elements in the promoters of ZmRCP members are predicted. The results of subcellular localization showed that ZmRCP3 and ZmRCP10 are targeted to mitochondria and ZmRCP2 is localized in the nucleus. A heatmap of expression levels among family members under abiotic stress conditions revealed varying degrees of induced expression, and the expression levels of 10 ZmRCP members were quantified using RT-qPCR under abiotic stress and plant hormone treatments. The results showed that ZmRCP members exhibit induced or inhibited responses to these abiotic stresses and plant hormones. These results contribute to a better understanding of the evolutionary history and potential role of the ZmRCP family in mediating responses to abiotic stress in maize.},
}
@article {pmid39536732,
year = {2024},
author = {Xuan, D and Qiang, F and Xu, H and Wang, L and Xia, Y},
title = {Screening for Mitochondrial tRNA Variants in 200 Patients with Systemic Lupus Erythematosus.},
journal = {Human heredity},
volume = {89},
number = {1},
pages = {84-97},
pmid = {39536732},
issn = {1423-0062},
mesh = {Humans ; *Lupus Erythematosus, Systemic/genetics ; *RNA, Transfer/genetics ; Female ; Male ; Adult ; DNA, Mitochondrial/genetics ; Middle Aged ; RNA, Mitochondrial/genetics ; Reactive Oxygen Species/metabolism ; Mitochondria/genetics ; Mutation/genetics ; Case-Control Studies ; Phylogeny ; Membrane Potential, Mitochondrial/genetics ; Genetic Predisposition to Disease ; },
abstract = {INTRODUCTION: Systemic lupus erythematosus (SLE) is a common autoimmune disease with unknown etiology. Recently, a growing number of evidence suggested that mitochondrial dysfunctions played active roles in the pathogenesis of SLE, but its detailed mechanism remains largely undetermined. The aim of this study was to analyze the frequencies of mitochondrial tRNA (mt-tRNA) variants in Chinese individuals with SLE.<br><br>METHODS: We carried out a mutational screening of mt-tRNA variants in a cohort of 200 patients with SLE and 200 control subjects by PCR-Sanger sequencing. The potential pathogenicity of mt-tRNA variants was evaluated by phylogenetic conservation and haplogroup analyses. In addition, trans-mitochondrial cybrid cell lines were established, and mitochondrial functions including ATP, reactive oxygen species (ROS), mitochondrial DNA (mtDNA) copy number, mitochondrial membrane potential (MMP), superoxide dismutase (SOD), and mt-RNA transcription were analyzed in cybrids with and without these putative pathogenic mt-tRNA variants.<br><br>RESULTS: We identified five possible pathogenic variants: tRNAVal G1606A, tRNALeu(UUR) A3243G, tRNAIle A4295G, tRNAGly T9997C, and tRNAThr A15924G that only found in SLE patients but were absent in controls. Interestingly, these variants were located at extremely conserved nucleotides of the corresponding tRNAs and may alter tRNAs' structure and function. Furthermore, cells carrying these tRNA variants had much lower levels of ATP, mtDNA copy number, MMP, and SOD than controls; by contrast, the levels of ROS increased significantly (p < 0.05 for all). Furthermore, a significant reduction in mt-ND1, ND2, ND3, ND5, and A6 mRNA expression was observed in cells with these mt-tRNA variants, while compared with controls. Thus, failures in tRNA metabolism caused by these variants would impair mitochondrial translation and subsequently lead to mitochondrial dysfunction that was involved in the progression and pathogenesis of SLE.<br><br>CONCLUSIONS: Our study suggested that mt-tRNA variants were important causes for SLE, and screening for mt-tRNA pathogenic variants was recommended for early detection and prevention for this disorder.},
}
@article {pmid39547447,
year = {2025},
author = {Xin, C and Wang, J and Chi, J and Xu, Y and Liang, R and Jian, L and Wang, L and Guo, J},
title = {Intragenic cytosine methylation modification regulates the response of SUCLα1 to lower temperature in Solanaceae.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {350},
number = {},
pages = {112320},
doi = {10.1016/j.plantsci.2024.112320},
pmid = {39547447},
issn = {1873-2259},
mesh = {*Cytosine/metabolism ; *Cold Temperature ; Plant Proteins/genetics/metabolism ; DNA Methylation ; Solanum tuberosum/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant ; Solanaceae/genetics/metabolism/physiology ; Nicotiana/genetics ; },
abstract = {The tricarboxylic acid cycle (TCAC) is a fundamental metabolic process governing matter and energy in plant cells, playing an indispensable role. However, its involvement in responding to low temperature stress in potato remains poorly understood. Previous studies have identified succinyl-CoA ligase (SUCL), which catalyzes the phosphorylation of TCAC substrates, as a gene associated with lower temperatures. Nevertheless, its function in potato's response to lower temperatures remains unclear. Phylogenetic analysis has revealed that Solanum tuberosum possesses α and β subunits of SUCL, which cluster with those of Solanum lycopersicum, Nicotiana tabacum and Nicotiana benthamiana. Further investigation has shown that StSUCLα1 is predominantly located within mitochondria. Low temperatures induce methylation modification alterations at 11 intragenic cytosine sites and lead to changes in StSUCLα1 expression levels. Correlation analysis suggests that alterations in intragenic cytosine methylation sites of SUCLα1 may be associated with MET1. Knocking down NbSUCLα1, the homologous gene of StSUCLα1 in N. benthamiana, results in increased susceptibility to low temperature stress in plants. In summary, we have confirmed that SUCLα1 is a key gene modulated by intragenic cytosine methylation in response to lower temperatures, providing a novel target for genetic breeding aimed at enhancing potato tolerance to low temperature stress.},
}
@article {pmid39567420,
year = {2025},
author = {Yun, BH and Kim, YH and Han, HS and Bang, IC},
title = {Population genetics analysis based on mitochondrial cytochrome c oxidase subunit I (CO1) gene sequences of Cottus koreanus in South Korea.},
journal = {Genes &amp; genomics},
volume = {47},
number = {2},
pages = {207-221},
pmid = {39567420},
issn = {2092-9293},
support = {NRF-2021R1A6A1A03039503//Ministry of Education/ ; Soonchunhyang University//Soonchunhyang University/ ; },
mesh = {*Electron Transport Complex IV/genetics ; Republic of Korea ; Animals ; Haplotypes ; Genetics, Population ; Genetic Variation ; Phylogeny ; Mitochondria/genetics ; *Fishes/genetics ; },
abstract = {BACKGROUND: The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species.<br><br>OBJECTIVE: To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis.<br><br>METHODS: We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea.<br><br>RESULTS: In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd&#x2005;=&#x2005;0.941) and low nucleotide diversity (&#x3c0;&#x2005;=&#x2005;0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak.<br><br>CONCLUSIONS: C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately.},
}
@article {pmid39581968,
year = {2024},
author = {Wang, Y and Chen, F and Chen, Y and Ren, K and Zhao, D and Li, K and Li, H and Wan, X and Peng, M and Xiang, Z and Tang, Q and Hou, Z and Fang, Q and Zhou, Y and Lu, Y},
title = {Identification and analysis of drought-responsive F-box genes in upland rice and involvement of OsFBX148 in ABA response and ROS accumulation.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1120},
pmid = {39581968},
issn = {1471-2229},
support = {32360075//the National Natural Science Foundation of China/ ; 2022CFB694//the Scientific Research Project of Department of Science and Technology of Hubei Province/ ; SCKJ-JYRC-2023-35//"Yazhou Bay" Elite Talent Science and Technology Program of Sanya Yazhou Bay Science and Technology City/ ; PY22005//the Incubation Project of Hubei Minzu University/ ; },
mesh = {*Oryza/genetics/physiology ; Drought Resistance ; *F-Box Proteins/chemistry/genetics/metabolism ; *Plant Proteins/chemistry/genetics/metabolism ; Phylogeny ; Promoter Regions, Genetic ; Gene Expression Profiling ; Abscisic Acid/metabolism ; Stress, Physiological ; Gene Expression Regulation, Plant ; Reactive Oxygen Species/metabolism ; Ubiquitin/metabolism ; },
abstract = {BACKGROUND: Upland rice varieties exhibit significant genetic diversity and broad environmental adaptability, making them ideal candidates for identifying consistently expressed stress-responsive genes. F-box proteins typically function as part of the SKP1-CUL1-F-box protein (SCF) ubiquitin ligase complexes to precisely regulate gene expression and protein level, playing essential roles in the modulation of abiotic stress responses. Therefore, utilizing upland rice varieties for screening stress-responsive F-box genes is a highly advantageous approach.<br><br>RESULTS: Through mRNA-seq analysis in the Brazilian upland rice (cv. IAPAR9), the research identified 29 drought-responsive F-box genes. Gene distribution and duplication analysis revealed these genes are distributed on 11 of the 12 chromosomes and 10 collinear gene pairs were identified on different chromosomes. 13 cis-elements or binding sites were identified in the promoters of the 29 drought-responsive F-box genes by analysis. Protein domain, stability and subcellular localization analysis results suggest that these F-box proteins possess F-box domain and several other domains, and they are mostly unstable proteins with subcellular localization in cytoplasm, nucleus, chloroplasts, mitochondria and endoplasmic reticulum. Most of drought-responsive F-box genes exhibited expression in various tissues such as root, stem, leaf, leaf sheath and panicle except for OsFBO10 and OsFBX283. These genes exhibited various responses to abiotic stresses such as osmotic, cold, heat, and salt stresses, along with ABA treatment. Importantly, a frame-shift mutation in OsFBX148 was created in the ZH11 variety, leading to altered ABA signal transduction and ROS accumulation. The study further elucidated the interaction of OsFBX148 with SKP1 family proteins OSK4/7/17 to form the SCF complex, dependent on the F-box domain.<br><br>CONCLUSIONS: The research identified and analyzed 29 drought-responsive F-box genes in upland rice and provides valuable insights into the role of OsFBX148 in ABA and ROS responses. It establishes a basis for future exploration of F-box genes in improving resistance to abiotic stresses, especially drought.},
}
@article {pmid39596001,
year = {2024},
author = {Wang, H and Charagh, S and Dong, N and Lu, F and Wang, Y and Cao, R and Ma, L and Wang, S and Jiao, G and Xie, L and Shao, G and Sheng, Z and Hu, S and Zhao, F and Tang, S and Chen, L and Hu, P and Wei, X},
title = {Genome-Wide Analysis of Heat Shock Protein Family and Identification of Their Functions in Rice Quality and Yield.},
journal = {International journal of molecular sciences},
volume = {25},
number = {22},
pages = {},
pmid = {39596001},
issn = {1422-0067},
support = {2023YFF1000500//National Key Research and Development Program of China/ ; 32372099//National Natural Science Foundation of China/ ; 32188102//National Natural Science Foundation of China/ ; },
mesh = {*Oryza/genetics/metabolism/growth &amp; development ; *Heat-Shock Proteins/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Gene Expression Regulation, Plant ; Multigene Family ; Genome, Plant ; Phylogeny ; Chromosomes, Plant/genetics ; Genome-Wide Association Study ; },
abstract = {Heat shock proteins (Hsps), acting as molecular chaperones, play a pivotal role in plant responses to environmental stress. In this study, we found a total of 192 genes encoding Hsps, which are distributed across all 12 chromosomes, with higher concentrations on chromosomes 1, 2, 3, and 5. These Hsps can be divided into six subfamilies (sHsp, Hsp40, Hsp60, Hsp70, Hsp90, and Hsp100) based on molecular weight and homology. Expression pattern data indicated that these Hsp genes can be categorized into three groups: generally high expression in almost all tissues, high tissue-specific expression, and low expression in all tissues. Further analysis of 15 representative genes found that the expression of 14 Hsp genes was upregulated by high temperatures. Subcellular localization analysis revealed seven proteins localized to the endoplasmic reticulum, while others localized to the mitochondria, chloroplasts, and nucleus. We successfully obtained the knockout mutants of above 15 Hsps by the CRISPR/Cas9 gene editing system. Under natural high-temperature conditions, the mutants of eight Hsps showed reduced yield mainly due to the seed setting rate or grain weight. Moreover, the rice quality of most of these mutants also changed, including increased grain chalkiness, decreased amylose content, and elevated total protein content, and the expressions of starch metabolism-related genes in the endosperm of these mutants were disturbed compared to the wild type under natural high-temperature conditions. In conclusion, our study provided new insights into the HSP gene family and found that it plays an important role in the formation of rice quality and yield.},
}
@article {pmid39604839,
year = {2024},
author = {Liao, R and Yao, J and Zhang, Y and Liu, Y and Pan, H and Han, B and Song, C},
title = {MYB transcription factors in Peucedanum Praeruptorum Dunn: the diverse roles of the R2R3-MYB subfamily in mediating coumarin biosynthesis.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {1135},
pmid = {39604839},
issn = {1471-2229},
support = {2023YFC3503804//National Key R&amp;D Program of China/ ; TCMRPSU-2022-04//Open Fund of Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resource/ ; TCMADM-2023-03//Open Fund of the Anhui Dabieshan Academy of Traditional Chinese Medicine/ ; },
mesh = {*Transcription Factors/metabolism/genetics ; *Plant Proteins/genetics/metabolism ; *Apiaceae/genetics/metabolism ; *Phylogeny ; *Coumarins/metabolism ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; },
abstract = {BACKGROUND: The MYB superfamily (v-myb avian myeloblastosis viral oncogene homolog) plays a role in plant growth and development, environmental stress defense, and synthesis of secondary metabolites. Little is known about the regulatory function of MYB genes in Peucedanum praeruptorum Dunn, although many MYB family members, especially R2R3-MYB genes, have been extensively studied in model plants.<br><br>RESULTS: A total of 157 R2R3-MYB transcription factors from P. praeruptorum were identified using bioinformatics analysis. Comprehensive analyses including chromosome location, microsynteny, gene structure, conserved motif, phylogenetic tree, and conserved domain were further performed. The length of the 157 transcription factors ranged from 120 to 1,688 amino acids (molecular weight between 14.21 and 182.69&#xa0;kDa). All proteins were hydrophilic. Subcellular localization predictions showed that 155 PpMYB proteins were localized in the nucleus, with PpMYB12 and PpMYB157 localized in the chloroplasts and mitochondria, respectively. Ten conserved motifs were identified in the PpMYBs, all of which contained typical MYB domains. Transcriptome analysis identified 47,902 unigenes. Kyoto Encyclopedia of Genes and Genomes analysis revealed 136 pathways, of which 524 genes were associated with the phenylpropanoid pathway. Differential expressed genes (DEGs) before and after bolting showed that 11 genes were enriched in the phenylpropanoid pathway. Moreover, the expression patterns of transcription genes were further verified by qRT-PCR. With high-performance liquid chromatography (HPLC), 8 coumarins were quantified from the root, stem, and leaf tissue samples of P. praeruptorum at different stages. Praeruptorin A was found in both roots and leaves before bolting, whereas praeruptorin B was mainly concentrated in the roots, and the content of both decreased in the roots and stems after bolting. Praeruptorin E content was highest in the leaves and increased with plant growth. The correlation analysis between transcription factors and coumarin content showed that the expression patterns of PpMYB3 and PpMYB103 in roots align with the accumulation trends of praeruptorin A, praeruptorin B, praeruptorin E, scopoletin, and isoscopoletin, which declined in content after bolting, suggesting that these genes may positively regulate the biosynthesis of coumarins. Eleven distinct metabolites and 48 DEGs were identified. Correlation analysis revealed that the expression of all DEGs were significantly related to the accumulation of coumarin metabolites, indicating that these genes are involved in the regulation of coumarin biosynthesis.<br><br>CONCLUSIONS: R2R3-MYB transcription factors may be involved in the synthesis of coumarin. Our findings provide basic data and a rationale for future an in-depth studies on the role of R2R3-MYB transcription factors in the growth and regulation of coumarin synthesis.},
}
@article {pmid39623304,
year = {2024},
author = {Zhang, C and Rasool, A and Qi, H and Zou, X and Wang, Y and Wang, Y and Wang, Y and Liu, Y and Yu, Y},
title = {Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1162},
pmid = {39623304},
issn = {1471-2164},
mesh = {*Genome, Mitochondrial ; *Medicine, Chinese Traditional ; *Viola/genetics ; Phylogeny ; Base Composition ; RNA, Transfer/genetics ; Genome, Plastid ; Codon Usage ; },
abstract = {BACKGROUND: Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.<br><br>RESULTS: This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721&#xa0;bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.<br><br>CONCLUSIONS: We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.},
}
@article {pmid39623987,
year = {2024},
author = {Zhang, Y and Zang, C and Pan, X and Gong, M and Liu, H},
title = {[Population genetic diversity of Culex tritaeniorhynchus in Jining City of Shandong Province based on the mitochondrial cytochrome C oxidase I gene].},
journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control},
volume = {36},
number = {5},
pages = {466-473},
doi = {10.16250/j.32.1915.2024119},
pmid = {39623987},
issn = {1005-6661},
support = {tsqn202312373//Shandong Provincial Taishan Scholar Program/ ; ZR2R2020KH001//Key Project of Natural Science Foundation t of Shandong Province/ ; 230726153807227//University-Industry Collaborative Education Program of Ministry of Education/ ; },
mesh = {Animals ; *Culex/genetics ; *Electron Transport Complex IV/genetics ; *Genetic Variation ; China ; Haplotypes ; Phylogeny ; Female ; Mitochondria/genetics ; },
abstract = {OBJECTIVE: To understand the genetic basis of the adaptation of Culex tritaeniorhynchus to different environmental ecology in Jining City, Shandong Province, so as to provide insights into understanding of the population structure or isolation pattern of Cx. tritaeniorhynchus in the city.<br><br>METHODS: Seven sampling sites were selected from urban, suburban and rural areas of Jining City, Shandong Province from June to August 2023, and mosquitoes were collected using mosquito-trapping lamps. All collected adult mosquitoes were identified morphologically. Genomic DNA was extracted from a single female Cx. tritaeniorhynchus mosquito, and the mitochondrial cytochrome C oxidase I (COI) gene was amplified using a PCR assay, sequenced and subjected to molecular identification. The number of haplotypes, haplotype diversity (Hd), nucleotide diversity (Pi), and average number of nucleotide differences (K) of Cx. tritaeniorhynchus DNA sequences were estimated among different sampling sites using the software DnaSP 6, and a neutrality test was performed. The fixation index (FST), and gene flow (number of migrants, Nm) of Cx. tritaeniorhynchus populations were calculated using the software Arlequin 3.5.2, and subjected to analysis of molecular variance (AMOVA). In addition, a haplotype network diagrams and a phylogenetic tree of Cx. tritaeniorhynchus populations were created using the software PopART and MEGA 11, respectively.<br><br>RESULTS: A total of 420 sequences were successfully amplified from the COI gene of Cx. tritaeniorhynchus samples collected from 7 sampling sites in Jining City, and a gene fragment sequence with a length of 603 bp was obtained, with 55 variable sites and 46 haplotypes and without insertion or deletion mutations. Of the 46 haplotypes, H01 was the dominant shared haplotype, and the haplotype frequency increased gradually from urban areas (34.00%) to rural areas (47.00%). The mean Hd, Pi and K values of Cx. tritaeniorhynchus COI genes were 0.814, 0.024 and 14.129, 0.489, 0.016 and 7.941 and 0.641, 0.016 and 10.393 in suburban, urban, and rural areas, respectively, with the highest population diversity of Cx. tritaeniorhynchus in suburban areas and the lowest in urban areas. Paired FST analysis among different types of sampling sites showed that the mean FST value was 0.029 between urban and suburban areas, indicating more frequent inter-population communication. AMOVA revealed that the percentage of intra-population variation (95.74%) was higher than that of inter-population variation (4.26%). Neutrality tests showed deviation from neutrality in Cx. tritaeniorhynchus populations collected from Nanyang Township (Tajima's D = 2.793, Fu's Fs = 6.429, both P values < 0.05). In addition, the mismatch distribution curves of Cx. tritaeniorhynchus COI gene appeared bimodal or multimodal patterns in Jining City, indicating a relatively stable overall population size.<br><br>CONCLUSIONS: The mitochondrial COI gene may be used as a molecular marker to investigate the population genetic diversity of Cx. tritaeniorhynchus. The population genetic diversity of Cx. tritaeniorhynchus is higher in the suburban areas of Jining City than in rural and urban areas, and there are frequent genetic exchanges between Cx. tritaeniorhynchus populations from urban and suburban areas.},
}
@article {pmid39633470,
year = {2024},
author = {Atherton, W and Ambrose, L and Wisdom, J and Lessard, BD and Kurucz, N and Webb, CE and Beebe, NW},
title = {Nuclear and mitochondrial population genetics of the Australasian arbovirus vector Culex annulirostris (Skuse) reveals strong geographic structure and cryptic species.},
journal = {Parasites &amp; vectors},
volume = {17},
number = {1},
pages = {501},
pmid = {39633470},
issn = {1756-3305},
support = {RG 18-19//Australian Biological Resources Study, Australia's Department of Climate Change, Energy, the Environment and Water/ ; },
mesh = {Animals ; *Culex/genetics/classification/virology ; *Microsatellite Repeats/genetics ; *Mosquito Vectors/genetics/classification/virology ; *Genetic Variation ; Australia ; *DNA, Mitochondrial/genetics ; Genetics, Population ; Arboviruses/genetics ; Australasia/epidemiology ; Papua New Guinea ; Electron Transport Complex IV/genetics ; Haplotypes ; Phylogeny ; Mitochondria/genetics ; },
abstract = {BACKGROUND: The mosquito Culex annulirostris Skuse (Diptera: Culicidae) is an important arbovirus vector in Australasia. It is part of the Culex sitiens subgroup that also includes Cx. palpalis and Cx. sitiens. Single locus mitochondrial and nuclear DNA sequencing studies suggest that Cx. annulirostris consists of a complex of at least two species. We tested this hypothesis by analysing both nuclear microsatellite data and additional mitochondrial sequence data to describe the population genetics of Cx. annulirostris through Australia, Papua New Guinea (PNG) and the Solomon Archipelago.<br><br>METHODS: Twelve novel microsatellite markers for Cx. annulirostris were developed and used on over 500 individuals identified as Cx. annulirostris by molecular diagnostics. Ten of the 12 microsatellites then used for analysis using Discriminant Analysis of Principal Components, a Bayesian clustering software, STRUCTURE, along with estimates of Jost's D statistic that is similar to FST but better suited to microsatellite data. Mitochondrial cytochrome oxidase I (COI) DNA sequence were also generated complementing previous work and analysed for sequence diversity (Haplotype diversity, Hd and Pi, &#x3c0;), Tadjima's D, and pairwise FST between populations. An allele specific molecular diagnostic with an internal control was developed.<br><br>RESULTS: We confirm the existence of multiple genetically and geographically restricted populations. Within mainland Australia, our findings show that Cx. annulirostris consists of two genetically and geographically distinct populations. One population extends through northern Australia and into the south-east coast of Queensland and New South Wales (NSW). The second Australian population occurs through inland NSW, Victoria, South Australia, extending west to southern Western Australia. These two Australian populations show evidence of possible admixture in central Australia and far north Queensland. Australia's Great Dividing Range that runs down southeast Australia presents a strong gene-flow barrier between these two populations which may be driven by climate, elevation or river basins. In PNG we find evidence of reproductive isolation between sympatric cryptic species occurring through PNG and Australia's northern Cape York Peninsula. A PCR-based molecular diagnostic was developed to distinguish these two cryptic species.<br><br>CONCLUSION: This study adds to the growing body of work suggesting that the taxon presently known as Cx. annulirostris now appears to consist of at least two cryptic species that co-occur in northern Australia and New Guinea and can be distinguished by a ITS1 PCR diagnostic. The Solomon Islands population may also represent a distinct species but in light its geographic isolation and lack of sympatry with other species would require further study. Additionally, the mitochondrial and nuclear DNA evidence of population structure between geographic regions within Australia appears latitudinal and elevational driven and may suggest an additional subspecies in that hybridise where they overlap.},
}
@article {pmid39662740,
year = {2025},
author = {de Quadros, T and Jaramillo, ML and Barreto, C and da Rosa, RD and de Melo, MS and Nazari, EM},
title = {Modulation of mitochondrial dynamics genes and mtDNA during embryonic development and under UVB exposure.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {300},
number = {},
pages = {111790},
doi = {10.1016/j.cbpa.2024.111790},
pmid = {39662740},
issn = {1531-4332},
mesh = {Animals ; *Ultraviolet Rays ; *DNA, Mitochondrial/genetics ; *Embryonic Development/radiation effects/genetics ; *Mitochondrial Dynamics/radiation effects ; Palaemonidae/genetics/embryology/radiation effects ; Phylogeny ; Mitochondria/metabolism/radiation effects/genetics ; Gene Expression Regulation, Developmental/radiation effects ; Embryo, Nonmammalian/radiation effects/metabolism ; },
abstract = {Studies using the embryos of the freshwater prawn Macrobrachium olfersii have reported changes in embryonic cells after exposure to ultraviolet B (UVB) radiation, such as DNA damage and apoptosis activation. Considering the importance of mitochondria in embryonic cells, this study aimed to characterize the aspects of mitochondrial morphofunctionality in M. olfersii embryos and mitochondrial responses to UVB radiation exposure. The coding sequences of genes Tfam, Nrf1, Mfn1, and Drp1 were identified from the transcriptome of M. olfersii embryos. The phylogenetic relationship showed strong amino acid identity and a highly conserved nature of the sequences. Additionally, the number of mitochondrial DNA (mtDNA) copies were higher in the early embryonic days. The results showed that the expression of the analyzed genes was highly regulated during embryonic development, increasing their levels near hatching. Furthermore, when embryos were exposed to UVB radiation, mitochondrial biogenesis was activated, recognized by higher levels of transcripts of genes Tfam and Nrf1, accompanied by mitochondrial fission. Additionally, these mitochondrial events were supported by an increase of mtDNA copies. Our results showed that UVB radiation was able to change the mitochondrial morphofunctionality, and under the current knowledge, certainly compromise embryonic cellular integrity. Additionally, mitochondria is an important cellular target of this radiation and its responses can be used to assess environmental stress caused by UVB radiation in embryos of aquatic species.},
}
@article {pmid39688736,
year = {2024},
author = {Singha, D and Patidar, A and Pal, S and Tyagi, K and Kumar, V},
title = {Mitochondrial genetic diversity of pest and vector species, Frankliniella schultzei (Thripidae: Thripinae).},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {55},
pmid = {39688736},
issn = {1573-4978},
support = {CRG/2023/000498//Science and Engineering Research Board/ ; },
mesh = {Animals ; *Phylogeny ; *Genetic Variation/genetics ; *Haplotypes/genetics ; India ; *Thysanoptera/genetics/classification ; DNA Barcoding, Taxonomic/methods ; Australia ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Insect Vectors/genetics/classification ; Bayes Theorem ; Gene Flow ; },
abstract = {BACKGROUND: Frankliniella schultzei (Trybom) is a serious pest and a carrier of tospoviruses in major agricultural crops. This species is a historical and unresolved species complex that contains genetically different cryptic species across the globe.<br><br>METHODS AND RESULTS: DNA barcodes were generated from freshly collected specimens of F. schultzei from India and Australia using the sanger sequencing. Seventy-five COI sequences were generated from India and Australia. Moreover, 318 sequences were downloaded (India, Australia, Pakistan, and Africa) from the NCBI GenBank to explore the genetic diversity and phylogeny. The minimum and maximum mean interspecific distance between 393 sequences was found to be 7.97% and 21.50%, respectively. Bayesian and Neighbour joining clustering indicated the presence of five putative species within F. schultzei that had sympatry and allopatry. Moreover, 20 haplotypes and 140 polymorphic sites were identified. The African clade is unique; it does not share haplotypes with any other countries, suggesting it may represent the true F. schultzei. Haplotype network analysis showed shallow gene flow and deep genetic variation between the populations. Signatures of recent population history events were measured using Fu's Fs test and Tajima's D test. Morphometric analysis based on seven characters is also carried out.<br><br>CONCLUSION: Phylogeny and genetic distance revealed the presence of five putative species within F. schultzei. On the contrary, morphology does not unequivocally corroborate the phylogenetic results, as morphometric analysis showed overlap among these clades. To resolve F. schultzei species complex, whole genome-based sequencing data are very much necessitated.},
}
@article {pmid39738580,
year = {2025},
author = {Ahmed, S and Nadeem, MS and Johansson, AM and Jonas, E and Muhammad, K and Mehmood, SA},
title = {Molecular diversity and phylogenetic analysis of ten sheep breeds from Khyber Pakhtunkhwa, Pakistan, based on mitochondrial D-loop sequences.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {36},
number = {1},
pages = {129-139},
pmid = {39738580},
issn = {1432-1777},
mesh = {Animals ; *Phylogeny ; Pakistan ; *DNA, Mitochondrial/genetics/chemistry ; Sheep/genetics/classification ; *Genetic Variation ; Haplotypes ; Female ; Breeding ; *Mitochondria/genetics ; },
abstract = {Livestock farming has a key role in many rural communities both economically and culturally. It plays an important role in overcoming the deficiencies of meat, milk, wool and various by-products. Pakistan has a large number of livestock, well-adapted to local conditions. and has some of the best tropical dairy breeds. Native sheep breeds stand a vital asset to the country's livestock sector because of their adaptability and unique genetic traits. However, knowledge of the genetic diversity of these sheep breeds remains limited. This study aims to investigate the genetic diversity of 10 local sheep breeds from Khyber Pakhtunkhwa by analyzing the mitochondrial D-loop from 159 individual samples of females. The sequenced data from the mtDNA D-loop showed 106 different haplotypes, with a haplotype diversity of 0.9854 ± 0.0041. Analysis of the mitochondrial D-loop revealed three distinct haplogroups (HapA, HapB, and HapC). Out of the 159 sequences, 125 (77.99%) grouped with HapA, 30 (18.87%) with HapB, and 5 (3.14%) with HapC. While HapA and HapB are commonly found in sheep breeds worldwide, the identification of 5 sequences belonging to HapC was unexpected. This haplogroup was seen in four sheep breeds: Afghani, Australian, Gauder and Waziri. Most interestingly, the two Pakistani-origin breeds, the Waziri sheep breed, from South of Waziristan and the Gauder, a crossbreed, have been identified with HapC haplogroup. This indicates that the sheep breeds of Khyber Pakhtunkhwa belong to three distinct phylogenetic lineages, suggesting a probable gene flow from the southwest to the northeast regions of the province.},
}
@article {pmid39819387,
year = {2025},
author = {Li, H and Liu, L and Qiu, Z and He, F and Dong, W},
title = {Complete mitochondrial genome assembly and comparative analysis of Colocasia esculenta.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {67},
pmid = {39819387},
issn = {1471-2229},
support = {2021GXNSFBA196012, 2022GXNSFAA035493//Natural Science Foundation of Guangxi/ ; TS202113//the Lipu C. esculenta Test Station Project of Guangxi/ ; Gui nongke 2023YM91, Gui nongke 2024YP081//Basic Scientific Research Business Project of Guangxi Academy of Agricultural Sciences/ ; },
mesh = {*Colocasia/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Genome, Plant ; RNA Editing ; },
abstract = {Colocasia esculenta ranks as the fifth most important tuber crop and is known for its high nutritional and medicinal value. However, there is no research on its mitochondrial genome, hindering in-depth exploration of its genomic resources and genetic relationships. Using second- and third-generation sequencing technologies, we assembled and annotated the mitogenome of C. esculenta. Its mitogenome mainly consists of five circular DNA molecules, with a total length of 594,811 bp and a GC content of 46.25%. A total of 55 genes, 157 simple sequence repeats, 29 tandem repeat sequences, 202 dispersed repeat sequences, and 625 RNA editing sites were detected. Most protein-coding genes use ATG as the start codon, and the third position of the codon tends to be A or T (U). GAA, AUU, and UUU are the most common codons in C. esculenta mitochondria. Finally, based on 28 representative plant species, a phylogenetic tree was constructed, revealing a close relationship between C. esculenta and Araceae. This study provides comprehensive information on C. esculenta, laying a foundation for crop genetics and molecular breeding.},
}
@article {pmid39834790,
year = {2025},
author = {Arias, E and Crawford, AJ and Hertz, A and Parra Olea, G},
title = {Deep cryptic diversity in the Craugastor podiciferus Species Group (Anura: Craugastoridae) of Isthmian Central America revealed by mitochondrial and nuclear data.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18212},
pmid = {39834790},
issn = {2167-8359},
mesh = {Animals ; Phylogeny ; *Anura/genetics/classification ; *DNA, Mitochondrial/genetics ; Central America ; Panama ; *Cell Nucleus/genetics ; *Genetic Variation ; *Mitochondria/genetics ; },
abstract = {The Craugastor podiciferus Species Group contains eleven species of terraranan frogs distributed from eastern Honduras to eastern Panama. All species have remarkable color pattern polymorphisms, which may contribute to potential taxonomic problems. We performed exhaustive sampling throughout the geographic distribution of the group to evaluate the phylogenetic relationships and biogeographic history of all named species based on two mitochondrial markers and nuclear ddRAD loci. We also implemented various species delimitation methods to test for the presence of unconfirmed candidate species within the group. Molecular phylogenetic analyses showed that the group contains four major clades. All currently named species are supported by molecular data, yet species richness within the group is clearly underestimated. Species delimitation was discordant between the mitochondrial and nuclear datasets and among analytical methods. Adopting a conservative approach, we propose that the C. podiciferus species group contains at least 12 unconfirmed candidate species. Ancestral area reconstruction showed that the group originated and diversified in the highlands of the Talamancan montane forest ecoregion of Costa Rica and western Panama.},
}
@article {pmid39860980,
year = {2024},
author = {Han, L and Yang, Y and Lu, M and Yu, H and Lu, Y and Zhou, M and Liu, T and Zhang, R and Chen, B and Hou, Z},
title = {Mitogenome Phylogenetics of Spiruromorpha Porpoise Parasite: Insights Into Phylogeny of Crassicauda magna.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {1},
pages = {},
pmid = {39860980},
issn = {2076-0817},
support = {415471//the Postdoctoral Funding Program of Heilongjiang Province, China/ ; GZC20230394//the State-sponsored Postdoctoral Researcher program/ ; },
mesh = {Animals ; *Phylogeny ; *Genome, Mitochondrial ; *Porpoises/parasitology ; },
abstract = {(1) Background: Crassicauda magna is a major parasite of large porpoises and whales and has been classified in the Habronematoidea family. However, there has been a great controversy regarding its classification. Mitochondria have an important function in revealing taxonomic and evolutionary history. (2) Methods: In this study, we sequenced the mitochondrial genome of C. magna and conducted a phylogenetic analysis with the mitochondrial sequences of species belonging to the Habronematoidea family. (3) Results: The complete mitochondrial genome was 13,604 bp and it has an AT-rich sequence and one non-coding region (NCR). The reconstruction of the ancestral state showed that the gene orders of all species in Spirurina were conserved. The phylogenetic tree indicates that C. magna is closer to Heliconema longissimum (Physalopteroidea) than Tetrameres grusi (Habronematoidea). (4) Conclusions: This study provides new evidence that C. magna is phylogenetically closer to Physalopteroidea at the molecular taxonomic level.},
}
@article {pmid39893979,
year = {2025},
author = {Duan, C and Zhao, Y and Xiao, Y and Hou, Y and Gong, W and Zhang, H and Wang, Y and Nie, X},
title = {Lithium with environmentally relevant concentrations interferes with mitochondrial function, antioxidant response, and autophagy processes in Daphnia magna, leading to changes in life-history traits and behavior.},
journal = {Journal of hazardous materials},
volume = {488},
number = {},
pages = {137420},
doi = {10.1016/j.jhazmat.2025.137420},
pmid = {39893979},
issn = {1873-3336},
mesh = {Animals ; *Daphnia/drug effects/physiology/metabolism ; Autophagy/drug effects ; *Water Pollutants, Chemical/toxicity ; *Mitochondria/drug effects/metabolism ; *Lithium/toxicity ; *Antioxidants/metabolism ; Behavior, Animal/drug effects ; Life History Traits ; Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; Daphnia magna ; },
abstract = {With the increasing production and use of lithium-based products, concerns over lithium pollution in aquatic ecosystems are increasing, whereas research on its toxicity mechanisms in aquatic organisms remains limited. The main objective of the present study was to explore the effects of environmentally relevant concentrations of lithium exposure on the life-history strategy, behavior, antioxidant system, and autophagy process of Daphnia magna. Acute (24-96 h) and chronic (21 days) exposure experiments under three lithium treatments (low: 8.34 μg/L, medium: 83.44 μg/L, and high: 834.41 μg/L) were conducted. The results indicated that exposure to medium and high lithium concentrations led to eye and tail deformities in D. magna. Furthermore, developmental and reproductive parameters such as body length, total neonates per female, and average neonates per time were negatively influenced. Lithium also interfered with energy metabolism to cause the decreasing swimming speed and the reduction in the swimming range. In addition, lithium exposure affected the expression of gsk-3β, further disrupting the dynamic balance of mitochondrial fission, fusion, and regeneration, which caused ROS accumulation and induced oxidative stress. D. magna attenuated the stress by activating the FoxO/SESN and Nrf2/Keap1 pathways, synergistically enhancing downstream antioxidant enzymes expression. Concurrently, D. magna also mitigated oxidative stress and mitochondrial damage by promoting autophagy and inhibiting apoptosis. In summary, lithium harmed the physiological and biochemical functions of D. magna through multiple mechanisms, suggesting that environmental lithium pollution may pose a potential threat to aquatic organisms.},
}
@article {pmid39940743,
year = {2025},
author = {Zeng, Q and Yu, Q and Mo, Y and Liang, H and Chen, B and Meng, J},
title = {Genome-Wide Identification and Functional Characterization of the Acyl-CoA Dehydrogenase (ACAD) Family in Fusarium sacchari.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
pmid = {39940743},
issn = {1422-0067},
support = {31960031//National Natural Science Foundation of China/ ; 2024GXNSFAA010041//Guangxi Natural Science Foundation/ ; },
mesh = {*Fusarium/genetics/enzymology/pathogenicity ; Phylogeny ; Fatty Acids/metabolism ; *Acyl-CoA Dehydrogenase/genetics/metabolism ; *Genome, Fungal ; Gene Expression Regulation, Fungal ; *Fungal Proteins/genetics/metabolism ; Plant Diseases/microbiology ; Multigene Family ; },
abstract = {Fusarium sacchari is one of the primary causal agents of Pokkah boeng disease (PBD), an important disease of sugarcane worldwide. The acyl-CoA dehydrogenases (ACADs) constitute a family of flavoenzymes involved in the β-oxidation of fatty acids and amino acid catabolism in mitochondria. However, the role of ACADs in the pathogenesis of F. sacchari is unclear. Here, 14 ACAD-encoding genes (FsACAD-1-FsACAD-14) were identified by screening the entire genome sequence of F. sacchari. The FsACAD genes are distributed across seven chromosomes and were classified into seven clades based on phylogenetic analysis of the protein sequences. In vivo mRNA quantification revealed that the FsACAD genes are differentially expressed during sugarcane infection, and their expression patterns differ significantly in response to the in vitro induction of fatty acids of different classes. Fatty acid utilization assays of the FsACAD-deletion mutants revealed that the FsACADs varied in their preference and ability to break down different fatty acids and amino acids. There was variation in the adverse impact of FsACAD-deletion mutants on fungal traits, including growth, conidiation, stress tolerance, and virulence. These findings provide insights into the roles of FsACADs in F. sacchari, and the identification of FsACADs offers potential new targets for the improved control of PBD.},
}
@article {pmid39950816,
year = {2025},
author = {Guo, B and Guo, G and Qi, W and Aizezi, M and Wu, C and Tian, M and Casulli, A and Zhang, W and Li, J},
title = {The genetic variation of mitochondrial sequences and pathological differences of Echinococcus multilocularis strains from different continents.},
journal = {Microbiology spectrum},
volume = {13},
number = {4},
pages = {e0131824},
pmid = {39950816},
issn = {2165-0497},
support = {2023TSYCTD0017//Tianshan talent training program/ ; 32072886,U1803282//MOST | National Natural Science Foundation of China (NSFC)/ ; 81830066//MOST | National Natural Science Foundation of China (NSFC)/ ; SKLHIDCA-2022-BC4//State Key Laboratory/ ; },
mesh = {Animals ; *Echinococcus multilocularis/genetics/classification/pathogenicity/isolation &amp; purification ; *Genetic Variation ; Phylogeny ; *Echinococcosis/parasitology/pathology ; Mice ; Japan ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Disease Models, Animal ; Liver/parasitology/pathology ; },
abstract = {Alveolar echinococcosis is a lethal zoonotic disease caused by the fox tapeworm Echinococcus multilocularis. The parasite is widely distributed in the Northern Hemisphere and exhibits low genetic diversity among populations. To compare the differences among four E. multilocularis strains from different geographical locations, namely, Alaska (EM-AK), Japan (EM-JP), Xinjiang (EM-XJ), and Ningxia (EM-NX), their complete mitochondrial (mt) sequences were compared, and their induced pathological lesions were analyzed in mouse models. The complete mt sequence of EM-AK resulted in 0.84%-0.86% variation as compared with the other strains, which had a lower variation. Phylogenetic analysis and parsimony network indicated that EM-AK resulted in 30,000 years of evolutionary distance from the other three strains. EM-AK induced more pathological damage than the other three strains, which was likely to induce more host cell infiltration and acute granuloma in the liver. More importantly, EM-AK produced more protoscoleces than the other three strains, which may impact the transmission dynamics of the parasite. Given the geographical location of four strains, which is far from each other, and also the pathological differences, the strains of E. multilocularis are likely models for addressing the relationship and interfacial immune response between the host and the helminth.IMPORTANCEEchinococcus multilocularis is the causative agent of alveolar echinococcosis, which is considered the most serious parasitic disease in the Northern Hemisphere. There are many genotypes, but the pathogenic and mitochondria sequence and differences are still unclear. Therefore, this study showed both pathological and genetic differences between the four strains of E. multilocularis. EM-AK induced more severe immune responses and especially induced more host cell infiltration, which resulted in more severe granuloma in the liver. EM-JP has metacestode lesions morphologically closer to those of E. granulosus with clear cyst fluid. However, this strain produced much fewer protoscoleces (PSCs). Genetically, EM-AK is more distant from other strains.},
}
@article {pmid39980249,
year = {2025},
author = {de Bont, L and Donnay, N and Favier, F and Couturier, J and Didierjean, C and Rouhier, N},
title = {Novel atypical thioredoxins with potential redox activity in eukaryote photosynthetic organisms.},
journal = {Journal of experimental botany},
volume = {76},
number = {13},
pages = {3834-3850},
doi = {10.1093/jxb/eraf066},
pmid = {39980249},
issn = {1460-2431},
support = {//Nationale de la Recherche/ ; },
mesh = {Oxidation-Reduction ; *Thioredoxins/metabolism/genetics/chemistry ; *Photosynthesis ; *Arabidopsis/metabolism/genetics ; Amino Acid Sequence ; *Arabidopsis Proteins/metabolism/genetics/chemistry ; Phylogeny ; },
abstract = {Photosynthetic organisms have a high diversity of proteins belonging to the thioredoxin (TRX) superfamily. It comprises more than 150 proteins distributed in different families and classes, including thioredoxins, glutaredoxins, protein disulfide isomerases, thiol peroxidases, and glutathione transferases, which all share the thioredoxin structural fold. Many of them have one or two redox-active cysteines and a characteristic cis-proline at specific positions, and additional domains or secondary structures at either end or inserted into the protein core. With the aim of further describing the TRX family in plants, we have identified a set of 17 atypical TRX-like proteins from Arabidopsis, which have not been considered before despite having both a TRX fold and the CxxC/S signature typical of redox-active TRXs. In silico sequence and structure analyses revealed that they are divided into eight distinct classes with unique active-site signatures and structures, some with disulfide bond-forming protein A (DsbA) and peroxiredoxin-like folds. Their distinct subcellular localizations (plastids, mitochondria, extracellular space) and gene expression profiles suggest that these proteins are involved in diverse cellular processes, further expanding the set of proteins involved in redox regulation and/or stress adaptation. Our results reveal additional diversity in the structure and function of atypical TRXs in plants.},
}
@article {pmid39993485,
year = {2025},
author = {Li, W and Yang, G and Fan, Y and Yan, X and Li, Z and Guo, Y and Wang, Q and Li, X and Gu, W and Ning, M and Zhou, J and Meng, Q},
title = {Eriocheir sinensis CD63 activate mitochondria-mediated apoptosis to resist Spiroplasma eriocheiris infection.},
journal = {Fish &amp; shellfish immunology},
volume = {161},
number = {},
pages = {110227},
doi = {10.1016/j.fsi.2025.110227},
pmid = {39993485},
issn = {1095-9947},
mesh = {Animals ; *Spiroplasma/physiology ; *Tetraspanin 30/genetics/immunology/chemistry ; *Apoptosis ; *Brachyura/immunology/genetics/microbiology ; Mitochondria ; *Arthropod Proteins/genetics/immunology/chemistry ; *Immunity, Innate/genetics ; Hemocytes/immunology ; Phylogeny ; Amino Acid Sequence ; Sequence Alignment ; },
abstract = {CD63, a member of the tetraspanins, is involved in cell movement, adhesion, immune response. Nevertheless, the role of CD63 in combating pathogen infections in invertebrates remains largely unclear. Tremor disease, whose pathogen is Spiroplasma eriocheiris, is one of the most prevalent illnesses affecting Eriocheir sinensis. EsCD63 is 1474 bp, with a 756 bp open reading frame that encodes for 252 amino acids. The qPCR data demonstrated that gills showed significant levels of transcription for EsCD63, followed by hemocytes, hepatopancreas, intestines and nerves, while showing low levels of transcription in the heart and muscles. After infection with S. eriocheiris, an obvious drop in the transcription level of EsCD63 was observed. Both the amount of S. eriocheiris copies in hemocytes and the mortality of E. sinensis significantly increased after the injection of chemically synthesized EsCD63 siRNA and stimulation with S. eriocheiris. After EsCD63 interference, the phagocytosis of hemocytes to S. eriocheiris, the apoptosis of hemocytes, and reactive oxygen species level of hemocytes were all decreased significantly, by laser scanning confocal microscopy and flow cytometry analysis. Meanwhile, the mitochondrial membrane potential of hemocytes was increased after EsCD63 interference. These findings indicated that EsCD63 was crucial for E. sinensis immunity and defense mechanisms against infection of S. eriocheiris.},
}
@article {pmid39993486,
year = {2025},
author = {He, M and Li, S and Sun, J and Lv, X and Li, Y and Song, L},
title = {CgVDAC2 participated in haemocyte mitophagy induced by Vibrio splendidus in the Pacific oyster Crassostrea gigas.},
journal = {Fish &amp; shellfish immunology},
volume = {160},
number = {},
pages = {110226},
doi = {10.1016/j.fsi.2025.110226},
pmid = {39993486},
issn = {1095-9947},
mesh = {Animals ; *Crassostrea/immunology/genetics/microbiology ; *Vibrio/physiology ; *Mitophagy/genetics ; Hemocytes/immunology ; *Immunity, Innate/genetics ; *Voltage-Dependent Anion Channel 2/genetics/immunology/chemistry ; Phylogeny ; *Gene Expression Regulation/immunology ; Sequence Alignment ; Amino Acid Sequence ; },
abstract = {VDAC2 (Voltage dependent anion channel 2) is a highly conserved pore-forming protein expressed in the outer membrane of eukaryotic mitochondria. In the present study, CgVDAC2 identified from Crassostrea gigas regulated the mitophagy of haemocytes induced by Vibrio splendidus. CgVDAC2 was distributed in the cytoplasm of three subpopulations of haemocytes. After V. splendidus stimulation, the mRNA and protein expressions of CgVDAC2 were induced in haemocytes. Furthermore, the green signals of CgVDAC2 were colocalized with the red signals of mitochondria and Mtphagy Dye, respectively. And their co-localization values were both increased significantly in haemocytes at 12 h after V. splendidus stimulation, respectively. In siCgVDAC2-treated oysters, the mRNA expressions of mitophagy-related genes (CgLC3, CgPINK1, CgParkin1, CgPHB2, and CgATG16L) and the levels of mitophagy decreased significantly in haemocytes after V. splendidus stimulation. In addition, both the fluorescence intensities of the JC-1 monomer/aggregate ratio (Q4/Q2) and mitochondrial reactive oxygen species (mtROS) increased significantly. Collectively, all the results indicated that CgVDAC2 participated in oyster antibacterial immune response through regulating the haemocyte mitophagy.},
}
@article {pmid40000832,
year = {2025},
author = {Du, W and Sun, Q and Hu, S and Yu, P and Kan, S and Zhang, W},
title = {Equus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {6803},
pmid = {40000832},
issn = {2045-2322},
support = {ZR2023QC278//Natural Science Foundation of Shandong Province/ ; 2022YFC3341002-2//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Horses/genetics ; *Equidae/genetics ; *Genome, Mitochondrial ; Phylogeny ; *Domestication ; Genetic Variation ; *Mitochondria/genetics ; China ; },
abstract = {Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes of all species within Equus and conducted a comprehensive pan-mitochondrial genome analysis. We found that the mitochondrial genomes of Equus are highly conserved, each encoding 37 genes, including 13 protein-coding genes (PCGs). Phylogenetic analysis based on mitochondrial genomes supports previous research, indicating that the extant species in Equus are divided into three main branches: horses, donkeys, and zebras. Specifically, 761 genetic variants were identified between donkeys and horses, 68 of which were non-synonymous mutations in PCGs, potentially linked to their different locomotor abilities. Structural protein modeling indicated that despite genetic differences, the overall protein structures between donkeys and horses remain similar. This study revealed the mitochondrial genome variation patterns of domesticated animals, offering novelty perspectives on domestication imprints. Additionally, it provides reliable candidate molecular markers for the identification of donkeys and horses.},
}
@article {pmid40185233,
year = {2025},
author = {Zhao, HF and Wang, Y and Liu, XH and Liu, XH and Geng, Z and Gao, ZQ and Huang, L and Weng, CJ and Dong, YH and Zhang, H},
title = {Structure-function insights into the dual role of African swine fever virus pB318L: A typical geranylgeranyl-diphosphate synthase and a nuclear import protein.},
journal = {Virologica Sinica},
volume = {40},
number = {2},
pages = {236-246},
pmid = {40185233},
issn = {1995-820X},
mesh = {*African Swine Fever Virus/genetics/enzymology/physiology ; Animals ; *Viral Proteins/genetics/metabolism/chemistry ; Structure-Activity Relationship ; Swine ; Phylogeny ; Virus Replication ; Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Nuclear Localization Signals/genetics ; },
abstract = {African swine fever virus (ASFV) pB318L is an important protein for viral replication that acts as a membrane-bound trans-geranylgeranyl-diphosphate synthase (GGPPS) catalyzing the condensation of isopentenyl diphosphate (IPP) with allylic diphosphates. Recently we solved the crystal structure pB318L lacking N-terminal transmembrane region and performed a preliminary structural analysis. In this study, structure-based mutagenesis study and geranylgeranyl pyrophosphate (GGPP) production assay further revealed the key residues for the GGPPS activity. Structural comparison showed pB318L displays a strong similarity to typical GGPPSs instead of protein prenyltransferases. The phylogenetic analysis indicated pB318L may share a common ancestor with the GGPPSs from Brassicaceae plants rather than from its natural host. The subcellular localization analysis showed pB318L is localized in both nucleus and cytoplasm (including the endoplasmic reticulum membrane and mitochondria outer membrane). A unique N-terminal nuclear localization signal (NLS) following the transmembrane region was discovered in pB318L and the NLS was confirmed to be required for the nuclear import. We further revealed the NLS plays an essential role in the interaction with nuclear transporter karyopherin subunit alpha 1 (KPNA1). Their interaction may suppress signal transducers and activators of transcription 1 (STAT1) translocation and subsequently competitively inhibit nuclear import of IFN-stimulated gene factor 3 (ISGF3) complex. Our biochemical, structural and cellular analyses provide novel insights to pB318L that acts as an essential GGPPS that promotes viral replication and as a nuclear import protein that may be involved in immune evasion of ASFV.},
}
@article {pmid40214180,
year = {2025},
author = {Takahashi, K and Lum, WM and Hehenberger, E and Iwataki, M},
title = {Kapelodiniopsis flava n. g., n. sp. (Dinophyceae), a new katodinioid with haptophyte-derived plastids of multiple origins: Implications for the plastid integration process.},
journal = {The Journal of eukaryotic microbiology},
volume = {72},
number = {3},
pages = {e13082},
doi = {10.1111/jeu.13082},
pmid = {40214180},
issn = {1550-7408},
support = {LQ200962204//The Czech Academy of Sciences, Lumina Quaeruntur fellowship/ ; 19KK0160//Japan Society for the Promotion of Science/ ; 21K15150//Japan Society for the Promotion of Science/ ; },
mesh = {*Plastids/genetics/ultrastructure ; Phylogeny ; *Dinoflagellida/genetics/classification/ultrastructure/isolation &amp; purification ; *Haptophyta/genetics/ultrastructure ; DNA, Protozoan/genetics/chemistry ; Japan ; DNA, Ribosomal/genetics/chemistry ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {An autotrophic unarmored dinoflagellate species with haptophyte-derived plastids, Kapelodiniopsis flava n. g., n. sp., was described as a sister taxon of Kapelodinium vestifici, which was formerly well characterized by its low-positioned cingulum and heterotrophic nature. The isolates from several Japanese coastal locations were observed using light microscopy, scanning and transmission electron microscopy, and their phylogeny was inferred from nuclear-encoded rRNA genes and multiple plastid-encoded genes. To date of this publication, a representative culture of Ks. flava has grown autotrophically for 98 months in the absence of prey or organic matter. This dinoflagellate lacked nonplastid haptophyte cell components (e.g. nucleus or mitochondria). In the host dinoflagellate phylogeny, Ks. flava was distantly related to the other two dinoflagellate lineages known to be associated with haptophyte-derived plastids, thus representing the third of such lineage. Plastid origins differed among Ks. flava strains (>99.8% 18S rRNA gene identity), with plastids being derived from at least three haptophytes and an especially strong genetic similarity to two distantly related extant haptophytes (>99.9% 16S rRNA gene identity). This indicates that Ks. flava recently integrated plastids from multiple haptophyte lineages to an extent that allows the host to replicate the plastids without other haptophyte components.},
}
@article {pmid40229680,
year = {2025},
author = {Liu, M and Fan, R and Wang, C and Dai, L and Chu, S},
title = {Complete analysis and phylogenetic analysis of Polygonatum sibiricum mitochondria.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {471},
pmid = {40229680},
issn = {1471-2229},
mesh = {*Polygonatum/genetics/classification ; *Phylogeny ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; Base Composition ; RNA, Ribosomal/genetics ; },
abstract = {In this project, we studied the complete mitogenome of the liliaceae medicinal plant Polygonatum sibiricum. The genome is represented by a circular ring molecule with a length of 691,910 bp and a GC content of 46.33%. Mitochondrial genome composition is slightly biased towards A+T, with AT accounting for 53.67%, and AT skewness slightly positive (0.092%). The complete mitogenome has a total of sixty-three unique genes, including thirty-nine protein-coding genes, twenty-one transfer RNAs (tRNAs) and three ribosomal RNAs (rRNAs). We examined codon use, repeat sequence, RNA editing in the mitogenome of P. sibiricum, and elucidated species classification based on phylogenetic trees of mitogenome of twenty-three species. Our results provide comprehensive information on the mitogenome of P. sibiricum and show for the first time the evolutionary relationship between the mitogenome of P. sibiricum and Chlorophytum comosum in the Asparagales family.},
}
@article {pmid40238856,
year = {2025},
author = {Lawson, LP and Bittencourt-Silva, GB and Conradie, W and Portik, DM and Loader, SP},
title = {A phylogenomic perspective reveals mitochondrial-nuclear discordance and previously undescribed species nested within a widespread East African Reed frog species (Hyperolius substriatus Ahl, 1931).},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0318951},
pmid = {40238856},
issn = {1932-6203},
mesh = {Animals ; Female ; Africa, Eastern ; *Anura/genetics/classification ; *Cell Nucleus/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; *Phylogeny ; Phylogeography ; },
abstract = {The sub-montane East African Reed Frog, Hyperolius substriatus Ahl, 1931 (Spotted Reed Frog) has a fragmented highland distribution throughout East Africa. Previous studies show extensive mitochondrial divergence between four lineages of African Spotted Reed Frogs that roughly correspond to previously-recognized subspecies. These may have conservation implications if formally described. However, as mitochondrial-based population models only track maternal patterns, further genomic datasets are necessary to assess the distinctness of these lineages in relation to historically recognized morphological subspecies. In this study, we expanded sampling to newly discovered localities and assessed mitochondrial and genomic data to better understand phylogeography and landscape genomics of this species. We found that genomic clades (biparentally inherited) confirm some of the mitochondrial structure (female inherited), but also revealed multiple cases of mitonuclear discordance particularly within the Udzungwa Mountain block, which may have two separate founding events based on peripatric mitochondrial lineages and panmictic genomic signals. Taken together, the three clades within the geographical range of H. substriatus through Tanzania, Malawi, and Mozambique correspond to three previously-identified subspecies and lineages, and have both spatially cohesive and population-specific patterns of geneflow and isolation with neighboring highland locations.},
}
@article {pmid40338339,
year = {2025},
author = {Li, X and Liu, D and Han, B and Huang, S and Deng, H},
title = {Genome-wide identification of CYP450 in Ganoderma lucidum and expression analysis of genes related to ganoderic acid synthesis.},
journal = {Archives of microbiology},
volume = {207},
number = {6},
pages = {137},
pmid = {40338339},
issn = {1432-072X},
support = {2023YFC3503804//The National Key Research and Development Program of China/ ; 2023AH052637//Special Funds for Anhui Dabie Mountain Institute of Traditional Chinese Medicine/ ; Anhui [2023] TG07//the 2023 Central Finance Forestry Science and Technology Promotion Demonstration Funds Project/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism ; *Reishi/genetics/enzymology/metabolism ; *Triterpenes/metabolism ; *Fungal Proteins/genetics/metabolism ; *Genome, Fungal ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Phylogeny ; Transcriptome ; },
abstract = {The biosynthesis mechanism of ganoderic acid, a class of secondary metabolites of Ganoderma lucidum, is currently unknown. Members of G. lucidum's CYP450 gene family were found in this study by genome-wide analysis. Determination of ganoderic acid content in Jilin, Zhejiang, Jinzhai, Fujian, Yunnan and Shandong regions was performed using high performance liquid chromatography. Expression of CYP450 gene of G. lucidum from Jilin, Jinzhai and Shandong origins was analyzed by transcriptome sequencing. The findings indicated that, through comprehensive sequence analysis and functional annotation, 189 CYP450 genes were detected in the G. lucidum genome, among which 34 CYP450 genes were significantly differentially expressed in transcriptome analysis, and the gene expression was positively correlated with ganoderic acid content. Bioinformatics analysis predicted the conserved motifs, structural features, and subcellular localization of 189 CYP genes, revealing significant differences in gene structure and protein motif composition among GlCYP450 family members. Subcellular localization revealed that they are located in the plasma membrane, cytoplasm, nucleus, mitochondria, peroxisome, endoplasmic reticulum, extracellular space, and cytoskeleton, suggesting that they have multiple functions. A number of cis-regulatory elements associated with stress responses and phytohormones were identified in the promoter regions of these genes. It demonstrates that ganoderic acid production has been significantly controlled by these P450 genes. These findings offer a crucial theoretical foundation for a thorough comprehension of the process of ganoderic acid production, the bioinformatics role of CYP450 genes in G. lucidum, and the selection and breeding of superior G. lucidum resources.},
}
@article {pmid40398836,
year = {2025},
author = {Chen, X and Chen, Z and Xu, Y and Zou, P and Shen, W and Zhang, Z and Wang, Y},
title = {Genome-wide identification of heat shock protein 90 family in Larimichthys crocea and expression analysis in response to thermal stress and Vibrio parahaemolyticus infection.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {279},
number = {},
pages = {111112},
doi = {10.1016/j.cbpb.2025.111112},
pmid = {40398836},
issn = {1879-1107},
mesh = {Animals ; *Vibrio parahaemolyticus/physiology ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Vibrio Infections/genetics/veterinary/metabolism ; *Perciformes/genetics/microbiology/metabolism ; *Fish Proteins/genetics/metabolism ; *Fish Diseases/genetics/microbiology/metabolism ; *Heat-Shock Response ; Gene Expression Regulation ; Phylogeny ; },
abstract = {Members of the heat shock protein 90 family (HSP90s) are evolutionarily conserved and play crucial roles in protein transport, immune regulation and antigen presentation. In this study, five hsp90s were identified from the genome of large yellow croaker (Larimichthys crocea) and analyzed using bioinformatics. All five identified hsp90s encode proteins with HATPase_c and HSP90 domains, and are mainly localized in the cytoplasm, mitochondria and endoplasmic reticulum. Chromosomal mapping revealed their distribution across three distinct chromosomes. Quantitative real-time PCR (qPCR) analysis showed differential expression patterns of the five hsp90s in 11 tissues. Additionally, their expression dynamics in the liver, spleen, head kidney, gill and blood were analyzed at 3 h, 12 h, 24 h and 48 h post thermal stress, Vibrio parahaemolyticus infection or under a combination of these two stressors. Results showed that the L. crocea hsp90s exhibited distinct expression patterns in response to the above three stimuli in different immune tissues. Notably, hsp90s in the spleen were most responsive. This study systematically clarified for the first time the gene structure characteristics, tissue expression patterns, and environmental stress response mechanisms of the HSP90 family in L. crocea. It confirmed that hsp90s show significant functional differentiation and synergy in response to biotic (pathogen infection) and abiotic (thermal stress) stresses, and provides important clues for a deeper understanding of the genetic basis of environmental adaptation in L. crocea.},
}
@article {pmid40471698,
year = {2025},
author = {Eddo, D and Hodur, Z and Wang, S},
title = {The Hidden Figures at Species Boundaries: The Mitochondrial Energetics Behind Mating Signal Divergence.},
journal = {Integrative and comparative biology},
volume = {65},
number = {2},
pages = {472-480},
doi = {10.1093/icb/icaf058},
pmid = {40471698},
issn = {1557-7023},
support = {//SUNY Research Foundation/ ; },
mesh = {Animals ; *Mitochondria/genetics/physiology/metabolism ; *Energy Metabolism ; *Genetic Speciation ; *Sexual Behavior, Animal ; Gene Flow ; Hybridization, Genetic ; *Animal Communication ; },
abstract = {The energy expenditures of mating signals are often divergent between species and influence heterospecific mating, thus mediating the direction of gene flow across the species boundaries. The relative energetics of the mating signals can be underpinned by mitochondrial haplotype divergence between species, which contributes to hybrid mitonuclear incompatibility and speciation. Here, we discuss the connection between mitochondrial variation, mating signal energetics, and their impact on gene flow across the species boundaries. Using multiple case studies, we highlighted the connections between mitochondrial functions, mating signal energetics, and hybridization across visual, acoustic, kinesthetic, and chemosensory signaling modalities. Integrating mitochondrial functions and mating signal energetics at the species boundaries will illuminate the organismal mechanisms underlying the formation and maintenance of species boundaries.},
}
@article {pmid40527445,
year = {2026},
author = {Fan, Y and Wang, N and Wang, S and Yang, Z and Chen, X and Lu, X and Huang, H and Chen, X and Zhao, L and Zhang, M and Sun, Y and Wang, J and Guo, L and Wang, L and Song, R and Wang, J and Zhang, X and Yu, X and Liu, Y and Zhou, XR and Meng, J and Feng, K and Dai, M and Ye, W},
title = {GhGLDH35A gene-mediated ROS homeostasis and stomatal movement via the ascorbic acid pathway confers alkaline stress tolerance.},
journal = {Journal of advanced research},
volume = {81},
number = {},
pages = {75-94},
pmid = {40527445},
issn = {2090-1224},
mesh = {*Ascorbic Acid/metabolism ; *Reactive Oxygen Species/metabolism ; Homeostasis ; *Plant Stomata/physiology/metabolism ; *Stress, Physiological/genetics ; Arabidopsis/genetics/metabolism ; Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism ; *Alcohol Oxidoreductases/genetics/metabolism ; Phylogeny ; Plants, Genetically Modified ; Oxidoreductases Acting on CH-CH Group Donors ; },
abstract = {INTRODUCTION: Ascorbic acid (AsA) is involved in plant responses to various abiotic stresses. However, its specific function in alkaline stress tolerance remains poorly understood. The L-galactono-1,4-lactone dehydrogenase (GLDH) gene is crucial for AsA synthesis, yet the precise role of GLDH in modulating plant resistance to alkaline stress has not been comprehensively characterized.<br><br>OBJECTIVES: To investigate the role of GLDH genes in enhancing tolerance to alkaline stress.<br><br>METHODS: Bioinformatics analysis of the GLDH gene family members was conducted, and an evolutionary tree was constructed using MEGA software. Cis-acting elements and gene structures were analyzed using TBtools. Gene expression levels were quantified by qRT-PCR, while the function of the GhGLDH35A gene was validated through VIGS (Virus-induced gene silencing) in cotton, heterologous overexpression in Arabidopsis thaliana, and complementation assays in yeast.<br><br>RESULTS: Our study investigated the effects of salt-alkaline stress on cotton and found that alkaline stress caused significantly more severe damage than salt stress. The GLDH family genes were identified and analyzed, revealing a high degree of evolutionary conservation. Most GhGLDH genes exhibited a positive response to alkaline stress and were regulated by light. Among them, GhGLDH35A, which is highly expressed within the GLDH family, was found to play a key role in conferring tolerance to alkaline stress. Subcellular localization analysis indicated that GhGLDH35A is localized in the mitochondria. Silencing of GhGLDH35A in cotton resulted in reduced tolerance to alkaline stress, disruption of ROS homeostasis, and impairment of photosynthesis and stomatal function. Conversely, overexpression of GhGLDH35A in Arabidopsis enhanced alkaline stress resistance by elevating AsA levels, increasing antioxidant enzyme activities to enhance ROS scavenging, sustaining photosynthesis, and promoting stomatal closure. Furthermore, heterologous expression of GhGLDH35A in yeast also improved its tolerance to alkaline stress.<br><br>CONCLUSIONS: GhGLDH35A positively regulates alkaline stress tolerance by enhancing antioxidant defenses and regulating stomatal movement.},
}
@article {pmid40580793,
year = {2025},
author = {Nishu, and Sharma, Y and Deepika, and Kaur, A and Upadhyay, SK},
title = {Exploration of mitochondrial calcium uniporters suggested their role in abiotic stress response in bread wheat.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110180},
doi = {10.1016/j.plaphy.2025.110180},
pmid = {40580793},
issn = {1873-2690},
mesh = {*Triticum/genetics/metabolism/physiology ; *Stress, Physiological/genetics ; *Calcium Channels/metabolism/genetics ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; Phylogeny ; Mitochondria/metabolism ; MicroRNAs/genetics/metabolism ; },
abstract = {Mitochondrial calcium uniporters (MCUs) play a crucial role in calcium transport, signaling, and homeostasis, which is vital for plant growth, development, and stress responses. In this study, we identified 17 TaMCU genes classified into seven homoeologous groups with conserved gene architecture in the bread wheat genome. The structural analysis revealed the presence of MCU domain, DVME motif, transmembrane helices, and various key amino acid residues, which are conserved across all TaMCU proteins. Each TaMCU protein consisted of a mitochondrial targeting peptide and predicted to be localized in the mitochondria. The phylogenetic and synteny analyses provided insights into their evolutionary diverged and conserved nature. Cis-regulatory element analysis suggested that TaMCU genes are involved in abiotic stress responses, involving key transcription factors such as MYB, MBS, W-box, and ERF. Protein-protein interaction study suggested that TaMCUs interact with other mitochondrial and stress-related proteins, such as MICU, PHB, and FREE1. Additionally, six miRNAs related to plant development and stress-response such as miR5384-3p, tae-miR5050 etc., exhibited interactions with a few TaMCU transcripts. RNA-seq expression profiling revealed differential expression of various TaMCU genes in tissue developmental stages and under various stress conditions. qRT-PCR under salinity and drought treatments confirmed the involvement of TaMCU1-D, TaMCU3-A, and TaMCU5-B genes in these stress conditions. These findings provide insights into the potential roles of TaMCU genes and suggest their future applications in the development of abiotic stress-resilient crop plants.},
}
@article {pmid40594503,
year = {2025},
author = {Li, XY and Wang, JQ and Zheng, KW and Li, YT},
title = {Characterization of glutamine synthetase involved in the fecundity of Rhopalosiphum padi.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20461},
pmid = {40594503},
issn = {2045-2322},
support = {31801733//National Natural Science Foundation of China/ ; 31801733//National Natural Science Foundation of China/ ; 31801733//National Natural Science Foundation of China/ ; S202110157032//College Students' Innovation and Entrepreneurship Program of Liaoning Province/ ; S202110157032//College Students' Innovation and Entrepreneurship Program of Liaoning Province/ ; },
mesh = {Animals ; *Aphids/enzymology/genetics/physiology/microbiology ; *Glutamate-Ammonia Ligase/genetics/metabolism ; Fertility/genetics ; *Insect Proteins/genetics/metabolism ; Buchnera/physiology ; Phylogeny ; Symbiosis ; Amino Acid Sequence ; Cloning, Molecular ; },
abstract = {Glutamine synthetase (GS) is a pivotal enzyme crucial for the synthesis of glutamine (Gln), an important precursor in amino acid biosynthesis, essential for the growth, development, and reproduction of insects through its involvement in nitrogen metabolism. Despite its recognized significance in insect biology, the specific functions of GS in aphids have not been fully elucidated. Here, we cloned and characterized two GS genes, RpGS1 and RpGS2, from Rhopalosiphum padi and analyzed their expression profiles and explored the contribution of RpGS to aphid fecundity. The two isoforms, which are predicted to localize in the mitochondria and cytoplasm respectively, were successfully cloned and heterologously expressed in Escherichia coli. Despite exhibiting 92% amino acid similarity, the isoforms displayed distinct enzymatic kinetic properties and demonstrated variations in mRNA expression levels across developmental stages and tissues. Notably, RpGS1 was highly expressed in the head, whereas RpGS2 was highly expressed in the intestine. Both RpGS genes were significantly expressed in alate adult aphids. Treatment with the specific inhibitor L-methionine S-sulfoximine (MSX) not only suppressed enzyme activity but also downregulated gene expression. Furthermore, inhibition of RpGS led to a marked decrease in the abundance of the obligate symbiont Buchnera and reduced the fecundity of R. padi. The transcript levels of RpVg and RpGT were also downregulated. These findings underscore the significant role of RpGS in regulating fecundity, suggesting its potential as a target for insecticide development in pest management strategies.},
}
@article {pmid40603484,
year = {2025},
author = {Gardellin, JV and Gestich, CC and Galetti, PM and Portela, L and Guimarães, VY and de Melo, FR and Goldberg, A and de Freitas, PD},
title = {Genetic diversity and structure of red handed howler monkeys assessed by mitochondrial and genotyping by sequencing analyses.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23418},
pmid = {40603484},
issn = {2045-2322},
support = {CEPID-CBioClima 2021/10639-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; R35 GM133481/GM/NIGMS NIH HHS/United States ; 303524/2019-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2021/05923-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; R01 AI175622/NH/NIH HHS/United States ; R01 AI175622/AI/NIAID NIH HHS/United States ; 150808/2019-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 317345/2021-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; *Genetic Variation ; *Alouatta/genetics/classification ; Phylogeny ; Haplotypes ; *DNA, Mitochondrial/genetics ; Genotype ; Brazil ; *Mitochondria/genetics ; Sequence Analysis, DNA ; Genotyping Techniques ; },
abstract = {The red-handed howler monkey, Alouatta belzebul, has an uncertain taxonomy complex that includes A. belzebul, A. discolor and A. ululata. These primates are endemic to Brazil and are classified as vulnerable or endangered by the IUCN Red List due to population declines over the past 40 years. Damming by hydroelectric power plants is the greatest threat to the taxa. The recent implantation of the fourth largest dam worldwide (Belo Monte Hydroelectric Dam, UHBM) threatens their populations, because its flooding zone covers areas where A. belzebul and A. discolor may co-occur. Determining species classification is crucial for conservation efforts. Here, we characterized the genetic diversity and structure of howler monkeys rescued before the flooding. We performed Genotyping by Sequencing (GBS) analyses and constructed a mitochondrial-based phylogenetic tree and a haplotype network in specimens identified as A. belzebul, based on their coat color, from both banks of the Xingu River and three islands. The study revealed the occurrence of both taxa, indicating high genetic diversity. These findings are valuable for understanding group diversity, providing reference data for monitoring populations in the region and implementing conservation actions, as well as serving as a model for similar studies of other taxa.},
}
@article {pmid40652880,
year = {2025},
author = {Zhang, X and Lu, X and Dai, M and Fan, Y and Yang, Z and Sun, Y and Yu, X and Song, R and Zhang, M and Lan, H and Chen, X and Wang, S and Wang, J and Guo, L and Li, L and Li, Y and Zhao, L and Hao, F and Ye, W},
title = {Citrate accumulation mediated through GhCS6 enhances antioxidant modulation under Cd[2+] stress in cotton.},
journal = {Plant physiology and biochemistry : PPB},
volume = {228},
number = {},
pages = {110226},
doi = {10.1016/j.plaphy.2025.110226},
pmid = {40652880},
issn = {1873-2690},
mesh = {*Cadmium/toxicity/metabolism ; *Gossypium/metabolism/genetics/drug effects ; *Antioxidants/metabolism ; *Plant Proteins/metabolism/genetics ; *Citric Acid/metabolism ; *Citrate (si)-Synthase/metabolism/genetics ; Gene Expression Regulation, Plant/drug effects ; Reactive Oxygen Species/metabolism ; Oxidative Stress/drug effects ; *Stress, Physiological/drug effects ; Hydrogen Peroxide/metabolism ; Phylogeny ; },
abstract = {Citrate synthase (CS) catalyzes the biosynthesis of citrate (CA), a tricarboxylic acid metabolite that serves as a pivotal biochemical regulator in plant cellular metabolism. This investigation conducted systematic genome-wide identification of CS family, integrating structural, phylogenetic relationships, collinearity analysis, cis-acting elements and expression analysis. GhCS6 protein is localized in the mitochondria. The pivotal cadmium-responsive regulatory candidate gene GhCS6 was identified, followed by its silencing mediation through virus-induced gene silencing (VIGS), silenced plants displaying phenotypic evidence of enhanced Cd[2+] susceptibility. Simultaneously, CA content in the silenced plants was also significantly decreased, which reduced the chelating capacity for Cd[2+] and consequently exacerbates the accumulation of Cd[2+]. The silenced plants showed an imbalance in the reactive oxygen species (ROS) scavenging system, as evidenced by lower superoxide dismutase (SOD) activity and a marked increase in H2O2 content, causing increased oxidative damage. This oxidative stress further compromised the integrity of cellular membranes, resulting in elevated malondialdehyde (MDA) content and compromised cellular structure. These changes ultimately impaired photosynthetic efficiency and plant growth and development. This study contributes significantly to understanding the function of the GhCS6 in plant Cd[2+] tolerance, and identifies potential gene targets for breeding Cd[2+] tolerant cotton varieties.},
}
@article {pmid40654039,
year = {2025},
author = {Saha, S and Hearn-Thomas, B and Marisa, V and Depiazzi, K and Schaefer, M and Murcha, MW},
title = {Structural and Functional Perspectives on Mitochondrial LYR-Domain Proteins in Plants.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70393},
pmid = {40654039},
issn = {1399-3054},
support = {DP210103258//Australian Research Council/ ; //Australian Government's Research Training Program/ ; //University of Western Australia/ ; },
mesh = {*Arabidopsis/metabolism/genetics ; *Mitochondrial Proteins/metabolism/genetics/chemistry ; *Arabidopsis Proteins/metabolism/genetics/chemistry ; *Mitochondria/metabolism ; Gene Expression Regulation, Plant ; Protein Domains ; Phylogeny ; },
abstract = {Arabidopsis thaliana contains 12 nuclear-encoded mitochondrial LYR (leucine/tyrosine/arginine) motif-containing proteins (LYRMs). Four of these proteins have been previously characterized in plants and were found to be involved in iron-sulfur cluster biogenesis and/or respiratory complex assembly. The function of the remaining eight is yet to be determined. Evolutionary analysis revealed that several LYRM proteins are unique to plants, while others share evolutionary ties with metazoans and fungi. Protein localization studies confirmed mitochondrial targeting for all 12 proteins, and expression profiles indicated high transcript abundance during germination and in developing tissues. Structural modeling highlighted the potential role of the LYR domain in protein-protein interactions with mitochondrial acyl carrier proteins, subunits of respiratory complexes, and chaperones. These findings enhance our understanding of the diverse roles of LYRM proteins in mitochondrial function in plants.},
}
@article {pmid40660128,
year = {2025},
author = {Miyata, M and Nomura, M and Kageyama, D},
title = {Elusive origin of mitochondria shared by two sister species of Eurema butterflies.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {71},
pmid = {40660128},
issn = {2730-7182},
support = {18J21090//JSPS KAKENHI/ ; 23K26922//JSPS KAKENHI/ ; },
mesh = {Animals ; *Butterflies/genetics/microbiology/classification ; *Wolbachia/genetics/physiology ; Phylogeny ; DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Haplotypes ; Japan ; Symbiosis ; },
abstract = {BACKGROUND: Wolbachia are maternally inherited arthropod endosymbionts known for their diverse effects on host reproduction, which serve to increase their prevalence in host populations. As Wolbachia spreads, the frequency of the associated mitochondrial DNA (mtDNA) haplotypes tends to increase within the host population. Two distinct Wolbachia strains, wCI and wFem, are shared by two pierid butterfly sister species: Eurema mandarina and Eurema hecabe. The congruence of mtDNA phylogeny and Wolbachia infection status suggests hybrid introgression of mtDNA from E. hecabe to E. mandarina. This inference is based on the observation that uninfected E. mandarina have unique mtDNA haplotypes, distinct from the mtDNA haplotypes found in Wolbachia-infected E. mandarina and E. hecabe. In E. hecabe, Wolbachia infection has been considered fixed, with no expectation of uninfected individuals.<br><br>RESULTS: Unexpectedly, Wolbachia-free E. hecabe individuals were discovered on the Yonaguni Island of Japan. We included these individuals in the phylogenetic analyses to reassess the impact of Wolbachia infection on Eurema butterflies. The nuclear Triosephosphate isomerase gene-based phylogenetic tree formed two discrete clades corresponding to E. mandarina and E. hecabe. Contrastingly, the mitochondrial cytochrome c oxidase subunit I gene-based tree consisted of three clades, Wolbachia-free E. mandarina, Wolbachia-free E. hecabe, and a clade consisting of Wolbachia-infected E. mandarina and E. hecabe, as well as two other Eurema species, Eurema ada and Eurema lacteola.<br><br>CONCLUSIONS: Our findings indicate that the mitochondria shared by E. mandarina and E. hecabe likely originate from a different species of Eurema (E. ada, E. lacteola, or others). Although the origin was not identified, our results indicate that Wolbachia provides significant evolutionary advantages to the associated mtDNA haplotypes across multiple Eurema species, leading to a complex mtDNA phylogeny.},
}
@article {pmid40757463,
year = {2025},
author = {Elwan, MM and Madkour, FA and Salem, MM and El-Nahass, EE},
title = {Kidney Morphology in Marine and Terrestrial Birds and Its Phylogenetic Links to Mammals via Aquaporin (AQP) Genome Sequences.},
journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology},
volume = {343},
number = {9},
pages = {1072-1089},
doi = {10.1002/jez.70018},
pmid = {40757463},
issn = {2471-5646},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Animals ; *Phylogeny ; *Kidney/anatomy &amp; histology/ultrastructure ; *Chickens/anatomy &amp; histology/genetics ; *Ducks/anatomy &amp; histology/genetics ; *Aquaporins/genetics ; Genome ; },
abstract = {The kidney is the main osmoregulatory organ in terrestrial vertebrates and depends on water conservation for survival. Only birds, among vertebrates other than mammals, can concentrate their urine as an adaptation to live in terrestrial environments. The water inflow of collecting duct epithelial cells is controlled by aquaporin 2 (AQP2) and an arginine vasotocin (AVT)-sensitive water channel expressed along cortical and medullary collecting ducts. This study aims to examine the anatomical, histological, histochemical, and ultrastructural variations in the kidneys of two avian species: marine birds, mallard duck (Anas platyrhynchos), and terrestrial birds, domestic chicken (Gallus gallus domesticus). Furthermore, phylogenetic relationships have been used to compare the AQP2 genome sequences of these two species with those of mammalian vertebrates. Histologically, the kidneys of the two studied species did not differ in structure. In the mallard, the renal lobule was comparatively divided into an elongated medulla (30%) and cortex (70%) and had more abundant cortical reptilian nephrons. However, the chicken renal lobule was a larger cortical region (85%) than the medullary region (15%) and had more mammalian nephrons. The brush border of the proximal convoluted tubules and the basement membrane of the nephron lining cells were positive for PAS stain but negative for AB, whereas the collecting ducts and the luminal surfaces of the distal convoluted tubules were positive for AB. Glomeruli and proximal convoluted tubules were more likely to react with bromophenol blue stain in chicken than in duck. TEM revealed that the cells lining the proximal, distal, and collecting renal tubules, as well as collecting ducts in duck, contained active and hypertrophied mitochondria, so the kidneys were more active in duck than in chicken. Multiple sequence alignment and phylogenetic tree analysis revealed that the anticipated genomic sequences of AQP2 are relatively conserved among avian species. In conclusion, studies of nephrons have identified both interspecies similarities and intraspecies differences among avian species.},
}
@article {pmid40759308,
year = {2025},
author = {Capodifoglio, KRH and Schneberger, F and Maia, AAM and Ranzani-Paiva, MJT},
title = {Mitochondrial dynamics and description of a novel Myxobolus species infecting Piaractus mesopotamicus in Brazil.},
journal = {Acta tropica},
volume = {269},
number = {},
pages = {107767},
doi = {10.1016/j.actatropica.2025.107767},
pmid = {40759308},
issn = {1873-6254},
mesh = {Brazil ; Animals ; *Myxobolus/classification/isolation &amp; purification/genetics/cytology/ultrastructure ; Phylogeny ; *Fish Diseases/parasitology ; *Parasitic Diseases, Animal/parasitology ; *Mitochondria/ultrastructure ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Gills/parasitology ; Characiformes/parasitology ; },
abstract = {A new Myxobolus species was identified infecting the gill arch of Piaractus mesopotamicus from a fish farm in São Paulo State, Brazil, and is described based on morphological, molecular, and biological data. Mature myxospores of Myxobolus naldonensis n.sp. were round in frontal view, with a length of 9.0 ± 0.3 µm, a width of 5.9 ± 0.3 µm, and a thickness of 5.2 ± 0.1 µm in the lateral view. Its polar capsules were elongated and equal size, occupying more than half of the myxospore, measuring 4.4 ± 0.2 µm in length, 1.7 ± 0.1 µm in width, and the polar tubules had 5 - 7 coils. Ultrastructural analysis revealed that the plasmodial wall was composed of a single membrane and that the sporogenesis process was asynchronous, with early developmental stages of myxospores in the periphery of the plasmodia and mature myxospores in the central part. Numerous mitochondria and pinocytotic channels were observed in the ectoplasm. Confocal analysis showed labeling of the nuclei of the sporoplasm, as well as of the valves and polar capsules. In mature myxospores a volume mitochondrial could be detected, but no labeling indicative of mitochondrial activity was observed. Molecular analysis based on the amplification and sequencing of small subunit ribosomal DNA (SSU rDNA) resulted in a 1968 bp sequence. Phylogenetic analysis grouped Myxobolus naldonensis n. sp. as sister species of Myxobolus tambaquiensis, which infects Colossoma macropomum, a fish belonging to the family Serrasalmidae.},
}
@article {pmid40812757,
year = {2025},
author = {Xi, K and Jin, Y and Lin, L and Fang, J and Wei, W and Lin, J and Huang, X and Huang, Y and Zhang, Y and Qin, Q},
title = {Grouper SPL promotes STING- and IRF3-mediated antiviral immune response against iridovirus infection.},
journal = {Fish &amp; shellfish immunology},
volume = {166},
number = {},
pages = {110654},
doi = {10.1016/j.fsi.2025.110654},
pmid = {40812757},
issn = {1095-9947},
mesh = {Animals ; *Fish Diseases/immunology/virology ; *Immunity, Innate/genetics ; *DNA Virus Infections/immunology/veterinary ; Fish Proteins/genetics/immunology/chemistry ; Ranavirus/physiology ; *Bass/immunology/genetics ; *Gene Expression Regulation/immunology ; Interferon Regulatory Factor-3/genetics/immunology ; Phylogeny ; Gene Expression Profiling/veterinary ; Sequence Alignment/veterinary ; },
abstract = {Sphingosine-1-phosphate (S1P) lyase (SPL) was an intracellular enzyme that catalyzes the degradation of the bioactive lipid S1P. Singapore grouper iridovirus (SGIV), a highly pathogenic large cytoplasmic dsDNA virus, had caused significant economic losses in aquaculture and threatened biodiversity. Though SPL had been reported to be crucial for several crucial cellular functions due to its roles in S1P metabolism, the roles of SPL in fish virus infection remained poorly understood. Herein, we found the positive regulatory role of grouper SPL (EcSPL) on the host's innate immune responses against SGIV infection. EcSPL encoded a 563 amino acid protein, containing one DOPA domain (140-502 aa). Quantitative real time PCR (qPCR) analysis showed that EcSPL was constitutively expressed in all examined tissues, and the expression of EcSPL was induced by SGIV infection in a time dependent manner. Subcellular localization revealed that EcSPL was distributed in the cytoplasm, and partly colocalized with the endoplasmic reticulum, mitochondria, and lysosomes. Overexpression of EcSPL significantly reduced the transcription and protein expression of the viral genes, as well as the severity of the cytopathic effects (CPEs) caused by SGIV, thereby suppressing SGIV replication. Meanwhile, EcSPL overexpression potently increased the promoter activity of interferon1 (IFN1), interferon3 (IFN3), and nuclear factor kappa-B (NF-κB), as well as the expression of pro-inflammatory cytokines and interferon related genes. Furthermore, EcSPL overexpression further augmented the promoter activity of IFN1, IFN3, and NF-κB triggered by STING (stimulator of interferon genes) and IRF3 (interferon regulatory factor 3), but not TBK1 (TANK-binding kinase 1). Mechanistically, EcSPL interacted with EcSTING and EcIRF3. Consistently, these key adaptors were found to be co-located with EcSPL. The study provided the first evidence that EcSPL as an antiviral host factor, restricted SGIV replication by directly enhancing EcSTING- or EcIRF3-mediated antiviral immune response. Our findings revealed a novel role for EcSPL in teleost immune defense against viral infection.},
}
@article {pmid40897671,
year = {2025},
author = {Meyer, EH and Lopez-Lopez, A and Keech, O and Rouhier, N},
title = {The Expanded LYR Motif-Containing Protein Family in Archaeplastida.},
journal = {Physiologia plantarum},
volume = {177},
number = {5},
pages = {e70482},
doi = {10.1111/ppl.70482},
pmid = {40897671},
issn = {1399-3054},
support = {FFF20-0008//Swedish Foundation for Strategic Research/ ; ME 4174/3-1//Deutsche Forschungsgemeinschaft/ ; ANR-11-LABX-0002-01//Agence Nationale de la Recherche/ ; //Lorraine University of Excellence (LUE)/ ; //Knut and Alice Wallenberg Foundation/ ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; *Eukaryota/genetics/metabolism ; Plants/genetics/metabolism ; },
abstract = {The LYR motif (LYRM)-containing proteins are small eukaryote-specific proteins that have been defined based on the presence of a Lys-Tyr-Arg amino acid motif and a conserved triplet of α-helices. Twelve LYRM proteins were described in humans. They are involved in core mitochondrial processes as subunits or assembly/stabilising factors of mitochondrial complexes. Their function depends on their ability to interact with the acylated form of acyl-carrier proteins (mtACPs), which places these proteins as direct contributors to two intertwined functional processes, energy metabolism and mitochondrial biogenesis. To gain insight into LYRM proteins in Archaeplastida, we first analyzed the Arabidopsis thaliana genome and then a set of organisms representing the different groups of the Archaeplastida clade. This analysis revealed the existence of 17 classes encompassing 10 of the 12 LYRM classes found in humans. Eleven classes exist in Arabidopsis, and six additional classes are present in some organisms but not in Arabidopsis, thus expanding previous observations. Subsequent data mining based on literature, gene expression, and in silico analyses allowed us to speculate about the possible molecular function of some currently uncharacterised LYRMs in plants. Altogether, this study revealed the diversification of the LYRM protein family in Archaeplastida and more globally among eukaryotes, in which the LYRM-mtACP associations represent central molecular systems to regulate mitochondrial biogenesis upon fluctuating growth conditions.},
}
@article {pmid40911529,
year = {2025},
author = {Adler, MJ and Martin, MM and Rozo-Lopez, P and Parker, BJ},
title = {A novel mitovirus associated with the fungal entomopathogen Zoophthora radicans.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331239},
pmid = {40911529},
issn = {1932-6203},
mesh = {Animals ; *Aphids/microbiology/virology ; *Entomophthorales/virology/genetics ; Phylogeny ; Genome, Viral ; *RNA Viruses/genetics ; },
abstract = {Metatranscriptome sequencing has emerged as a powerful tool for uncovering viral diversity in insects and their associated microbes. To explore viruses linked to the pea aphid (Acyrthosiphon pisum), we performed metatranscriptome sequencing on field-collected samples. In addition to several known plant viruses, we assembled the genome of a new virus homologous to species in the family Mitoviridae, which are positive-sense single-stranded RNA viruses that encode only an RNA-dependent RNA polymerase and typically replicate in mitochondria. Given the frequent association of mitoviruses with fungi and the presence of entomopathogenic fungal reads in our dataset, we conducted 18S amplicon sequencing and PCR screening on individual aphids. These analyses identified two fungal entomopathogens and uncovered an association between the mitovirus and Zoophthora radicans, a generalist aphid pathogen. Our findings shed light on the hidden microbial diversity in natural pea aphid populations and emphasize the utility of metatranscriptomics in identifying novel virus-host associations.},
}
@article {pmid40914435,
year = {2026},
author = {Yang, X and Li, X and Li, H and Yu, Y and Qin, C},
title = {MdBACT5 and MdBACT8 contribute to the formation of branched-chain volatiles in apple.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {362},
number = {},
pages = {112742},
doi = {10.1016/j.plantsci.2025.112742},
pmid = {40914435},
issn = {1873-2259},
mesh = {*Malus/genetics/metabolism/enzymology ; *Plant Proteins/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; Phylogeny ; *Transaminases/genetics/metabolism ; Gene Expression Regulation, Plant ; *Amino Acids, Branched-Chain/metabolism ; },
abstract = {Branched-chain amino acid aminotransferases (BCATs) catalyze both the final anabolic step and the initial catabolic step of branched-chain amino acids (BCAAs), which are pivotal for the formation of plant branched-chain volatiles (BCVs). However, the members of BCAT family in apple (Malus domestica Borkh.) remain poorly characterized. In the current study, we identified nine BCAT genes in the apple genome. Phylogenetic analysis classified these MdBCATs into two groups distributed across five chromosomes, with conserved gene structures within each group. Physicochemical analysis revealed coding sequence (CDS) lengths ranging from 852 to 1248 bp, encoding proteins with molecular weights of 31.13 45-41 kDa and isoelectric points (pI) of 5.86-8.35. Collinearity analysis indicated that segmental duplication predominantly drove the expansion of the apple BCAT family. Promoter regions of MdBCATs harbored cis-acting elements associated with growth and development, stress responses, and hormone signaling. RT-qPCR analysis demonstrated differential expression patterns of MdBCATs in the peel tissue of 'Oregon Spur II' apples during ambient storage. Subcellular localization revealed plastid- and mitochondrial-targeting of specific MdBCATs. Notably, transient overexpression of mitochondrially-localized MdBACT5 and MdBACT8 significantly enhanced BCV biosynthesis. Taken together, this study provides critical insights into the role of BCATs in apple fruit aroma quality.},
}
@article {pmid40919755,
year = {2025},
author = {Xu, L and Guo, P and Kuang, Y and Su, K and Hu, K and Gan, D},
title = {Characteristics of the MAPK gene family in Zizania latifolia and MAPK3 role in response to fungal pathogen infection.},
journal = {Journal of genetics},
volume = {104},
number = {},
pages = {},
pmid = {40919755},
issn = {0973-7731},
mesh = {*Plant Diseases/microbiology/genetics ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; *Mitogen-Activated Protein Kinases/genetics/metabolism ; *Poaceae/genetics/microbiology ; *Plant Proteins/genetics/metabolism ; Phylogeny ; Multigene Family ; Ustilago/pathogenicity ; Host-Pathogen Interactions/genetics ; Arabidopsis/genetics/microbiology ; },
abstract = {The stems of Zizania latifolia, an important vegetable in China, are targeted by the pathogen Ustilago esculenta, triggering a response through the mitogen-activated protein kinase (MAPK) signalling pathway. To investigate the characteristics and the role of MAPK gene family in the biological stress response, a bioinformatics-based analysis was performed, and the expression patterns of ZlMPKs and MAPK-infection pathway-related genes were detected in male plants inoculated with U. esculenta. Twenty-five ZlMPK genes were identified and divided into four subgroups A, B, C and D: carried a conserved TEY motif, while D had a conserved TDY motif. The ZlMPKs were located in the nucleus, cytoplasm, chloroplast, mitochondria, and peroxisome, and most exhibited evidence of gene duplication events. The relative expression of most ZlMPKs was the highest at 3 h after inoculation with U. esculenta, with 21 ZlMPKs being upregulated and four being downregulated. Additionally, nine of 11 MAPK-infection pathway-related genes were upregulated at 3 h after inoculation. ZlMPK3 was cloned and transformed into Arabidopsis thaliana, and two overexpression lines were identified by resistance screening and molecular detection. Their responses to Botrytis cinerea infection were studied. The leaf inoculation sites of ZlMPK3-overexpression plants revealed damage, while those of wild-type plants did not. The relative expression of MAPK pathogen related genes was altered after inoculation. Specifically, the expression levels of the ethylene biosynthetic pathway gene AtACS6 and five cysteine-rich secretory protein CAP genes were significantly upregulated, while those of systemic acquired resistance marker gene, pathogenesis-related 1 AtPR1 and early defense signalling gene AtFRK1 were significantly downregulated, indicating that resistance to B. cinerea was weakened in the ZlMPK3-overexpression lines.},
}
@article {pmid40943134,
year = {2025},
author = {Lin, D and Zhao, X and Hu, Q and Wang, S and Zhang, Y and Xu, Z},
title = {Genome-Wide Identification, Phylogenetic Analysis, and Expression Pattern of Polyamine Biosynthesis Gene Family in Pepper.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943134},
issn = {1422-0067},
support = {2024LZGC013//Key R&amp;D Program of Shandong Province/ ; 25-1-5-xdny-13-nsh//Science &amp; Technology for Public Benefit Demonstration Project of Qingdao/ ; 2024TZXD019//Sci-Tech Innovation Action Plan for Rural Vitalization of Shandong Province/ ; SDAIT0507//Vegetable Industrial Technology System of Shandong Province/ ; 24-4-4-zrjj-27-jch//Natural Science Foundation of Qingdao/ ; },
mesh = {*Capsicum/genetics/metabolism ; *Polyamines/metabolism ; *Gene Expression Regulation, Plant ; Phylogeny ; Stress, Physiological/genetics ; Multigene Family ; *Plant Proteins/genetics/metabolism ; *Genome, Plant ; Plant Growth Regulators/metabolism ; Promoter Regions, Genetic ; },
abstract = {Polyamines (PAs), including putrescine, spermidine, spermine, and thermospermine, play essential roles in plant growth, development, and responses to stress. However, the structure and function of PA biosynthetic genes in pepper remain poorly characterized. This study aimed to identify PA biosynthesis genes in the pepper genome using bioinformatics approaches and to assess their expression under various stress conditions. A total of 16 PA biosynthesis-related genes were identified, representing members of the arginine decarboxylase (ADC), ornithine decarboxylase (ODC), agmatine iminohydrolase (AIH), N-carbamoylputrescine amidohydrolase (CPA), S-adenosylmethionine decarboxylase (SAMDC), spermidine synthase (SPDS), spermine synthase (SPMS), and ACAULIS5 (ACL5) gene families. These genes encode proteins with an average molecular weight of approximately 40 kDa, primarily localized in the mitochondria and cytoplasm. Promoter analysis revealed multiple cis-acting elements associated with stress and phytohormone responsiveness. Gene expression was induced by various abiotic stresses, including saline-alkaline, drought, heat, cold, and hydrogen peroxide, as well as by phytohormones such as abscisic acid, ethylene, salicylic acid, auxin, and gibberellin. Overall, this study provides a comprehensive analysis of PA biosynthesis genes in pepper and highlights their potential roles in stress adaptation and hormone signalling, offering a foundation for further exploration of PA-mediated stress tolerance mechanisms.},
}
@article {pmid40980060,
year = {2025},
author = {Russell, JE and Mizera, N and Brown, CG and Chuang, A and Coyle, DR and Nelsen, DR},
title = {Mitochondrial and Wolbachia phylogenetics of the introduced Jorō spider, Trichonephila clavata (Araneae: Araneidae) in North America.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19952},
pmid = {40980060},
issn = {2167-8359},
mesh = {Animals ; *Wolbachia/genetics/classification ; *Phylogeny ; *Spiders/microbiology/genetics ; Genetic Variation ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Mitochondria/genetics ; Sequence Analysis, DNA ; North America ; Georgia ; },
abstract = {The introduction of Trichonephila clavata (L. Koch, 1878) (Araneae: Araneidae: subfamily Nephilinae) in the United States was first recorded in Georgia in 2014. Since its introduction, T. clavata has become a prominent feature of the arthropod fauna in several southeastern US states. Many questions regarding the introduction event(s) remain unanswered; for instance, was the introduction a single discrete event followed by rapid spread, or were there multiple introductions? The mitochondrial cytochrome c oxidase subunit one gene region (COI), which was used to characterize the initial T. clavata observation in the US, has also been used to characterize within- and between-population genetic variation. One confounding factor for COI as a population genetic molecular marker, though, is the presence of cytoplasmic agents of selection such as intracellular bacteria in the genus Wolbachia. Given that Wolbachia infections have been detected in potential source populations of T. clavata, the present study sought to characterize mitochondrial genetic diversity and the status of Wolbachia infection in the North American population(s) closest to the originally proposed introduction site in Georgia. DNA sequencing revealed no mitochondrial genetic variation in the T. clavata population sampled in North America, and an exact sequence match to the previously reported T. clavata in Georgia and a sequence sample from Yunnan, China. Wolbachia was detected in the North American samples. However, phylogenetic analysis on a concatenated multi-locus type sequence suggested two distinct Wolbachia clades, one represented by samples collected in Georgia and another represented by a single sample collected in South Carolina. Sequence analyses of the multi-locus gene regions suggested that the Georgia T. clavata may be infected with two strains of Wolbachia (super-infection), and the South Carolina sample represented a separate single infection. The study's results emphasize the need for further research, including expanded sampling in the introduced and potential source population regions, as well as a more detailed molecular characterization of the populations.},
}
@article {pmid41009599,
year = {2025},
author = {Gong, Y and Chen, R and Yang, C and Lu, Y and Fu, Z and Feng, Y and Li, X and Li, L and Li, X},
title = {Genomic-Encoded Mitovirus RdRp Is Required for Embryo Development and Maintaining Mitochondrial Dynamics in Arabidopsis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
pmid = {41009599},
issn = {1422-0067},
support = {No.32171920//National Natural Science Foundation of China/ ; },
mesh = {*Arabidopsis/genetics/virology/embryology/growth &amp; development/metabolism ; *RNA-Dependent RNA Polymerase/genetics/metabolism ; *Mitochondrial Dynamics/genetics ; Mitochondria/metabolism/genetics ; Phylogeny ; *Seeds/genetics/growth &amp; development ; *Arabidopsis Proteins/genetics/metabolism ; *Viral Proteins/genetics/metabolism ; Gene Expression Regulation, Plant ; },
abstract = {Mitoviral-derived sequences are frequently detected in plant genomes, encoding an RNA-dependent RNA polymerase (RdRp). These sequences share many similarities with mitoviruses that are known to commonly infect plant mitochondria. However, the functional characterization of nuclear-encoded mitoviral-RdRp remains unclear. This study elucidates the critical role of mRdRp (AT2G07749) in maintaining mitochondrial homeostasis and embryo viability, highlighting the dual role of viral-derived genes in plant development and stress response. Phylogenetic analysis reveals that mRdRp shares 96.8% identity with the mitoviral RdRp encoded by mitochondrial-genomes, suggesting that this nuclear mRdRp gene originated from horizontal transfer events following ancestral plant-mitovirus infections. To dissect mRdRp function, we generated a mRdRp knockout mutant via CRISPR-Cas9 or knockdown mutant by RNA interference (RNAi). These mRdRp mutants exhibited severe developmental defects, including dwarfism, embryo lethality, and sterility. Phenotypic assays further showed that mRdRp mutants displayed heightened susceptibility to ABA and rotenone, indicating impaired adaptive capacity to both hormonal and metabolic stress. Loss of mRdRp led to fragmented mitochondrial networks and a significant reduction in mitochondrial abundance in both leaf protoplasts and root meristematic cells. Additionally, mitochondrial-derived small RNA (sRNA) aberrantly accumulated in mRdRp mutants, which potentially disrupts endogenous RNA-silencing pathways that rely on sRNA-mediated gene regulation. Collectively, these results provide mechanistic insights into the function integration of a virus-derived gene into plant cellular networks, advancing our understanding of host-virus coevolution and the role of horizontally transferred viral genes in shaping plant physiology.},
}
@article {pmid41009977,
year = {2025},
author = {Zhou, B and Guan, C and Guan, M},
title = {Genome-Wide Identification of the BnaRFS Gene Family and Functional Characterization of BnaRFS6 in Brassica napus.},
journal = {Genes},
volume = {16},
number = {9},
pages = {},
pmid = {41009977},
issn = {2073-4425},
support = {HARS-03//Hunan Agriculture Research System/ ; },
mesh = {*Brassica napus/genetics/metabolism/growth &amp; development ; *Plant Proteins/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant ; Multigene Family ; *Galactosyltransferases/genetics/metabolism ; },
abstract = {BACKGROUND: Raffinose synthase (RFS) plays a crucial role in plant growth and development, as well as in responses to biotic and abiotic stresses. However, its functions in Brassica napus remain poorly understood.<br><br>METHODS: To investigate the characteristics of the RFS gene family in B. napus (rapeseed), five Arabidopsis thaliana RFS gene sequences were used as references to identify thirteen RFS genes in B. napus, four in Brassica rapa, and six in Brassica oleracea. A comprehensive analysis was conducted, including molecular characteristics, phylogenetic relationships, conserved protein motifs, gene structures, and chromosomal localization.<br><br>RESULTS: BnaC02G0100500ZS was selected as a candidate gene due to its unique expression profile. Sequence alignment identified it as BnaRFS6, and subcellular localization revealed that its encoded protein is localized in the mitochondria. Overexpression of BnaRFS6 in rapeseed significantly affected the soluble sugar and starch content in the stalks, resulting in increased levels of fructose, glucose, and raffinose, and a decreased starch content.<br><br>CONCLUSIONS: These findings highlight the role of BnaRFS6 in enhancing sugar metabolism in B. napus, particularly in relation to fructose, glucose, and raffinose accumulation. Understanding its potential function provides a foundation for improving the sugar content and taste of rapeseed stalks through genetic engineering in the future.},
}
@article {pmid41023160,
year = {2025},
author = {Brocklebank, JW and Davies, L and Hancock, J and Metta, M and Juani, K and Engkias, J and Goossens, B and Orozco-terWengel, P},
title = {Maternal origins and genetic diversity of Sabahan swamp buffalo using mitochondrial cytochrome b gene.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33685},
pmid = {41023160},
issn = {2045-2322},
support = {NE/X016714/1//Natural Environment, Biotechnology and Biological Sciences and Medical Research Councils/ ; NE/X016714/1//Natural Environment, Biotechnology and Biological Sciences and Medical Research Councils/ ; NE/X016714/1//Natural Environment, Biotechnology and Biological Sciences and Medical Research Councils/ ; NE/X016714/1//Natural Environment, Biotechnology and Biological Sciences and Medical Research Councils/ ; },
mesh = {Animals ; *Buffaloes/genetics ; *Cytochromes b/genetics ; *Genetic Variation ; Haplotypes ; Phylogeny ; Malaysia ; Female ; Genetics, Population ; DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; },
abstract = {The swamp buffalo (Bubalus bubalis carabanensis) plays a crucial role in agriculture across Southeast Asia but is increasingly underutilized in regions like Sabah, Malaysia. This study presents the first comprehensive statewide genetic assessment of Sabahan swamp buffalo using mitochondrial cytochrome b (cytb) gene sequences to investigate maternal origins and assess genetic diversity. Blood samples were collected from 211 individuals across eight locations in Sabah. DNA extraction and PCR amplification successfully yielded 198 high-quality cytb sequences. Comparative analysis with 1745 publicly available sequences revealed that 197 Sabahan buffalo belong to the SA1 haplogroup, which is common across Southeast Asia. Only four haplotypes were identified, with one dominant haplotype found in 190 individuals, indicating remarkably low genetic diversity (haplotype diversity = 0.088; nucleotide diversity = 0.00031). An additional river buffalo haplotype detected in one phenotypically swamp buffalo suggests introgression from Murrah buffalo. Analysis of molecular variance (AMOVA) showed that 96.29% of genetic variation occurred within populations, with minimal differentiation among them. ΦST comparisons suggest Sabah's buffalo are genetically closer to Chinese swamp buffalo populations than those from South Asia, supporting a maternal lineage via the China-Taiwan-Philippines dispersal route. Spatial autocorrelation analysis indicated localized gene flow, while demographic reconstruction via Bayesian Skyline Plot suggested long-term population stability with recent expansion. These findings highlight the limited maternal genetic variation within Sabahan swamp buffalo, likely stemming from a founder effect during introduction to Borneo and minimal subsequent genetic inflow. The study provides critical insight into the evolutionary history and population structure of Sabah's swamp buffalo, with implications for conservation and livestock improvement strategies aimed at bolstering genetic diversity and productivity in the region.},
}
@article {pmid41130487,
year = {2025},
author = {Hu, Y and Chen, S and Sun, Q and Song, L and Liu, L and Zhang, D and Liu, H and Wang, S},
title = {HSP70-mediated survival mechanisms and thermotolerance plasticity in the corn aphid, Rhopalosiphum maidis, across developmental stages.},
journal = {International journal of biological macromolecules},
volume = {331},
number = {Pt 2},
pages = {148462},
doi = {10.1016/j.ijbiomac.2025.148462},
pmid = {41130487},
issn = {1879-0003},
mesh = {Animals ; *Aphids/genetics/growth &amp; development/physiology/metabolism ; *HSP70 Heat-Shock Proteins/genetics/metabolism/chemistry ; *Thermotolerance/genetics ; *Insect Proteins/genetics/metabolism ; Heat-Shock Response ; Phylogeny ; Gene Expression Regulation, Developmental ; },
abstract = {Heat shock proteins (HSPs) play a fundamental role in mediating thermotolerance in insects; however, their stage-specific contributions to thermal adaptation in the corn aphid, Rhopalosiphum maidis, remain poorly characterized. Here, we systematically characterized Hsp70-mediated thermotolerance mechanisms across the developmental stages of this devastating maize pest. A total of 15 Hsp70 genes were identified, each containing conserved functional domains such as EEVD and GIDLGTTYS motifs, ATP-binding sites, and nuclear localization signals. Subcellular localization predictions revealed a typical eukaryotic distribution pattern, with 12 localized to the cytosol, two to the endoplasmic reticulum, and one to the mitochondria. Following sequence alignment, nine non-redundant Hsp70 genes were selected for further functional analysis. Thermotolerance assays supported that third-instar nymphs were the most susceptible to heat stress, showing only 53.0 % survival at 40 °C, whereas adults exhibited the highest tolerance, with an LT50 of 43.11 °C. Expression profiling revealed significant upregulation of five Hsp70 genes-R. maidis Hsp70-8, -11, -12, -13 and -14-specifically in third-instar nymphs at 36 °C. RNAi-mediated silencing of these genes resulted in a 56.0-68.0 % increase in mortality among third-instar nymphs. Additionally, the recombinant R. maidis HSP70-7 (55 kDa) was successfully expressed. These findings underscore the existence of developmental trade-offs in thermotolerance in R. maidis and emphasize the functional diversification of Hsp70 genes, supporting their potential as RNAi targets for pest management under increasing climatic temperatures.},
}
@article {pmid41144527,
year = {2025},
author = {Rabbi, MA and Hossain, MM and Shuvo, MRK and Bhuya, AR and Ghosh, A},
title = {Comprehensive analysis of proline metabolizing genes reveals their functional diversification and abiotic stress response in Solanum lycopersicum.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335608},
pmid = {41144527},
issn = {1932-6203},
mesh = {*Solanum lycopersicum/genetics/metabolism ; *Proline/metabolism ; *Stress, Physiological/genetics ; Gene Expression Regulation, Plant ; Phylogeny ; *Plant Proteins/genetics/metabolism ; *Genes, Plant ; Droughts ; Multigene Family ; },
abstract = {Proline plays a crucial role in plant stress responses. Proline metabolizing genes (PMGs) are a group of enzymes involved in its catabolism in mitochondria and the biosynthesis in the chloroplast and cytoplasm. A total of 21 PMGs were identified in Solanum lycopersicum. Among them, 2 gene pairs were identified as tandemly duplicated, and 6 gene pairs were segmentally duplicated. Phylogenetic analysis revealed distinct gene clusters, suggesting functional diversification. Gene structure analysis provided insights into the arrangement of coding and non-coding regions, while domain analysis highlighted conserved sequences for functional predictions and evolutionary conservation. Microarray expression data of the identified genes revealed that SlOAT8 exhibited maximum expression in different anatomical tissues, particularly in ovules, and SlOAT9 showed maximum response at developmental stages associated with shoot growth. Under stress conditions, SlOAT8 and SlP5CS1 were upregulated in exposure to drought stress but downregulated in response to heat and salt stress. Meanwhile, SlOAT4 was strongly expressed only in roots during salt stress. The qRT-PCR analysis demonstrated significant upregulation of SlOAT8, SlP5CDH2, and SlP5CR alongside a significant downregulation of SlP5CS1 under abiotic stress conditions. Furthermore, biochemical assay indicates the accumulation of proline and H2O2 under stressed conditions. These findings provide an extensive study on the PMGs, which will help in the development of a stress-resilient tomato plant in further.},
}
@article {pmid41151232,
year = {2026},
author = {Ye, M and Zhou, D and Kong, L and Zhang, Y and Pan, C and Huang, C and Li, G and Chen, H and Tian, C},
title = {Genome-wide characterization of the Hsp40 gene family in Clarias fuscus reveals their roles in thermal stress adaptation and immune modulation.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {57},
number = {},
pages = {101661},
doi = {10.1016/j.cbd.2025.101661},
pmid = {41151232},
issn = {1878-0407},
mesh = {Animals ; *HSP40 Heat-Shock Proteins/genetics/immunology/chemistry/metabolism ; Phylogeny ; *Catfishes/genetics/immunology/physiology ; *Fish Proteins/genetics/immunology/metabolism/chemistry ; Multigene Family ; Genome ; *Heat-Shock Response ; },
abstract = {Thermal stress poses a significant challenge to fish physiology and aquaculture sustainability, necessitating an in-depth understanding of molecular responses to temperature fluctuations. This study characterizes the Hsp40 gene family in Hong Kong catfish (Clarias fuscus), a species known for its thermal resilience, to elucidate their roles in proteostasis and immune modulation. A total of 55 Hsp40 genes were identified and categorized into three subfamilies: DnaJa (n = 6), DnaJb (n = 16), and DnaJc (n = 33). These genes exhibit conserved J-domains and diverse motifs, indicating adaptations to aquatic stressors. Phylogenetic analysis reveals that the Hsp40 gene family in C. fuscus exhibits the closest evolutionary relationship to Ictalurus punctatus, followed by Danio rerio, with distinct clustering patterns across the subtypes. Collinearity and synteny analyses indicated substantial genomic conservation of Hsp40 genes between C. fuscus, I. punctatus, and D. rerio, with evidence of gene duplication and homologous relationships. The subcellular localization of Hsp40 proteins was observed in the cytoplasm, endoplasmic reticulum, mitochondria, nucleus, and extracellular regions, supporting their roles in chaperone activity and immune response regulation. Protein interaction networks identified two major clusters: one associated with protein folding and another with Hsp90-dependent immune signaling. Molecular docking confirmed stable interactions between Hsp40 and Hsp70, aiding in the mitigation of thermal-induced protein misfolding. Transcriptomic analysis under thermal stress showed significant differential expression of 30 Hsp40 genes, with dnajb11 and dnajc5.1 notably differentially expressed in the liver, gills, and kidneys. Under normal-temperature conditions, 10, 6, and 12 genes were differentially expressed in the liver, gills, and kidneys, respectively. High-temperature acclimation significantly increased the number of differentially expressed genes in the kidneys (20 genes), indicating enhanced thermal tolerance. These genes bolster immunity by stabilizing proteins and modulating inflammatory pathways. These findings suggest that key Hsp40s, such as dnajb11 and dnajc5.1, serve as biomarkers for selective breeding and support the development of strategies like immunomodulatory feed additives to enhance thermal resilience in C. fuscus aquaculture.},
}
@article {pmid41174841,
year = {2026},
author = {Yuan, J and Yang, W and Zhao, Z and Cao, J and Yang, W and Deng, W and Zhong, S and Liu, J and Yu, Y},
title = {A new small subunit of the mitochondrial F-ATPase, PhDC, determines flower color by acidifying vacuoles.},
journal = {The New phytologist},
volume = {249},
number = {1},
pages = {232-251},
doi = {10.1111/nph.70676},
pmid = {41174841},
issn = {1469-8137},
support = {32202527//National Natural Science Foundation of China/ ; 32271939//National Natural Science Foundation of China/ ; 32302591//National Natural Science Foundation of China/ ; },
mesh = {*Vacuoles/metabolism ; *Flowers/genetics/enzymology ; Hydrogen-Ion Concentration ; Mitochondria/enzymology/metabolism ; *Petunia/genetics/enzymology/metabolism ; *Plant Proteins/metabolism/genetics/chemistry ; Anthocyanins/metabolism ; Protein Subunits/metabolism/chemistry ; Gene Silencing ; Gene Expression Regulation, Plant ; *Pigmentation/genetics ; *Proton-Translocating ATPases/metabolism/genetics/chemistry ; Phylogeny ; },
abstract = {The pH within the plant vacuole determines the anthocyanin absorption spectrum and affects flower color. V-ATPase, P-ATPase, and pyrophosphatase proton pumps involved in vacuolar acidification have been reported. However, whether other proteins regulate vacuolar pH in Petunia hybrida remains unclear. Here, by using VIGS technology to silence numerous genes annotated as 'unknown protein', we identified a gene whose silencing darkened petal color and named it PhDC (DEEPENING COLOR). PhDC silencing mediated by RNAi also darkened petal color. PhDC has low similarity to yeast mitochondrial F-ATPase subunit and Arabidopsis ATP17 (a predicted mitochondrial F-ATPase subunit). PhATPd and PhATPO, encoding the mitochondrial F-ATPase subunit d and OSCP, respectively, shared similar spatiotemporal expression with PhDC. PhDC localized to mitochondria and interacted with four subunits of mitochondrial F-ATPase. PhDC, PhATPd, and PhATPO silencing led to a similar phenotype in petunia. PhDC silencing reduced mitochondrial F-ATPase activity and impaired mitochondria. The anthocyanin content in PhDC-silenced petals did not significantly change, while the vacuoles of petal cells were alkalized, and the P-ATPase activity and ATP content were reduced. These results suggest that PhDC is a new subunit of the mitochondrial F-ATPase. Furthermore, PhDC silencing affects petal color by altering the vacuole pH and P-ATPase activity.},
}
@article {pmid41178341,
year = {2026},
author = {Dong, Y and Li, G and Zhang, Y and Wu, S and Liu, K and Yu, D and Wang, Z and Yang, Y and Guo, S and Li, Z and Guo, F and Huang, B and Wang, Y},
title = {Gluconolactonase SMP30 deletion worsens fungal degeneration through ROS accumulation and mitochondrial dysfunction in an insect fungal pathogen.},
journal = {Pest management science},
volume = {82},
number = {2},
pages = {1912-1920},
doi = {10.1002/ps.70337},
pmid = {41178341},
issn = {1526-4998},
support = {32102274//National Science Foundation of China/ ; 202312/WT_/Wellcome Trust/United Kingdom ; 202312/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Reactive Oxygen Species/metabolism ; Animals ; *Carboxylic Ester Hydrolases/genetics/metabolism ; *Mitochondria/metabolism ; *Fungal Proteins/genetics/metabolism ; *Metarhizium/genetics/pathogenicity/enzymology/physiology ; Virulence ; Phylogeny ; Gene Deletion ; },
abstract = {BACKGROUND: Gluconolactonase/Senescence marker protein 30 (SMP30) is a multifunctional enzyme involved in L-ascorbic acid biosynthesis, ROS scavenging, and aging in mammals, but its role in fungi remains partially understood.<br><br>RESULTS: Here, we demonstrate that an SMP30 (MrSMP30-1) from the entomopathogenic fungus Metarhizium robertsii is essential for ROS elimination and mitochondrial function. Phylogenetic analysis shows that MrSMP30-1 is more closely related to SMP30 proteins from phytopathogenic fungi than to those from other entomopathogens. Recombinant MrSMP30-1 displays maximum lactonase activity at pH&#x2009;6.5 and 25&#x2009;&#xb0;C. Deletion of MrSMP30-1 results in intracellular ROS buildup, a significant decrease in lipid droplets, and collapse of mitochondrial membrane potential, leading to accelerated, spontaneous fungal degeneration. Virulence tests indicate that the loss of MrSMP30-1 reduces pathogenicity. Immunoprecipitation combined with mass spectrometry identified seven proteins, including polyketide synthase 3, that potentially interact physically with MrSMP30-1.<br><br>CONCLUSION: Our results indicate that the gluconolactonase MrSMP30-1 is essential for ROS detoxification and preserving mitochondrial integrity in M. robertsii. This not only enhances our understanding of SMP30's proposed role in fungi but also suggests that it could serve as a biomarker for monitoring fungal culture degeneration. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid41318756,
year = {2025},
author = {Talarico, L and Petrosino, G and Rossi, AR and Franchini, P and Gratton, P and Tancioni, L},
title = {Efficient eDNA-based assessment of mitochondrial lineage diversity in wild brown trout populations.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {317},
pmid = {41318756},
issn = {2045-2322},
support = {PRIN 2022 - 2022JJ7STN//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; },
mesh = {Animals ; *Trout/genetics ; *Genetic Variation ; *DNA, Mitochondrial/genetics ; *DNA, Environmental/genetics/analysis ; Phylogeography ; Phylogeny ; Genotype ; *Mitochondria/genetics ; },
abstract = {Among the numerous applications of environmental DNA (eDNA), the assessment of genetic diversity in wild populations of target taxa remains moderately investigated. Focusing on 10 selected sites inhabited by brown trout (Salmo trutta complex) in central Italian watercourses, we: (1) developed a non-invasive genetic monitoring protocol combining environmental DNA sampling, amplicon sequencing with custom-designed primers targeting a 192 bp fragment of the mitochondrial Control Region (CR) - whose evolutionary lineages are informative for brown trout phylogeography and genetic conservation status-and a curated reference database; (2) validate it comparing CR lineages assemblages revealed by eDNA with those obtained through traditional CR genotyping of trouts collected by electrofishing in recent surveys, while accounting for uncertainty associated with sample size of genotyped individuals. The two methods returned strongly correlated per-site raw frequencies of CR lineages (Pearson r = 0.93, p < 0.0001), and remarkably similar lineage assemblages (Mantel r = 0.832, p = 0.0001). Concordances between (semi-quantitative) lineage assemblages retrieved by the two methods increased at increasing trout densities and decreased at warmer water temperatures. Discordances mostly involved low-frequency lineages that were not detected by traditional CR genotyping. This study supports the effectiveness of eDNA for reliably characterising mitochondrial intra-population diversity in brown trout, a widely distributed and actively managed taxon of important conservation and economic value, offering a valuable tool to assist the genetic monitoring of wild populations, including the identification and quantification of exotic lineages.},
}
@article {pmid41345699,
year = {2025},
author = {Yilmaz, A and Kasap, OE},
title = {Prevalence of Wolbachia in natural sand fly (diptera: psychodidae) populations from Türkiye and its potential role in mitochondrial divergence.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {16},
pmid = {41345699},
issn = {1756-3305},
support = {2211-A National PhD Scholarship Program//T&#xdc;B&#x130;TAK/ ; 101057690//European Commission/ ; 10038150 and 10038150//UK Research and Innovation/ ; TBAG 105T205 and SBAG 114S999//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; 09D01601002 and 01001601001//Hacettepe University Scientific Research Unit/ ; W911QY-16-C-0160//AFHSB-GEIS/ ; },
mesh = {Animals ; *Wolbachia/genetics/isolation &amp; purification ; *Psychodidae/microbiology/classification/genetics ; *Genetic Variation ; Multilocus Sequence Typing ; Phylogeny ; Female ; Male ; Prevalence ; *Mitochondria/genetics ; Insect Vectors/microbiology ; Phlebotomus/microbiology ; },
abstract = {BACKGROUND: Phlebotomine sand flies are vectors of various pathogens, most notably Leishmania spp. Symbiotic bacteria have recently gained considerable attention owing to their effects on hosts and on other organisms co-infecting the same host. In this study, we investigated the natural Wolbachia infection status of sand fly taxa distributed in Türkiye and examined its potential role in driving the deep mitochondrial divergence observed within certain taxa.<br><br>METHODS: We analysed 858 sand fly specimens, mostly collected between 2005 and 2016, with additional samples obtained in 2023. Specimens were morphologically identified, and the mitochondrial cox1 gene was sequenced for DNA barcoding. For selected taxa showing marked mitochondrial divergence, species delimitation methods were applied, and genetic diversity indices and neutrality tests were calculated. Wolbachia infection was detected via PCR amplification of the wsp gene, and strain diversity was characterised using multilocus sequence typing (MLST) of five housekeeping genes. Logistic regression was used to evaluate associations between infection status and mitochondrial lineage, sex or collection period.<br><br>RESULTS: Wolbachia infection was detected in 16.67% of specimens, occurring exclusively in Phlebotomus papatasi, Ph. major s.l., Ph. tobbi, Ph. economidesi and Sergentomyia minuta. Analyses of wsp and MLST data identified all sequences as belonging to Supergroup A, with multiple strains present within and across host taxa. Infection among the five Ph. major s.l. lineages delineated by species delimitation was significantly associated with lineage, with lineages 3-5 showing a higher probability of infection. The reduced haplotype and nucleotide diversity, along with a significant negative deviation from neutrality observed in lineage 5, suggest a selective sweep likely driven by Wolbachia infection.<br><br>CONCLUSIONS: This study represents the first comprehensive screening of Wolbachia infection in sand fly taxa distributed across T&#xfc;rkiye, during which several novel Wolbachia strains were identified. Our findings suggest a potential role of Wolbachia infection in driving lineage differentiation within certain sand fly taxa. However, further detailed investigations are required to elucidate the mechanisms by which Wolbachia influences sand fly diversification and to assess the broader epidemiological implications related to sand fly-borne diseases (SFBDs).},
}
@article {pmid41367310,
year = {2025},
author = {Nguyen, THM and Klein, DA and Weklar, OS and Wengrow, ER and Rockman, MV},
title = {Abundant Recurrent Mitochondrial Mutations and Widespread Mitonuclear Epistasis in Caenorhabditis elegans.},
journal = {Molecular biology and evolution},
volume = {42},
number = {12},
pages = {},
pmid = {41367310},
issn = {1537-1719},
support = {R01 ES029930/ES/NIEHS NIH HHS/United States ; R35 GM141906/GM/NIGMS NIH HHS/United States ; ES029930/NH/NIH HHS/United States ; GM141906/NH/NIH HHS/United States ; },
mesh = {Animals ; *Caenorhabditis elegans/genetics ; *Epistasis, Genetic ; Genome, Mitochondrial ; *Mitochondria/genetics ; Mutation ; Cell Nucleus/genetics ; Phylogeny ; Caenorhabditis elegans Proteins/genetics ; },
abstract = {Coordinated genetic and physical interactions between mitochondrial and nuclear gene products regulate ATP production in the mitochondria. Linking mitochondrial genotypes and mitonuclear genetic interactions to phenotypes remains a complex challenge. Here, we have developed Caenorhabditis elegans as a model for mitonuclear epistasis studies. In a sample of 540 genetically distinct wild isolates, 10% of sites in the mitochondrial genome vary, with hundreds of missense mutations segregating in the species. Recurrent mutations and triallelic sites are common. Phylogenetic analyses of mitogenome sequences identified 8 distinct lineages, each with diagnostic variants. Principal component analysis of the nuclear genomes showed considerable concordance between mitochondrial and nuclear genomes in C. elegans populations, suggesting that disrupting coevolved mitonuclear genetic combinations could reveal substantial epistasis. We used GPR-1 overexpression, which disrupts the first mitotic division, to efficiently exchange nuclear and mitochondrial genomes between all pairs of 18 naturally isolated C. elegans strains, generating the largest-to-date animal mitonuclear exchange panel, with 323 unique viable mitonuclear genotypes. We phenotyped development of a subset of strains, with 30 unique genotypes, under 6 different environmental conditions, including high temperature and exposure to heavy metals. Mitonuclear epistasis contributed significantly to phenotypic variance across all tested conditions. We also tested for mitonuclear coadaptation by comparing the stress resistance of matched and mismatched cybrids. Interestingly, some mismatched strains exhibited greater resistance, highlighting the complexity and context dependence of mitonuclear interactions.},
}
@article {pmid41383010,
year = {2026},
author = {Li, G and Zhang, Y and Yu, H and Xie, Y and Luo, H and Wang, Y and Tang, J and Zhang, J and Xie, X and Zong, W and Liu, K and Wang, X and Long, Y and Song, Q and Wu, Z and Liu, YG and Chen, L},
title = {A tripartite pollen killer-protector system confers temperature-sensitive inter-subspecific reproductive isolation in rice.},
journal = {Molecular plant},
volume = {19},
number = {2},
pages = {295-312},
doi = {10.1016/j.molp.2025.12.008},
pmid = {41383010},
issn = {1752-9867},
mesh = {*Oryza/genetics/physiology ; *Pollen/genetics/physiology ; *Reproductive Isolation ; *Plant Proteins/metabolism/genetics ; Temperature ; Plant Infertility/genetics ; },
abstract = {Hybrid-sterility-mediated reproductive isolation is pivotal for speciation, yet the underlying molecular mechanisms and environmental responses remain unclear. Here, we report a temperature-sensitive pollen killer-protector system at a three-gene Sa locus for indica-japonica rice hybrid sterility. Genetic analyses identified SaFL[+], a strong pollen protector from Sa-i (indica allele), and SaFL[-], a weak japonica allele from Sa-j, which is exclusively functional under high temperatures. Protein interaction, ubiquitination, and degradation assays showed that SaF[+] and SaM[+] from Sa-i form a pollen-killer complex to bind and ubiquitinate the reactive oxygen species scavenger COX11 for degradation in mitochondria, causing male sterility of the Sa-j pollen. Protein affinity and competitive binding assays indicated that in the Sa-i pollen, SaFL[+] binds SaM[+] to disrupt the killer complex and restore fertility. However, the weak protector SaFL[-] can bind SaM[+] under high temperatures, sparing the Sa-j pollen from sterility. Synteny comparisons and haplotype analyses showed that the Sa locus originated in ancient wild rice and underwent divergence within the Oryza genus during expansion from tropical to temperate environments, which might have driven latitudinal adaptation and reproductive isolation in rice populations. Thus, Sa represents a temperature-sensitive reproductive-isolation system associated with domestication and environmental adaptation in rice.},
}
@article {pmid41528575,
year = {2026},
author = {Punia, V and Das, G and Kumar, S and Verma, R and Nath, S and Choudhary, R and Chourasia, R and Nayak, A and Singh, AP},
title = {Comparative diagnostic performance of microscopy and PCR assays with preliminary mitochondrial sequence analysis of Babesia species infecting dogs in Jabalpur, central India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {286},
pmid = {41528575},
issn = {1573-4978},
mesh = {Animals ; Dogs ; *Babesia/genetics/isolation &amp; purification ; India ; *Babesiosis/diagnosis/parasitology/genetics ; *Polymerase Chain Reaction/methods/veterinary ; *Dog Diseases/parasitology/diagnosis/genetics ; *Microscopy/methods ; Phylogeny ; Mitochondria/genetics ; Sequence Analysis, DNA/methods ; Sensitivity and Specificity ; Electron Transport Complex IV/genetics ; DNA, Mitochondrial/genetics ; },
abstract = {BACKGROUND: The present study evaluated the diagnostic performance of conventional microscopy and polymerase chain reaction (PCR) based assays for the detection of Babesia infections in dogs, including semi-nested PCR (SN-PCR) targeting the 18 S rRNA gene and single-round PCR (SR-PCR) assays targeting the mitochondrial cytochrome b (cytb) and cytochrome c oxidase subunit 1 (cox1) genes for B. gibsoni and B. vogeli, respectively. Mitochondrial sequence variation was further assessed by integrating newly generated sequences from Jabalpur, Madhya Pradesh (central India), with global reference datasets.<br><br>METHODS AND RESULTS: A total of 100 blood samples from dogs suspected of having haemoprotozoan infections were analysed between June 2022 and May 2023. Microscopic examination of Giemsa-stained smears detected Babesia parasites in 13% of the samples, whereas the 18&#xa0;S rRNA SN-PCR assay identified infections in 29%, comprising B. gibsoni (25%) and B. vogeli (4%). Representative sequences showed 98-99% identity with corresponding GenBank reference sequences. Representative sequences showed 98-99% identity with corresponding GenBank reference sequences. Compared with SN-PCR, microscopy demonstrated moderate sensitivity but perfect specificity, resulting in an overall diagnostic accuracy of 84.0% (p&#x2009;<&#x2009;0.01). Mitochondrial SR-PCR assays detected B. gibsoni and B. vogeli in 5% and 4% of the samples, respectively. The cytb-based assay showed higher sensitivity and a significant diagnostic association (p&#x2009;<&#x2009;0.01) than the cox1 assay, whereas the cox1 assay demonstrated lower sensitivity with a non-significant association (p&#x2009;>&#x2009;0.05). All PCR assays showed 100% specificity and positive predictive value. Bayesian phylogenetic and haplotype analyses indicated that B. gibsoni cytb sequences formed a monophyletic lineage with limited regional structuring, with Indian isolates clustering within a distinct sub-lineage. In contrast, B. vogeli cox1 sequences exhibited low global diversity with a dominant shared haplotype across geographic regions.<br><br>CONCLUSIONS: The 18S rRNA SN-PCR assay showed the highest sensitive method for detecting Babesia infections in dogs. Mitochondrial markers (cytb and cox1) supported species confirmation and comparative phylogenetic assessment, highlighting the complementary value of nuclear and mitochondrial gene targets for molecular surveillance and control of canine babesiosis in India.},
}
@article {pmid41563631,
year = {2026},
author = {Nehela, Y and Killiny, N},
title = {Not just a cycle: mitochondrial CsgabD is involved in GABA metabolism during citrus defense against biotic stress.},
journal = {Plant molecular biology},
volume = {116},
number = {1},
pages = {11},
pmid = {41563631},
issn = {1573-5028},
mesh = {*gamma-Aminobutyric Acid/metabolism ; *Succinate-Semialdehyde Dehydrogenase/metabolism/genetics/chemistry ; Phylogeny ; *Plant Proteins/metabolism/genetics/chemistry ; *Mitochondria/metabolism ; Amino Acid Sequence ; *Stress, Physiological ; *Citrus sinensis/genetics/microbiology/metabolism ; Gene Expression Regulation, Plant ; *Citrus/genetics/metabolism/microbiology ; Plant Diseases/microbiology/immunology ; Rhizobiaceae/physiology ; Liberibacter/physiology ; Succinic Acid/metabolism ; Sequence Alignment ; Molecular Docking Simulation ; },
abstract = {While the role of succinic semialdehyde (SSA) dehydrogenase (SSADH; also known as gabD) is well-reported from model plants, the lack of functionality and structure of SSADH from citrus represents a significant knowledge gap. Herein, genome-wide analyses identified 17 high-confidence SSADH-like proteins from Citrus sinensis, among which three putative SSADHs have potential GABA dehydrogenase function. Sequence alignment, phylogenetic analyses, and domain architecture demonstrated high conservation among CsSSADHs (aka CsgabD) and their homologs across diverse plant taxa. Notably, CsSSADH-2 lacked a conserved QGIVC motif found in CsSSADH-1/-3. Secondary structure analyses indicated conserved aldehyde dehydrogenase domains. Homology-based 3D modeling predicted CsSSADH-1 and 2 as homo-tetramers; however, AlphaFold2-based modeling suggested their full-length monomer structures. PPI networks revealed CsSSADH-1 interacts with 10 proteins, primarily involved in GABA/succinate metabolism and the TCA cycle. Docking studies indicated that CsSSADH-1 displayed acceptable affinity and binding modes with GABA, SSA, and succinate. GABA supplementation enhances CsSSADH expression, GABA, and succinate content in a dose-dependent manner in both healthy and infected citrus plants under greenhouse conditions. CsSSADH was involved in citrus responses to 'Candidatus Liberibacter asiaticus' and/or its vector, Diaphorina citri. Nevertheless, GABA accumulation under biotic stress leads to condition-specific rerouting of GABA metabolism. Chemical inhibition of CsSSADH resulted in increased GABA accumulation but reduced succinate levels in both healthy and infected plants. This study offers the first comprehensive characterization of C. sinensis SSADH isoforms, providing insights into their evolutionary divergence, structural features, and potential functions, and enhancing our understanding of their possible roles in GABA metabolism and citrus defense responses.},
}
@article {pmid41564688,
year = {2026},
author = {Bhalodi, JA and Surm, JM and Reitzel, AM},
title = {Transcription dynamics and regulation of heat shock protein genes during stress and development in the estuarine cnidarian Nematostella vectensis.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {58},
number = {},
pages = {101754},
doi = {10.1016/j.cbd.2026.101754},
pmid = {41564688},
issn = {1878-0407},
mesh = {Animals ; *HSP90 Heat-Shock Proteins/genetics ; *HSP70 Heat-Shock Proteins/genetics ; *Stress, Physiological/genetics ; Phylogeny ; *Transcription, Genetic ; *Gene Expression Regulation, Developmental ; *Sea Anemones/genetics/growth &amp; development ; *Cnidaria/genetics/growth &amp; development ; },
abstract = {Heat shock proteins (HSPs) are molecular chaperones that function in protecting cells from proteotoxicity. Eukaryotes have multiple HSPs that localize in the cytoplasm, endoplasmic reticulum (ER), and mitochondria. In cnidarian species, where HSPs are often used as biomarkers of environmental stress, little is known about how particular HSPs vary in copy number, expression, inducibility, and regulation within a species. Here, we characterized the full repertoire of HSP70 and HSP90 genes in an emerging model cnidarian, Nematostella vectensis. We identified five HSP70 and three HSP90 genes, with at least one homolog from each family belonging to the three primary clades based on subcellular localization. Although transcriptional induction remained insignificant by a 10 °C temperature change, two cytosolic HSP70s and one cytosolic HSP90 were significantly upregulated with a 20 °C temperature increase. Most HSPs exhibited similar developmental expression patterns, with elevated expression during the early larval stage followed by reduced expression in the juvenile stage. HSPs showed evidence for differential expression across cell types, with multiple cytosolic and ER HSPs being highly expressed in neuronal and cnidocyte populations. Moreover, the putative promoters of N. vectensis HSPs differed in both the abundance and sequences of regulatory heat shock element motifs, providing a potential mechanism of functional diversification in response to temperature and development. By characterizing expression of all HSP70 and HSP90 genes in this cnidarian, we reveal distinct roles of these core chaperones in the proteostasis response, providing a foundation for future functional studies on contributions of HSPs to cnidarian life cycle and stress resilience.},
}
@article {pmid41570014,
year = {2026},
author = {Hu, H and He, L and Chen, R and Jing, Z and Wan, H and Xiao, Z and Cheng, H and Wu, C and Liu, X},
title = {Genome-wide identification and multi-dimensional functional characterization of the SIR2 family in Brassica napus L.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340688},
pmid = {41570014},
issn = {1932-6203},
mesh = {*Brassica napus/genetics/metabolism ; Phylogeny ; Gene Expression Regulation, Plant ; *Plant Proteins/genetics/metabolism/chemistry ; Genome, Plant ; *Histone Deacetylases/genetics/metabolism/chemistry ; Stress, Physiological/genetics ; Promoter Regions, Genetic ; Multigene Family ; Synteny ; Amino Acid Sequence ; Epigenesis, Genetic ; },
abstract = {Silent Information Regulator 2 (SIR2) family proteins are NAD+-dependent histone deacetylases that play key roles in epigenetic regulation, plant development, and stress responses; however, systematic characterization of this family (hereafter SRTs) in the important oilseed crop Brassica napus (rapeseed) remains limited. In this study, we identified 4 SRT genes in the rapeseed genome, designated BnaASRT1/2 and BnaCSRT1/2, based on their homology to Arabidopsis SRTs and chromosomal localization. These genes encode proteins with conserved SIR2 domains, sharing >80% sequence identity and >95% coverage with Arabidopsis SRTs, and exhibit similar subcellular localizations (SRT1s in the nucleus, SRT2s in mitochondria). Phylogenetic and synteny analyses confirmed the evolutionary conservation of rapeseed SRTs, which originated from whole-genome duplication events and were stably inherited from its diploid ancestors (Brassica rapa and Brassica oleracea). Structural analysis indicates that gene structure, motifs, and promoter elements related to stress and hormone responses are conserved, although subtle differences in the promoters suggest functional specialization. Notably, GO enrichment and molecular docking assays demonstrated that BnaSRTs possess histone deacetylase activity, with strong binding affinity to key acetylation sites (e.g., H3K9ac). Treatment with the SIRT-specific inhibitor nicotinamide (NAM) significantly elevated histone acetylation levels and altered the expression of genes involved in photosynthesis, metabolism, and stress responses-further supporting BnaSRTs' ole in epigenetic regulation. Furthermore, expression profiling via the BnIR database showed tissue-specific expression of BnaSRTs (e.g., high BnaASRT2 expression in buds, flowers, and siliques) and dynamic responses to abiotic stresses (salt, drought, cold) and hormones (ABA, JA, IAA), with BnaSRT2s showing the most prominent expression changes. Collectively, these findings clarify the evolutionary conservation, structural features, and functional roles of the SIR2 family in rapeseed, laying a foundation for epigenetic improvement of its agronomic traits.},
}
@article {pmid41618126,
year = {2026},
author = {Usmani, SF and Saddique, MAB and Fiaz, S and Tahir, MHN and Waheed, U and Abdalla, MA and Ahmed, UAH and Alharthi, B and Farid, HN and Pan, R and Yang, SH},
title = {Genome-wide identification of ADK gene family associated with heat stress tolerance in chili (Capsicum annuum L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {41618126},
issn = {2730-6844},
mesh = {*Capsicum/genetics/physiology ; Phylogeny ; *Thermotolerance/genetics ; Multigene Family ; *Plant Proteins/genetics/metabolism ; *Heat-Shock Response/genetics ; Genome, Plant ; Gene Expression Regulation, Plant ; },
abstract = {Chili (Capsicum annuum), also known as hot pepper, is a major vegetable crop in the Solanaceae family. It originated from C. annuum var. minimum, native to Mexico, Southern Peru, and Bolivia. High temperatures negatively affect all key development stages of chili, including fruit set, pollen viability, floral aberration, and the number of seeds per fruit. Heat stress tolerance is a crucial trait in chili and may be regulated by the Adenylate Kinase (ADK) gene family. Although ADK genes have been studied in Arabidopsis thaliana, Oryza sativa, Glycine max, Solanum lycopersicum, and Solanum tuberosum, they remain uncharacterized in C. annuum. This study presents the first genome-wide analysis of the ADK gene family in chili, including gene identification, phylogenetics, motif analysis, expression profiling, and stress-related interaction networks. This study identified nine ADK genes in C. annuum and 70 orthologs from four other species using BLASTp. Phylogenetic analysis grouped the genes into four clades, while gene structure analysis revealed gene lengths ranging from 1,204 to 13,304 bp, with 4 to 17 exons. Conserved motifs and ADK domains were identified. Chromosomal mapping placed the genes across nine chromosomes, with segmental duplications aiding expansion. Predicted subcellular localization suggested that most CaADK proteins localize to chloroplasts and mitochondria. In silico expression profiling showed that CaADK1 and CaADK8 had the highest expression under heat stress, indicating their potential role in thermotolerance. These findings provide novel insights into the CDK gene family in chili and offer molecular targets for enhancing heat stress tolerance in C. annuum.},
}
@article {pmid41621609,
year = {2026},
author = {Gusmão, IV and Figueredo, RTA and Corrêa, LL and Maia, AAM and Adriano, EA},
title = {Integrative taxonomy reveals a novel Ceratomyxa (Cnidaria: Myxozoa) parasitizing the gallbladder of the Amazonian fish Pellona castelnaeana.},
journal = {Acta tropica},
volume = {275},
number = {},
pages = {108005},
doi = {10.1016/j.actatropica.2026.108005},
pmid = {41621609},
issn = {1873-6254},
mesh = {Animals ; *Myxozoa/classification/isolation &amp; purification/genetics/ultrastructure ; *Gallbladder/parasitology ; Phylogeny ; *Fish Diseases/parasitology/epidemiology ; DNA, Ribosomal/chemistry/genetics ; *Parasitic Diseases, Animal/parasitology/epidemiology ; Sequence Analysis, DNA ; Molecular Sequence Data ; Fishes ; Cluster Analysis ; Microscopy, Electron, Transmission ; Prevalence ; },
abstract = {Freshwater species of the myxozoan genus Ceratomyxa have recently emerged as a diverse group of parasites infecting fish in South America, many of which exhibit vermiform plasmodia with dynamic motility. In this integrative taxonomic study, we describe Ceratomyxa souzapintorum n. sp., a novel species infecting the gallbladder of the Amazonian clupeiform fish Pellona castelnaeana. The prevalence of infection was 73%, and the parasite displayed worm-like plasmodia exhibiting nematode-like motility. Arcuate myxospores measured 14.8 ± 1.7 µm in thickness and 6.1 ± 0.7 µm in length, with a posterior angle of 59° (42-78°). The two spherical nematocysts measured 2.0 µm and contained filaments with 3-4 coils. Ultrastructural analyses revealed plasmodia consisting of an outer cytoplasmic region containing sporogonic stages and numerous tubular mitochondria, and internally a large central vacuole. Mature plasmodia exhibited a thin cytoplasmic layer, with mature myxospores apparently free within the central vacuole. Phylogenetic analyses positioned C. souzapintorum n. sp. within the clade of Amazonian Ceratomyxa species.},
}
@article {pmid41628193,
year = {2026},
author = {Owaresat, JK and Dey, D and Siam, MAH and Anam, MA and Siddiki, AZ},
title = {Genetic diversity, phylogeography, population structure, and demographic history of wild Catla catla at a transboundary scale across South Asia revealed by Mitochondrial COI sequences.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0341820},
pmid = {41628193},
issn = {1932-6203},
mesh = {Animals ; *Genetic Variation ; Phylogeography ; *Electron Transport Complex IV/genetics ; Haplotypes ; Phylogeny ; *DNA, Mitochondrial/genetics ; Genetics, Population ; Asia, Southern ; Asia ; *Mitochondria/genetics/enzymology ; },
abstract = {This study presents the first assessment of mitochondrial cytochrome c oxidase I (COI) sequences from multiple countries to evaluate the genetic diversity, phylogeographic relationships, population structure, and demographic history of wild Catla catla in South Asia. A total of 18 haplotypes, with moderate haplotype diversity (Hd = 0.599), low nucleotide diversity (π = 0.017), and limited mutational steps among most haplotypes, were identified after analyzing 133 COI sequences collected from Bangladesh, India, and Pakistan. The results revealed low genetic differentiation among all wild Catla samples, influenced by introgression from hatchery-reared fry and population bottlenecks. Phylogenetic analyses identified two distinct haplogroups for Pakistani populations, supporting the existence of divergent mitochondrial lineages. AMOVA test showed that most genetic variation occurred within populations (74.46.%) rather than among the seven river basin populations (25.54%). The high pairwise genetic distance (FST= 0.255), together with the presence of numerous population-specific haplotypes and low gene flow (Nm = 0.729), indicated significant population structure among these river populations. A positive Mantel test (r = 0.12) confirmed a significant increase in genetic divergence with increasing geographic distance. The neutrality test and mismatch distribution presented a contrasting demographic history. A significantly negative Fu's Fs (Fu's Fs = -24.431) pointed to recent population expansion, whereas a significant Harpending's raggedness index (r = 0.009) and a multimodal mismatch distribution suggested long-term demographic substructure. These findings provide essential COI-based baseline genetic information for conserving the genetic integrity of the wild Catla catla and guiding sustainable transboundary fisheries management in South Asia.},
}
@article {pmid41630175,
year = {2026},
author = {Lim, SJ and Breitbart, M},
title = {Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {2},
pages = {e70065},
pmid = {41630175},
issn = {1550-7408},
support = {//University of South Florida/ ; OCE- 2527605//National Science Foundation/ ; },
mesh = {Animals ; *Sea Urchins/parasitology ; *Ciliophora/genetics/isolation &amp; purification/pathogenicity/classification ; Phylogeny ; Genome, Mitochondrial ; Base Composition ; Sequence Analysis, DNA ; },
abstract = {A scuticociliate most closely related to Philaster apodigitiformis caused mass mortalities of diadematoid sea urchins and was cultured as Philaster sp. isolate FWC2. We sequenced the metagenomic content of this isolate, which was predicted to represent ≤ 56% of the complete genome. Based on k-mer counts, the haploid genome size was predicted to be 122-136 Mbp. We assembled and annotated a 4,088 bp nuclear ribosomal operon, a 41,396 bp mitochondrial genome with 19.22% G + C content, 24 protein-coding genes, 6 tRNA genes, and 2 rRNA genes, and a protein sequence homologous to β-PKA in Philaster apodigitiformis potentially involved in host infection.},
}
@article {pmid41740769,
year = {2026},
author = {Wang, L and Li, H and Shi, Y and Li, W and Gao, W and Wu, D and Wang, S and Qin, Q},
title = {Functional characterization of the Rab11 and its response to SGIV infection in the orange-spotted grouper (Epinephelus coioides).},
journal = {Fish &amp; shellfish immunology},
volume = {172},
number = {},
pages = {111230},
doi = {10.1016/j.fsi.2026.111230},
pmid = {41740769},
issn = {1095-9947},
mesh = {Animals ; *rab GTP-Binding Proteins/genetics/chemistry/immunology/metabolism ; Amino Acid Sequence ; *Fish Diseases/immunology/virology/genetics ; Sequence Alignment/veterinary ; *Fish Proteins/genetics/chemistry/metabolism/immunology ; *DNA Virus Infections/immunology/veterinary/genetics/virology ; *Immunity, Innate/genetics ; *Bass/genetics/immunology ; Ranavirus/physiology ; Phylogeny ; rab11 GTP-Binding Proteins ; *Gene Expression Regulation/immunology ; Gene Expression Profiling/veterinary ; },
abstract = {Rab11, a member of the Rab GTPase family, serves as a key regulator of vesicular trafficking and modulates viral infection in mammals, yet its functional role in aquatic viral infection remains largely uncharacterized. Singapore grouper iridovirus (SGIV), a member of the genus Ranavirus in the family Iridoviridae, is one of the most important viral pathogens afflicting grouper aquaculture. In this study, we investigated the influence of a novel Rab11 homolog (EcRab11) from the orange-spotted grouper (Epinephelus coioides) on SGIV infection and the role in host innate immune responses. EcRab11 shares high amino acid sequence identity with Rab11 orthologs spanning from mammals to teleost fishes, indicating evolutionary conservation of this GTPase. In healthy groupers, EcRab11 was predominantly expressed in major immune organs including the liver and spleen, and its transcript levels were significantly upregulated following immune challenges. Confocal imaging revealed that EcRab11 localizes to the cytoplasm as distinct punctate and vesicle-like structures. In contrast, overexpression of a constitutively active EcRab11 mutant (CA-EcRab11, with a GTP-locked mutation at the conserved Q70L site that renders the protein persistently activated and unable to hydrolyze GTP to GDP) induced the formation of enlarged vesicular structures, whereas overexpression of a dominant-negative EcRab11 mutant (DN-EcRab11, with a GDP-locked mutation at the conserved S25N site that abrogates GTP binding and locks the protein in an inactive state) resulted in a marked reduction in vesicle formation. Co-localization analyses further demonstrated that EcRab11 extensively colocalizes with the Golgi apparatus, early endosomes and late endosomes, and partially with the endoplasmic reticulum or lysosomes, but did not colocalize with mitochondria. Functional assays revealed that EcRab11 overexpression significantly suppressed SGIV infection, whereas overexpression of either CA-EcRab11 or DN-EcRab11 enhanced viral replication. Moreover, EcRab11 was found to positively regulate both autophagy and IFN immune responses in grouper cells. Taken together, our findings demonstrate that EcRab11 modulates SGIV infection by orchestrating host innate immune responses, thereby uncovering a novel antiviral mechanism of Rab11 against SGIV and providing new insights for the development of antiviral strategies for grouper aquaculture.},
}
@article {pmid41752171,
year = {2026},
author = {Khan, A and Ziyi, Y and Rahman, FU and Luo, H and Hu, Z},
title = {The Impact of Mitochondrial DNA Depletion on Mitochondrial Ultrastructure, Photosynthesis, and the mTERF Gene Family in Chlamydomonas reinhardtii.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752171},
issn = {1422-0067},
support = {32273118//National Natural Science Foundation of China/ ; GuikeAA24263042//Guangxi Major Program for Science and Technology/ ; 2018YFA0902500//Chinese National Key 576 R&amp;D Project for Synthetic Biology/ ; KCXFZ20211020164013021//Shenzhen Special Fund for Sustainable Development/ ; 2022B1111070005//Guangdong Key R&amp;D Project/ ; 2022B010//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Chlamydomonas reinhardtii/genetics/metabolism/ultrastructure ; *DNA, Mitochondrial/genetics/metabolism ; *Photosynthesis/genetics ; *Mitochondria/ultrastructure/genetics/metabolism ; Phylogeny ; Multigene Family ; *Mitochondrial Proteins/genetics/metabolism ; Chloroplasts/metabolism/genetics ; },
abstract = {Mitochondrial biogenesis requires coordinated expression from both nuclear and mitochondrial genomes. To understand the consequences of mitochondrial genome loss, we generated a mitochondrial DNA-depleted line (crm[-]) in Chlamydomonas reinhardtii via long-term ethidium bromide treatment. We then examined how mtDNA disruption affects mitochondrial ultrastructure, chloroplast function, and the mitochondrial transcription termination factor (mTERF) gene family. Our results reveal that mitochondrial dysfunction is associated with severe organelle remodeling, including mitochondrial elongation, matrix condensation, and cristae collapse. Consequently, mitochondria reduce the electron sink capacity which appears to over-reduce the chloroplast electron transport chain, correlating with causing damage to photosystem II (PSII), as indicated by higher plastoquinone PQ redox state and PSII excitation pressure and lower non-photochemical quantum yield [Y(NPQ)]. Furthermore, we identified and characterized eight nuclear-encoded mTERF genes in C. reinhardtii (CrmTERFs). Phylogenetic analysis grouped them into three clades with potential functional conservation. Collinearity analysis suggested potential evolutionary relationships between mTERF genes in Chlamydomonas and Marchantia polymorpha. Gene ontology annotation linked CrmTERFs to transcription termination and RNA biosynthesis regulation. Additionally, in silico prediction identified twelve putative miRNAs targeting seven of the eight CrmTERFs, with CrmTERF3 as the only exception, providing candidates for future experimental validation. This study provides the first comprehensive analysis of the nuclear encoded mTERF gene family in Chlamydomonas and demonstrates that mtDNA loss is correlated with mTERF genes expression, as well as mitochondrial structure and chloroplast photoprotective impairments. These findings suggest a potential role for CrmTERFs in mitochondrial retrograde signaling and organellar crosstalk, though functional validation is required to establish causality.},
}
@article {pmid41781574,
year = {2026},
author = {Bhardwaj, P and Prajapati, MR and Gupta, N and Majumder, S and Baranwal, VK and Sharma, SK},
title = {Identification of a novel mitovirus in Colocasia esculenta through high‑throughput sequencing and in-silico miRNA prediction for sequence-specific gene silencing.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {4},
pages = {423-431},
pmid = {41781574},
issn = {1618-1905},
mesh = {*Colocasia/virology ; *MicroRNAs/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; RNA-Dependent RNA Polymerase/genetics ; *Gene Silencing ; Plant Diseases/virology ; Genome, Viral ; RNA, Viral/genetics ; Open Reading Frames ; Plant Leaves/virology ; },
abstract = {Mitoviruses are simple RNA viruses typically associated with fungal mitochondria, although recent studies suggest their presence in plant transcriptomes. In this study, we report the identification and molecular characterization of a novel mitovirus from Colocasia esculenta using high-throughput sequencing (HTS). Analysis of symptomatic leaf tissues revealed a 2,644 nucleotide-long viral genome encoding a single open reading frame (ORF) for an RNA-dependent RNA polymerase (RdRp) of 544 amino acids. The viral sequence, tentatively named Colocasia esculenta associated mitovirus 2 (CeaMV2), showed 60.76% amino acid identity with known mitoviruses, supporting its classification as a novel species within the family Mitoviridae. Phylogenetic analysis showed that CeaMV2 clustered within the family Mitoviridae, grouped with other plant-associated mitoviruses, supporting its placement within the family Mitoviridae. The conserved domain searches confirmed the presence of the mitovirus-specific RdRp domain (Pfam: PF05919). RT-PCR and Sanger sequencing further validated the presence of CeaMV2 in C. esculenta leaf samples. The relatively short RdRp and its expression in plant transcriptome suggest possible association with plant mitochondria. Furthermore, in-silico analysis identified several plant-derived mature miRNAs, such as sbi-miR6231-3p, with high binding affinity to the CeaMV2 RdRp gene, suggesting a potential role for RNA interference in the host-virus interaction. This finding expands the known diversity of mitoviruses and highlights the utility of HTS in uncovering cryptic viral infections and potential RNAi-based defense mechanisms in economically important crops.},
}
@article {pmid41807573,
year = {2026},
author = {Ghosh, D and Thakur, S and Bali, S and Sharma, S and Dogra, V},
title = {Comparative genome-wide analysis in Setaria italica and Arabidopsis thaliana revealed functional conservation of specific FtsH proteases under high light and heat stress.},
journal = {Plant cell reports},
volume = {45},
number = {4},
pages = {},
pmid = {41807573},
issn = {1432-203X},
support = {6/1/FIRST/2020-RPPBDD-TMD-SeMI//Council of Scientific and Industrial Research, India/ ; BT/RLF/Re-entry/02/2019//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Arabidopsis/genetics/radiation effects/physiology/enzymology ; Gene Expression Regulation, Plant/radiation effects ; *Light ; *Heat-Shock Response/genetics ; *Arabidopsis Proteins/genetics/metabolism ; *ATP-Dependent Proteases/genetics/metabolism ; Hot Temperature ; Promoter Regions, Genetic/genetics ; Phylogeny ; Photosystem II Protein Complex/metabolism/genetics ; Metalloproteases/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Genome, Plant ; Stress, Physiological ; },
abstract = {The study identified and characterized FtsH gene family in Setaria italica, where a comparative analysis with Arabidopsis thaliana revealed a conservation of expression patterns and functioning of specific FtsH proteases under heat and high light stress. The filamentation temperature-sensitive H (FtsH) metalloproteases maintain proteostasis in chloroplasts and mitochondria under both normal and stress conditions. Here, we compared the specificity of FtsH proteases to heat (HS) and high light (HL) stress (HLS) in C3 model plant Arabidopsis thaliana and an important C4 model crop with high nutritional value, Setaria italica. We identified 9 FtsH genes representing all homologs of functional AtFtsH genes, except for the homologs of AtFtsH12 in S. italica. Gene ontology (GO) analysis revealed a significant enrichment towards the photosynthetic process. Promoter analysis revealed the presence of cis-elements responsive to HL and HS. Interestingly, only selective genes encoding photosystem (PS) II-repairing FtsHs (AtFtsH1, AtFtsH2, AtFtsH5, and AtFtsH8), and FtsHs involved in PSII biogenesis and protein import regulation (AtFtsH4 and AtFtsH11, respectively), and their homologs in S. italica, showed transcriptional upregulation in response to HL, revealing their conserved function under photoinhibitory stresses, which is further reinforced by a rapid induction of FtsH2 and concurrent degradation of PSII reaction center proteins (D1 and D2). On the contrary, almost all FtsH genes were upregulated in response to elevated temperature, establishing their critical and conserved function in maintaining chloroplast proteostasis under HS. AtFtsH6 and its homolog, SiFtsH4, showed a marked induction in both transcript and protein levels with concurrent degradation of PSII-LHC proteins upon elevated temperatures, indicating their possible role in PSII-LHC proteostasis under HS. In summary, this study highlights the specificity of FtsHs in maintaining proteostasis under HS and HLS conditions in C3 and C4 plants.},
}
@article {pmid41812958,
year = {2026},
author = {Zhang, J and Liu, B and Meng, L and You, L and Liu, Z and Wu, Y and Zhang, C and Zhou, Y and Chen, R and Cao, Z and Sun, Y},
title = {Identification and functional analysis of Bcl2-associated agonist of cell death (Bad) reveals its pro-apoptotic and antibacterial roles in Cromileptes altivelis.},
journal = {Fish &amp; shellfish immunology},
volume = {173},
number = {},
pages = {111264},
doi = {10.1016/j.fsi.2026.111264},
pmid = {41812958},
issn = {1095-9947},
mesh = {Animals ; Vibrio/physiology ; Fish Proteins/genetics/immunology/chemistry ; *Apoptosis/genetics ; *Fish Diseases/immunology ; Vibrio Infections/immunology/veterinary ; *Gene Expression Regulation/immunology ; Amino Acid Sequence ; Sequence Alignment/veterinary ; *bcl-Associated Death Protein/genetics/immunology/chemistry ; Gene Expression Profiling/veterinary ; *Immunity, Innate/genetics ; *Perciformes/immunology/genetics ; Phylogeny ; Base Sequence ; },
abstract = {Bcl-2-associated agonist of cell death (Bad) is a pro-apoptotic member of the Bcl-2 family that contains only the BH3 domain and plays a critical role in mitochondrial apoptosis in mammals. However, its functional role in teleosts remains to be fully elucidated. In this study, we identified and characterized the Bad homolog from Cromileptes altivelis (designated CaBad). The complete coding sequence of CaBad comprises 504 bp, encoding a protein of 167 amino acids with only one conserved BH3 domain. CaBad was ubiquitously expressed in healthy C. altivelis, with highest transcript levels detected in immune-related tissues including liver, spleen, and head kidney. Following challenge with Vibrio harveyi, CaBad expression was significantly upregulated in the liver, spleen, and head kidney. Subcellular localization analysis revealed that CaBad was distributed in the cytoplasm and nucleus, and showed enhanced mitochondrial translocation during apoptosis. Flow cytometry assays demonstrated that CaBad promoted apoptosis of C. altivelis brain (CAB) cells upon V. harveyi flagellin B (Fla B) stimulation. This pro-apoptotic effect was mediated through the mitochondrial pathway, as demonstrated by loss of mitochondrial membrane potential, increased DNA fragmentation, activation of Caspase 9 and Caspase 3, and upregulation of key pro-apoptotic proteins including cytochrome c and p53. Furthermore, CaBad was found to inhibit the NF-κB signaling pathway, as evidenced by suppressed IKKα phosphorylation and downregulated transcription of NF-κB subunits and pro-inflammatory cytokines both in vitro and in vivo. Importantly, in vivo infection experiments showed that CaBad overexpression significantly reduced bacterial loads in immune tissues, whereas CaBad knockdown led to increased bacterial colonization. Collectively, our results indicate that CaBad exerts a conserved pro-apoptotic function via the mitochondrial pathway and contributes to antibacterial immunity in C. altivelis, providing new insights into the role of BH3-only proteins in teleosts host defense.},
}
@article {pmid41821201,
year = {2026},
author = {Aoudache, Y and Inturri, S and Das Neves, B and de Bont, L and Remacle, C and Rouhier, N},
title = {Updated Inventory and Refined Classification of the Ferredoxin Family in Archaeplastida.},
journal = {Physiologia plantarum},
volume = {178},
number = {2},
pages = {e70836},
doi = {10.1111/ppl.70836},
pmid = {41821201},
issn = {1399-3054},
support = {CDR J.0149.23//Fonds De La Recherche Scientifique - FNRS/ ; ANR-11-LABX-0002-01//Agence Nationale de la Recherche/ ; },
mesh = {Arabidopsis/genetics/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; *Ferredoxins/metabolism/genetics/classification ; Iron-Sulfur Proteins/metabolism ; Mitochondria/metabolism ; Phylogeny ; Plastids/metabolism/genetics ; },
abstract = {Ferredoxins (FDXs) are ubiquitous proteins that bind iron-sulfur (Fe-S) clusters and usually catalyse electron transfer reactions. In eukaryotic photosynthetic organisms, a relatively high number of [2Fe-2S] cluster-containing FDXs is present in plastids and mitochondria. These are mostly redox-active FDXs, except one mitochondrial FDX that no longer binds an Fe-S cluster and is a component of the respiratory complex I. We have performed a phylogenomic study to describe the content and distribution of FDXs in different phylogenetic groups of the Archaeplastida clade, including the two models Arabidopsis thaliana and Chlamydomonas reinhardtii. Important differences exist since the number of FDXs ranges from four to 19. From the sequence characteristics and phylogenetic analyses, they cluster in 10 clades: eight containing plastidial FDXs and two mitochondrial FDXs. Six clades are present in most organisms, while four clades comprising plastidial FDXs (FDX5, FDX7, FDX8, and FDX9) are present in a small subset of organisms, mostly algae and lower Embryophytes; the FDX5 and FDX9 clades are even only present in Chlorophyceae. The expression patterns of these two FDXs in Chlamydomonas combined with the physiological and biochemical studies performed with FDX5 suggest specific roles of FDX5 in anoxia and of FDX9 in the dark. Structural analyses provide additional support to the functional divergence among plastidial FDXs. Overall, these analyses revealed the existence of an important diversity within the FDX family and allowed refining the FDX classification in Archaeplastida. It also provides clues for future physiological analyses to decipher the functions of the uncharacterised FDXs.},
}
@article {pmid41833805,
year = {2026},
author = {Huang, R and Yan, C and Lv, Y and Jin, Y and Zhang, D},
title = {Immunological functional studies of a putative lipocalin member LcApoM_AGPRP in large yellow croaker (Larimichthys crocea).},
journal = {Fish &amp; shellfish immunology},
volume = {173},
number = {},
pages = {111274},
doi = {10.1016/j.fsi.2026.111274},
pmid = {41833805},
issn = {1095-9947},
mesh = {Animals ; *Perciformes/immunology/genetics ; *Immunity, Innate/genetics ; Fish Proteins/genetics/immunology/chemistry ; Poly I-C/pharmacology ; Sequence Alignment/veterinary ; *Fish Diseases/immunology ; Amino Acid Sequence ; *Gene Expression Regulation/immunology ; *Lipocalins/genetics/immunology/chemistry ; Phylogeny ; Lipopolysaccharides/pharmacology ; Gene Expression Profiling/veterinary ; },
abstract = {Lipocalins play crucial roles in immune defense in vertebrates; however, their functional mechanisms in teleost fish remain poorly understood. In this study, the economically important marine fish large yellow croaker (Larimichthys crocea) was used as a model to investigate a novel lipocalin-like protein, LcApoM_AGPRP, and to elucidate its role in immune responses. A putative antibacterial protein, LcApoM_AGPRP, which lacks functional annotation in the genome, was identified in large yellow croaker. LcApoM_AGPRP was highly constitutively expressed in the liver, head kidney, ovary, gill and spermary of healthy large yellow croaker. It expression was significantly upregulated following LPS and Poly(I:C) stimulation, indicating a potential role in innate immune responses. Subcellular localization analysis demonstrated that LcApoM_AGPRP is predominantly localized in lysosomes, mainly distributed in the Golgi apparatus and mitochondria and partially distributed in the endoplasmic reticulum, implying its involvement in organelle-mediated immune defense. Functional assays showed that LcApoM_AGPRP possesses broad-spectrum antimicrobial activity. The recombinant protein exerts its antibacterial effects through multiple mechanisms, including disruption of bacterial membrane integrity, inhibition of bacterial motility, and interference with biofilm formation. Stability assays further confirmed that its antibacterial activity is maintained over a wide range of temperatures (25-100 °C) and salinities (0-40 ‰), highlighting its strong environmental adaptability. These properties suggest that LcApoM_AGPRP has considerable potential for application as an antibacterial agent, aquaculture feed additive, or food preservative. This study provides the first systematic identification and functional characterization of LcApoM_AGPRP, offering new insights into the innate immune system of teleost fish.},
}
@article {pmid41931186,
year = {2026},
author = {Akhilesh, K and Naik, VCB and Chandrakar, G and Sindhura, KAV and Rao, VP and Prabhulinga, T and Sundaram, RM},
title = {MtCOI-based genetic diversity and population structure of the White-Backed Planthopper, Sogatella furcifera Horváth across major rice ecosystems of India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41931186},
issn = {1573-4978},
support = {IF230039//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Hemiptera/genetics ; India ; Genetic Variation/genetics ; Phylogeny ; Haplotypes/genetics ; *Electron Transport Complex IV/genetics ; *Oryza/parasitology ; Ecosystem ; Genetics, Population/methods ; Bayes Theorem ; Gene Flow ; Mitochondria/genetics ; },
abstract = {BACKGROUND: The white-backed planthopper, Sogatella furcifera Horváth is a major rice pest in Asia, causing direct phloem-feeding damage and transmitting Southern rice black-streaked dwarf virus (SRBSDV). Despite its economic importance in India, information on its genetic diversity, population connectivity and demographic history remains limited. METHODS AND RESULTS: Mitochondrial cytochrome oxidase I (mtCOI) sequences (710 bp) from 44 individuals representing 16 populations across nine Indian states were analysed to assess genetic structure. Phylogenetic analyses using Maximum Likelihood and Bayesian inference recovered a single monophyletic cluster with shallow divergence and no region-specific lineages. Three closely related haplotypes were detected, differing by a single mutation, with one dominant haplotype (H1) comprising 88.63% of individuals. Overall haplotype and nucleotide diversity were low (Hd = 0.342; π = 0.00057) and southern populations showed mitochondrial monomorphism under current sampling. AMOVA indicated that most genetic variation occurred within populations (92.68%), with only 7.32% among populations. Pairwise FST and gene flow analyses indicated heterogeneous connectivity, while isolation-by-distance analysis detected a significant positive correlation between genetic and geographic distances (r ≈ 0.50, P < 0.05). Neutrality tests (Tajima’s D; Fu and Li’s D and F) were negative but non-significant. Bayesian Skyline Plot analysis indicated moderate historical fluctuations in effective population size without evidence of recent rapid expansion or severe bottlenecks. CONCLUSIONS: Indian populations of S. furcifera exhibit low mitochondrial genetic differentiation, shallow spatial structuring and moderate isolation by distance. The overall pattern suggests demographic stability and substantial dispersal potential; however, inference is limited by the resolution of a single mitochondrial marker. These findings provide a baseline for understanding WBPH population dynamics in India and highlight the need for high-resolution nuclear markers to better resolve fine-scale structure relevant to migration monitoring and pest management.},
}
@article {pmid41963795,
year = {2026},
author = {Stuehler, DS and Cano, LM and Heck, M},
title = {Rapid and reproducible haplotyping of complete mitochondrial genomes using split k-mers.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41963795},
issn = {1471-2164},
support = {2022-70029-038503//National Institute of Food and Agriculture/ ; 8062-22410-007-000-D//Agricultural Research Service/ ; 2020-70029-33176//Emergency Citrus Disease Research and Extension Program/ ; },
mesh = {*Genome, Mitochondrial ; *Haplotypes ; Animals ; Phylogeny ; Hemiptera/genetics ; Reproducibility of Results ; },
abstract = {Accurate phylogenetic analysis of mitochondrial haplotypes underpins a wide spectrum of biological inquiry. While multilocus sequence-based phylogenies are standard, inconsistent gene selection and removal of terminal overhangs during alignment trimming disregard non-coding sequence as well as limit the reproducibility of haplotyping methods. To examine alternative approaches, we tested split k-mer analysis (SKA) to reassess published mitogenome datasets of one mammalian and two insect species. SKA accurately haplotyped each dataset, improved polymorphism detection in the hemipteran Diaphorina citri and aided in the identification of D. citri haplotypes associated with the titer of “Candidatus Liberibacter asiaticus”, the bacterium associated with citrus greening disease. We present a new mitogenome haplotyping method and script, ska-mtdna.py.},
}
@article {pmid42079717,
year = {2026},
author = {Alther, E and Abdelmula, AA and Elsanosi, HA and Mostafa, S and Zhou, G},
title = {Comprehensive genome characterization and expression analysis of the DUF4228 gene family in Sorghum (Sorghum bicolor L.) under salt stress conditions.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21175},
pmid = {42079717},
issn = {2167-8359},
mesh = {*Sorghum/genetics ; *Gene Expression Regulation, Plant ; Phylogeny ; *Salt Stress/genetics ; *Plant Proteins/genetics/metabolism ; *Genome, Plant ; Multigene Family ; Gene Expression Profiling ; Chromosome Mapping ; *Genes, Plant ; Promoter Regions, Genetic ; Stress, Physiological/genetics ; },
abstract = {Sorghum (Sorghum bicolor L.) is recognized for its resilience to environmental adversities; the DUF4228 gene family plays vital roles in development, growth, and response to stress in number of plant species such as Arabidopsis thaliana, and Glycine max, however, the systematic analysis of these gene families lacks reports in Sorghum. In this study, we identified and characterized members of the DUF4228 gene family in the Sorghum genome through comprehensive bioinformatics analyses. A total of 25 SbDUF4228 genes were discovered and mapped across eight chromosomes. Phylogenetic analysis divided these genes into six different groupings. Subcellular localization indicated that SbDUF4228 proteins are distributed across the nucleus, mitochondria, cytoplasm, and plasma membrane, indicating potential functional diversity. Expression analysis based on Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values revealed that SbDUF4228 genes are differentially expressed across distinct tissues. Furthermore, the promoter regions of the DUF4228 gene were enriched with cis-regulatory elements associated with stress responses (MYB, MYC) and hormone signaling (ABA, MeJA). To further examine their role in abiotic stress response, we preformed quantitative real-time polymerase chain reaction (qRT-PCR) on seven SbDUF4228 genes under salt stress conditions. The results indicated SbDUF4228-4, SbDUF4228-14, SbDUF4228-1, and SbDUF4228-15 genes were significantly up-regulated following salt treatment, indicating their crucial role in salt stress tolerance. Overall, this study identifies key stress-responsive members of the SbDUF4228 family and provides a foundation for future functional research and Sorghum improvement strategies.},
}
@article {pmid42116196,
year = {2026},
author = {Abreu, FVS and Mosmann, LB and Martins, CB and da Silva Xavier, A and da Rocha Corpas Maciel, IM and Nascimento-Pereira, AC and Ribeiro, PS and Alencar, J and Tubaki, RM and Motta, MA and Lourenço-de-Oliveira, R and Pavan, MG},
title = {Mitochondrial introgression hampers the DNA barcoding of cryptic yellow fever vectors Haemagogus capricornii Lutz and Hg. janthinomys in the Atlantic Forest, Brazil.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42116196},
issn = {1756-3305},
support = {309577/2013-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Animals ; Brazil/epidemiology ; Phylogeny ; Female ; Male ; *Yellow Fever/transmission/epidemiology ; *DNA Barcoding, Taxonomic ; *Culicidae/genetics/classification/anatomy &amp; histology ; *Mosquito Vectors/genetics/classification ; DNA, Mitochondrial/genetics ; Forests ; *Genetic Introgression ; *Mitochondria/genetics ; Bayes Theorem ; },
abstract = {BACKGROUND: Yellow fever is a major public health concern in Brazil, transmitted in sylvatic cycles by Haemagogus and Sabethes mosquitoes. Among them, Haemagogus janthinomys and Hg. capricornii occur in sympatry in the Atlantic Forest and females are morphologically indistinguishable, complicating vector identification during outbreaks. Here, we aimed to investigate their taxonomic status and evolutionary history using an integrative approach including morphological and phylogenetic analyses.<br><br>METHODS: Mosquitoes were collected in 17 municipalities across nine Brazilian states, including simultaneous captures of both species in sympatric areas. Males were identified by genitalia morphology and molecular analyses were performed using three mitochondrial and two nuclear genes. Diversity analyses and neutrality tests were performed, and phylogenies were reconstructed with Maximum Likelihood and Bayesian inferences. Divergence times were estimated using strict molecular clock, and population history was assessed through mismatch distribution analysis and Bayesian Skyline Plots.<br><br>RESULTS: A total of 79 specimens were morphologically identified, with Hg. janthinomys showing a broader geographic and altitudinal distribution than Hg. capricornii, which was usually restricted to higher elevations. Phylogenetic analyses based on mitochondrial markers revealed two clades, but did not recover clear reciprocal monophyly, thus evidencing that these markers alone cannot separate the two species. The inclusion of nuclear markers evidenced introgression events of Hg. janthinomys mitochondria in Hg. capricornii specimens in the Para&#xed;ba River Valley and Esp&#xed;rito Santo State, and successive breeding of Hg. capricornii on few samples morphologically identified as Hg. janthinomys in S&#xe3;o Paulo State. Molecular clock and population history analyses evidenced that these species have probably speciated in peripatry or parapatry during the Pleistocene era at approximately 1.2 million years ago, and a recent sudden expansion of Hg. capricornii in the last 10 thousand years ago has tripled its population and likely led to a secondary contact between the two species.<br><br>CONCLUSIONS: Haemagogus janthinomys and Hg. capricornii are valid and closely related species with evolutionary histories shaped by divergence during the Pleistocene era and subsequent introgression events. The use of cytochrome c oxidase subunit I gene (COI) DNA barcoding alone could not reliably distinguish them, and integrating morphology with multiple molecular markers is essential for accurate identification. Future work is needed for a finer resolution of hybridization patterns to help clarify if the observed mito-nuclear discordance reflects historical introgression or active genetic exchange between species.},
}
@article {pmid42167054,
year = {2026},
author = {Mège, M and Berquier, F and Bonsergent, C and Malandrin, L},
title = {Theileria equi sensu lato genetic diversity and phylogeny: new insights from mitochondrion, apicoplast and nucleus multilocus gene analysis.},
journal = {Ticks and tick-borne diseases},
volume = {17},
number = {3},
pages = {102656},
doi = {10.1016/j.ttbdis.2026.102656},
pmid = {42167054},
issn = {1877-9603},
mesh = {*Phylogeny ; *Theileria/genetics/classification ; *Genetic Variation ; Animals ; Horses ; *Theileriasis/parasitology ; Cell Nucleus/genetics ; Multilocus Sequence Typing ; *Horse Diseases/parasitology ; Mitochondria/genetics ; DNA, Protozoan/genetics ; Molecular Sequence Data ; },
abstract = {Equine piroplasmosis is a significant tick-borne disease with a global distribution. Among the two causative agents, Theileria equi has undergone numerous taxonomic reclassifications over time, reflecting advances in our understanding of its biology, molecular characteristics, and phylogenetic relationships. Formerly named Babesia equi, now classified in the Equus group apart from Babesia and Theileria species, its genus name will again certainly change. The genetic diversity also within T. equi lead to the renaming of one lineage as Theileria haneyi. Theileria equi should better now be considered as T. equi sensu lato (including T. haneyi) with a set of different cryptic species awaiting for formal taxonomical changes to be taken. A better knowledge within this group is therefore essential as this diversity has an impact on the diagnostic of this disease which is submitted to strict regulations governing the international movement of horses. In the present study, we designed primers to study the same five genes from the nucleus (hsp70, clamp and ama-1), the mitochondria (cox1) and the apicoplast (tufA), on a set of 36 mono-infected samples of the lineages A, C (T. haneyi) and E of T. equi sensu lato. The phylogenetic separation in lineages A, C and E based on 18S rRNA sequencing was confirmed by this multi-locus analysis. Genetic diversity and phylogenetic separation within lineage A into two sub-lineages A1 and A2 were demonstrated on the basis of all five genes, with an additional A3 sub-lineage on the basis of nuclear (hsp70) and mitochondrial (cox1) markers. All these sub-lineages would deserve the rank of species based on cox1 divergence confirmed by other markers. Phylogenetic and haplotype networks analyses were also conducted on genes used in molecular or serological diagnostic, ema-1 and ema-11, to evaluate the impact of this diversity on currently used tests. We confirmed the absence of molecular detection of the lineage E DNA with any of these two gene targets. We linked the sub-lineages A1 and A3 to the ema-1 clades A and B, with a worldwide distribution. We confirmed the link of the rare A2 sub-lineage from France to a new ema-1 clade D, with additional Eurasian sequences from Croatia, Mongolia and China. A fifth ema-1 clade E was also confirmed. Separation of lineage C (T. haneyi) into at least two sub-lineages was also confirmed with the few ema-11 sequences available, based on their genetic diversity, and their phylogenetic and haplotype network analyses. From this study, it becomes clear that the division of T. equi sensu lato into species corresponding either to the lineage (5 species) or to the sub-lineage (at least 10) should await a more comprehensive knowledge of its genetic diversity worldwide, as it may impact the diagnostic tools to be developed.},
}
@article {pmid42218085,
year = {2026},
author = {Wang, C and Kassem, S and Suo, X and Soldati-Favre, D and Jia, Y},
title = {Fragmented rRNAs and lineage-specific RNA-binding proteins define myzozoan mitoribosomes.},
journal = {Trends in parasitology},
volume = {42},
number = {8},
pages = {749-762},
doi = {10.1016/j.pt.2026.05.008},
pmid = {42218085},
issn = {1471-5007},
mesh = {*RNA-Binding Proteins/genetics/metabolism ; *RNA, Ribosomal/genetics ; Animals ; *Mitochondrial Ribosomes ; Apicomplexa/genetics ; },
abstract = {Myzozoa, a clade of alveolate protists including Apicomplexa, Chromerida, Perkinsozoa, and dinoflagellates, possesses the most reduced mitochondrial genomes among eukaryotes. Apicomplexan parasites, such as Toxoplasma gondii and Plasmodium spp., retain mitochondrial genomes encoding only three proteins and highly fragmented rRNAs. Despite this reduction, recent structural studies show that T. gondii mitoribosome incorporates lineage-specific RNA-binding proteins as integral components to maintain a functional complex composed of over 50 rRNA fragments. The conservation of rRNA fragmentation and protein repertoire observed among Apicomplexa suggests a shared evolution within the phylum. This radical divergence from all other currently investigated cytoplasmic and mitochondrial ribosomes highlights evolutionary plasticity and common ancestry, providing a model for studying mitochondrial evolution and potential antiparasitic drug discovery.},
}
@article {pmid42247036,
year = {2026},
author = {Sahraoui, N and Belkahia, H and Ben Said, M and Boukert, R and Ben Ali, S and Denis, F},
title = {Global cytochrome c oxidase subunit I analysis reveals mitochondrial conservation in Camelus dromedarius with clear interspecific separation from other camelids.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42247036},
issn = {1573-4978},
mesh = {Animals ; *Camelus/genetics/classification ; Phylogeny ; *Electron Transport Complex IV/genetics ; *Mitochondria/genetics ; Genetic Variation ; Species Specificity ; DNA Barcoding, Taxonomic/methods ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; Algeria ; Genotype ; },
abstract = {BACKGROUND: The mitochondrial cytochrome c oxidase subunit I (COI) gene is widely used as a DNA barcoding marker; however, its ability to discriminate closely related camelid species and capture intraspecific variation in Camelus dromedarius remains insufficiently assessed at a global scale.<br><br>METHODS AND RESULTS: In this study, we sequenced COI from 20 Algerian dromedaries and combined these data with publicly available sequences covering the same fragment, along with representative sequences from the six other extant camelid species and Bos taurus as an outgroup. Sequence alignment, diversity indices, and neutrality tests were performed using DnaSP, while genetic distances and phylogenetic relationships were inferred using Maximum Likelihood under the Tamura-Nei model. Analysis of 136 C. dromedarius COI sequences (625&#xa0;bp) revealed only five polymorphic sites and four genotypes worldwide, with very low genotype diversity (Gd&#x2009;=&#x2009;0.277), nucleotide diversity (&#x3c0;&#x2009;=&#x2009;0.00145), and mean nucleotide differences (k&#x2009;=&#x2009;0.905). The Algerian genotypes (G1 and G2) fell within this limited variation, showing&#x2009;&#x2265;&#x2009;99.2% identity and minimal genetic distances (&#x2264;&#x2009;0.008) relative to reference sequences. In contrast, interspecific distances between dromedaries and other camelids were substantially higher (&#x2248;&#x2009;0.014-0.188). Phylogenetic analysis recovered well-supported clades corresponding to C. dromedarius, Bactrian camels, and New World camelids, with no overlap between intra- and interspecific variation.<br><br>CONCLUSIONS: These findings indicate that the COI region is highly conserved within C. dromedarius but remains effective for species discrimination. The inclusion of Algerian sequences supports the low mitochondrial diversity of dromedaries and suggests a recent shared maternal ancestry across their global range.},
}
@article {pmid42278388,
year = {2026},
author = {Fan, H and Yu, J and Wang, W and Lv, Z and Zhu, S and Li, C},
title = {Perilipin 2 Stabilizes Lipid Droplets and Coordinates Mitochondrial Fatty Acid Flux and ER Stress Adaptation in Apostichopus japonicus.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
pmid = {42278388},
issn = {1422-0067},
support = {32303042//National Natural Science Foundation of China/ ; 32325050//National Science Fund for Distinguished Young Scholars of China/ ; LQ24C190001//Zhejiang Provincial Natural Science Foundation/ ; LZ25C190002//Zhejiang Provincial Natural Science Foundation/ ; 2024JCYJ070//Yantai Science and Technology Innovation Development Plan-Basic Research Project/ ; },
mesh = {Animals ; *Mitochondria/metabolism ; *Stichopus/metabolism/genetics/microbiology ; *Lipid Droplets/metabolism ; *Fatty Acids/metabolism ; *Perilipin-2/metabolism/genetics/chemistry ; Phylogeny ; *Endoplasmic Reticulum Stress ; Endoplasmic Reticulum/metabolism ; Vibrio ; Lipolysis ; Adaptation, Physiological ; },
abstract = {Perilipins (PLINs) are lipid droplet-associated proteins that regulate lipid storage, mobilization, and metabolism, yet their roles in invertebrates remain poorly characterized. This study aimed to investigate the evolutionary conservation and functional adaptation of PLIN2 in the sea cucumber Apostichopus japonicus. Phylogenetic analysis placed A. japonicus PLIN2 within the PLIN2 clade, forming an echinoderm-specific branch distinct from vertebrate PLIN2s. Structural prediction revealed an N-terminal PAT domain containing an amphipathic helix that was required for lipid droplet targeting, as deletion of this region abolished its localization to lipid droplet. Functionally, PLIN2 abundance positively correlated with lipid droplet formation, and its knockdown reduced triacylglycerol accumulation while upregulating lipolysis-related genes. Pull-down and co-immunoprecipitation assays identified interactions between PLIN2 and the endoplasmic reticulum protein ERP44, as well as the mitochondrial protein TRXR2, suggesting a role in lipid droplet-organelle coupling. Consistently, disruption of the PLIN2-TRXR2 module impaired fatty acid transfer from lipid droplets to mitochondria, leading to suppressed β-oxidation and decreased ATP production. In addition, PLIN2 mediates the protective role of lipid droplets against Vibrio splendidus-induced ER stress. Together, these findings establish A. japonicus PLIN2 as a multifunctional lipid droplet-associated protein that coordinates lipid droplet stability with organelle communication, energy metabolism, and ER homeostasis.},
}
@article {pmid42342450,
year = {2026},
author = {Chowdhury, S and Kruger, AJ and Roger, LM},
title = {Conserved HSP60 structure with lineage- and context-specific regulation in cnidarians.},
journal = {Life science alliance},
volume = {9},
number = {9},
pages = {},
pmid = {42342450},
issn = {2575-1077},
mesh = {Animals ; *Chaperonin 60/genetics/metabolism/chemistry ; Phylogeny ; Heat-Shock Response ; *Cnidaria/metabolism/genetics ; Sea Anemones/metabolism/genetics ; Mitochondria/metabolism ; Stress, Physiological ; },
abstract = {Heat shock proteins safeguard proteostasis under stress. We examined mitochondrial chaperonin HSP60 in three cnidarians to assess stress responses. We evaluated HSP60 expression in Pocillopora acuta (hard coral), Exaiptasia diaphana (sea anemone), and Cassiopea xamachana (upside-down jellyfish) using immunoblotting. In P. acuta, HSP60 was not detected at the fragment level under either control (25°C) or heat-stress (30°C). In contrast, isolated cells showed transient HSP60 expression under both temperature conditions, indicating context-dependent regulation in coral. E. diaphana and C. xamachana showed elevated HSP60 expression over 24 h when stressed (+5°C above laboratory optima). These patterns indicate lineage-specific regulatory mechanisms underlying chaperone-mediated stress response pathways. Thus, thermal sensitivity varies among species and across biological contexts. Consistent antibody cross-reactivity prompted evolutionary analysis. Phylogenetic analyses confirmed cnidarian HSP60 proteins are orthologous to vertebrate HSP60, demonstrating deep conservation across Metazoa. Although HSP60 is ancient and highly conserved, its role in regulating mitochondrial proteostasis varies across early-diverging metazoans. This study underlines the role of chaperone plasticity in cnidarian thermotolerance and diverging bleaching susceptibility of symbiotic cnidarians.},
}
@article {pmid42353767,
year = {2026},
author = {Lin, B and Zhang, X and Yu, Z and Zhao, W and Ma, G and Song, S and Li, X and Zhuang, Y and Zhang, J and Zhang, D and Chen, B},
title = {Genome-Wide Identification and Expression Analysis of the Soybean GmHSP100 Gene Family in Response to Heat and Salt Stresses.},
journal = {Genes},
volume = {17},
number = {6},
pages = {},
pmid = {42353767},
issn = {2073-4425},
support = {2023LZGC006, 32572365, 32322062, 32441057, SRICSPYF-BS2025109, ZR2023JQ009, SDARS-28-01, and SDARS-28-06//Shandong Agricultural University/ ; },
mesh = {*Glycine max/genetics/metabolism ; Gene Expression Regulation, Plant ; *Salt Stress/genetics ; Multigene Family ; *Plant Proteins/genetics/metabolism ; *Heat-Shock Proteins/genetics/metabolism ; *Heat-Shock Response/genetics ; Phylogeny ; Gene Expression Profiling ; Promoter Regions, Genetic ; Genome-Wide Association Study ; *Soybean Proteins/genetics ; Genome, Plant ; },
abstract = {BACKGROUND: Heat shock protein 100 (HSP100) is a key molecular chaperone that maintains intracellular proteostasis and enhances plant tolerance. However, the HSP100 gene family in soybean (Glycine max) has not been systematically characterized.<br><br>METHODS: In this study, we performed genome-wide identification and comprehensive analysis of the GmHSP100 gene family and analyzed their phylogeny, genomic distribution, synteny, protein structures, subcellular localization, promoter cis-elements, and expression patterns under heat and salt stresses via bioinformatics approaches and quantitative real-time PCR (qRT-PCR) validation.<br><br>RESULTS: Thirteen GmHSP100 members were identified, which were classified into CLPB, CLPC and CLPD subfamilies. Segmental and whole-genome duplications primarily drove the expansion of this gene family. All encoded proteins possessed conserved AAA+ ATPase domains, with distinct motifs across subfamilies. Most proteins localized to the cytoplasm, while CLPC and CLPD targeted chloroplasts and GmCLPB4 localized to mitochondria. Promoter analysis identified numerous elements associated with light, hormone and stress responses. Expression profiling showed strong tissue specificity and time-dependent stress-treatment induction. Heat stress triggered rapid and strong upregulation of the GmHSP100s, whereas salt stress salt stress induced their relatively delayed and sustained expression.<br><br>CONCLUSIONS: These findings reveal the evolutionary conservation and diversification of the GmHSP100 gene family in soybean, providing a foundational framework for understanding the functions of GmHSP100 in stress adaptation.},
}
@article {pmid42377538,
year = {2026},
author = {Wang, X and Li, J and Li, S and Zhang, X and Wang, J and Hou, T and He, J},
title = {Identification of the R2R3-MYB transcription factor family in goji and LbaR2R3-MYB3 mediated wax biosynthesis enhancing powdery mildew resistance in tobacco.},
journal = {Plant cell reports},
volume = {45},
number = {7},
pages = {},
pmid = {42377538},
issn = {1432-203X},
support = {24JRRA650//Gansu Province Natural Science Foundation/ ; 2026A-063//Gansu Provincial Education Science and Technology Innovation Project/ ; 32060341//National Natural Science Foundation of China/ ; },
mesh = {*Transcription Factors/metabolism/genetics ; *Plant Proteins/genetics/metabolism ; *Nicotiana/genetics/microbiology/metabolism/immunology ; *Disease Resistance/genetics ; *Plant Diseases/microbiology/immunology/genetics ; Gene Expression Regulation, Plant ; *Ascomycota/physiology/pathogenicity ; *Waxes/metabolism ; Plants, Genetically Modified ; Phylogeny ; Plant Leaves/genetics/microbiology/metabolism ; Amino Acid Sequence ; Multigene Family ; },
abstract = {The transcription factor LbaR2R3-MYB3 of goji promotes the biosynthesis of wax components including alkanes, alcohols, fatty acids, and ketones, increases total leaf cuticular wax load, and consequently enhances tobacco resistance to powdery mildew. Goji (Lycium barbarum) is one of the important economic forest species in northwest China. Powdery mildew is a common disease of goji plants that significantly reduces yield and quality, causing substantial economic losses for growers. Cuticular wax serves as the first physical barrier protecting plants against both biotic and abiotic stresses. Members of the R2R3-MYB transcription factor family in goji have not been previously reported, and the relationship between the key member LbaR2R3-MYB3 and cuticular wax biosynthesis and powdery mildew resistance remains unclear. Therefore, this study employed "Ningqi I" goji as the experimental material and identified 75 R2R3-MYB transcription factor family members distributed across 11 chromosomes in the genome. The goji LbaR2R3-MYB proteins mainly localized in the nucleus, mitochondria, cytoplasm, and chloroplasts. Ten conserved motifs were identified in LbaR2R3-MYB3 proteins, with Motif1, Motif2, and Motif3 being the most widely distributed. The promoters of these family members contain multiple cis-acting elements responsive to hormones and abiotic stress. Members of the LbaR2R3-MYB transcription factor family exhibited evolutionary instability. The LbaR2R3-MYB3 gene was cloned from goji leaves yielding a 756 bp fragment. Heterologous expression vectors were successfully constructed, and transgenic tobacco lines overexpressing LbaR2R3-MYB3 (LbaR2R3-MYB3-OE) were obtained. Compared with wild-type tobacco, the cuticular wax load in transgenic tobacco leaves was significantly increased by 1.82-fold, with significant increases in alkanes, alcohols, fatty acids, and ketones. The transgenic tobacco lines showed a 38.2% reduction in powdery mildew incidence and a 59.8% decrease in disease index compared to WT, indicating significantly enhanced resistance to powdery mildew. These results demonstrate that the transcription factor LbaR2R3-MYB3 promotes the biosynthesis of wax components including alkanes, alcohols, fatty acids, and ketones, increases total leaf cuticular wax load, and consequently enhances tobacco resistance to powdery mildew.},
}
@article {pmid42409135,
year = {2026},
author = {Li, C and Qi, S and Zhang, M and Zhang, Y and Zhou, S and Dong, J and Kong, X},
title = {Common carp USP30s restrict SVCV replication by attenuating mitophagy.},
journal = {Fish &amp; shellfish immunology},
volume = {177},
number = {},
pages = {111583},
doi = {10.1016/j.fsi.2026.111583},
pmid = {42409135},
issn = {1095-9947},
mesh = {Animals ; *Carps/immunology/genetics ; *Mitophagy/immunology ; Rhabdoviridae/physiology ; *Virus Replication ; *Fish Diseases/immunology ; Fish Proteins/genetics/immunology/chemistry ; Rhabdoviridae Infections/immunology/veterinary/virology ; Sequence Alignment/veterinary ; *Immunity, Innate/genetics ; Amino Acid Sequence ; *Gene Expression Regulation/immunology ; Phylogeny ; },
abstract = {As a selective autophagic process, mitophagy is deeply involved in antiviral immunity by eliminating damaged mitochondria and requires the participation of various enzymes. Among these, the deubiquitinating enzyme USP30 is known to regulate mitophagy in mammals, yet its function in teleost antiviral defense remains entirely unexplored. In this study, we identified two USP30 homologs from the common carp (Cyprinus carpio), CcUSP30-A and CcUSP30-B, both containing a conserved USP domain and the atypical catalytic triad (Cys73, His445, Ser470). In vitro, spring viremia of carp virus (SVCV) infection induced PINK1-Parkin-dependent mitophagy that was subsequently exploited to promote viral replication. Overexpression of CcUSP30-A and CcUSP30-B significantly upregulated mitochondrial protein levels, reduced SVCV-induced mitophagy, and restricted SVCV replication. Notably, CcUSP30-B displayed stronger anti-mitophagy and anti-SVCV activities than CcUSP30-A. These findings demonstrate that CcUSP30s antagonize the PINK1-Parkin pathway, thereby counteracting excessive SVCV-induced mitophagy and ultimately limiting viral replication. This study provides the first evidence that USP30 acts as an antiviral regulator by preserving mitochondrial integrity in teleosts, and it may serve as a promising target for a novel strategy to control SVCV infection in aquaculture.},
}
@article {pmid42475569,
year = {2026},
author = {Chitnis, M and Kaub, L and Vďačný, P and Beiers, LM and Sturm, S and Coskun, &#xd6;K and Mills, DB and Gomez-Saez, GV and Mengue, L and Gottschaldt, KD and Gilder, SA and Obert, T and Rurik, I and Sturm, EV and Orsi, WD},
title = {Magnetotaxis in an anaerobic ciliate via tripartite syntrophy.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {30},
pages = {e2609513123},
pmid = {42475569},
issn = {1091-6490},
support = {OR417/9-1//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Magnetosomes/metabolism/genetics ; *Ciliophora/physiology/microbiology/genetics ; *Deltaproteobacteria/genetics/physiology ; Anaerobiosis ; Phylogeny ; Ferrosoferric Oxide/metabolism ; },
abstract = {Magnetotaxis has evolved independently numerous times in bacteria, whereby genetically controlled biomineralization of nano-crystalline magnets results in swimming along Earth's magnetic field lines. Compared to magnetotactic bacteria (MTB), evolutionary mechanisms of magnetotaxis as a trait in eukaryotes remain poorly understood. Here, we report a magnetotactic ciliate, Tropidoatractus magnetotacticus sp. nov., that acquires magnetotaxis via syntrophy. T. magnetotacticus exhibits magnetotaxis due to the magnetic moment of internal ferrimagnetic magnetite (Fe3O4) nanoparticles forming ellipsoidal "necklace-shaped" parallel chains. Electron microscopy revealed T. magnetotacticus hosts numerous internal rod-shaped bacteria containing these magnetosome chains. Consistent with this, a genomic population of MTB (Thermodesulfobacteriota) in magnetically sorted T. magnetotacticus cells was found that encoded and expressed a magnetosome gene cluster responsible for magnetosome Fe3O4 biomineralization closely related to that of the ectosymbiont "Candidatus Desulfarcum epimagneticum." T. magnetotacticus also housed a second genomic population affiliated with the endosymbiotic methanogen Methanoregula. Metatranscriptomes of sorted T. magnetotacticus cells show eukaryotic hydrogenosomal Fe-hydrogenase gene expression, and expression of genes encoding proteins in an electron transport chain indicative of H2-producing mitochondria-related organelles. Active gene expression of energy metabolism pathways indicates a tripartite syntrophic network whereby anaerobic fermentation products from T. magnetotacticus are consumed by two syntrophic partners: MTB producing the magnetosome chains and hydrogenotrophic methanogens. Our findings show how magnetotaxis can emerge as a trait in eukaryotes via syntrophic cooperation.},
}
@article {pmid42511689,
year = {2026},
author = {Peng, R and Huang, F and He, Y and Xu, J and Zhu, Y and Ren, M and Hao, Y and Tian, Z},
title = {Research Advances in Plant Pyruvate Kinase.},
journal = {International journal of molecular sciences},
volume = {27},
number = {14},
pages = {},
pmid = {42511689},
issn = {1422-0067},
support = {SKLCUSA-b202305//State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ ; 2021C02063-1//the Major Projects of Rice Breeding in the 14th Five Year Plan of Zhejiang Province/ ; LQ23C130005//Zhejiang Provincial Natural Science Foundation/ ; },
mesh = {*Pyruvate Kinase/metabolism/genetics/chemistry ; *Plants/enzymology/genetics ; *Plant Proteins/metabolism/genetics/chemistry ; Gene Expression Regulation, Plant ; Phylogeny ; Plastids/enzymology ; },
abstract = {Pyruvate kinase (PK) is the terminal rate-limiting enzyme of glycolysis and occupies a central position in plant energy metabolism and carbon skeleton allocation. Plant PK isoenzymes comprise the cytosolic pyruvate kinase (PKc) and the plastidic pyruvate kinase (PKp), which differ markedly in gene origin, protein structure, subcellular localization, and physiological function, exhibiting independent evolutionary histories and functional diversification. Recent studies have revealed that PKc possesses dynamic subcellular distribution, allowing it to shuttle among the cytosol, mitochondria, and nucleus, where it participates in stress responses and epigenetic regulation through protein-protein interactions. PKp is localized to plastids and connects carbon metabolism with lipid biosynthesis and the methylerythritol phosphate (MEP) pathway by supplying pyruvate, thereby playing critical roles in seed development and oil accumulation. This review comprehensively summarizes recent advances in plant PKc and PKp concerning protein structure and subunit composition, tissue-specific expression, subcellular localization, protein interaction networks, activity regulation, and their effects on plant growth, development, and stress responses. In addition, phylogenetic tree, motif, and domain analyses of pyruvate kinase genes from Oryza sativa (rice), Glycine max (soybean), Gossypium hirsutum (cotton), Solanum tuberosum (potato), Arachis hypogaea (peanut), and Arabidopsis thaliana, as well as promoter cis-element analyses, are performed. This review aims to provide theoretical references for crop quality improvement and stress-resilient breeding.},
}
@article {pmid42518108,
year = {2026},
author = {Khan, R and Chengbo, Z and Zahid, A and Ali, N and Tariq, A and Mutahari, A and Khaliq, B and Shah, AA and Batool, A and Chao, C and Nisa, ZU and Gatasheh, MK},
title = {Genome-wide identification and characterization of the glutaredoxin (GRX) family genes in wild soybean and their expression dynamics under salt and alkali conditions.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42518108},
issn = {1573-4978},
support = {YQ2023C034//Heilongjiang Natural Science Foundation/ ; HSDSSCX2022-140//Graduate innovation research project of Harbin Normal University/ ; ORF-2026-393//Ongoing Research Funding program/ ; },
mesh = {*Glycine max/genetics/metabolism ; *Glutaredoxins/genetics/metabolism ; Gene Expression Regulation, Plant/genetics ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; Salt Tolerance/genetics ; Phylogeny ; Multigene Family ; Salt Stress/genetics ; Genome-Wide Association Study/methods ; Genome, Plant/genetics ; Gene Expression Profiling/methods ; Promoter Regions, Genetic ; },
abstract = {BACKGROUND: Glutaredoxins (GRXs) are vital oxidoreductases governing plant redox homeostasis, growth, development and stress adaptation. Although GRXs carry essential biological functions, the GRX gene family in wild soybean (Glycine soja Sieb and Zucc.) lacks systematic characterization. This genome-wide study aimed to identify and profile wild soybean GRX genes and explore their functions in salt stress tolerance.<br><br>METHODS AND RESULTS: Hidden Markov Model screening retrieved 196 candidate GRX proteins; 54 non-redundant GsGRX genes were validated via domain identification and redundancy filtering (sample set: whole wild soybean genome). The encoded proteins varied widely in sequence length, molecular weight, isoelectric point, stability and hydropathicity. Most GsGRXs localized to chloroplasts, with partial distribution in mitochondria, cytoplasm and nucleus. Segmental and tandem duplications drove GsGRX family expansion, and collinearity confirmed conserved evolutionary relationships with Arabidopsis thaliana and Oryza sativa. Promoters contained abundant cis-elements linked to light, hormone and abiotic stress signaling. qRT-PCR showed time-dependent (0, 3, 6&#xa0;h) transcriptional fluctuations of GsGRX genes under saline-alkali stress.<br><br>CONCLUSIONS: Transcriptional dynamics under stress verify the participation of GsGRX genes in plant stress regulatory networks. This work establishes the first full-scale characterization of the G. soja GRX family, uncovering novel evidence for their core roles in cellular redox control and salt stress resistance in wild soybean.},
}
@article {pmid42574932,
year = {2026},
author = {Kim, HS and Shin, J and Kim, T and Ki, JS},
title = {pH changes differently affect carbonic anhydrases (Ap-CAs) transcriptions in the marine toxic dinoflagellate Alexandrium pacificum.},
journal = {Marine environmental research},
volume = {221},
number = {},
pages = {108329},
doi = {10.1016/j.marenvres.2026.108329},
pmid = {42574932},
issn = {1879-0291},
mesh = {*Carbonic Anhydrases/metabolism/genetics ; Hydrogen-Ion Concentration ; *Dinoflagellida/genetics/enzymology/physiology ; Seawater/chemistry ; Phylogeny ; Ocean Acidification ; Carbon Dioxide/metabolism ; Photosynthesis ; },
abstract = {Carbonic anhydrases (CAs) involve carbon dioxide (CO2) concentration in photosynthetic microalgae. They are known to function under low CO2 level in seawater, possibly affected by pH conditions. In the present study, we determined four novel CA genes, namely Ap-αCA, -βCA, -δCA1, and -δCA2, from the toxic marine dinoflagellate Alexandrium pacificum. The Ap-CAs were divided into three classes, alpha (α), beta (β), and delta (δ) via their phylogeny and motif features. Individual Ap-CA might be differently located to chloroplast, cytoplasm, mitochondria, or extracellular as judged by signal peptides. In addition, we evaluated the photosynthetic responses and transcriptional levels of the CAs and three photosynthesis genes (rbcL, atpB, and psbA) in the cells exposed to various pH conditions. The relative gene expressions of Ap-αCA and Ap-βCA were upregulated at higher pH conditions (pH 8.5 and 8.9) compared to the control (pH 8.1), but showed no significant changes in lower pH conditions (pH 7.3 and 7.7). In contrast, the Ap-δCAs expression was little changed. Expression patterns of rbcL, a carbon fixation gene marker, were similar to those of Ap-αCA and Ap-βCA, while there were no significant changes in atpB and psbA. These results suggest that photosynthetically available CO2 levels may decrease with increasing pH conditions, and the CAs function as a carbon concentration mechanism in marine environments.},
}
@article {pmid42660915,
year = {2026},
author = {Wang, J and Jin, J and Feng, X and Li, J and Han, L and Lyu, T and Zhang, W and Pan, J and Xu, X and Feng, S and Hu, Z and Zhou, W and Zhou, J and Xia, X and Yu, J and Last, RL and Fan, P},
title = {Evolutionary hijacking of fatty acid biosynthesis drives insecticidal acylsugar diversity in tomato.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42660915},
issn = {2041-1723},
support = {No. 32472718//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 325B2079//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 1546617//National Science Foundation (NSF)/ ; No. LZ22C150005//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; },
mesh = {*Solanum lycopersicum/metabolism/genetics ; *Fatty Acids/biosynthesis ; Coenzyme A Ligases/metabolism/genetics ; Plant Proteins/metabolism/genetics ; Gene Expression Regulation, Plant ; Evolution, Molecular ; *Insecticides/metabolism ; },
abstract = {The evolution of plant defensive specialized metabolites often involves repurposing existing primary metabolic pathways for novel roles. However, the relative contribution of changes in protein function versus gene regulation and localization in driving such divergency remains less well understood. Here, we investigate the evolutionary origin of long-branched-chain acylsugars-a class of insecticidal metabolites found in wild tomatoes but absent from their domesticated counterpart. We show that this chemical divergency is enabled by a single enzyme, an acyl-CoA synthetase (SpBACS1), that was repurposed to bridge two distinct primary metabolic pathways. We demonstrate that SpBACS1 activates products of amino acid catabolism and primes them as non-canonical starters for elongation by the plastidial fatty acid synthase machinery for acylsugar assembly. Strikingly, the loss of this trait during domestication was not due to impaired enzyme function. Instead, we describe two distinct regulatory mechanisms. First, the cultivated ortholog, SlBACS1, lacks expression in acylsugar-producing trichomes due to promoter sequence divergence, despite retaining enzyme catalytic activity. Concurrently, their paralogs, BACS2, were neolocalized to the mitochondria, functionally isolating them from the chloroplast-based primary fatty acid metabolic elongation pathway. These findings demonstrate how divergence in cis-regulatory elements and subcellular targeting, in the absence of protein function modification, were potent drivers of metabolic evolution, providing a strategy for re-engineering valuable chemical diversity into cultivated crops.},
}
@article {pmid14975754,
year = {2004},
author = {Karlgren, M and Backlund, M and Johansson, I and Oscarson, M and Ingelman-Sundberg, M},
title = {Characterization and tissue distribution of a novel human cytochrome P450-CYP2U1.},
journal = {Biochemical and biophysical research communications},
volume = {315},
number = {3},
pages = {679-685},
doi = {10.1016/j.bbrc.2004.01.110},
pmid = {14975754},
issn = {0006-291X},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/*genetics/*metabolism ; Cytoplasm/enzymology ; DNA, Complementary/genetics ; Humans ; Isoenzymes/genetics/metabolism ; Microsomes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Oligonucleotide Probes/chemistry/genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Rats ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Tissue Distribution ; },
abstract = {A novel human cytochrome P450 cDNA designated CYP2U1 was identified using homology searches, and the corresponding gene is located on chromosome 4. The deduced 544 amino acid sequence displays up to 39% identity to other CYP2 family members, with closest resemblance to CYP2R1 and is highly conserved between species. CYP2U1 shows some structural differences compared to other CYP2 family members. The gene has only five exons and the enzyme harbors two insertions in the N-terminal region. Northern blot analysis revealed high mRNA expression in human thymus, with weaker expression in heart and brain, whereas in the rat similar mRNA levels were detected in thymus and brain. Western blot analysis revealed much higher CYP2U1 protein expression in rat brain than in thymus, particularly in limbic structures and in cortex. The physiological and toxicological role of this novel P450 is still unknown, but the selective tissue distribution suggests an important endogenous function.},
}
@article {pmid14984837,
year = {2004},
author = {Agatsuma, T and Rajapakse, RP and Kuruwita, VY and Iwagami, M and Rajapakse, RC},
title = {Molecular taxonomic position of the elephant schistosome, Bivitellobilharzia nairi, newly discovered in Sri Lanka.},
journal = {Parasitology international},
volume = {53},
number = {1},
pages = {69-75},
doi = {10.1016/j.parint.2003.11.003},
pmid = {14984837},
issn = {1383-5769},
mesh = {Animals ; Base Sequence ; DNA, Helminth/analysis ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/genetics ; Elephants/*parasitology ; Male ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Schistosomatidae/*classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sri Lanka ; Trematode Infections/parasitology/*veterinary ; },
abstract = {Bivitellobilharzia nairi (Mudaliar and Ramanujachar, 1945) Dutt and Srivastava, 1955 was first recorded in India. A number of adult worm specimens of this schistosome species were recovered from a domestic elephant, which died in 1999 in Sri Lanka. This is the first report of this schistosome from Sri Lanka. In the present study, in order to clarify the phylogenetic relationship with other species of schistosomes, sequences from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene from B. nairi were analyzed. Two intraspecific variations were seen within 13 individuals in the ITS2 region. In the CO1 region of the mitochondrial DNA, there were four haplotypes in the nucleotide sequences and two haplotypes in the amino acid sequences. Phylogenetic analysis using the nuclear DNA showed that B. nairi was basal to all of species of the genus Schistosoma. The 28S tree also showed that the mammalian lineage was monophyletic. However, phylogenetic analysis using the mitochondrial DNA showed that B. nairi was nested within the genus Schistosoma. The taxonomical position for this species as well as the contradiction between the results from the nuclear and mitochondrial genes were discussed.},
}
@article {pmid14984933,
year = {2004},
author = {Wang, YS and Harding, SA and Tsai, CJ},
title = {Expression of a glycine decarboxylase complex H-protein in non-photosynthetic tissues of Populus tremuloides.},
journal = {Biochimica et biophysica acta},
volume = {1676},
number = {3},
pages = {266-272},
doi = {10.1016/j.bbaexp.2003.12.004},
pmid = {14984933},
issn = {0006-3002},
mesh = {Amino Acid Oxidoreductases/biosynthesis/chemistry/*genetics ; Amino Acid Sequence ; Cloning, Molecular ; DNA, Complementary/analysis/biosynthesis/chemistry ; Gene Expression Regulation, Enzymologic ; Glycine Decarboxylase Complex ; Glycine Decarboxylase Complex H-Protein ; Glycine Dehydrogenase (Decarboxylating) ; Molecular Sequence Data ; Phylogeny ; Plant Roots/enzymology ; Populus/enzymology/growth &amp; development/*metabolism ; Protein Isoforms/genetics ; Sequence Alignment ; },
abstract = {The Gly decarboxylase complex (GDC) is abundant in mitochondria of C3 leaves and functions in photorespiratory carbon recovery. However, expression of GDC component proteins has generally been less evident in non-green tissues. Here we report an aspen (Populus tremuloides Michx.) PtgdcH1 gene, encoding a GDC subunit H-protein that is phylogenetically distinct from previously characterized photorespiratory H-proteins. Strong expression of PtgdcH1 in root tips and developing xylem suggests that GDC supports a very active C1 metabolism in non-photosynthetic tissues of aspen.},
}
@article {pmid14994549,
year = {2003},
author = {Nikolaev, SI and Berney, S and Fahrni, J and Mylnikov, AP and Petrov, NB and Pawlowski, J},
title = {Genetic relationships between desmothoracid heliozoa and gymnophryid amoebas as evidenced by comparison of the nucleotide sequences of 18S rRNA genes.},
journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections},
volume = {393},
number = {},
pages = {553-556},
pmid = {14994549},
issn = {0012-4966},
mesh = {Amoeba ; Animals ; Base Sequence ; DNA, Complementary/metabolism ; Genes, rRNA ; Likelihood Functions ; Mitochondria/pathology ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; *Sequence Analysis, DNA ; },
}
@article {pmid14998395,
year = {2004},
author = {Yamada, Y and Makimura, K and Uchida, K and Yamaguchi, H and Osumi, M},
title = {Phylogenetic relationships among medically important yeasts based on sequences of mitochondrial large subunit ribosomal RNA gene.},
journal = {Mycoses},
volume = {47},
number = {1-2},
pages = {24-28},
doi = {10.1046/j.0933-7407.2003.00942.x},
pmid = {14998395},
issn = {0933-7407},
mesh = {Base Sequence ; Candida/classification/genetics/isolation &amp; purification ; Cluster Analysis ; Cryptococcus/classification/genetics/isolation &amp; purification ; DNA, Fungal/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Genes, Fungal ; *Genes, rRNA ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Yeasts/*classification/*genetics/isolation &amp; purification ; },
abstract = {Sequences of the mitochondrial large subunit ribosomal RNA (mtLsurRNA) gene of medically important yeasts were analysed. Sixteen strains of eight species including two varieties were subjected to sequencing. Sequencing enabled us to recognize the differences between all the species and varieties. Alignment analysis revealed that these sequences consisted of three clusters: the Candida albicans group, the C. glabrata group, and the basidiomycetous group. It is possible, therefore, that the mtLsurRNA gene is one of the targets not only for species identification but also for phylogenetic analysis of closely related yeasts. The dendrogram of each group, obtained from this gene, supports the previous study of yeasts based upon the chromosomal genes.},
}
@article {pmid15003237,
year = {2004},
author = {Picault, N and Hodges, M and Palmieri, L and Palmieri, F},
title = {The growing family of mitochondrial carriers in Arabidopsis.},
journal = {Trends in plant science},
volume = {9},
number = {3},
pages = {138-146},
doi = {10.1016/j.tplants.2004.01.007},
pmid = {15003237},
issn = {1360-1385},
mesh = {Arabidopsis/*genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant ; Genomics/methods ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Phylogeny ; },
}
@article {pmid15014069,
year = {2004},
author = {Hoffmeister, M and van der Klei, A and Rotte, C and van Grinsven, KW and van Hellemond, JJ and Henze, K and Tielens, AG and Martin, W},
title = {Euglena gracilis rhodoquinone:ubiquinone ratio and mitochondrial proteome differ under aerobic and anaerobic conditions.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {21},
pages = {22422-22429},
doi = {10.1074/jbc.M400913200},
pmid = {15014069},
issn = {0021-9258},
mesh = {Animals ; Biochemistry/methods ; Cloning, Molecular ; DNA, Complementary/metabolism ; Databases as Topic ; Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Euglena gracilis/*metabolism ; Expressed Sequence Tags ; Gene Expression Regulation, Bacterial ; Hydrogen/chemistry ; Mitochondria/enzymology/*metabolism ; Models, Chemical ; Molecular Sequence Data ; Oxygen/*metabolism ; Peptides/chemistry ; Phylogeny ; Protein Structure, Tertiary ; Proteome ; Pyruvic Acid/chemistry ; Trypsin/chemistry ; Ubiquinone/*analogs &amp; derivatives/*chemistry ; },
abstract = {Euglena gracilis cells grown under aerobic and anaerobic conditions were compared for their whole cell rhodoquinone and ubiquinone content and for major protein spots contained in isolated mitochondria as assayed by two-dimensional gel electrophoresis and mass spectrometry sequencing. Anaerobically grown cells had higher rhodoquinone levels than aerobically grown cells in agreement with earlier findings indicating the need for fumarate reductase activity in anaerobic wax ester fermentation in Euglena. Microsequencing revealed components of complex III and complex IV of the respiratory chain and the E1beta subunit of pyruvate dehydrogenase to be present in mitochondria of aerobically grown cells but lacking in mitochondria from anaerobically grown cells. No proteins were identified as specific to mitochondria from anaerobically grown cells. cDNAs for the E1alpha, E2, and E3 subunits of mitochondrial pyruvate dehydrogenase were cloned and shown to be differentially expressed under aerobic and anaerobic conditions. Their expression patterns differed from that of mitochondrial pyruvate:NADP(+) oxidoreductase, the N-terminal domain of which is pyruvate:ferredoxin oxidoreductase, an enzyme otherwise typical of hydrogenosomes, hydrogen-producing forms of mitochondria found among anaerobic protists. The Euglena mitochondrion is thus a long sought intermediate that unites biochemical properties of aerobic and anaerobic mitochondria and hydrogenosomes because it contains both pyruvate:ferredoxin oxidoreductase and rhodoquinone typical of hydrogenosomes and anaerobic mitochondria as well as pyruvate dehydrogenase and ubiquinone typical of aerobic mitochondria. Our data show that under aerobic conditions Euglena mitochondria are prepared for anaerobic function and furthermore suggest that the ancestor of mitochondria was a facultative anaerobe, segments of whose physiology have been preserved in the Euglena lineage.},
}
@article {pmid15024005,
year = {2004},
author = {Ravanel, S and Block, MA and Rippert, P and Jabrin, S and Curien, G and Rébeillé, F and Douce, R},
title = {Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {21},
pages = {22548-22557},
doi = {10.1074/jbc.M313250200},
pmid = {15024005},
issn = {0021-9258},
mesh = {Arabidopsis/metabolism ; Blotting, Western ; Chloroplasts/*metabolism ; Cloning, Molecular ; Cytosol/*metabolism ; DNA, Complementary/metabolism ; Diffusion ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Green Fluorescent Proteins ; Homocysteine/chemistry ; Immunoblotting ; Kinetics ; Luminescent Proteins/metabolism ; Methionine/*chemistry/*metabolism ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Pisum sativum ; Phylogeny ; Plastids/metabolism ; Protein Isoforms ; S-Adenosylmethionine/*chemistry ; Time Factors ; Vitamin B 12/metabolism ; },
abstract = {The subcellular distribution of Met and S-adenosylmethionine (AdoMet) metabolism in plant cells discloses a complex partition between the cytosol and the organelles. In the present work we show that Arabidopsis contains three functional isoforms of vitamin B(12)-independent methionine synthase (MS), the enzyme that catalyzes the methylation of homocysteine to Met with 5-methyltetrahydrofolate as methyl group donor. One MS isoform is present in chloroplasts and is most likely required to methylate homocysteine that is synthesized de novo in this compartment. Thus, chloroplasts are autonomous and are the unique site for de novo Met synthesis in plant cells. The additional MS isoforms are present in the cytosol and are most probably involved in the regeneration of Met from homocysteine produced in the course of the activated methyl cycle. Although Met synthesis can occur in chloroplasts, there is no evidence that AdoMet is synthesized anywhere but the cytosol. In accordance with this proposal, we show that AdoMet is transported into chloroplasts by a carrier-mediated facilitated diffusion process. This carrier is able to catalyze the uniport uptake of AdoMet into chloroplasts as well as the exchange between cytosolic AdoMet and chloroplastic AdoMet or S-adenosylhomocysteine. The obvious function for the carrier is to sustain methylation reactions and other AdoMet-dependent functions in chloroplasts and probably to remove S-adenosylhomocysteine generated in the stroma by methyltransferase activities. Therefore, the chloroplastic AdoMet carrier serves as a link between cytosolic and chloroplastic one-carbon metabolism.},
}
@article {pmid15033531,
year = {2004},
author = {Dolezal, P and Vanácová, S and Tachezy, J and Hrdý, I},
title = {Malic enzymes of Trichomonas vaginalis: two enzyme families, two distinct origins.},
journal = {Gene},
volume = {329},
number = {},
pages = {81-92},
doi = {10.1016/j.gene.2003.12.022},
pmid = {15033531},
issn = {0378-1119},
support = {1 R03 TW05536-01/TW/FIC NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Protozoan/chemistry/genetics ; Isoenzymes/genetics/isolation &amp; purification/metabolism ; Kinetics ; Malate Dehydrogenase/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; },
abstract = {The cytosolic malic enzyme of the amitochondriate protist Trichomonas vaginalis was purified to homogeneity and characterized. The corresponding gene was sequenced and compared with its hydrogenosomal homologue from the same organism. The enzymes were found to differ in coenzyme specificity, molecular mass and physiological role. The cytosolic malic enzyme is a dimer consisting of two 42-kDa subunits with strict specificity for nicotinamide adenine dinucleotide phosphate (NADP(+)), and has a presumed function of pyruvate and NADPH production. The hydrogenosomal malic enzyme is a tetramer of 60-kDa subunits that preferentially utilizes nicotinamide adenine dinucleotide (NAD(+)) to NADP(+). The hydrogenosomal enzyme supplies the hydrogenosome with pyruvate for further catabolic processes linked with substrate-level phosphorylation. Phylogenetic analysis of malic enzymes showed the existence of two distinct families of these enzymes in nature, which differ in subunit size. The trichomonad cytosolic malic enzyme belongs to the small subunit-type family that occurs almost exclusively in prokaryotes. In contrast, the hydrogenosomal malic enzyme displays a close relationship with the large subunit-type family of the enzyme, which is found in mitochondria, plastids and the cytosol of eukaryotes. The eubacterial origin of trichomonad cytosolic malic enzyme suggests an occurrence of horizontal gene transfer from a eubacterium to the ancestor of T. vaginalis. The presence of both prokaryotic and eukaryotic type of malic enzyme in different compartments of a single eukaryotic cell appears to be unique in nature.},
}
@article {pmid15041416,
year = {2004},
author = {Gwo, JC and Kuo, MC and Chiu, JY and Cheng, HY},
title = {Ultrastructure of Pagrus major and Rhabdosargus sarba spermatozoa (Perciformes: Sparidae: Sparinae).},
journal = {Tissue &amp; cell},
volume = {36},
number = {2},
pages = {141-147},
doi = {10.1016/j.tice.2003.11.003},
pmid = {15041416},
issn = {0040-8166},
mesh = {Animals ; Cell Nucleus/*ultrastructure ; Male ; Mitochondria/*ultrastructure ; Perciformes/*anatomy &amp; histology ; Phylogeny ; Sperm Head/*ultrastructure ; Sperm Midpiece/*ultrastructure ; },
abstract = {Transmission and scanning electron microscopy were used to investigate the ultrastructure of spermatozoa in two Sparinae species Pagrus major and Rhabdosargus sarba. Ultrastructurally, the spermatozoa of P. major and R. sarba both consist of a spherical, homogeneously electron-dense nucleus with a deep axial nuclear fossa, and an unusual notch, in the nuclear region. The midpiece contains two spherical mitochondria in R. sarba and one in P. major. The comparison of spermatozoal ultrastructure of these two species of Sparidae shows that they closely resemble one another and suggests that they are closely related. Variation in the geometry and dimensions of the mitochondrion and nucleus is substantial in these two Sparidae species. It is concluded that the spermatozoa of both species are of primitive type, and they are distinguished by several unique features which may provide useful systematic characteristics.},
}
@article {pmid15047880,
year = {2004},
author = {Sakaguchi, S and Fukuda, T and Takano, H and Ono, K and Takio, S},
title = {Photosynthetic electron transport differentially regulates the expression of superoxide dismutase genes in liverwort, Marchantia paleacea var. diptera.},
journal = {Plant &amp; cell physiology},
volume = {45},
number = {3},
pages = {318-324},
doi = {10.1093/pcp/pch039},
pmid = {15047880},
issn = {0032-0781},
mesh = {Amino Acid Sequence ; Deoxyadenosines/pharmacology ; Dibromothymoquinone/pharmacology ; Diuron/pharmacology ; Electron Transport/drug effects/radiation effects ; Gene Expression Regulation, Enzymologic/drug effects/radiation effects ; Gene Expression Regulation, Plant/drug effects/radiation effects ; Hepatophyta/enzymology/genetics/*physiology ; Light ; Molecular Sequence Data ; Photosynthesis/drug effects/radiation effects ; Photosynthetic Reaction Center Complex Proteins/*genetics/physiology ; Phylogeny ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*genetics/metabolism ; Transcription Factors/genetics/physiology ; },
abstract = {Liverwort, Marchantia paleacea var. diptera, contains Mn-superoxide dismutase (Mn-SOD) in mitochondria, Fe-SOD in chloroplast and CuZn-SOD in cytosol. An Mn-SOD gene (MpMnSOD) was isolated from the liverwort. Using this clone together with the liverwort Fe-SOD and CuZn-SOD genes as probes, the expression of three SOD genes was investigated. Under heterotrophic conditions, the transcript of three SOD genes was accumulated light independently. On the other hand, under photoautotrophic conditions, the transcript levels of Fe-SOD and Mn-SOD increased in the light while that of CuZn-SOD decreased. The reverse occurred in the dark. In contrast to the transcript level, the activity of the three SODs was barely affected by light. The transcription inhibitor, cordycepin, inhibited either the light-promoted accumulation of Fe-SOD and Mn-SOD transcript or the light-induced reduction of the CuZn-SOD transcript. Photosynthetic electron transport inhibitors, DCMU and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, inhibited the photo-response in three SOD genes. These results suggest that the transcript abundance of three SOD genes in liverwort is regulated by photosynthetic electron transport but the mechanism regulating the transcript abundance of the CuZn-SOD gene is different from that of the Fe-SOD and Mn-SOD genes.},
}
@article {pmid15051864,
year = {2004},
author = {Romano, PG and Horton, P and Gray, JE},
title = {The Arabidopsis cyclophilin gene family.},
journal = {Plant physiology},
volume = {134},
number = {4},
pages = {1268-1282},
pmid = {15051864},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Cyclophilin A/chemistry/genetics/metabolism ; Cyclophilins/*genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Molecular Sequence Data ; Multigene Family ; Photosynthetic Reaction Center Complex Proteins/*genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness.},
}
@article {pmid15054102,
year = {2004},
author = {del Arco, A and Satrústegui, J},
title = {Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains.},
journal = {The Journal of biological chemistry},
volume = {279},
number = {23},
pages = {24701-24713},
doi = {10.1074/jbc.M401417200},
pmid = {15054102},
issn = {0021-9258},
mesh = {Alternative Splicing ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Transport Systems ; Amino Acid Transport Systems, Acidic ; Animals ; Antiporters ; Blotting, Northern ; Blotting, Western ; COS Cells ; Calcium/*chemistry/metabolism ; Calcium-Binding Proteins/*chemistry/physiology ; Calmodulin/chemistry ; Cell Line ; DNA, Complementary/metabolism ; Databases as Topic ; Dexamethasone/pharmacology ; Exons ; Expressed Sequence Tags ; Genome, Human ; Humans ; Immunoblotting ; Introns ; Lung/metabolism ; Membrane Transport Proteins/*chemistry/physiology ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Proteins/physiology ; Molecular Sequence Data ; Multigene Family ; Organic Anion Transporters/physiology ; Peptides/chemistry ; Peroxisomes/metabolism ; Phylogeny ; Plasmids/metabolism ; Promoter Regions, Genetic ; Protein Isoforms ; Protein Structure, Tertiary ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Tissue Distribution ; Up-Regulation ; },
abstract = {Aralar1 and citrin were identified as calcium binding aspartate/glutamate carriers (AGC) in mitochondria. The presence of calcium binding motifs facing the extramitochondrial space allows the regulation of the transport activity of these carriers by cytosolic calcium and provides a new mechanism to transduce calcium signals in mitochondria without the requirement of calcium entry in the organelle. We now report the complete characterization of a second subfamily of human calcium binding mitochondrial carriers named SCaMC (short calcium-binding mitochondrial carriers). We have identified three SCaMC genes in the human genome. All code for highly conserved proteins (about 70-80% identity), of about 500 amino acids with a characteristic mitochondrial carrier domain at the C terminus, and an N-terminal extension harboring four EF-hand binding motifs with high similarity to calmodulin. All SCaMC proteins were found to be located exclusively in mitochondria, and their N-terminal extensions were dispensable for the correct mitochondrial targeting of the polypeptides. SCaMC-1 is the human orthologue of the rabbit Efinal protein, which was reported to be located in peroxisomes, and SCaMC-2 is the human orthologue of the rat MCSC protein, described as up-regulated by dexamethasone in AR42J cells. One of the SCaMC genes, SCaMC-2, has four variants generated by alternative splicing, resulting in proteins with a common C terminus but with variations in their N-terminal halves, including the loss of one to three EF-hand motifs. These results make SCaMC one of most complex subfamilies of mitochondrial carriers and suggest that the large number of isoforms and splice variants may confer different calcium sensitivity to the transport activity of these carriers.},
}
@article {pmid15062797,
year = {2004},
author = {Dreyer, H and Steiner, G},
title = {The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca).},
journal = {Molecular phylogenetics and evolution},
volume = {31},
number = {2},
pages = {605-617},
doi = {10.1016/j.ympev.2003.08.007},
pmid = {15062797},
issn = {1055-7903},
mesh = {Amino Acid Sequence ; Animals ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; *Genome ; Mitochondria/genetics ; Molecular Sequence Data ; Mollusca/*classification/*genetics ; *Phylogeny ; Proteins/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; },
abstract = {Comparisons of mitochondrial gene sequences and gene arrangements can be informative for reconstructing high-level phylogenetic relationships. We determined the complete sequence of the mitochondrial genome of Siphonodentalium lobatum, (Mollusca, Scaphopoda). With only 13,932 bases, it is the shortest molluscan mitochondrial genome reported so far. The genome contains the usual 13 protein-coding genes, two rRNA and 22 tRNA genes. The ATPase subunit 8 gene is exceptionally short. Several transfer RNAs show truncated TpsiC arms or DHU arms. The gene arrangement of S. lobatum is markedly different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod. Phylogenetic analyses of all available complete molluscan mitochondrial genomes based on amino acid sequences of 11 protein-coding genes yield trees with low support for the basal branches. None of the traditionally accepted molluscan taxa and phylogenies are recovered in all analyses, except for the euthyneuran Gastropoda. S. lobatum appears as the sister taxon to two of the three bivalve species. We conclude that the deep molluscan phylogeny is probably beyond the resolution of mitochondrial protein sequences. Moreover, assessing the phylogenetic signal in gene order data requires a much larger taxon sample than is currently available, given the exceptional diversity of this character set in the Mollusca.},
}
@article {pmid15065427,
year = {2004},
author = {Palenko, MV and Mukha, DV and Zakharov, IA},
title = {[Variability of the mitochondrial gene for cytochrome oxidase I within the Adalia bipunctata species and within species of ladybird beetles (Coleoptera: Coccinellidae)].},
journal = {Genetika},
volume = {40},
number = {2},
pages = {205-209},
pmid = {15065427},
issn = {0016-6758},
mesh = {Animals ; Base Sequence ; Coleoptera/classification/*genetics ; DNA ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Intergeneric, interspecific, and intraspecific genetic variation of the 310-bp 3'-end region of the mitochondrial gene of cytochrome oxidase I (COI) has been assessed in ladybirds (Coleoptera: Coccinnellidae). The phylogenetic distances between eight species of ladybirds have been determined. Mitochondrial DNA (mtDNA) nucleotide sequences have been compared in Adalia bipunctata L. differing in the elytron and pronotum colors that have been sampled from several geographically remote populations. The taxonomic statuses of two morphs from the genus Adalia, A. bipunctata bipunctata and A. bipunctata fasciatopunctata, have been identified.},
}
@article {pmid15075277,
year = {2004},
author = {Slapeta, J and Keithly, JS},
title = {Cryptosporidium parvum mitochondrial-type HSP70 targets homologous and heterologous mitochondria.},
journal = {Eukaryotic cell},
volume = {3},
number = {2},
pages = {483-494},
pmid = {15075277},
issn = {1535-9778},
support = {D43 TW000915/TW/FIC NIH HHS/United States ; TW00915-05/TW/FIC NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Cryptosporidium parvum/genetics/*metabolism/ultrastructure ; Escherichia coli Proteins/genetics ; Gene Expression ; HSP70 Heat-Shock Proteins/chemistry/genetics/*metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/genetics/*metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Transport ; Sequence Alignment ; Sporozoites/ultrastructure ; },
abstract = {A mitochondrial HSP70 gene (Cp-mtHSP70) is described for the apicomplexan Cryptosporidium parvum, an agent of diarrhea in humans and animals. Mitochondrial HSP70 is known to have been acquired from the proto-mitochondrial endosymbiont. The amino acid sequence of Cp-mtHSP70 shares common domains with mitochondrial and proteobacterial homologues, including 34 amino acids of an NH2-terminal mitochondrion-like targeting presequence. Phylogenetic reconstruction places Cp-mtHSP70 within the mitochondrial clade of HSP70 homologues. Using reverse transcription-PCR, Cp-mtHSP70 mRNA was observed in C. parvum intracellular stages cultured in HCT-8 cells. Polyclonal antibodies to Cp-mtHSP70 recognize a approximately 70-kDa protein in Western blot analysis of sporozoite extracts. Both fluorescein- and immunogold-labeled anti-Cp-mtHSP70 localize to a single mitochondrial compartment in close apposition to the nucleus. Furthermore, the NH2-terminal presequence of Cp-mtHSP70 can correctly target green fluorescent protein to the single mitochondrion of the apicomplexan Toxoplasma gondii and the mitochondrial network of the yeast Saccharomyces cerevisiae. When this presequence was truncated, the predicted amphiphilic alpha-helix was shown to be essential for import into the yeast mitochondrion. These data further support the presence of a secondarily reduced relict mitochondrion in C. parvum.},
}
@article {pmid15086795,
year = {2004},
author = {Emanuel, C and Weihe, A and Graner, A and Hess, WR and Börner, T},
title = {Chloroplast development affects expression of phage-type RNA polymerases in barley leaves.},
journal = {The Plant journal : for cell and molecular biology},
volume = {38},
number = {3},
pages = {460-472},
doi = {10.1111/j.0960-7412.2004.02060.x},
pmid = {15086795},
issn = {0960-7412},
mesh = {Amino Acid Sequence ; Chloroplasts/*enzymology/genetics/physiology ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Hordeum/*enzymology/genetics/growth &amp; development ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/*enzymology/genetics/growth &amp; development ; Plant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription Factors/genetics/metabolism ; },
abstract = {We have identified the barley gene and cDNA encoding the plastid phage-type RNA polymerase (RNAP), nuclear-encoded plastid RNAP (RpoTp), and the nearly full-length cDNA of the mitochondrial RNAP, nuclear-encoded mitochondrial RNAP (RpoTm). RpoTp spans more than 9000 nt, consists of 19 exons and 18 introns, gives rise to a 3632-nt mRNA and is localized to the long arm of chromosome 1 (7H). The length of the deduced polypeptide is 948 residues. The mRNA levels of RpoTp and RpoTm were determined in roots and primary leaf sections of 7-day-old barley seedlings of the albostrians mutant, which were either phenotypically normal and exhibited a gradient of chloroplast development, or contained ribosome-deficient undifferentiated plastids. Transcript levels of RpoTp and RpoTm in almost all sections reached higher concentrations in plastid ribosome-deficient leaves than in the wild-type material, except in the most basal part of the leaf. These data indicate a role of plastid-to-nucleus signalling in the expression of the two RpoT genes. The mRNA levels of the plastid genes, beta-subunit of plastid-encoded RNAP (rpoB), proteolytic subunit of the Clp protease (clpP) and ribosomal protein Rpl2 (rpl2), all known to be transcribed by the nuclear-encoded RNAP (NEP), followed closely the pattern of RpoTp mRNA accumulation, strongly suggesting that RpoTp and NEP are identical. Transcripts of RpoTm and RpoTm-transcribed mitochondrial genes cytochrome oxidase subunit 2 (coxII) and ATPase subunit 9 (atp9) accumulated to the highest levels in the most basal parts of the leaf and declined considerably towards the leaf tip with a pronounced reduction in green versus white leaves. Our data revealed a marked influence of the developmental stage of the plastid on the expression and activity of organellar phage-type RNAPs and their target genes. Thus, interorganellar cross-talk in the regulated expression of nuclear-encoded plastid and mitochondrial RNAP genes might be a key element governing the concerted expression of genes located within plastids, mitochondria and the nucleus of the plant cell.},
}
@article {pmid15120112,
year = {2004},
author = {Hourton-Cabassa, C and Rita Matos, A and Zachowski, A and Moreau, F},
title = {The plant uncoupling protein homologues: a new family of energy-dissipating proteins in plant mitochondria.},
journal = {Plant physiology and biochemistry : PPB},
volume = {42},
number = {4},
pages = {283-290},
doi = {10.1016/j.plaphy.2004.01.007},
pmid = {15120112},
issn = {0981-9428},
mesh = {Carrier Proteins/chemistry/genetics/metabolism ; Energy Metabolism ; Ion Channels ; Membrane Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/*metabolism ; Phylogeny ; Plant Proteins/chemistry/*genetics/*metabolism ; Uncoupling Protein 1 ; },
abstract = {Uncoupling proteins (UCPs) form a subfamily within the mitochondrial carrier protein family, which catalyze a free fatty acid-mediated proton recycling and can modulate the tightness of coupling between mitochondrial respiration and ATP synthesis. As in mammalian tissues, UCPs are rather ubiquitous in the plant kingdom and widespread in plant tissues in which they could have various physiological roles, such as heat production or protection against free oxygen radicals. The simultaneous occurrence in plant mitochondria of two putative energy-dissipating systems, namely UCP which dissipates the proton motive force, and alternative oxidase (AOX) which dissipates the redox potential, raises the question of their functional interactions.},
}
@article {pmid15120381,
year = {2004},
author = {Lumbsch, HT and Schmitt, I and Palice, Z and Wiklund, E and Ekman, S and Wedin, M},
title = {Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {31},
number = {3},
pages = {822-832},
doi = {10.1016/j.ympev.2003.11.001},
pmid = {15120381},
issn = {1055-7903},
mesh = {Ascomycota/genetics/*metabolism ; Bayes Theorem ; Cell Nucleus/*metabolism ; DNA/chemistry ; DNA, Ribosomal/chemistry ; Databases as Topic ; Mitochondria/*metabolism ; Monte Carlo Method ; Phylogeny ; Species Specificity ; },
abstract = {Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.},
}
@article {pmid15126279,
year = {2004},
author = {Tanaka, M and Takeyasu, T and Fuku, N and Li-Jun, G and Kurata, M},
title = {Mitochondrial genome single nucleotide polymorphisms and their phenotypes in the Japanese.},
journal = {Annals of the New York Academy of Sciences},
volume = {1011},
number = {},
pages = {7-20},
doi = {10.1007/978-3-662-41088-2_2},
pmid = {15126279},
issn = {0077-8923},
mesh = {Brain/physiology ; DNA, Mitochondrial/*genetics ; Haplotypes ; Humans ; Japan ; Life Expectancy ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics ; Nucleic Acid Conformation ; Obesity/genetics/metabolism ; Phenotype ; Phylogeny ; *Polymorphism, Single Nucleotide ; Protein Conformation ; },
abstract = {Polymorphisms in the human mitochondrial genome have been used for the elucidation of phylogenetic relationships among various ethnic groups. Because analysis by mitochondrial genetics has detected pathogenic mutations causing mitochondrial encephalomyopathy or cardiomyopathy, most of the mitochondrial single nucleotide polymorphisms (mtSNPs) found in control subjects have been regarded as merely normal variants. However, we cannot exclude the possibility that the mitochondrial functional differences among individuals are ascribable at least in part to the mtSNPs of each individual. Human lifespan in ancient history was much shorter than that at the present time. Therefore, it is reasonable to speculate that certain mtSNPs that predispose one toward susceptibility to adult- or elderly-onset diseases, such as Parkinson's disease and Alzheimer's disease, have never been a target for natural selection in the past. Similarly, thrifty mtSNPs that had been advantageous for survival under severe famine or cold climate conditions might turn out to be related to satiation-related diseases, such as diabetes mellitus and obesity. To examine these hypotheses, we have constructed a mtSNP database by sequencing the entire mitochondrial genomes of 672 subjects: 96 in each of seven groups (i.e., centenarians, young obese or non-obese subjects, diabetic patients with or without major vascular involvement, patients with Parkinson's disease, and those with Alzheimer's disease).},
}
@article {pmid15126405,
year = {2004},
author = {Arnason, E},
title = {Mitochondrial cytochrome B DNA variation in the high-fecundity atlantic cod: trans-atlantic clines and shallow gene genealogy.},
journal = {Genetics},
volume = {166},
number = {4},
pages = {1871-1885},
pmid = {15126405},
issn = {0016-6731},
mesh = {Analysis of Variance ; Animals ; Atlantic Ocean ; Base Sequence ; Cytochromes b/*genetics ; Fertility/*genetics ; Fishes/*genetics/physiology ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes/genetics ; Molecular Sequence Data ; *Phylogeny ; Population Density ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {An analysis of sequence variation of 250 bp of the mitochondrial cytochrome b gene of 1278 Atlantic cod Gadus morhua ranging from Newfoundland to the Baltic shows four high-frequency (>8%) haplotypes and a number of rare and singleton haplotypes. Variation is primarily synonymous mutations. Natural selection acting directly on these variants is either absent or very weak. Common haplotypes show regular trans-Atlantic clines in frequencies and each of them reaches its highest frequency in a particular country. A shallow multifurcating constellation gene genealogy implies young age and recent turnover of polymorphism. Haplotypes characterizing populations at opposite ends of the geographic distribution in Newfoundland and the Baltic are mutationally closest together. The haplotypes are young and have risen rapidly in frequency. Observed differentiation among countries is due primarily to clinal variation. Hypotheses of historical isolation and polymorphisms balanced by local selection and gene flow are unlikely. Instead the results are explained by demic selection of mitochondria carried by highly fit females winning reproductive sweepstakes. By inference the Atlantic cod, a very high-fecundity vertebrate, is characterized by a high variance of offspring number and strong natural selection that leads to very low effective to actual population sizes.},
}
@article {pmid15128508,
year = {2004},
author = {Beninati, T and Lo, N and Sacchi, L and Genchi, C and Noda, H and Bandi, C},
title = {A novel alpha-Proteobacterium resides in the mitochondria of ovarian cells of the tick Ixodes ricinus.},
journal = {Applied and environmental microbiology},
volume = {70},
number = {5},
pages = {2596-2602},
pmid = {15128508},
issn = {0099-2240},
mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification ; Animals ; DNA, Ribosomal/analysis ; Female ; In Situ Hybridization ; Ixodes/*microbiology ; Male ; Microscopy, Electron ; Mitochondria/*microbiology ; Molecular Sequence Data ; Ovary/cytology/microbiology/ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {An intracellular bacterium from Ixodes ricinus ticks collected in Italy was characterized by electron microscopy (EM), PCR sequencing of the 16S rRNA gene, molecular phylogenetic analysis, and in situ hybridization (ISH). This bacterium was shown by EM to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. When universal 16S rRNA bacterial primers were used, PCR amplification of ovarian DNA followed by cloning and sequencing resulted in the same sequence being found in each sample. Phylogenetic analysis of this sequence showed that the bacterium from which it was derived, tentatively designated IricES1, is part of a novel clade in the alpha subdivision of the Proteobacterium: ISH and PCR assays of various tissues performed with oligonucleotides specific for the IricES1 16S rRNA showed that IricES1 is restricted to ovarian cells. Based on the results obtained, we inferred that the bacteria seen by EM in ovarian cells are a single type of bacteria, corresponding to IricES1. PCR screening of 166 ticks from various parts of Italy and one site in England showed that IricES1 was present in 96% of adult females and 44% of nymphs (unsexed). No adult males were found to be infected. Despite the apparent parasitism of host mitochondria by IricES1, the available information suggests that the bacterium has an obligate relationship with its host, although this must be confirmed.},
}
@article {pmid15134648,
year = {2004},
author = {Ceccarelli, EA and Arakaki, AK and Cortez, N and Carrillo, N},
title = {Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases.},
journal = {Biochimica et biophysica acta},
volume = {1698},
number = {2},
pages = {155-165},
doi = {10.1016/j.bbapap.2003.12.005},
pmid = {15134648},
issn = {0006-3002},
mesh = {Bacteria/*enzymology ; Ferredoxin-NADP Reductase/*physiology ; Mitochondria/enzymology ; Phylogeny ; Plants/*enzymology ; Protein Structure, Tertiary ; },
abstract = {Ferredoxin (flavodoxin)-NADP(H) reductases (FNRs) are ubiquitous flavoenzymes that deliver NADPH or low potential one-electron donors (ferredoxin, flavodoxin, adrenodoxin) to redox-based metabolisms in plastids, mitochondria and bacteria. Two great families of FAD-containing proteins displaying FNR activity have evolved from different and independent origins. The enzymes present in mitochondria and some bacterial genera are members of the structural superfamily of disulfide oxidoreductases whose prototype is glutathione reductase. A second group, comprising the FNRs from plastids and most eubacteria, constitutes a unique family, the plant-type FNRs, totally unrelated in sequence with the former. The two-domain structure of the plant family of FNR also provides the basic scaffold for an extended superfamily of electron transfer flavoproteins. In this article we compare FNR flavoenzymes from very different origins and describe how the natural history of these reductases shaped structure, flavin conformation and catalytic activity to face the very different metabolic demands they have to deal with in their hosts. We show that plant-type FNRs can be classified into a plastidic class, characterised by extended FAD conformation and high catalytic efficiency, and a bacterial class displaying a folded FAD molecule and low turnover rates. Sequence alignments supported this classification, providing a criterion to predict the structural and biochemical properties of newly identified members of the family.},
}
@article {pmid15141947,
year = {2004},
author = {Sánchez Puerta, MV and Bachvaroff, TR and Delwiche, CF},
title = {The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to heterokonts (supplement).},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {11},
number = {1},
pages = {67-68},
doi = {10.1093/dnares/11.1.67},
pmid = {15141947},
issn = {1340-2838},
mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Phytoplankton/*genetics ; },
}
@article {pmid15162115,
year = {2004},
author = {Lo Brutto, S and Azeuleo, M and Sarà, M},
title = {Mitochondrial simple sequence repeats and 12S-rRNA gene reveal two distinct lineages of Crocidura russula (Mammalia, Soricidae).},
journal = {Heredity},
volume = {92},
number = {6},
pages = {527-533},
doi = {10.1038/sj.hdy.6800448},
pmid = {15162115},
issn = {0018-067X},
mesh = {Africa, Northern ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Europe ; Genes, rRNA/*genetics ; Genetics, Population ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Analysis ; Sequence Homology, Nucleic Acid ; Shrews/*genetics ; },
abstract = {A short segment (135 bp) of the control region and a partial sequence (394 bp) of the 12S-rRNA gene in the mitochondrial DNA of Crocidura russula were analyzed in order to test a previous hypothesis regarding the presence of a gene flow disruption in northern Africa. This breakpoint would have separated northeast-African C. russula populations from the European (plus the northwest-African) populations. The analysis was carried out on specimens from Tunisia (C. r. cf agilis), Sardinia (C. r. ichnusae), and Pantelleria (C. r. cossyrensis), and on C. r. russula from Spain and Belgium. Two C. russula lineages were identified; they both shared R2 tandem repeated motifs of the same length (12 bp), but not the same primary structure. These simple sequence repeats were present in 12-23 copies in the right domain of the control region. Within the northeast-African populations, a polymorphism of repeat variants, not yet found in Europe, was recorded. A neighbor-join tree, which was built by sequences of the conserved 12S-rRNA gene, separated the two sister groups; it permitted us to date a divergence time of 0.5 Myr. Our data discriminated two different mitochondrial lineages in accordance with the previous morphological and karyological data. Ecoclimatic barriers formed during the Middle Pleistocene broke the range of ancestral species in the Eastern Algeria (Kabile Mountains), leading to two genetically separate and modern lineages. The northeast-African lineage can today be located in Tunisia, Pantelleria, and Sardinia. The northwest-African lineage (Morocco and West Algeria), reaching Spain by anthropogenic introduction, spread over north Europe in modern times. The Palaearctic C. russula species is monophyletic, but a taxonomical revision (ie, to provide a full species rank for the northeast taxa and to put in synonymy some insular taxa) is required.},
}
@article {pmid15173569,
year = {2004},
author = {LeClere, S and Rampey, RA and Bartel, B},
title = {IAR4, a gene required for auxin conjugate sensitivity in Arabidopsis, encodes a pyruvate dehydrogenase E1alpha homolog.},
journal = {Plant physiology},
volume = {135},
number = {2},
pages = {989-999},
pmid = {15173569},
issn = {0032-0889},
support = {R29 GM054749/GM/NIGMS NIH HHS/United States ; R29-GM54749/GM/NIGMS NIH HHS/United States ; T32-GM08362/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Indoleacetic Acids/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutation ; Phylogeny ; Pyruvate Decarboxylase/*genetics/metabolism ; Pyruvate Dehydrogenase (Lipoamide)/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {The formation and hydrolysis of indole-3-acetic acid (IAA) conjugates represent a potentially important means for plants to regulate IAA levels and thereby auxin responses. The identification and characterization of mutants defective in these processes is advancing the understanding of auxin regulation and response. Here we report the isolation and characterization of the Arabidopsis iar4 mutant, which has reduced sensitivity to several IAA-amino acid conjugates. iar4 is less sensitive to a synthetic auxin and low concentrations of an ethylene precursor but responds to free IAA and other hormones tested similarly to wild type. The gene defective in iar4 encodes a homolog of the E1alpha-subunit of mitochondrial pyruvate dehydrogenase, which converts pyruvate to acetyl-coenzyme A. We did not detect glycolysis or Krebs-cycle-related defects in the iar4 mutant, and a T-DNA insertion in the IAR4 coding sequence conferred similar phenotypes as the originally identified missense allele. In contrast, we found that disruption of the previously described mitochondrial pyruvate dehydrogenase E1alpha-subunit does not alter IAA-Ala responsiveness or confer any obvious phenotypes. It is possible that IAR4 acts in the conversion of indole-3-pyruvate to indole-3-acetyl-coenzyme A, which is a potential precursor of IAA and IAA conjugates.},
}
@article {pmid15179056,
year = {2004},
author = {Min, MS and Okumura, H and Jo, DJ and An, JH and Kim, KS and Kim, CB and Shin, NS and Lee, MH and Han, CH and Voloshina, IV and Lee, H},
title = {Molecular phylogenetic status of the Korean goral and Japanese serow based on partial sequences of the mitochondrial cytochrome b gene.},
journal = {Molecules and cells},
volume = {17},
number = {2},
pages = {365-372},
pmid = {15179056},
issn = {1016-8478},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*analysis ; Genetic Variation ; Goats/*classification/*genetics ; Haplotypes ; Japan ; Korea ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {To investigate the molecular phylogenetic status of the Korean goral, Nemorhaedus caudatus raddeanus, and Japanese serow, Capricornis crispus, we determined partial sequences of the mitochondrial cytochrome b gene of twelve Korean gorals and sixteen Japanese serows, and compared them with those of the major lineages of Rupicaprini species including two other Nemorhaedus species and two other Capricornis species. The Korean gorals examined possessed two haplotypes with only one nucleotide difference between them, while the Japanese serows showed slightly higher sequence diversity with five haplotypes. Genetic distances and molecular phylogenetic trees indicated that there is considerable genetic divergence between the Korean goral and N. caudatus (the Chinese goral) [Groves and Shields (1996)], but virtually none between Korean and Russian gorals. The Korean and Russian gorals may therefore be distinct from the Chinese goral. The data highlight the importance of conservation of the goral populations of these regions, and the need to reconsider the taxonomic status of Korean and Russian gorals. Our study also clearly demonstrated sufficient genetic distance between serows and gorals to justify their assignment to separate genera. Of the three species of Capricornis, the Formosan serow, C. swinhoei is more closely related to C. sumatraensis than to the Japanese serow, suggesting that the Formosan serow is a distinct species. Preliminary data on intraspecific genetic variation in the Japanese serow are also presented.},
}
@article {pmid15186796,
year = {2004},
author = {Monteiro, FA and Donnelly, MJ and Beard, CB and Costa, J},
title = {Nested clade and phylogeographic analyses of the Chagas disease vector Triatoma brasiliensis in Northeast Brazil.},
journal = {Molecular phylogenetics and evolution},
volume = {32},
number = {1},
pages = {46-56},
doi = {10.1016/j.ympev.2003.12.011},
pmid = {15186796},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Chagas Disease/*parasitology/transmission ; Cytochromes b/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Species Specificity ; Triatoma/*genetics ; },
abstract = {Triatoma brasiliensis (Hemiptera: Reduviidae: Triatominae) is the most important Chagas disease vector in the semiarid areas of Northeast Brazil. We analyzed mitochondrial cytochrome b sequence variation among 136 individuals representing 16 populations from across the species' distribution. Neighbor-joining and parsimony tree-building methods were used in conjunction with nested clade analysis to describe the systematics and phylogeography of this species. Our results indicate that T. brasiliensis is composed of four genetically distinct chromatic forms (referred to as brasiliensis, macromelasoma, juazeiro, and melanica) that present inter-population divergence values (0.027-0.119, corrected K2-p) and a pattern of haplotype geographic distribution compatible with the existence of a species complex. As a consequence, such forms can be treated as isolated targets in vector control programs. We were unable to infer what is shaping the population structure of the brasiliensis form as we obtained mutually exclusive causes of structure, namely a barrier to gene flow caused by past population fragmentation, and isolation by distance between populations (which would permit gene flow). We found indication of mitochondrial DNA introgression occurring among forms in putative hybrid zones.},
}
@article {pmid15197470,
year = {2004},
author = {Giglione, C and Boularot, A and Meinnel, T},
title = {Protein N-terminal methionine excision.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {61},
number = {12},
pages = {1455-1474},
doi = {10.1007/s00018-004-3466-8},
pmid = {15197470},
issn = {1420-682X},
mesh = {Amidohydrolases/*chemistry ; Aminopeptidases/chemistry ; Animals ; Cations ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Humans ; Metalloproteases/metabolism ; Methionine/*chemistry ; Mitochondria/metabolism ; Models, Chemical ; Phylogeny ; Plastids/metabolism ; Protein Structure, Tertiary ; Proteins/*chemistry ; Proteome/chemistry ; },
abstract = {N-terminal methionine excision (NME) is the major proteolytic pathway responsible for the diversity of N-terminal amino acids in proteins. Dedicated NME components have been identified in all organisms, in all compartments in which protein synthesis occurs: cytoplasm, plastids and mitochondria. Recent studies have revealed that NME is regulated at various levels and plays an important role in controlling protein turnover. NME is essential in Eubacteria and lower eukaryotes and is the target of many natural and synthetic inhibitors. Such inhibitors have considerable potential for use in the treatment of various human diseases, from cancer to bacterial and parasitic infections.},
}
@article {pmid15252706,
year = {2004},
author = {Seo, D and Kamino, K and Inoue, K and Sakurai, H},
title = {Purification and characterization of ferredoxin-NADP+ reductase encoded by Bacillus subtilis yumC.},
journal = {Archives of microbiology},
volume = {182},
number = {1},
pages = {80-89},
doi = {10.1007/s00203-004-0701-5},
pmid = {15252706},
issn = {0302-8933},
mesh = {Bacillus subtilis/*enzymology/genetics ; Ferredoxin-NADP Reductase/chemistry/genetics/*isolation &amp; purification ; Ferredoxins/*metabolism ; Phylogeny ; },
abstract = {From Bacillus subtilis cell extracts, ferredoxin-NADP+ reductase (FNR) was purified to homogeneity and found to be the yumC gene product by N-terminal amino acid sequencing. YumC is a approximately 94-kDa homodimeric protein with one molecule of non-covalently bound FAD per subunit. In a diaphorase assay with 2,6-dichlorophenol-indophenol as electron acceptor, the affinity for NADPH was much higher than that for NADH, with Km values of 0.57 microM vs >200 microM. Kcat values of YumC with NADPH were 22.7 s(-1) and 35.4 s(-1) in diaphorase and in a ferredoxin-dependent NADPH-cytochrome c reduction assay, respectively. The cell extracts contained another diaphorase-active enzyme, the yfkO gene product, but its affinity for ferredoxin was very low. The deduced YumC amino acid sequence has high identity to that of the recently identified Chlorobium tepidum FNR. A genomic database search indicated that there are more than 20 genes encoding proteins that share a high level of amino acid sequence identity with YumC and which have been annotated variously as NADH oxidase, thioredoxin reductase, thioredoxin reductase-like protein, etc. These genes are found notably in gram-positive bacteria, except Clostridia, and less frequently in archaea and proteobacteria. We propose that YumC and C. tepidum FNR constitute a new group of FNR that should be added to the already established plant-type, bacteria-type, and mitochondria-type FNR groups.},
}
@article {pmid15255480,
year = {2004},
author = {Bonhomme, F and Orth, A and Cucchi, T and Hadjisterkotis, E and Vigne, JD and Auffray, JC},
title = {[A new species of wild mice on the Island of Cyprus].},
journal = {Comptes rendus biologies},
volume = {327},
number = {5},
pages = {501-507},
doi = {10.1016/j.crvi.2004.03.001},
pmid = {15255480},
issn = {1631-0691},
mesh = {Animals ; Climate ; Cyprus ; Geography ; Mitochondria/genetics ; Muridae/*classification/genetics ; Phylogeny ; },
abstract = {A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.},
}
@article {pmid15256617,
year = {2004},
author = {Davis, CC and Wurdack, KJ},
title = {Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales.},
journal = {Science (New York, N.Y.)},
volume = {305},
number = {5684},
pages = {676-678},
doi = {10.1126/science.1100671},
pmid = {15256617},
issn = {1095-9203},
mesh = {Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Flowers ; *Gene Transfer, Horizontal ; Genes, Plant ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Plant Proteins/genetics ; Vitaceae/*classification/*genetics/parasitology ; },
abstract = {Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochondrial (matR) and nuclear loci (18S ribosomal DNA and PHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrial nad1B-C, however, groups them within Vitaceae, near their obligate host Tetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.},
}
@article {pmid15258168,
year = {2004},
author = {Wirtz, M and Droux, M and Hell, R},
title = {O-acetylserine (thiol) lyase: an enigmatic enzyme of plant cysteine biosynthesis revisited in Arabidopsis thaliana.},
journal = {Journal of experimental botany},
volume = {55},
number = {404},
pages = {1785-1798},
doi = {10.1093/jxb/erh201},
pmid = {15258168},
issn = {0022-0957},
mesh = {Arabidopsis/*enzymology ; Carbon-Oxygen Lyases/*chemistry/isolation &amp; purification/metabolism ; Cysteine/*biosynthesis ; Cytosol/enzymology ; Enzyme Stability ; Escherichia coli/genetics ; Gene Expression Regulation, Plant ; Isoenzymes ; Kinetics ; Mitochondria/enzymology ; Phylogeny ; Plastids/enzymology ; Protein Binding ; Recombinant Proteins/*chemistry/isolation &amp; purification/metabolism ; Substrate Specificity ; },
abstract = {The synthesis of cysteine is positioned at a decisive stage of assimilatory sulphate reduction, marking the fixation of inorganic sulphide into a carbon skeleton. O-acetylserine (thiol) lyase (OAS-TL) catalyses the reaction of inorganic sulphide with O-acetylserine (OAS). Despite its prominent position in the pathway OAS-TL is generally regarded as a non-limiting enzyme without regulatory function, due to low substrate affinities and semi-constitutive expression patterns. To resolve this apparent contradiction, the kinetic properties of three OAS-TLs from Arabidopsis thaliana, localized in the cytosol (A), plastids (B), and mitochondria (C), were analysed. The recombinant expressed OAS-TLs were purified to apparent homogeneity without any fusion tag to maintain their native forms. The proteins displayed high specific activities of 550-900 micromol min(-1) mg(-1). Using an improved and highly sensitive assay method for cysteine determination, the apparent K(m)(sulphide) was 3-6 microM for OAS-TL A, B, and C and thus 10-100 times lower than previously reported for plant OAS-TLs. K(m)(OAS) was between 310 microM and 690 microM for OAS-TL isoform A, B, and C, whereas the apparent dissociation binding constant for OAS was much lower (K(d)<1 microM OAS). A HPLC method was developed for OAS quantification that revealed fast increases of the cellular OAS concentration in response to sulphate deprivation. The observed fluctuations of intracellular OAS concentrations, combined with the OAS dissociation constant and the catalytic properties of OAS-TL, support the model of a dynamic cysteine synthesis system with regulatory function as can be expected from the position of the reaction in the sulphur assimilation pathway.},
}
@article {pmid15260141,
year = {2004},
author = {Aldrich, BT and Krafsur, E and Kambhampati, S},
title = {Species-specific allozyme markers for Appalachian wood-feeding cockroaches (Dictyoptera: Cryptocercidae).},
journal = {Biochemical genetics},
volume = {42},
number = {5-6},
pages = {149-164},
doi = {10.1023/b:bigi.0000026631.46010.ca},
pmid = {15260141},
issn = {0006-2928},
mesh = {Alleles ; Animals ; Appalachian Region ; Cockroaches/*enzymology/*genetics ; Genetic Markers/genetics ; Heterozygote ; Hybridization, Genetic ; Isoenzymes/analysis/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Members of the genus Cryptocercus are wood-feeding cockroaches that live in the temperate forests. Nine species are recognized in the genus worldwide: two in eastern Eurasia, two in China, and five in the United States. Within the United States, one species occurs in the Pacific Northwest and four occur in the Appalachian Mountains. Previous studies have revealed the presence of potential zones of overlap in distribution among the Appalachian species, raising the possibility of hybridization among them. Differences in mitochondrial DNA have previously been identified for the Appalachian species. However, to identify hybrid individuals one or more species-specific, codominant nuclear markers are required. Therefore, our objective was to undertake allozyme analysis of enzymatic loci to identify fixed, species-specific alleles for the four Appalachian species. We assayed a mean of 42 individuals each from 16 sites for allozyme variation for the four species. At 6 of the 33 loci examined, fixed alternate alleles were identified; a combination of 2 loci enabled the identification of all four species. To identify hybrids in the field, we examined 42 individuals each from 13 sites in which two or more of the above species occur in close proximity for presence of heterozygous individuals at one or more of the six fixed loci. No heterozygous individuals were found suggesting the lack of hybridization among the Appalachian species.},
}
@article {pmid15267107,
year = {2004},
author = {Putignani, L and Tait, A and Smith, HV and Horner, D and Tovar, J and Tetley, L and Wastling, JM},
title = {Characterization of a mitochondrion-like organelle in Cryptosporidium parvum.},
journal = {Parasitology},
volume = {129},
number = {Pt 1},
pages = {1-18},
doi = {10.1017/s003118200400527x},
pmid = {15267107},
issn = {0031-1820},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carrier Proteins/chemistry/genetics ; Chaperonin 60/metabolism ; Cloning, Molecular ; Cryptosporidium parvum/genetics/metabolism/*ultrastructure ; DNA, Protozoan/chemistry/genetics ; Fluorescent Dyes/chemistry ; Indoles/chemistry ; Microscopy, Electron ; Microscopy, Fluorescence ; Mitochondria/metabolism/*ultrastructure ; Models, Biological ; Molecular Sequence Data ; Organic Chemicals ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; },
abstract = {Cryptosporidium parvum is a protozoan parasite that causes widespread diarrhoeal disease in humans and other animals and is responsible for large waterborne outbreaks of cryptosporidiosis. Unlike many organisms belonging to the phylum Apicomplexa, such as Plasmodium spp. and Toxoplasma gondii, there is no clinically proven drug treatment against this parasite. Aspects of the basic biology of C. parvum remain poorly understood, including a detailed knowledge of key metabolic pathways, its genome organization and organellar complement. Previous studies have proposed that C. parvum lacks a relic plastid organelle, or 'apicoplast', but that it may possess a mitochondrion. Here we characterize a mitochondrion-like organelle in C. parvum by (i) ultrastructural and morphological description (ii) localization of heterologous mitochondrial chaperonin antibody probes (iii) phylogenetic analysis of genes encoding mitochondrial transport proteins (iv) identification and analysis of mitochondrion-associated gene sequences. Our descriptive morphological analysis was performed by energy-filtering transmission electron microscopy (EFTEM) of C. hominis and C. parvum. The 'mitochondrion-like' organelle was characterized by labelling the structure with a heterologous mitochondrial chaperonin probe (hsp60) both in immunoelectron microscopy (IMEM) and immunofluorescence (IMF). Phylogenetic analysis of the mitochondrial import system and housekeeping components (hsp60 and hsp70-dnaK) suggested that the C. parvum mitochondrion-like organelle is likely to have descended from a common ancestral apicomplexan mitochondrion. We also identified a partial cDNA sequence coding for an alternative oxidase (AOX) gene, a component of the electron transport chain which can act as an alternative to the terminal mitochondrial respiratory complexes III and IV, which has not yet been reported in any other member of this phylum. Degenerate primers developed to identify selected mitochondrial genes failed to identify either cytochrome oxidase subunit I, or cytochrome b. Taken together, our data aim to provide new insights into the characterization of this Cryptosporidium organelle and a logical framework for future functional investigation.},
}
@article {pmid15279958,
year = {2004},
author = {Sienkiewicz, N and Daher, W and Dive, D and Wrenger, C and Viscogliosi, E and Wintjens, R and Jouin, H and Capron, M and Müller, S and Khalife, J},
title = {Identification of a mitochondrial superoxide dismutase with an unusual targeting sequence in Plasmodium falciparum.},
journal = {Molecular and biochemical parasitology},
volume = {137},
number = {1},
pages = {121-132},
doi = {10.1016/j.molbiopara.2004.05.005},
pmid = {15279958},
issn = {0166-6851},
mesh = {Adaptation, Psychological ; Amino Acid Sequence ; Animals ; Cytoplasm/enzymology ; DNA, Complementary ; DNA, Protozoan/chemistry ; Erythrocytes/parasitology ; Fluorescent Antibody Technique, Indirect ; Gene Duplication ; Gene Expression Regulation ; Introns/genetics ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Plasmodium falciparum/*enzymology/genetics/growth &amp; development ; *Protein Sorting Signals ; *Protein Transport ; RNA, Messenger/analysis ; RNA, Protozoan/analysis ; Recombinant Fusion Proteins/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; Superoxide Dismutase/*chemistry/*genetics/metabolism ; Superoxide Dismutase-1 ; Superoxide Dismutase 2 ; },
abstract = {The intraerythrocytic stages of Plasmodium falciparum are exposed to oxidative stress and require functional anti-oxidant systems to survive. In addition to the parasite's known iron-dependent superoxide dismutase PfSOD1, a second SOD gene (PfSOD2) interrupted by 8 introns was identified on chromosome 6. Molecular modelling shows that the structure of PfSOD2 is similar to other iron-dependent SODs and phylogenetic analysis suggests PfSOD1 and PfSOD2 are the result of an ancestral gene duplication. The deduced amino acid sequence of PfSOD2 is similar to PfSOD1 but has a long N-terminal extension. Immunofluorescence studies show that PfSOD1 is cytosolic, whereas the N-terminal extension of PfSOD2 targets a green fluorescent protein fusion into the parasite's mitochondrion. Both SOD genes are transcribed during the erythrocytic cycle with PfSOD1 mRNA levels up to 35-fold higher than those of PfSOD2. Northern blots demonstrated that the mRNA levels of both SOD genes are up-regulated upon exposure to oxidative stress.},
}
@article {pmid15283236,
year = {2004},
author = {Kawasaki, M and Mochizuki, T and Ishizaki, H and Fujihiro, M},
title = {Ascospore-derived isolate of Arthroderma benhamiae with morphology suggestive of Trichophyton verrucosum.},
journal = {Medical mycology},
volume = {42},
number = {3},
pages = {223-228},
doi = {10.1080/13693780310001644699},
pmid = {15283236},
issn = {1369-3786},
mesh = {Arthrodermataceae/*classification/*genetics/growth &amp; development/metabolism ; DNA Fingerprinting ; DNA, Fungal/analysis/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/chemistry/isolation &amp; purification ; Glucose/metabolism ; Inositol/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Homology ; Thiamine/metabolism ; Trichophyton/*classification/*genetics/growth &amp; development ; },
abstract = {Sixty-one ascospores were isolated from an ascocarp produced by the mating of two Arthroderma benhamiae strains, RV 26678 and KMU4169, that differed in their mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) patterns and in the sequences of their nuclear ribosomal internal transcribed spacer (ITS) regions. RV 26678 is a genetically typical A. benhamiae isolate, while KMU4169, though morphologically indistinguishable from A. benhamiae, is an isolate with a deviating ITS sequence and with a mtDNA RFLP profile identical to that of T. verrucosum. One of the 61 progeny ascospores formed a colony, KMU5-46, that was quite different from both parental isolates. KMU5-46 is a faviform colony morphologically similar to Trichophyton verrucosum, although its mtDNA RFLP patterns and ITS sequences were identical to those of A. benhamiae parental strain RV 26678. The morphological alteration manifested in KMU5-46, as well as this isolate's complete loss of sexual response, indicates the possibility that the asexual T. verrucosum and the sexual A. benhamiae are conspecific.},
}
@article {pmid15284954,
year = {2004},
author = {Bortolini, MC and Da Silva, WA and Zago, MA and Elion, J and Krishnamoorthy, R and Goncalves, VF and Pena, SD},
title = {The phylogeography of mitochondrial DNA haplogroup L3g in Africa and the Atlantic slave trade.},
journal = {American journal of human genetics},
volume = {75},
number = {3},
pages = {522-4; author reply 524-6},
doi = {10.1086/423823},
pmid = {15284954},
issn = {0002-9297},
mesh = {Black People/*genetics ; *DNA, Mitochondrial ; *Data Interpretation, Statistical ; Haplotypes ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Mitochondria/genetics ; Mutation ; Phylogeny ; Social Problems/history ; },
}
@article {pmid15341915,
year = {2004},
author = {Kouvelis, VN and Ghikas, DV and Typas, MA},
title = {The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {41},
number = {10},
pages = {930-940},
doi = {10.1016/j.fgb.2004.07.003},
pmid = {15341915},
issn = {1087-1845},
mesh = {Codon ; DNA, Intergenic ; DNA, Mitochondrial/chemistry/*genetics ; Gene Order ; Genes, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Regulatory Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny ; Verticillium/*genetics ; },
abstract = {The mitochondrial genome (mtDNA) of the entomopathogenic fungus Lecanicillium muscarium (synonym Verticillium lecanii) with a total size of 24,499-bp has been analyzed. So far, it is the smallest known mitochondrial genome among Pezizomycotina, with an extremely compact gene organization and only one group-I intron in its large ribosomal RNA (rnl) gene. It contains the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, one intronic ORF coding for a possible ribosomal protein (rps), and a set of 25 tRNA genes which recognize codons for all amino acids, except alanine and cysteine. All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed some characteristic common features like uninterrupted gene pairs, overlapping genes, and extremely variable intergenic regions, that can all be exploited for the study of fungal mitochondrial genomes. Moreover, a minimum common mtDNA gene order could be detected, in two units, for all known Sordariomycetes namely nad1-nad4-atp8-atp6 and rns-cox3-rnl, which can be extended in Hypocreales, to nad4L-nad5-cob-cox1-nad1-nad4-atp8-atp6 and rns-cox3-rnl nad2-nad3, respectively. Phylogenetic analysis of all fungal mtDNA essential protein-coding genes as one unit, clearly demonstrated the superiority of small genome (mtDNA) over single gene comparisons.},
}
@article {pmid15370881,
year = {2004},
author = {McDonald, A and Vanlerberghe, G},
title = {Branched mitochondrial electron transport in the Animalia: presence of alternative oxidase in several animal phyla.},
journal = {IUBMB life},
volume = {56},
number = {6},
pages = {333-341},
doi = {10.1080/1521-6540400000876},
pmid = {15370881},
issn = {1521-6543},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Ciona intestinalis/enzymology/genetics ; Electron Transport ; Humans ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Oxidoreductases/*classification/*genetics/metabolism ; Phylogeny ; Plant Proteins ; Sequence Alignment ; Tylenchoidea/enzymology/genetics ; Alternative Oxidase ; },
abstract = {The mitochondrion of most eukaryotes has multiple electron transport components that increase the points of entry and/or exit of electrons, thus giving a branched nature to the respiratory chain. In plants and many other organisms, a prominent example is alternative oxidase, a non-energy conserving branch in the respiratory chain and an additional terminal oxidase for the exit of electrons. Our genome database searches have now revealed the presence of alternative oxidase in four animal species from three different phyla (Mollusca, Nematoda and Chordata), consistent with frequent reports of cyanide-resistant respiration in the Animalia. In Ciona intestinalis and Crassostrea gigas, alternative oxidase is expressed in several different tissues. Phylogenetic analysis is consistent with the animal proteins having originated by vertical inheritance. We hypothesize that alternative oxidase is likely widespread in the Animalia and discuss some of the potential role(s) for such a branched respiratory chain.},
}
@article {pmid15385674,
year = {2004},
author = {Gelhaye, E and Rouhier, N and Gérard, J and Jolivet, Y and Gualberto, J and Navrot, N and Ohlsson, PI and Wingsle, G and Hirasawa, M and Knaff, DB and Wang, H and Dizengremel, P and Meyer, Y and Jacquot, JP},
title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {101},
number = {40},
pages = {14545-14550},
pmid = {15385674},
issn = {0027-8424},
mesh = {Base Sequence ; DNA, Recombinant/genetics ; Glutathione Peroxidase/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/genetics/*metabolism ; Plants, Genetically Modified ; Populus/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Thioredoxin h ; Alternative Oxidase ; },
abstract = {The plant mitochondrial thioredoxin (Trx) system has been described as containing an NADPH-dependent Trx reductase and Trx o. In addition to the mitochondrial isoform, Trx o, plants are known to contain several chloroplastic Trx isoforms and the cytosolic Trx h isoforms. We report here the presence in plant mitochondria of a Trx isoform (PtTrxh2) belonging to the Trx h group. Western blot analyses with mitochondrial proteins isolated from both poplar and GFP fusion constructs indicate that PtTrxh2 is targeted to plant mitochondria. The recombinant protein, PtTrxh2, has been shown to be reduced efficiently by the mitochondrial Trx reductase AtNTRA. PtTrxh2 is also able to reduce alternative oxidase homodimers and to allow its activation by pyruvate. In contrast, neither PtTrxh2 nor AtTrxo1 exhibits activity with several poplar glutathione peroxidases and especially a putative mitochondrial isoform. Incubation of PtTrxh2 with glutathione disulfide led to the formation of glutathionylated Trx, identified by mass spectrometry. The formation of a glutathione adduct increases the redox potential of PtTrxh2 from -290 to -225 mV. In addition to Trx o, this study shows that Trx h could also be present in mitochondria. This previously unrecognized complexity is not unexpected, considering the multiple redox-regulated processes found in plant mitochondria.},
}
@article {pmid15474311,
year = {2004},
author = {Krücken, J and Schroetel, RM and Müller, IU and Saïdani, N and Marinovski, P and Benten, WP and Stamm, O and Wunderlich, F},
title = {Comparative analysis of the human gimap gene cluster encoding a novel GTPase family.},
journal = {Gene},
volume = {341},
number = {},
pages = {291-304},
doi = {10.1016/j.gene.2004.07.005},
pmid = {15474311},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; CHO Cells ; Cricetinae ; Cricetulus ; Exons ; Female ; GTP-Binding Proteins/*genetics/metabolism ; Gene Expression Profiling ; Gene Order ; Genes/genetics ; Humans ; Introns ; Jurkat Cells ; Luminescent Proteins/genetics/metabolism ; Male ; Membrane Proteins/*genetics/metabolism ; Microscopy, Confocal ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Plasmids/genetics ; Protein Isoforms/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Tissue Array Analysis ; Transfection ; },
abstract = {There is a growing family of novel GTPases conserved among higher plants and vertebrates, abbreviated as AIG1, IAP, IMAP, and IAN, respectively. Here, we comparatively analyze the human gene family encoding GTPases of the immunity-associated protein family recently re-termed GIMAP. Chromosome 7q36.1 contains, within 300 kb, a gimap gene cluster with seven functional genes and one pseudogene (hgimap3). The six genes hgimap1, hgimap2, hgimap4, hgimap5, hgimap6, and hgimap7 encode 33-46 kDa proteins with one GTP-binding domain, whereas hgimap8 encodes a very unusual 75-kDa protein with three GTP-binding domains. All hgimap genes except hgimap2 have orthologs in the mouse. Major expression sites of hgimap mRNAs are the spleen and lymph nodes, but also other organs such as muscle, heart, placenta, and digestive tract display detectable hgimap mRNA levels. The proteins hGIMAP4 and hGIMAP7 can be localized at ER and Golgi apparatus, but not in mitochondria, lysosomes and nuclei. All hgimap genes were expressed at very low levels-if at all-in diverse cancer cell lines. Our data support the view that the GIMAP proteins are involved in the control of cell survival not only in cells of the immune system as commonly anticipated.},
}
@article {pmid15483054,
year = {2005},
author = {Fuchs, F and Westermann, B},
title = {Role of Unc104/KIF1-related motor proteins in mitochondrial transport in Neurospora crassa.},
journal = {Molecular biology of the cell},
volume = {16},
number = {1},
pages = {153-161},
pmid = {15483054},
issn = {1059-1524},
mesh = {Animals ; Biological Transport ; Caenorhabditis elegans Proteins/metabolism/*physiology ; Cell Movement ; Cell Proliferation ; Microscopy ; Microtubules/metabolism/ultrastructure ; Mitochondria/*metabolism ; Mutation ; Nerve Tissue Proteins/metabolism/*physiology ; Neurospora crassa/*metabolism ; Phylogeny ; Plasmids/metabolism ; Protein Binding ; Subcellular Fractions ; Time Factors ; Up-Regulation ; },
abstract = {Eukaryotic cells use diverse cytoskeleton-dependent machineries to control inheritance and intracellular positioning of mitochondria. In particular, microtubules play a major role in mitochondrial motility in the filamentous fungus Neurospora crassa and in mammalian cells. We examined the role of two novel Unc104/KIF1-related members of the kinesin family, Nkin2 and Nkin3, in mitochondrial motility in Neurospora. The Nkin2 protein is required for mitochondrial interactions with microtubules in vitro. Mutant hyphae lacking Nkin2 show mitochondrial motility defects in vivo early after germination of conidiospores. Nkin3, a member of a unique fungal-specific subgroup of small Unc104/KIF1-related proteins, is not associated with mitochondria in wild-type cells. However, it is highly expressed and recruited to mitochondria in Deltankin-2 mutants. Mitochondria lacking Nkin2 require Nkin3 for binding to microtubules in vitro, and mitochondrial motility defects in Deltankin-2 mutants disappear with up-regulation of Nkin3 in vivo. We propose that mitochondrial transport is mediated by Nkin2 in Neurospora, and organelle motility defects in Deltankin-2 mutants are rescued by Nkin3. Apparently, a highly versatile complement of organelle motors allows the cell to efficiently respond to exogenous challenges, a process that might also account for the great variety of different mitochondrial transport systems that have evolved in eukaryotic cells.},
}
@article {pmid15486098,
year = {2004},
author = {Hwang, YT and Pelitire, SM and Henderson, MP and Andrews, DW and Dyer, JM and Mullen, RT},
title = {Novel targeting signals mediate the sorting of different isoforms of the tail-anchored membrane protein cytochrome b5 to either endoplasmic reticulum or mitochondria.},
journal = {The Plant cell},
volume = {16},
number = {11},
pages = {3002-3019},
pmid = {15486098},
issn = {1040-4651},
mesh = {Aleurites/*genetics/*metabolism ; Amino Acid Motifs/genetics ; Amino Acid Sequence ; Cytochromes b5/chemistry/genetics/isolation &amp; purification/*metabolism ; Endoplasmic Reticulum/*metabolism ; Gene Expression Regulation, Plant/physiology ; Intracellular Membranes/metabolism ; Membrane Proteins/chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Sorting Signals/*genetics ; Protein Structure, Tertiary ; Protein Transport/physiology ; Signal Transduction/genetics ; },
abstract = {Tail-anchored membrane proteins are a class of proteins that are targeted posttranslationally to various organelles and integrated by a single segment of hydrophobic amino acids located near the C terminus. Although the localization of tail-anchored proteins in specific subcellular compartments in plant cells is essential for their biological function, the molecular targeting signals responsible for sorting these proteins are not well defined. Here, we describe the biogenesis of four closely related tung (Aleurites fordii) cytochrome b5 isoforms (Cb5-A, -B, -C, and -D), which are small tail-anchored proteins that play an essential role in many cellular processes, including lipid biosynthesis. Using a combination of in vivo and in vitro assays, we show that Cb5-A, -B, and -C are targeted exclusively to the endoplasmic reticulum (ER), whereas Cb5-D is targeted specifically to mitochondrial outer membranes. Comprehensive mutational analyses of ER and mitochondrial Cb5s revealed that their C termini, including transmembrane domains (TMD) and tail regions, contained several unique physicochemical and sequence-specific characteristics that defined organelle-specific targeting motifs. Mitochondrial targeting of Cb5 was mediated by a combination of hydrophilic amino acids along one face of the TMD, an enrichment of branched beta-carbon-containing residues in the medial portion of the TMD, and a dibasic -R-R/K/H-x motif in the C-terminal tail. By contrast, ER targeting of Cb5 depended primarily upon the overall length and hydrophobicity of the TMD, although an -R/H-x-Y/F- motif in the tail was also a targeting determinant. Collectively, the results presented provide significant insight into the early biogenetic events required for entry of tail-anchored proteins into either the ER or mitochondrial targeting pathways.},
}
@article {pmid15496229,
year = {2004},
author = {Nickrent, DL and Blarer, A and Qiu, YL and Vidal-Russell, R and Anderson, FE},
title = {Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer.},
journal = {BMC evolutionary biology},
volume = {4},
number = {},
pages = {40},
pmid = {15496229},
issn = {1471-2148},
mesh = {Bayes Theorem ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Likelihood Functions ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.<br><br>RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.<br><br>CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.},
}
@article {pmid15507320,
year = {2004},
author = {Tone, Y and Kawai-Yamada, M and Uchimiya, H},
title = {Isolation and characterization of Arabidopsis thaliana ISU1 gene.},
journal = {Biochimica et biophysica acta},
volume = {1680},
number = {3},
pages = {171-175},
doi = {10.1016/j.bbaexp.2004.09.005},
pmid = {15507320},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/*metabolism ; Blotting, Northern ; Cloning, Molecular ; DNA, Plant/genetics/*isolation &amp; purification ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Proteins/*genetics/isolation &amp; purification ; Plasmids ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {We describe the isolation of a cDNA encoding Arabidopsis thaliana ISU1 (AtISU1), which regulates iron homeostasis in the mitochondria. The AtISU1 gene contained an open reading frame that encoded 167 amino acid residues. Northern blot analysis demonstrated that AtISU1 gene was ubiquitously expressed in plant tissues examined. The yeast seo5-1, which harbors a single base-pair deletion in ScISU1, is a suppressor of oxidative damage in sod1-deficient mutant. Based on comparative expression analyses using yeast ISU1 gene (ScISU1) in seo5-1 mutant, we found that AtISU1 acts as a counterpart of ScISU1.},
}
@article {pmid15516736,
year = {2004},
author = {Zhou, C and Zhou, K and Zhang, S},
title = {Molecular authentication of the animal crude drug Sailonggu (bone of Myospalax baileyi).},
journal = {Biological &amp; pharmaceutical bulletin},
volume = {27},
number = {11},
pages = {1850-1858},
doi = {10.1248/bpb.27.1850},
pmid = {15516736},
issn = {0918-6158},
mesh = {Alleles ; Animals ; Bone and Bones/*chemistry ; Cytochromes c/genetics ; DNA Primers ; Medicine, Chinese Traditional ; Mitochondria/chemistry ; Pharmaceutical Preparations/*analysis ; Phylogeny ; Polymerase Chain Reaction ; Rodentia/*genetics ; Sequence Alignment ; },
abstract = {Two pairs of allele-specific diagnostic primers (SL1L/SL1H and SL2L/SL2H) for distinguishing the Chinese crude drug Sailonggu (bone of plateau zokor, Myospalax baileyi) from its substitutes were designed based on complete sequences of mitochondrial 12S rRNA and cytochrome b genes of the original animals of Myospalacinae, bamboo rat Rhizomys sinensis and black lipped pika Ochotona curzoniae. Total DNA was extracted from crude drug samples and original animals. Allele-specific diagnostic PCRs were performed using these primers with the total DNA as a template annealing at 65 degrees C. Positive amplifications were obtained from all DNA templates of Sailonggu and M. baileyi, whereas negative amplifications resulted from those of other zokors, the bamboo rat and black lipped pika. These results indicate that Sailonggu samples can be definitely distinguished from their substitutes by diagnostic PCR, and no incorrect discrimination was found under the same reaction conditions. Each of the two diagnostic primer pairs can be used to distinguish crude drug Sailonggu from its substitutes or adulterants. The three Sailonggu samples studied were diagnosed as genuine Sailonggu. In addition, the results of sequence alignment and phylogenetic analysis are congruent with that of the allele-specific diagnostic PCR.},
}
@article {pmid15526035,
year = {2004},
author = {Vahsen, N and Candé, C and Brière, JJ and Bénit, P and Joza, N and Larochette, N and Mastroberardino, PG and Pequignot, MO and Casares, N and Lazar, V and Feraud, O and Debili, N and Wissing, S and Engelhardt, S and Madeo, F and Piacentini, M and Penninger, JM and Schägger, H and Rustin, P and Kroemer, G},
title = {AIF deficiency compromises oxidative phosphorylation.},
journal = {The EMBO journal},
volume = {23},
number = {23},
pages = {4679-4689},
pmid = {15526035},
issn = {0261-4189},
mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Apoptosis ; Apoptosis Inducing Factor ; Brain/metabolism ; Cells, Cultured ; Electron Transport Complex I/biosynthesis ; Electron Transport Complex III/biosynthesis ; Flavoproteins/genetics/metabolism ; Glucose/metabolism ; Humans ; Lactic Acid/biosynthesis ; Membrane Proteins/*deficiency/genetics/metabolism ; Mice ; Mice, Transgenic ; Mitochondria/metabolism ; Myocardium/metabolism ; Organ Specificity ; Oxidative Phosphorylation ; Phylogeny ; RNA, Small Interfering/metabolism ; Retina/metabolism ; Yeasts/genetics/growth &amp; development/metabolism ; },
abstract = {Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein that, after apoptosis induction, translocates to the nucleus where it participates in apoptotic chromatinolysis. Here, we show that human or mouse cells lacking AIF as a result of homologous recombination or small interfering RNA exhibit high lactate production and enhanced dependency on glycolytic ATP generation, due to severe reduction of respiratory chain complex I activity. Although AIF itself is not a part of complex I, AIF-deficient cells exhibit a reduced content of complex I and of its components, pointing to a role of AIF in the biogenesis and/or maintenance of this polyprotein complex. Harlequin mice with reduced AIF expression due to a retroviral insertion into the AIF gene also manifest a reduced oxidative phosphorylation (OXPHOS) in the retina and in the brain, correlating with reduced expression of complex I subunits, retinal degeneration, and neuronal defects. Altogether, these data point to a role of AIF in OXPHOS and emphasize the dual role of AIF in life and death.},
}
@article {pmid15548286,
year = {2004},
author = {Smith, MA and Green, DM},
title = {Phylogeography of Bufo fowleri at its northern range limit.},
journal = {Molecular ecology},
volume = {13},
number = {12},
pages = {3723-3733},
doi = {10.1111/j.1365-294X.2004.02301.x},
pmid = {15548286},
issn = {0962-1083},
mesh = {Analysis of Variance ; Animals ; Base Sequence ; Bufonidae/*genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; *Demography ; *Genetic Variation ; Geography ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Ohio ; Ontario ; Pennsylvania ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Many of the species that recolonized previously glaciated areas in the Great Lakes basin of North America over the past 10-12,000 years exhibit genetic evidence of multiple invasion routes and present-day secondary contact between deeply divergent lineages. With this in mind, we investigated the phylogeographical structure of genetic variability in Fowler's toads (Bufo fowleri) at the northern edge of its distribution where its range encircles the Lake Erie basin. Because B. fowleri is so closely tied to habitats along the Lake Erie shoreline, we would expect to find clear evidence of the number of invasions leading to the species' colonization of the northern shore. A 540 bp sequence from the mitochondrial control region was amplified and analysed for 158 individuals from 21 populations. Interpopulation sequence variation ranged from 0% to 6%. Phylogenetic analysis of p-distance using the neighbor-joining method revealed two deeply divergent (6% sequence divergence) mtDNA lineages (Phylogroup 1 and 2), possibly arising as a result of secondary contact of populations that entered the region from two separate glacial refugia. However, the phylogeographical pattern was not simple. The populations at Long Point, on the north shore of Lake Erie, clustered with the population from Indiana Dunes on Lake Michigan to form Phylogroup 2 whereas all other B. fowleri populations examined from both sides of Lake Erie constituted Phylogroup 1. Furthermore, mtDNA sequences from the related species Bufo americanus, obtained from populations outside the range of B. fowleri, clustered with mtDNA haplotypes of B. fowleri Phylogroup 1, indicating the possibility of partial introgression of mitochondria from one species to the other.},
}
@article {pmid15556293,
year = {2004},
author = {Guy, L and Roten, CA},
title = {Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication.},
journal = {Gene},
volume = {340},
number = {1},
pages = {45-52},
doi = {10.1016/j.gene.2004.06.056},
pmid = {15556293},
issn = {0378-1119},
mesh = {Base Composition/genetics ; Chromosomes, Archaeal/*genetics ; Chromosomes, Bacterial/*genetics ; DNA Replication/genetics ; DNA, Circular/genetics ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; *Genome, Archaeal ; *Genome, Bacterial ; Humans ; Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; Replication Origin/genetics ; Transcription, Genetic/genetics ; },
abstract = {Selective pressures related to gene function and chromosomal architecture are acting on genome sequences and can be revealed, for instance, by appropriate genometric methods. Cumulative nucleotide skew analyses, i.e., GC, TA, and ORF orientation skews, predict the location of the origin of DNA replication for 88 out of 100 completely sequenced bacterial chromosomes. These methods appear fully reliable for proteobacteria, Gram-positives, and spirochetes as well as for euryarchaeotes. Based on this genome architecture information, coorientation analyses reveal that in prokaryotes, ribosomal RNA (rRNA) genes encoding the small and large ribosomal subunits are all transcribed in the same direction as DNA replication; that is, they are located along the leading strand. This result offers a simple and reliable method for circumscribing the region containing the origin of the DNA replication and reveals a strong selective pressure acting on the orientation of rRNA genes similar to the weaker one acting on the orientation of ORFs. Rate of coorientation of transfer RNA (tRNA) genes with DNA replication appears to be taxon-specific. Analyzing nucleotide biases such as GC and TA skews of genes and plotting one against the other reveals a taxonomic clusterization of species. All ribosomal RNA genes are enriched in Gs and depleted in Cs, the only so far known exception being the rRNA genes of deuterostomian mitochondria. However, this exception can be explained by the fact that in the chromosome of the human mitochondrion, the model of the deuterostomian organelle genome, DNA replication, and rRNA transcription proceed in opposite directions. A general rule is deduced from prokaryotic and mitochondrial genomes: ribosomal RNA genes that are transcribed in the same direction as the DNA replication are enriched in Gs, and those transcribed in the opposite direction are depleted in Gs.},
}
@article {pmid15562597,
year = {2004},
author = {DeJong, RJ and Emery, AM and Adema, CM},
title = {The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni.},
journal = {The Journal of parasitology},
volume = {90},
number = {5},
pages = {991-997},
doi = {10.1645/GE-284R},
pmid = {15562597},
issn = {0022-3395},
support = {AI052363/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Biomphalaria/classification/*genetics/parasitology ; DNA, Complementary/chemistry ; DNA, Mitochondrial/*chemistry/genetics ; Disease Vectors ; *Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; },
abstract = {The complete mitochondrial (Mt) genome of the gastropod Biomphalaria glabrata, a major intermediate host for the human parasite Schistosoma mansoni, was sequenced. The circular genome, the first determined from a basommatophoran snail, is AT rich (74.6%) and the smallest Mt genome (13,670 nucleotides [nt]) characterized from mollusks to date. Sequences from 2 B. glabrata strains, M-line and 1742, differed by only 18 nt. Phylogenetic analysis of 16S and ND1 sequences confirmed the Brazilian ancestry of both B. glabrata strains. Gene predictions indicated 22 transfer RNA, 12S and 16S ribosomal RNA (rRNA), and 13 protein-encoding genes, as is typical for metazoans. Of the mollusk Mt genomes currently known, the gene order was most similar to that of stylommatophoran gastropods, concordant with the monophyly of pulmonate gastropods. Screening of GenBank (expressed sequence tags database [dbEST]) with the Mt sequence identified 108 entries from B. glabrata as Mt-derived sequences, including 12S and 16S rRNA sequences. Moreover, 11 sequences originating from the Mt genome of B. glabrata were identified among EST entries ascribed to intramolluskan stages of S. mansoni. The availability of this Mt sequence will facilitate further molecular investigations into the biology of Biomphalaria sp. and interactions between this intermediate host and intramolluskan stages of S. mansoni.},
}
@article {pmid15567032,
year = {2005},
author = {Osaki, H and Nakamura, H and Nomura, K and Matsumoto, N and Yoshida, K},
title = {Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka.},
journal = {Virus research},
volume = {107},
number = {1},
pages = {39-46},
doi = {10.1016/j.virusres.2004.06.010},
pmid = {15567032},
issn = {0168-1702},
mesh = {Amino Acid Sequence ; Base Sequence ; Basidiomycota/genetics/*virology ; DNA, Viral/genetics ; Mitochondria/virology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/microbiology ; RNA Viruses/classification/*genetics/isolation &amp; purification ; RNA, Double-Stranded/chemistry/genetics ; RNA, Viral/chemistry/genetics ; Sequence Homology, Amino Acid ; },
abstract = {A double-stranded (ds) RNA (2411 bp) from a strain V18 of the violet root rot basidiomycetous fungus, Helicobasidium mompa was sequenced. Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive strand of V18 dsRNA was found to contain a long open-reading frame with the potential to encode a protein of 700 amino acids (molecular mass 79,805 Da), including conserved motifs characteristic of RNA-dependent RNA polymerase (RDRP). This putative RDRP was shown to be related to putative RDRPs of several fungal mitochondrial viruses. It is proposed that V18 dsRNA is assigned to the genus Mitovirus in the family Narnaviridae and designated as H. mompa mitovirus 1-18 (HmMV1-18). Like other mitoviruses, HmMV1-18 RNA can be folded into potentially stable stem-loop structures at both the 5'- and 3'-termini, and both terminal sequences have inverted complementarity with the potential to form panhandle structure. BLAST analysis indicates that the RDRP encoded by HmMV1-18 is more closely related to those encoded by mitochondrial viruses of some ascomycetes than to that of the unassigned RsM2-1A1 dsRNA in the basidiomycetous Rhizoctonia solani. HmMV1-18 is the first member of the genus Mitovirus from basidiomycete fungi.},
}
@article {pmid15577909,
year = {2004},
author = {Hrdy, I and Hirt, RP and Dolezal, P and Bardonová, L and Foster, PG and Tachezy, J and Embley, TM},
title = {Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I.},
journal = {Nature},
volume = {432},
number = {7017},
pages = {618-622},
doi = {10.1038/nature03149},
pmid = {15577909},
issn = {1476-4687},
mesh = {Aerobiosis ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Electron Transport Complex I/chemistry/*metabolism ; Hydrogen/*metabolism ; Malates/metabolism ; Mitochondria/*enzymology/metabolism ; Models, Biological ; Molecular Sequence Data ; NAD/metabolism ; NADH Dehydrogenase/chemistry/*metabolism ; Organelles/*enzymology/metabolism ; Phylogeny ; Protein Subunits/chemistry/metabolism ; Protozoan Proteins/chemistry/metabolism ; Sequence Alignment ; Symbiosis ; Trichomonas vaginalis/*cytology/*enzymology/metabolism ; },
abstract = {Hydrogenosomes are double-membraned ATP-producing and hydrogen-producing organelles of diverse anaerobic eukaryotes. In some versions of endosymbiotic theory they are suggested to be homologues of mitochondria, but alternative views suggest they arose from an anaerobic bacterium that was distinct from the mitochondrial endosymbiont. Here we show that the 51-kDa and 24-kDa subunits of the NADH dehydrogenase module in complex I, the first step in the mitochondrial respiratory chain, are active in hydrogenosomes of Trichomonas vaginalis. Like mitochondrial NADH dehydrogenase, the purified Trichomonas enzyme can reduce a variety of electron carriers including ubiquinone, but unlike the mitochondrial enzyme it can also reduce ferredoxin, the electron carrier used for hydrogen production. The presence of NADH dehydrogenase solves the long-standing conundrum of how hydrogenosomes regenerate NAD+ after malate oxidation. Phylogenetic analyses show that the Trichomonas 51-kDa homologue shares common ancestry with the mitochondrial enzyme. Recruitment of complex I subunits into a H2-producing pathway provides evidence that mitochondria and hydrogenosomes are aerobic and anaerobic homologues of the same endosymbiotically derived organelle.},
}
@article {pmid15579378,
year = {2005},
author = {Wüster, W and Dumbrell, AJ and Hay, C and Pook, CE and Williams, DJ and Fry, BG},
title = {Snakes across the Strait: trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus, and Pseudechis).},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {1},
pages = {1-14},
doi = {10.1016/j.ympev.2004.08.018},
pmid = {15579378},
issn = {1055-7903},
mesh = {Animals ; Australia ; DNA, Mitochondrial ; Elapidae/*genetics ; Geography ; Haplotypes ; Mitochondria/genetics ; New Guinea ; Phylogeny ; },
abstract = {We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis-death adders; Oxyuranus-taipans; Pseudechis-blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.},
}
@article {pmid15579384,
year = {2005},
author = {Van der Meij, MA and de Bakker, MA and Bout, RG},
title = {Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA.},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {1},
pages = {97-105},
doi = {10.1016/j.ympev.2004.09.006},
pmid = {15579384},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial ; Fibrinogen/genetics ; Finches/*genetics ; Genetic Variation ; Mitochondria/*genetics ; *Phylogeny ; Sequence Alignment ; },
abstract = {The complete mitochondrial gene cytochrome b in combination with a nuclear gene, beta-fibrinogen intron 7, is sequenced for different groups of mostly granivorous species in the superfamily Passeroidea, with a focus on the estrildids and fringillids. From our study we can conclude that within the group of granivorous finches two clades can be distinguished, the estrildid weaver clade and the cardueline, fringillid, emberizid, passerine sparrow clade. In contrast to many other studies the passerine sparrows are not placed within the weavers estrildid clade which is in agreement with other recent studies (e.g.,). Our study also shows that the estrildids do form a monophyletic group, but there is a division based on geographic origin: an African group and an Asian-Australian group. Within the Fringillidae the Fringilla species are the sister group of the carduelines.},
}
@article {pmid15579385,
year = {2005},
author = {Froufe, E and Knizhin, I and Weiss, S},
title = {Phylogenetic analysis of the genus Thymallus (grayling) based on mtDNA control region and ATPase 6 genes, with inferences on control region constraints and broad-scale Eurasian phylogeography.},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {1},
pages = {106-117},
doi = {10.1016/j.ympev.2004.09.009},
pmid = {15579385},
issn = {1055-7903},
mesh = {Animals ; Asia ; Base Sequence ; *DNA, Mitochondrial ; Europe ; Geography ; *Locus Control Region ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Phylogeny ; Salmonidae/*genetics ; Sequence Alignment ; },
abstract = {We present first insights into the molecular phylogeny of the grayling genus Thymallus (Salmonidae) using sequences from the mitochondrial control region and ATPase6 genes. A suite of analytical approaches were applied for each gene separately and for the combined data. The ATPase6 gene is shown to have a mean divergence rate across the genus of 2.46 times faster than the complete control region. Based on the combined data, four major (internal) clades, presumably originating in the Pliocene, were resolved with high support in all analyses and represented two distinct lineages in the Amur basin, one lineage in all remaining Siberian and Mongolian drainages, and one lineage corresponding to European grayling Thymallus thymallus. The resolution of multiple lineages, from both additional internal and terminal clades, within each major drainage basin underscores the complexity and effects that Pleistocene hydrological dynamics have had on the distribution of biodiversity in Siberia.},
}
@article {pmid15579392,
year = {2005},
author = {Moussalli, A and Hugall, AF and Moritz, C},
title = {A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984).},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {1},
pages = {190-202},
doi = {10.1016/j.ympev.2004.08.022},
pmid = {15579392},
issn = {1055-7903},
mesh = {Animals ; Australia ; Base Sequence ; Bayes Theorem ; Genetic Variation ; Geography ; Lizards/*genetics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; },
abstract = {The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.},
}
@article {pmid15585129,
year = {2004},
author = {Krishnan, NM and Seligmann, H and Raina, SZ and Pollock, DD},
title = {Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes.},
journal = {DNA and cell biology},
volume = {23},
number = {10},
pages = {707-714},
pmid = {15585129},
issn = {1044-5498},
support = {R24 GM065580/GM/NIGMS NIH HHS/United States ; R33 GM065612/GM/NIGMS NIH HHS/United States ; GM065580-01/GM/NIGMS NIH HHS/United States ; GM065612-01/GM/NIGMS NIH HHS/United States ; R21 GM065612/GM/NIGMS NIH HHS/United States ; },
mesh = {*Genome ; Markov Chains ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Messenger/chemistry/genetics ; },
abstract = {During mitochondrial replication, spontaneous mutations occur and accumulate asymmetrically during the time spent single stranded by the heavy strand (DssH). The predominant mutations appear to be deaminations from adenine to hypoxanthine (A --> H, which leads to an A --> G substitution) and cytosine to thymine (C --> T). Previous findings indicated that C --> T substitutions accumulate rapidly and then saturate at high DssH, suggesting protection or repair, whereas A --> G accumulates linearly with DssH. We describe here the implementation of a simple hidden Markov model (HMM) of among-site rate correlations to provide an almost continuous profile of the asymmetry in substitution response for any particular substitution type. We implement this model using a phylogeny-based Bayesian Markov chain Monte Carlo (MCMC) approach. We compare and contrast the relative asymmetries in all 12 possible substitution types, and find that the observed transition substitution responses determined using our new method agree quite well with previous predictions of a saturating curve for C --> T transition substitutions and a linear accumulation of A --> G transitions. The patterns seen in transversion substitutions show much lower among-site variation, and are nonlinear and more complex than those seen in transitions. We also find that, after accounting for the principal linear effect, some of the residual variation in A --> G/G --> A response ratios is explained by the average predicted nucleic acid secondary structure propensity at a site, possibly due to protection from mutation when secondary structure forms.},
}
@article {pmid15588583,
year = {2004},
author = {Mizumoto, K and Murai, K and Nakamura, C and Takumi, S},
title = {Preferential expression of a HLP homolog encoding a mitochondrial L14 ribosomal protein in stamens of common wheat.},
journal = {Gene},
volume = {343},
number = {2},
pages = {281-289},
doi = {10.1016/j.gene.2004.09.005},
pmid = {15588583},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Arabidopsis Proteins/*genetics ; Cell Nucleus/genetics ; Flowers/*genetics/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; Recombinant Proteins/*genetics ; Ribosomal Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; Triticum/*genetics ; },
abstract = {Interaction between nucleus and cytoplasm has essential roles in plant development, including that of floral organs. We isolated a wheat homolog Whlp of Arabidopsis HUELLENLOS PARALOG (HLP) gene encoding a mitochondrial (mt) ribosomal protein L14. Transient expression analysis using the green fluorescent protein (GFP) fusion protein showed that 50 amino residues located on the N-terminal of the wheat HLP homolog (WHLP) protein acted as a mt-targeting signal (MTS). Expression patterns of the Whlp gene were compared among floral organs of alloplasmic lines of wheat, in which intrinsic cytoplasms were replaced by the cytoplasm of a wild relative Aegilops crassa. In these alloplasmic lines, pistillody (homeotic transformation of stamens into pistil-like organs) is induced by the alien cytoplasm in the absence of nuclear restorer genes. The Whlp transcripts preferentially accumulated in stamens compared with pistils, leaves, and roots. The expression level of Whlp in the pistillate stamens of the alloplasmic lines was similar to that in genuine pistils of both euplasmic lines and fertile alloplasmic lines. The result suggested that the elevated expression of the Whlp gene plays a role in aiding the development of male reproductive organ but not in the determination of its whorl identity. A comparable expression pattern was observed in another nuclear-encoded mt ribosomal protein gene but not in a mt-encoded gene. The different expression patterns of different mt ribosomal protein genes suggest that the abundance of mt ribosomal proteins is differentially regulated in the organ/tissue development in wheat.},
}
@article {pmid15592471,
year = {2005},
author = {Roca, AL and Georgiadis, N and O'Brien, SJ},
title = {Cytonuclear genomic dissociation in African elephant species.},
journal = {Nature genetics},
volume = {37},
number = {1},
pages = {96-100},
doi = {10.1038/ng1485},
pmid = {15592471},
issn = {1061-4036},
mesh = {Africa South of the Sahara ; Animals ; DNA, Mitochondrial ; Elephants/*genetics ; Female ; *Gene Frequency ; *Genetics, Population ; Haplotypes ; Male ; Molecular Sequence Data ; Phylogeny ; },
abstract = {African forest and savanna elephants are distinct species separated by a hybrid zone. Because hybridization can affect the systematic and conservation status of populations, we examined gene flow between forest and savanna elephants at 21 African locations. We detected cytonuclear dissociation, indicative of different evolutionary histories for nuclear and mitochondrial genomes. Both paternally (n = 205 males) and biparentally (n = 2,123 X-chromosome segments) inherited gene sequences indicated that there was deep genetic separation between forest and savanna elephants. Yet in some savanna locales distant from present-day forest habitats, many individuals with savanna-specific nuclear genotypes carried maternally transmitted forest elephant mitochondrial DNA. This extreme cytonuclear dissociation implies that there were ancient episodes of hybridization between forest females and savanna males, which are larger and reproductively dominant to forest or hybrid males. Recurrent backcrossing of female hybrids to savanna bulls replaced the forest nuclear genome. The persistence of residual forest elephant mitochondria in savanna elephant herds renders evolutionary interpretations based on mitochondrial DNA alone misleading and preserves a genomic record of ancient habitat changes.},
}
@article {pmid15619004,
year = {2005},
author = {Gelhaye, E and Rouhier, N and Navrot, N and Jacquot, JP},
title = {The plant thioredoxin system.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {62},
number = {1},
pages = {24-35},
doi = {10.1007/s00018-004-4296-4},
pmid = {15619004},
issn = {1420-682X},
mesh = {Amino Acid Sequence ; Arabidopsis Proteins/classification/genetics/metabolism ; Chloroplasts/metabolism ; Genetic Variation/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/*classification/*metabolism ; Protein Isoforms/genetics/metabolism ; Sequence Homology, Amino Acid ; Thioredoxins/*classification/genetics/*metabolism ; },
abstract = {Thioredoxins are small proteins catalyzing thiol-disulfide interchange and are involved in the regulation of the redox environment of the cell. In plants, the thioredoxin system is particularly complex since at least 20 thioredoxin isoforms are found in the plant model Arabidopsis thaliana. Based upon primary sequence analysis and subcellular localization, thioredoxins can be classified into different groups and subgroups. Different pathways allowing thioredoxin reduction also coexist in the plant involving ferredoxin-thioredoxin reductase, thioredoxin reductases and the glutathione/glutaredoxin system. This review discusses the literature of plant thioredoxins with emphasis on recent findings in the field.},
}
@article {pmid15631992,
year = {2005},
author = {Dimmer, KS and Jakobs, S and Vogel, F and Altmann, K and Westermann, B},
title = {Mdm31 and Mdm32 are inner membrane proteins required for maintenance of mitochondrial shape and stability of mitochondrial DNA nucleoids in yeast.},
journal = {The Journal of cell biology},
volume = {168},
number = {1},
pages = {103-115},
pmid = {15631992},
issn = {0021-9525},
mesh = {Actins/metabolism ; DNA, Mitochondrial/*metabolism ; Epistasis, Genetic ; Genomic Instability ; Green Fluorescent Proteins/genetics/metabolism ; Humans ; Intracellular Membranes/*metabolism ; Membrane Proteins/classification/genetics/*metabolism ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/classification/genetics/*metabolism ; Multiprotein Complexes ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/cytology/metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; },
abstract = {The MDM31 and MDM32 genes are required for normal distribution and morphology of mitochondria in the yeast Saccharomyces cerevisiae. They encode two related proteins located in distinct protein complexes in the mitochondrial inner membrane. Cells lacking Mdm31 and Mdm32 harbor giant spherical mitochondria with highly aberrant internal structure. Mitochondrial DNA (mtDNA) is instable in the mutants, mtDNA nucleoids are disorganized, and their association with Mmm1-containing complexes in the outer membrane is abolished. Mutant mitochondria are largely immotile, resulting in a mitochondrial inheritance defect. Deletion of either one of the MDM31 and MDM32 genes is synthetically lethal with deletion of either one of the MMM1, MMM2, MDM10, and MDM12 genes, which encode outer membrane proteins involved in mitochondrial morphogenesis and mtDNA inheritance. We propose that Mdm31 and Mdm32 cooperate with Mmm1, Mmm2, Mdm10, and Mdm12 in maintenance of mitochondrial morphology and mtDNA.},
}
@article {pmid15634957,
year = {2005},
author = {Kurtzman, CP and Robnett, CJ and Ward, JM and Brayton, C and Gorelick, P and Walsh, TJ},
title = {Multigene phylogenetic analysis of pathogenic candida species in the Kazachstania (Arxiozyma) telluris complex and description of their ascosporic states as Kazachstania bovina sp. nov., K. heterogenica sp. nov., K. pintolopesii sp. nov., and K. slooffiae sp. nov.},
journal = {Journal of clinical microbiology},
volume = {43},
number = {1},
pages = {101-111},
pmid = {15634957},
issn = {0095-1137},
support = {N01-CO-56000/CO/NCI NIH HHS/United States ; },
mesh = {Animals ; Candida/*classification/genetics/*pathogenicity/physiology ; Candidiasis/microbiology/pathology ; Fungal Proteins/*genetics ; Genes, rRNA ; Humans ; Mice ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA Polymerase II/genetics ; RNA, Ribosomal/genetics ; Rats ; Saccharomycetales/*classification/genetics ; Sequence Analysis, DNA ; Spores, Fungal/physiology ; },
abstract = {A yeast causing widespread infection of laboratory mice was identified from 26S rRNA gene sequences as Candida pintolopesii. To determine the relationship of C. pintolopesii with other members of the Kazachstania (Arxiozyma) telluris species complex, nucleotide sequences from domains 1 and 2 of the 26S rRNA gene, the mitochondrial small-subunit rRNA gene, and the RNA polymerase II gene were phylogenetically analyzed. That analysis resolved the 48 strains examined into five closely related species: K. telluris, Candida bovina, C. pintolopesii, Candida slooffiae, and a previously unknown species. One or more strains of each of the last four species formed an ascosporic state much like that of K. telluris. To place these ascosporogenous strains taxonomically, it is proposed that they be assigned to the teleomorphic genus Kazachstania as K. bovina (type strain NRRL Y-7283, CBS 9732, from the nasal passage of a pigeon), K. heterogenica (type strain NRRL Y-27499, CBS 2675, from rodent feces), K. pintolopesii (type strain NRRL Y-27500, CBS 2985, from the peritoneal fluid of a dead guinea pig), and K. slooffiae (type strain NRRL YB-4349, CBS 9733, from the cecum of a horse). On the basis of multigene sequence analyses, K. heterogenica appears to be a hybrid of K. pintolopesii and a presently unknown species. With the exception of K. bovina, the phylogenetically defined species show a moderate degree of host specificity.},
}
@article {pmid15648215,
year = {2004},
author = {Davolos, D and Maclean, N and Pietrangeli, B},
title = {A molecular phylogenetic study of the freshwater talitrid amphipod Orchestia cavimana (Crustacea).},
journal = {Rivista di biologia},
volume = {97},
number = {1},
pages = {161-168},
pmid = {15648215},
issn = {0035-6050},
mesh = {Amino Acid Sequence ; Amphipoda/*genetics ; Animals ; Electron Transport Complex IV/genetics ; Mitochondria/genetics ; *Phylogeny ; Poisson Distribution ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {In this paper we performed a molecular phylogenetic study of Orchestia cavimana, the sole talitrid amphipod inhabiting beaches of European freshwater lakes and rivers. For that purpose, we have PCR amplified and sequenced regions of the mitochondrial cytochrome oxidase subunit I (COI) gene, basing our analysis on both nucleotide and amino acid sequences and considering also structural classes of the COI enzyme. Phylogenetic analyses were conducted by neighbour-joining (NJ) and maximum-parsimony (MP) methods comparing homologous sequences of talitrids and other Crustacea. In both NJ and MP trees, O. cavimana shows a basal placement with respect to other talitrid amphipods.},
}
@article {pmid15650813,
year = {2005},
author = {Nishikawa, T and Vaughan, DA and Kadowaki, K},
title = {Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {110},
number = {4},
pages = {696-705},
pmid = {15650813},
issn = {0040-5752},
mesh = {Base Sequence ; Chloroplasts/*genetics ; DNA, Mitochondrial ; DNA, Plant ; *Genome, Plant ; *Minisatellite Repeats ; Mitochondria/*genetics ; Oryza/*classification/genetics ; Phylogeny ; Polyploidy ; },
abstract = {Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.},
}
@article {pmid15665243,
year = {2005},
author = {Nunes-Nesi, A and Carrari, F and Lytovchenko, A and Smith, AM and Loureiro, ME and Ratcliffe, RG and Sweetlove, LJ and Fernie, AR},
title = {Enhanced photosynthetic performance and growth as a consequence of decreasing mitochondrial malate dehydrogenase activity in transgenic tomato plants.},
journal = {Plant physiology},
volume = {137},
number = {2},
pages = {611-622},
pmid = {15665243},
issn = {0032-0889},
mesh = {Ascorbic Acid/metabolism ; Chloroplasts/metabolism ; DNA, Complementary/genetics/physiology ; Electron Transport ; Solanum lycopersicum/enzymology/*genetics/growth &amp; development ; Malate Dehydrogenase/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oxygen Consumption ; Phenotype ; Photosynthesis/*physiology ; Phylogeny ; Plants, Genetically Modified ; },
abstract = {Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the mitochondrial malate dehydrogenase gene in the antisense orientation and exhibiting reduced activity of this isoform of malate dehydrogenase show enhanced photosynthetic activity and aerial growth under atmospheric conditions (360 ppm CO2). In comparison to wild-type plants, carbon dioxide assimilation rates and total plant dry matter were up to 11% and 19% enhanced in the transgenics, when assessed on a whole-plant basis. Accumulation of carbohydrates and redox-related compounds such as ascorbate was also markedly elevated in the transgenics. Also increased in the transgenic plants was the capacity to use L-galactono-lactone, the terminal precursor of ascorbate biosynthesis, as a respiratory substrate. Experiments in which ascorbate was fed to isolated leaf discs also resulted in increased rates of photosynthesis providing strong indication for an ascorbate-mediated link between the energy-generating processes of respiration and photosynthesis. This report thus shows that the repression of this mitochondrially localized enzyme improves both carbon assimilation and aerial growth in a crop species.},
}
@article {pmid15668256,
year = {2005},
author = {Zhang, L and Joshi, AK and Hofmann, J and Schweizer, E and Smith, S},
title = {Cloning, expression, and characterization of the human mitochondrial beta-ketoacyl synthase. Complementation of the yeast CEM1 knock-out strain.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {13},
pages = {12422-12429},
doi = {10.1074/jbc.M413686200},
pmid = {15668256},
issn = {0021-9258},
support = {DK 16073/DK/NIDDK NIH HHS/United States ; GM 69717/GM/NIGMS NIH HHS/United States ; },
mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/*biosynthesis/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Cell Nucleus/metabolism ; Cerulenin/chemistry ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/metabolism ; Dose-Response Relationship, Drug ; Esters/chemistry ; Genetic Complementation Test ; Humans ; Kinetics ; Mass Spectrometry ; Mice ; Mitochondria/*enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thioctic Acid/chemistry ; Tissue Distribution ; },
abstract = {A human beta-ketoacyl synthase implicated in a mitochondrial pathway for fatty acid synthesis has been identified, cloned, expressed, and characterized. Sequence analysis indicates that the protein is more closely related to freestanding counterparts found in prokaryotes and chloroplasts than it is to the beta-ketoacyl synthase domain of the human cytosolic fatty acid synthase. The full-length nuclear-encoded 459-residue protein includes an N-terminal sequence element of approximately 38 residues that functions as a mitochondrial targeting sequence. The enzyme can elongate acyl-chains containing 2-14 carbon atoms with malonyl moieties attached in thioester linkage to the human mitochondrial acyl carrier protein and is able to restore growth to the respiratory-deficient yeast mutant cem1 that lacks the endogenous mitochondrial beta-ketoacyl synthase and exhibits lowered lipoic acid levels. To date, four components of a putative type II mitochondrial fatty acid synthase pathway have been identified in humans: acyl carrier protein, malonyl transferase, beta-ketoacyl synthase, and enoyl reductase. The substrate specificity and complementation data for the beta-ketoacyl synthase suggest that, as in plants and fungi, in humans this pathway may play an important role in the generation of octanoyl-acyl carrier protein, the lipoic acid precursor, as well as longer chain fatty acids that are required for optimal mitochondrial function.},
}
@article {pmid15683923,
year = {2005},
author = {Jesus, J and Brehm, A and Harris, DJ},
title = {Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {3},
pages = {480-485},
doi = {10.1016/j.ympev.2004.11.006},
pmid = {15683923},
issn = {1055-7903},
mesh = {Africa, Western ; Animals ; Cytochromes b/genetics ; *Genes, mos ; Lizards/*genetics ; Mitochondria/*genetics ; Phosphopyruvate Hydratase/*genetics ; *Phylogeny ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; },
abstract = {Mitochondrial DNA (12S rRNA, 16S rRNA, and cytochrome b) sequences and nuclear sequences (C-mos and alpha-Enolase) were analyzed within all known Hemidactylus species from all three volcanic islands in the Gulf of Guinea that have never been connected to the continent. These comprise both endemic and widespread species. Our aim was to determine if the widespread species was introduced anthropogenically, to determine the number of distinct genetic lineages within the islands, and to determine if the endemic forms constituted a monophyletic group. Our results suggest that a previously undescribed species on São Tomé is the sister taxon to Hemidactylus newtoni, endemic to Annobon. Genetic variation between populations of Hemidactylus greefii from São Tomé and Principe is very high based on mtDNA sequences, but the forms cannot be distinguished using the nuclear DNA sequences. Hemidactylus mabouia appears to have been anthropogenically introduced to all three islands. The island endemics do not form a monophyletic group, suggesting multiple independent colonizations of the islands.},
}
@article {pmid15683930,
year = {2005},
author = {Iglésias, SP and Lecointre, G and Sellos, DY},
title = {Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes.},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {3},
pages = {569-583},
doi = {10.1016/j.ympev.2004.10.022},
pmid = {15683930},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Genes, RAG-1 ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S ; Sequence Alignment ; Sharks/classification/*genetics ; },
abstract = {Using nuclear coding and mitochondrial ribosomal genes we try to clarify relationships within Carcharhiniformes with special focus on the two most problematic groups: scyliorhinids and triakids. The mitochondrial aligned sequences are 1542 bp long, and include principally portion of 16S rRNA gene. They are obtained for two outgroup species and 43 Carcharhiniformes species, covering 5 of the 8 families and 15 of the 48 genera of the order. The nuclear RAG1 sequences are 1454 bp long, and are obtained for 17 species representative of the diversity of all species sampled. We used Maximum Parsimony and Maximum Likelihood criteria for tree reconstruction. Paraphylies within the family Scyliorhinidae was proposed for the first time by Maisey [Zool. J. Linn. Soc. 82, 33, 1984] in a morphological cladistic analysis. This result has never been proposed again until recently from molecular phylogenies [Mol. Phylogenet. Evol. 31, 214, 2004]. Here, independent and simultaneous analyses of nuclear and mitochondrial data are congruent in supporting the paraphyly of scyliorhinids. Two groups of scyliorhinids are obtained, thoroughly in line with discrimination proposed by previous authors, based on presence/absence of supraorbital crests on the chondrocranium. The first group (Scyliorhinus+Cephaloscyllium) is basal within carcharhiniforms and the second group (Apristurus+Asymbolus+Cephalurus+Galeus+Parmaturus) is sister group of all the other families investigated (Carcharhinidae, Proscyllidae, Pseudotriakidae, and Triakidae). The paraphyly of triakids appeared probable but more investigations are needed. In conclusion several independent morphological and molecular phylogenetic studies support paraphyly within scyliorhinids. So we propose a new classification for the group, with the redefinition of the family Scyliorhinidae sensu stricto and the resurrection of the family Pentanchidae with a new definition.},
}
@article {pmid15683933,
year = {2005},
author = {Trontelj, P and Utevsky, SY},
title = {Celebrity with a neglected taxonomy: molecular systematics of the medicinal leech (genus Hirudo).},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {3},
pages = {616-624},
doi = {10.1016/j.ympev.2004.10.012},
pmid = {15683933},
issn = {1055-7903},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Hirudo medicinalis/*classification/*genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal ; },
abstract = {The medicinal leech is the most famous representative of the Hirudinea. It is one of few invertebrates widely used in medicine and as a scientific model object. It has recently been given considerable conservation effort. Despite all attention there is confusion regarding the taxonomic status of different morphological forms, with many different species described in the past, but only two generally accepted at present. The results of the phylogenetic analysis of a nuclear (ITS2+5.8S rRNA) and two mitochondrial gene sequences (12S rRNA, COI) suggest that the genus Hirudo is monophyletic. It consists, apart form the type Hirudo medicinalis and the East Asian Hirudo nipponia, of three other, neglected species. All of them have already been described either as species or morphological variety, and can readily be identified by their coloration pattern. The type species is in weakly supported sister relation with Hirudo sp. n. (described as variety orientalis) from Transcaucasia and Iran. Sister to them stands Hirudo verbana from southeastern Europe and Turkey, which is nowadays predominantly bred in leech farms and used as 'medicinal leech.' The North African Hirudo troctina is the sister taxon to this group of Western Eurasian species, whereas the basal split is between H. nipponia and the Western Palaearctic clade.},
}
@article {pmid15683934,
year = {2005},
author = {Mallarino, R and Bermingham, E and Willmott, KR and Whinnett, A and Jiggins, CD},
title = {Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes.},
journal = {Molecular phylogenetics and evolution},
volume = {34},
number = {3},
pages = {625-644},
doi = {10.1016/j.ympev.2004.10.021},
pmid = {15683934},
issn = {1055-7903},
mesh = {Animals ; Butterflies/classification/*genetics ; DNA, Mitochondrial ; Microtubule Proteins/genetics ; Mitochondria/genetics ; *Phylogeny ; },
abstract = {Butterflies in the nymphalid subfamily Ithomiinae are brightly colored and involved in mimicry. Here we present a phylogenetic hypothesis for 23 of the 24 species in the genus Ithomia, based on seven different gene regions, representing 5 linkage groups and 4469 bp. We sequenced varying length regions of the following genes: (1) elongation factor 1alpha (Ef1alpha; 1028 bp); (2) tektin (tektin; 715 bp); (3) wingless (wg; 405 bp); (4) ribosomal protein L5 (RpL5; 722 bp, exons 1, 2, 3, and introns 1 and 2); and (5) mitochondrial cytochrome oxidase I, II (Co1 and Co2 and intervening leucine tRNA; 1599 bp). The results show incongruence between some genetic loci, although when alternate topologies are compared statistically it was generally true that one topology was supported by a majority of loci sampled. This highlights the need to sample widely across the genome in order to obtain a well-supported phylogenetic hypothesis. A combined evidence topology is presented based on a Bayesian analysis of all the gene regions, except the fast-evolving RpL5. The resulting hypothesis is concordant with the most probable relationships determined from our topological comparisons, although in some parts of the tree relationships remain weakly supported. The tree suggests diversification has largely occurred within biogeographic regions such as Central America, the Amazon, the southern and northern Andes, with only occasional dispersal (or vicariance) between such regions. This phylogenetic hypothesis can now be used to investigate patterns of diversification across the genus, such as the potential role of color pattern changes in speciation.},
}
@article {pmid15689432,
year = {2005},
author = {Seif, E and Leigh, J and Liu, Y and Roewer, I and Forget, L and Lang, BF},
title = {Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms.},
journal = {Nucleic acids research},
volume = {33},
number = {2},
pages = {734-744},
pmid = {15689432},
issn = {1362-4962},
mesh = {Bacteria/enzymology/genetics ; Base Sequence ; Conserved Sequence ; DNA Transposable Elements ; DNA, Mitochondrial/*chemistry ; Endonucleases/genetics ; Fungi/classification/*genetics ; Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Code ; *Genome, Fungal ; Introns ; Magnoliopsida/genetics ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/classification/genetics ; Molecular Sequence Data ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/genetics/metabolism ; RNA, Messenger/chemistry ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry ; Ribonuclease P/*genetics ; },
abstract = {To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.},
}
@article {pmid15700158,
year = {2005},
author = {Dee, CT and Moffat, KG},
title = {A novel family of mitochondrial proteins is represented by the Drosophila genes slmo, preli-like and real-time.},
journal = {Development genes and evolution},
volume = {215},
number = {5},
pages = {248-254},
pmid = {15700158},
issn = {0949-944X},
mesh = {Adaptor Proteins, Signal Transducing/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Drosophila/embryology/*genetics ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster ; Gene Expression Regulation, Developmental ; Homeodomain Proteins/*genetics ; Intestinal Mucosa/metabolism ; Intestines/embryology ; Membrane Proteins ; Mice ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; NIH 3T3 Cells ; Nervous System/embryology/metabolism ; Nuclear Proteins/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transfection ; },
abstract = {Mitochondria play essential roles in development and disease. The characterisation of mitochondrial proteins is therefore of particular importance. The slowmo (slmo) gene of Drosophila melanogaster has been shown to encode a novel type of mitochondrial protein, and is essential in the developing central nervous system. The Slmo protein contains a conserved PRELI/MSF1p' domain, found in proteins from a wide variety of eukaryotic organisms. However, the function of the proteins of this family is currently unknown. In this study, the evolutionary relationships between members of the PRELI/MSF1p' family are described, and we present the first analysis of two novel Drosophila genes predicted to encode proteins of this type. The first of these, preli-like (prel), is expressed ubiquitously during embryonic development, whilst the second, real-time (retm), is expressed dynamically in the developing gut and central nervous system. retm encodes a member of a novel conserved subclass of larger PRELI/MSF1p' domain proteins, which also contain the CRAL-TRIO motif thought to mediate the transport of small hydrophobic ligands. Here we provide evidence that, like Slmo, both the Prel and Retm proteins are localised to the mitochondria, indicating that the function of the PRELI/MSF1p' domain is specific to this organelle.},
}
@article {pmid15700763,
year = {2005},
author = {Hu, M and Gasser, RB and Chilton, NB and Beveridge, I},
title = {Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within three species of Progamotaenia (Cestoda: Anoplocephalidae) from macropodid marsupials.},
journal = {Parasitology},
volume = {130},
number = {Pt 1},
pages = {117-129},
doi = {10.1017/s0031182004006377},
pmid = {15700763},
issn = {0031-1820},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cestoda/*enzymology/*genetics ; Cestode Infections/parasitology/veterinary ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Macropodidae/*parasitology ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Sequence variation within 3 morphologically defined species of the anoplocephalid cestode genus Progamotaenia (P. ewersi, P. macropodis and P. zschokkei) was investigated using the cytochrome c oxidase subunit 1 gene. The magnitude of genetic variation detected within each morphospecies suggests that, in each instance, several cryptic species are present. Within P. ewersi, 5 genetically distict groups of cestodes were detected, 1 shared by Macropus robustus and M. parryi in Queensland, 1 in M. agilis from Queensland, 1 in Petrogale assimilis from Queensland, 1 in Macropus fuliginosus from South Australia and 1 in Wallabia bicolor from Victoria. In P. macropodis, cestodes from M. robustus from Queensland, Western Australia and the Northern Territory, M. parryi from Queensland and M. eugenii from South Australia were genetically distinct from those in Wallabia bicolor from Queensland and Victoria and from M. fuliginosus from South Australia. P. zschokkei consisted of a number of genetically distinct groups of cestodes, 1 in Lagorchestes conspicillatus and L. hirsutus from Queensland and the Northern Territory respectively, 1 in Petrogale herberti, P. assimilis and M. dorsalis from Queensland, 1 in Onychogalea fraenata from Queensland, 1 in M. agilis from Queensland and 1 in Thylogale stigmatica and T. thetis from Queensland. In general, genetic groups within each morphospecies were host specific and occurred predominantly in a particular macropodid host clade. Comparison of genetic relationships of cestodes with the phylogeny of their hosts revealed examples of colonization (P. zschokkei in M. agilis) and of host switching (P. zschokkei in M. dorsalis).},
}
@article {pmid15703189,
year = {2005},
author = {Srivastava, S and Moraes, CT},
title = {Double-strand breaks of mouse muscle mtDNA promote large deletions similar to multiple mtDNA deletions in humans.},
journal = {Human molecular genetics},
volume = {14},
number = {7},
pages = {893-902},
pmid = {15703189},
issn = {0964-6906},
support = {R01 EY010804/EY/NEI NIH HHS/United States ; EY 10804/EY/NEI NIH HHS/United States ; GM 55766/GM/NIGMS NIH HHS/United States ; R01 MH085801/MH/NIMH NIH HHS/United States ; R56 NS041777/NS/NINDS NIH HHS/United States ; NS 041777/NS/NINDS NIH HHS/United States ; R01 NS041777/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Blotting, Southern ; *DNA Damage ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics/metabolism ; Disease Models, Animal ; Electron Transport ; *Gene Deletion ; Humans ; Immunohistochemistry ; Mice ; Mice, Transgenic ; Microscopy, Electron ; Mitochondria/metabolism ; *Models, Genetic ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Muscles/*metabolism ; Muscular Diseases ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Transgenes ; },
abstract = {Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders and have been found to accumulate during normal aging. Despite the fact that hundreds of deletions have been characterized at the molecular level, their mechanisms of genesis are unknown. We tested the effect of double-strand breaks of muscle mtDNA by developing a mouse model in which a mitochondrially targeted restriction endonuclease (PstI) was expressed in skeletal muscle of mice. Because mouse mtDNA harbors two PstI sites, transgenic founders developed a mitochondrial myopathy associated with mtDNA depletion. The founders showed a chimeric pattern of transgene expression and their residual level of wild-type mtDNA in muscle was approximately 40% of controls. We were able to identify the formation of large mtDNA deletions in muscle of transgenic mice. A family of mtDNA deletions was identified, and most of these rearrangements involved one of the PstI sites and the 3' end of the D-loop region. The deletions had no or small direct repeats at the breakpoint region. These features are essentially identical to the ones observed in humans with multiple mtDNA deletions in muscle, suggesting that double-strand DNA breaks mediate the formation of large mtDNA deletions.},
}
@article {pmid15707358,
year = {2005},
author = {Arnesano, F and Banci, L and Bertini, I and Martinelli, M},
title = {Ortholog search of proteins involved in copper delivery to cytochrome C oxidase and functional analysis of paralogs and gene neighbors by genomic context.},
journal = {Journal of proteome research},
volume = {4},
number = {1},
pages = {63-70},
doi = {10.1021/pr049862f},
pmid = {15707358},
issn = {1535-3893},
mesh = {Animals ; Bacterial Proteins ; Carrier Proteins ; Cation Transport Proteins/genetics/*physiology ; Copper/*metabolism ; Copper Transport Proteins ; Databases, Protein ; Electron Transport Chain Complex Proteins ; Electron Transport Complex IV/*biosynthesis/genetics ; Genomics/*methods ; Humans ; Membrane Proteins/genetics/physiology ; Mitochondria/genetics ; Mitochondrial Proteins ; Molecular Chaperones ; Phylogeny ; Proteins/genetics/physiology ; },
abstract = {Cytochrome c oxidase (COX) is a multi-subunit enzyme of the mitochondrial respiratory chain. Delivery of metal cofactors to COX is essential for assembly, which represents a long-standing puzzle. The proteins Cox17, Sco1/2, and Cox11 are necessary for copper insertion into CuA and CuB redox centers of COX in eukaryotes. A genome-wide search in all prokaryotic genomes combined with genomic context reveals that only Sco and Cox11 have orthologs in prokaryotes. However, while Cox11 function is confined to COX assembly, Sco acts as a multifunctional linker connecting a variety of biological processes. Multifunctionality is achieved by gene duplication and paralogs. Neighbor genes of Sco paralogs often encode cuproenzymes and cytochrome c domains and, in some cases, Sco is fused to cytochrome c. This led us to suggest that cytochrome c might be relevant to Sco function and the two proteins might jointly be involved in COX assembly. Sco is also related, in terms of gene neighborhood and phylogenetic occurrence, to a newly detected protein involved in copper trafficking in bacteria and archaea, but with no sequence similarity to the mitochondrial copper chaperone Cox17. By linking the assembly system to the copper uptake system, Sco allows COX to face alternative copper trafficking pathways.},
}
@article {pmid15720402,
year = {2005},
author = {Riemenschneider, A and Wegele, R and Schmidt, A and Papenbrock, J},
title = {Isolation and characterization of a D-cysteine desulfhydrase protein from Arabidopsis thaliana.},
journal = {The FEBS journal},
volume = {272},
number = {5},
pages = {1291-1304},
doi = {10.1111/j.1742-4658.2005.04567.x},
pmid = {15720402},
issn = {1742-464X},
mesh = {Amino Acids, Cyclic/metabolism ; Arabidopsis/*enzymology ; Binding Sites ; Cell Nucleus/metabolism ; Cystathionine gamma-Lyase/chemistry/*isolation &amp; purification/*metabolism ; Cysteine/*metabolism ; Escherichia coli/metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/metabolism ; Phylogeny ; Pyridoxal Phosphate/*metabolism ; Pyruvic Acid/metabolism ; RNA, Plant/metabolism ; Recombinant Proteins/metabolism ; Subcellular Fractions ; },
abstract = {In several organisms D-cysteine desulfhydrase (D-CDes) activity (EC 4.1.99.4) was measured; this enzyme decomposes D-cysteine into pyruvate, H2S, and NH3. A gene encoding a putative D-CDes protein was identified in Arabidopsis thaliana (L) Heynh. based on high homology to an Escherichia coli protein called YedO that has D-CDes activity. The deduced Arabidopsis protein consists of 401 amino acids and has a molecular mass of 43.9 kDa. It contains a pyridoxal-5'-phosphate binding site. The purified recombinant mature protein had a Km for D-cysteine of 0.25 mm. Only D-cysteine but not L-cysteine was converted by D-CDes to pyruvate, H2S, and NH3. The activity was inhibited by aminooxy acetic acid and hydroxylamine, inhibitors specific for pyridoxal-5'-phosphate dependent proteins, at low micromolar concentrations. The protein did not exhibit 1-aminocyclopropane-1-carboxylate deaminase activity (EC 3.5.99.7) as homologous bacterial proteins. Western blot analysis of isolated organelles and localization studies using fusion constructs with the green fluorescent protein indicated an intracellular localization of the nuclear encoded D-CDes protein in the mitochondria. D-CDes RNA levels increased with proceeding development of Arabidopsis but decreased in senescent plants; D-CDes protein levels remained almost unchanged in the same plants whereas specific D-CDes activity was highest in senescent plants. In plants grown in a 12-h light/12-h dark rhythm D-CDes RNA levels were highest in the dark, whereas protein levels and enzyme activity were lower in the dark period than in the light indicating post-translational regulation. Plants grown under low sulfate concentration showed an accumulation of D-CDes RNA and increased protein levels, the D-CDes activity was almost unchanged. Putative in vivo functions of the Arabidopsisd-CDes protein are discussed.},
}
@article {pmid15721031,
year = {2005},
author = {Kunisawa, T},
title = {Branching orders among alpha-proteobacteria and mitochondria inferred from gene transpositions.},
journal = {Journal of theoretical biology},
volume = {234},
number = {1},
pages = {1-5},
doi = {10.1016/j.jtbi.2004.11.004},
pmid = {15721031},
issn = {0022-5193},
mesh = {Alphaproteobacteria/*genetics ; Gene Rearrangement ; *Genes, Bacterial ; Mitochondria/*genetics ; Phylogeny ; },
}
@article {pmid15737601,
year = {2005},
author = {Arnason, U},
title = {Comments on the paper "Phylogeny of mysticete whales based on mitochondrial and nuclear data" by Amanda L. Rychel, Tod W. Reeder, and Annalisa Berta [Mol. Phylogenet. Evol. 32 (2004) 892-901].},
journal = {Molecular phylogenetics and evolution},
volume = {35},
number = {1},
pages = {309-10; author reply 311-2},
doi = {10.1016/j.ympev.2004.11.013},
pmid = {15737601},
issn = {1055-7903},
mesh = {Animals ; Cell Nucleus/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Whales/*classification/*genetics ; },
}
@article {pmid15744282,
year = {2005},
author = {Gray, MW},
title = {Evolutionary biology: the hydrogenosome's murky past.},
journal = {Nature},
volume = {434},
number = {7029},
pages = {29-31},
doi = {10.1038/434029a},
pmid = {15744282},
issn = {1476-4687},
mesh = {Animals ; Ciliophora/*cytology/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Electron Transport ; Electron Transport Complex I/chemistry/metabolism ; Genome ; Hydrogen/*metabolism ; Isoptera/parasitology ; Mitochondria/enzymology/*genetics/*metabolism ; Organelles/enzymology/*genetics/*metabolism ; *Phylogeny ; Trichomonas vaginalis/cytology/genetics ; },
}
@article {pmid15744302,
year = {2005},
author = {Boxma, B and de Graaf, RM and van der Staay, GW and van Alen, TA and Ricard, G and Gabaldón, T and van Hoek, AH and Moon-van der Staay, SY and Koopman, WJ and van Hellemond, JJ and Tielens, AG and Friedrich, T and Veenhuis, M and Huynen, MA and Hackstein, JH},
title = {An anaerobic mitochondrion that produces hydrogen.},
journal = {Nature},
volume = {434},
number = {7029},
pages = {74-79},
doi = {10.1038/nature03343},
pmid = {15744302},
issn = {1476-4687},
mesh = {*Anaerobiosis ; Animals ; Ciliophora/*cytology/genetics/*metabolism/ultrastructure ; Cockroaches/parasitology ; DNA, Mitochondrial/genetics ; Electron Transport ; Electron Transport Complex I/antagonists &amp; inhibitors/metabolism ; Genome ; Glucose/metabolism ; Hydrogen/*metabolism ; Mitochondria/enzymology/genetics/*metabolism/ultrastructure ; Molecular Sequence Data ; Open Reading Frames/genetics ; Organelles/drug effects/genetics/metabolism/ultrastructure ; Phylogeny ; Proteome ; },
abstract = {Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product--biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes.},
}
@article {pmid15744502,
year = {2005},
author = {Edmondson, AC and Song, D and Alvarez, LA and Wall, MK and Almond, D and McClellan, DA and Maxwell, A and Nielsen, BL},
title = {Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.},
journal = {Molecular genetics and genomics : MGG},
volume = {273},
number = {2},
pages = {115-122},
pmid = {15744502},
issn = {1617-4615},
support = {BBS/E/J/00000201/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Biolistics ; Computational Biology ; DNA-Binding Proteins/*genetics ; Escherichia coli ; Gene Components ; Green Fluorescent Proteins ; Likelihood Functions ; Mitochondria/*metabolism ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Rec A Recombinases/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; },
abstract = {A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.},
}
@article {pmid15752446,
year = {2005},
author = {Chua, PK and Corkill, JE and Hooi, PS and Cheng, SC and Winstanley, C and Hart, CA},
title = {Isolation of Waddlia malaysiensis, a novel intracellular bacterium, from fruit bat (Eonycteris spelaea).},
journal = {Emerging infectious diseases},
volume = {11},
number = {2},
pages = {271-277},
pmid = {15752446},
issn = {1080-6040},
mesh = {3T3 Cells ; Acetylmuramyl-Alanyl-Isoglutamine/*analogs &amp; derivatives/chemistry/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Chiroptera/*microbiology/urine ; Chlamydiales/drug effects/genetics/*isolation &amp; purification/ultrastructure ; Chlorocebus aethiops ; Cricetinae ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Humans ; Mice ; Microbial Sensitivity Tests ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 23S/chemistry/genetics ; Sequence Alignment ; Vero Cells ; },
abstract = {An obligate intracellular bacterium was isolated from urine samples from 7 (3.5%) of 202 fruit bats (Eonycteris spelaea) in peninsular Malaysia. The bacterium produced large membrane-bound inclusions in human, simian, and rodent cell lines, including epithelial, fibroblastlike, and lymphoid cells. Thin-section electron microscopy showed reticulate bodies dividing by binary fission and elementary bodies in the inclusions; mitochondria surrounded the inclusions. The inclusions were positive for periodic acid-Schiff stain but could not be stained by fluorescein-labeled anti-Chlamydia trachomatis major outer membrane protein monoclonal antibody. The bacterium was resistant to penicillin and streptomycin (MICs > 256 mg/L) but susceptible to tetracycline (MIC = 0.25 mg/L) and chloramphenicol (MIC = 0.5 mg/L). Sequence analysis of the 16SrRNA gene indicated that it was most closely related to 2 isolates of Waddlia chondrophila (94% and 96% identity). The 16S and 23S rRNA gene signatures were only 91% identical. We propose this novel bacterium be called W. malaysiensis.},
}
@article {pmid15803323,
year = {2005},
author = {Purnell, MP and Skopelitis, DS and Roubelakis-Angelakis, KA and Botella, JR},
title = {Modulation of higher-plant NAD(H)-dependent glutamate dehydrogenase activity in transgenic tobacco via alteration of beta subunit levels.},
journal = {Planta},
volume = {222},
number = {1},
pages = {167-180},
pmid = {15803323},
issn = {0032-0935},
mesh = {Amino Acids/metabolism ; Cloning, Molecular ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Genotype ; Glutamate Dehydrogenase (NADP+)/*chemistry/genetics/*metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Mitochondria/enzymology ; Phylogeny ; Plants, Genetically Modified ; Protein Processing, Post-Translational ; Protein Subunits/biosynthesis/genetics/metabolism ; Quaternary Ammonium Compounds/metabolism ; RNA, Messenger/genetics/metabolism ; Nicotiana/*enzymology/*genetics ; Transformation, Genetic ; },
abstract = {Glutamate dehydrogenase (GDH; EC 1.4.1.2-1.4.1.4) catalyses in vitro the reversible amination of 2-oxoglutarate to glutamate. In vascular plants the in vivo direction(s) of the GDH reaction and hence the physiological role(s) of this enzyme remain obscure. A phylogenetic analysis identified two clearly separated groups of higher-plant GDH genes encoding either the alpha- or beta-subunit of the GDH holoenzyme. To help clarify the physiological role(s) of GDH, tobacco (Nicotiana tabacum L.) was transformed with either an antisense or sense copy of a beta-subunit gene, and transgenic plants recovered with between 0.5- and 34-times normal leaf GDH activity. This large modulation of GDH activity (shown to be via alteration of beta-subunit levels) had little effect on leaf ammonium or the leaf free amino acid pool, except that a large increase in GDH activity was associated with a significant decrease in leaf Asp (~51%, P=0.0045). Similarly, plant growth and development were not affected, suggesting that a large modulation of GDH beta-subunit titre does not affect plant viability under the ideal growing conditions employed. Reduction of GDH activity and protein levels in an antisense line was associated with a large increase in transcripts of a beta-subunit gene, suggesting that the reduction in beta-subunit levels might have been due to translational inhibition. In another experiment designed to detect post-translational up-regulation of GDH activity, GDH over-expressing plants were subjected to prolonged dark-stress. GDH activity increased, but this was found to be due more likely to resistance of the GDH protein to stress-induced proteolysis, rather than to post-translational up-regulation.},
}
@article {pmid15803417,
year = {2004},
author = {Woloszynska, M and Bocer, T and Mackiewicz, P and Janska, H},
title = {A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus.},
journal = {Plant molecular biology},
volume = {56},
number = {5},
pages = {811-820},
pmid = {15803417},
issn = {0167-4412},
mesh = {Base Sequence ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phaseolus/*genetics ; Phylogeny ; Plant Proteins/genetics ; RNA, Transfer, Ala/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron, named pvs-trnA for its location within the Phaseolus vulgaris sterility sequence (pvs). The purpose of this study was to determine the type of transfer (intracellular or horizontal) that gave rise to pvs-trnA. Using a PCR approach we could not find the respective portion of the trnA gene as a part of pvs outside the Phaseolus genus. However, a BLAST search revealed longer fragments of trnA present in the mitochondrial genomes of some Citrus species, Helianthus annuus and Zea mays. Basing on the identity or near-identity between these mitochondrial sequences and their chloroplast counterparts we concluded that they had relocated from chloroplasts to mitochondria via recent, independent, intracellular DNA transfers. In contrast, pvs-trnA displayed a relatively higher sequence divergence when compared with its chloroplast counterpart from Phaseolus vulgaris. Alignment of pvs-trnA with corresponding trnA fragments from 35 plant species as well as phylogenetic analysis revealed that pvs-trnA grouped with non-eudicot sequences and was well separated from all Fabales sequences. In conclusion, we propose that pvs-trnA arose via horizontal transfer of a trnA intron fragment from chloroplast of a non-eudicot plant to Phaseolus mitochondria. This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants.},
}
@article {pmid15809292,
year = {2005},
author = {Haguenauer, A and Raimbault, S and Masscheleyn, S and Gonzalez-Barroso, Mdel M and Criscuolo, F and Plamondon, J and Miroux, B and Ricquier, D and Richard, D and Bouillaud, F and Pecqueur, C},
title = {A new renal mitochondrial carrier, KMCP1, is up-regulated during tubular cell regeneration and induction of antioxidant enzymes.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {23},
pages = {22036-22043},
doi = {10.1074/jbc.M412136200},
pmid = {15809292},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Antioxidants/*pharmacology ; Blotting, Northern ; Blotting, Western ; Brain/metabolism ; COS Cells ; Carrier Proteins/*biosynthesis/*chemistry/metabolism/*physiology ; Cloning, Molecular ; DNA, Complementary/metabolism ; Glutamine/chemistry ; Glycerol/chemistry/metabolism ; Immunoprecipitation ; Ion Channels ; Kidney/*metabolism ; Kidney Tubules/*physiology ; Membrane Potentials ; Membrane Proteins/metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis/*physiology ; Molecular Sequence Data ; Oxidants/pharmacology ; Oxidation-Reduction ; Oxidative Stress ; Oxygen/metabolism ; Oxygen Consumption ; Phylogeny ; RNA/chemistry/metabolism ; *Regeneration ; Superoxide Dismutase/metabolism ; Time Factors ; Tissue Distribution ; Uncoupling Protein 1 ; *Up-Regulation ; },
abstract = {The mitochondrial carrier family transports a variety of metabolites across the inner mitochondrial membrane. We identified and cloned a new member of this family, KMCP1 (kidney mitochondrial carrier protein-1), that is highly homologous to the previously identified protein BMCP1 (brain mitochondrial carrier protein-1). Western blotting and in situ experiments showed that this carrier is expressed predominantly within the kidney cortex in the proximal and distal tubules. KMCP1 was increased during fasting and during the regenerative phase of glycerol-induced renal failure. We show that both situations are associated with transiently increased expression of superoxide-generating enzymes, followed by increased mitochondrial metabolism and antioxidant defenses. Given that KMCP1 expression occurs simultaneously with these latter events, we propose that KMCP1 is involved in situations in which mitochondrial metabolism is increased, in particular when the cellular redox balance tends toward a pro-oxidant status.},
}
@article {pmid15826309,
year = {2005},
author = {Mower, JP},
title = {PREP-Mt: predictive RNA editor for plant mitochondrial genes.},
journal = {BMC bioinformatics},
volume = {6},
number = {},
pages = {96},
pmid = {15826309},
issn = {1471-2105},
support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01-GM-35087/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chloroplasts ; Computational Biology/*methods ; Conserved Sequence ; Cytidine/chemistry ; DNA/chemistry ; DNA, Plant ; Databases, Protein ; *Genes, Plant ; *Genome, Plant ; Mitochondrial Proteins ; Models, Statistical ; Molecular Sequence Data ; Phylogeny ; Plant Proteins ; Protein Binding ; RNA/*chemistry ; *RNA Editing ; RNA, Chloroplast ; RNA, Mitochondrial ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Homology, Amino Acid ; Software ; },
abstract = {BACKGROUND: In plants, RNA editing is a process that converts specific cytidines to uridines and uridines to cytidines in transcripts from virtually all mitochondrial protein-coding genes. There are thousands of plant mitochondrial genes in the sequence databases, but sites of RNA editing have not been determined for most. Accurate methods of RNA editing site prediction will be important in filling in this information gap and could reduce or even eliminate the need for experimental determination of editing sites for many sequences. Because RNA editing tends to increase protein conservation across species by "correcting" codons that specify unconserved amino acids, this principle can be used to predict editing sites by identifying positions where an RNA editing event would increase the conservation of a protein to homologues from other plants. PREP-Mt takes this approach to predict editing sites for any protein-coding gene in plant mitochondria.<br><br>RESULTS: To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the 3,698 known sites of RNA editing (sensitivity = 82.2%) and 55,956 of the 56,565 known unedited sites (specificity = 98.9%). Accuracy and sensitivity increased to 98.7% and 94.7%, respectively, after excluding the 489 silent editing sites (which have no effect on protein sequence or function) from the test set.<br><br>CONCLUSION: These results indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein sequences for use in molecular, biochemical, and phylogenetic analyses. In addition, PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify particular sequences with unusual editing properties. The PREP-Mt methodology should be applicable to any system where RNA editing increases protein conservation across species.},
}
@article {pmid15830887,
year = {2004},
author = {Guo, KW and Niu, AO},
title = {[Studies on the genetic variation of two mitochondrial DNA molecules of Schistosoma japonicum].},
journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases},
volume = {22},
number = {5},
pages = {300-302},
pmid = {15830887},
issn = {1000-7423},
mesh = {Animals ; Base Sequence ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Schistosoma japonicum/*genetics ; },
abstract = {OBJECTIVE: To study the variation of Schistosoma japonicum through two mitochondrial DNA molecules.<br><br>METHODS: Genomic DNA was isolated with kit, and the mitochondrial NADH dehydrogenase 1 (ND1) and cytochrome c oxidase I (COI) gene fragments were amplified by polymerase chain reaction (PCR) and sequenced. The gene trees were constructed and the acquired data were analyzed with the help of bioinformatics.<br><br>RESULTS: The gene trees showed that the Taiwan isolate and the mainland isolates can be divided in two groups: a group from the hilly region (Yunnan and Sichuan), another group from the lake region (Hunan, Jiangxi and Anhui); isolates from Hubei are at a different position on the gene trees.<br><br>CONCLUSION: There are variations among the geographic isolates of Schistosoma japonicum in China, nevertheless, they have close kinship.},
}
@article {pmid15854906,
year = {2005},
author = {Chan, KW and Slotboom, DJ and Cox, S and Embley, TM and Fabre, O and van der Giezen, M and Harding, M and Horner, DS and Kunji, ER and León-Avila, G and Tovar, J},
title = {A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica.},
journal = {Current biology : CB},
volume = {15},
number = {8},
pages = {737-742},
doi = {10.1016/j.cub.2005.02.068},
pmid = {15854906},
issn = {0960-9822},
support = {MC_U105663139/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bayes Theorem ; Blotting, Western ; Cell Fractionation ; Computational Biology ; DNA, Complementary/genetics ; Electrophoresis, Polyacrylamide Gel ; Entamoeba histolytica/genetics/*metabolism ; Humans ; Lactococcus lactis ; Mitochondrial ADP, ATP Translocases/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Organelles/*metabolism ; *Phylogeny ; Protein Conformation ; Saccharomyces cerevisiae ; Sequence Analysis, DNA ; Transport Vesicles/metabolism ; },
abstract = {Recent data suggest that microaerophilic and parasitic protozoa, which lack oxidative phosphorylation, nevertheless contain mitochondrial homologs [1-6], organelles that share common ancestry with mitochondria. Such widespread retention suggests there may be a common function for mitochondrial homologs that makes them essential for eukaryotic cells. We determined the mitochondrial carrier family (MCF) complement of the Entamoeba histolytica mitochondrial homolog, also known as a crypton [5] or more commonly as a mitosome [3]. MCF proteins support mitochondrial metabolic energy generation, DNA replication, and amino-acid metabolism by linking biochemical pathways in the mitochondrial matrix with those in the cytosol [7]. MCF diversity thus closely mirrors important facets of mitochondrial metabolic diversity. The Entamoeba histolytica mitosome has lost all but a single type of MCF protein, which transports ATP and ADP via a novel mechanism that is not reliant on a membrane potential. Phylogenetic analyses confirm that the Entamoeba ADP/ATP carrier is distinct from archetypal mitochondrial ADP/ATP carriers, an observation that is supported by its different substrate and inhibitor specificity. Because many functions of yeast and human mitochondria rely on solutes transported by specialized members of this family, the Entamoeba mitosome must contain only a small subset of these processes requiring adenine nucleotide exchange.},
}
@article {pmid15861250,
year = {2004},
author = {Coates, BS and Sumerford, DV and Hellmich, RL},
title = {Geographic and voltinism differentiation among North American Ostrinia nubilalis (European corn borer) mitochondrial cytochrome c oxidase haplotypes.},
journal = {Journal of insect science (Online)},
volume = {4},
number = {},
pages = {35},
pmid = {15861250},
issn = {1536-2442},
mesh = {Animals ; Demography ; Ecosystem ; Electron Transport Complex IV/*genetics ; Gene Expression Regulation, Enzymologic ; Genetic Variation ; Haplotypes ; Insect Proteins/genetics ; Mitochondria/*enzymology ; Moths/*enzymology/genetics ; Phylogeny ; },
abstract = {DNA sequence of European corn borer, Ostrinia nubilalis (Hubner) (Lepidoptera: Crambidae), mitochondrial cytochrome c oxidase I (cox1) and II (cox2) genes were characterized and used for population genetic analysis. Twenty-six point mutations were identified from a 2,156 bp DNA sequence alignment. The frequency of polymorphic cox1DdeI and HaeIII, and cox2 Sau3AI and MspI restriction sites were determined from 1,414 individuals by polymerase chain reaction restriction fragment length polymorphism. Ten haplotypes were observed. A single haplotype was present among 90% of individuals examined, and a HaeIII haplotype was not present in samples from the Atlantic coast. Significant genetic differentiation existed between Atlantic coast and midwestern United States samples, and between sympatric uni- and bivoltine ecotypes. These genetic markers identify regional and ecotype differences in the North American O. nubilalis population.},
}
@article {pmid15878829,
year = {2005},
author = {Matsubara, M and Komatsu, M and Araki, T and Asakawa, S and Yokobori, S and Watanabe, K and Wada, H},
title = {The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {36},
number = {3},
pages = {598-605},
doi = {10.1016/j.ympev.2005.03.018},
pmid = {15878829},
issn = {1055-7903},
mesh = {Animals ; Base Composition ; Base Sequence ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Mitochondrial/*genetics ; Echinodermata/*classification/*genetics ; Genome ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; },
abstract = {One of the most important issues in asteroid phylogeny is the phylogenetic status of Paxillosida. This group lacks an anus and suckers on the tube feet in adults and does not develop the brachiolaria stage in early development. Two controversial hypotheses have been proposed for the phylogenetic status of Paxillosida, i.e., Paxillosida is primitive or rather specialized in asteroids. In this study, we determined the complete mitochondrial DNA nucleotide sequences from two paxillosidans (Astropecten polyacanthus and Luidia quinaria) and one forcipulatidan (Asterias amurensis). The mitochondrial genomes of the three asteroids were identical with respect to gene order and transcription direction, and were identical to the previously reported mitochondrial genomes of Asterina pectinifera (Valvatida) and Pisaster ochraceus (Forcipulatida) in this respect. Therefore, the comparison of genome structures was uninformative for the purposes of asteroid phylogeny. However, molecular phylogenetic analyses based on the amino acid sequences and the nucleotide sequences from the five asteroids supported the monophyly of the clade that included the two paxillosidans and Asterina. This suggests that the paxillosidan characters are secondarily derived ones.},
}
@article {pmid15888416,
year = {2005},
author = {Birdsey, GM and Lewin, J and Holbrook, JD and Simpson, VR and Cunningham, AA and Danpure, CJ},
title = {A comparative analysis of the evolutionary relationship between diet and enzyme targeting in bats, marsupials and other mammals.},
journal = {Proceedings. Biological sciences},
volume = {272},
number = {1565},
pages = {833-840},
pmid = {15888416},
issn = {0962-8452},
mesh = {Alanine Transaminase/*metabolism ; Animals ; Chiroptera/*metabolism ; *Diet ; Glyoxylates/*metabolism ; Immunohistochemistry ; Linear Models ; Liver/*metabolism ; Marsupialia/*metabolism ; Mitochondria/metabolism ; Peroxisomes/metabolism ; Phylogeny ; },
abstract = {The subcellular distribution of the enzyme alanine:glyoxylate aminotransferase (AGT) in the livers of different mammals appears to be related to their natural diets. Thus, AGT tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. To what extent this relationship is an incidental consequence of phylogenetic structure or an evolutionarily meaningful adaptive response to changes in dietary selection pressure is unknown. In order to distinguish between these two possibilities, we have determined the subcellular distribution of AGT in the livers of 22 new mammalian species, including members of three orders not studied before. In addition, we have analysed the statistical relationship between AGT distribution and diet in all 77 mammalian species, from 12 different orders, for which the distribution is currently known. Our analysis shows that there is a highly significant correlation between AGT distribution and diet, independent of phylogeny. This finding is compatible with the suggestion that the variable intracellular targeting of AGT is an adaptive response to episodic changes in dietary selection pressure. To our knowledge, this is the first example of such a response being manifested at the molecular and cellular levels across the breadth of Mammalia.},
}
@article {pmid15890885,
year = {2005},
author = {Macaulay, V and Hill, C and Achilli, A and Rengo, C and Clarke, D and Meehan, W and Blackburn, J and Semino, O and Scozzari, R and Cruciani, F and Taha, A and Shaari, NK and Raja, JM and Ismail, P and Zainuddin, Z and Goodwin, W and Bulbeck, D and Bandelt, HJ and Oppenheimer, S and Torroni, A and Richards, M},
title = {Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.},
journal = {Science (New York, N.Y.)},
volume = {308},
number = {5724},
pages = {1034-1036},
doi = {10.1126/science.1109792},
pmid = {15890885},
issn = {1095-9203},
mesh = {Africa ; Asia ; Australasia ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/*genetics ; Europe ; Founder Effect ; Genetic Drift ; *Genetic Variation ; Genetics, Population ; *Genome, Human ; Haplotypes ; History, Ancient ; Humans ; India ; Malaysia ; Mitochondria/*genetics ; Mutation ; Phylogeny ; *Population Dynamics ; Time ; },
abstract = {A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.},
}
@article {pmid15904985,
year = {2005},
author = {Pütz, S and Gelius-Dietrich, G and Piotrowski, M and Henze, K},
title = {Rubrerythrin and peroxiredoxin: two novel putative peroxidases in the hydrogenosomes of the microaerophilic protozoon Trichomonas vaginalis.},
journal = {Molecular and biochemical parasitology},
volume = {142},
number = {2},
pages = {212-223},
doi = {10.1016/j.molbiopara.2005.04.003},
pmid = {15904985},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins ; Ferredoxins ; Hemerythrin ; Hydrogen/*metabolism ; Molecular Sequence Data ; Organelles/*enzymology ; Oxidative Stress ; Oxygen/pharmacology ; Peroxidases/chemistry/genetics/*metabolism ; Peroxiredoxins ; Phylogeny ; Proteome ; Protozoan Proteins/chemistry/genetics/*metabolism ; Rubredoxins ; Sequence Alignment ; Trichomonas vaginalis/*enzymology/genetics/physiology ; },
abstract = {The parasitic flagellate Trichomonas vaginalis contains hydrogenosomes, anaerobic organelles related to mitochondria, that generate ATP from the fermentative conversion of pyruvate to acetate, CO2 and molecular hydrogen. Although an essentially anaerobic organism, Trichomonas encounters low oxygen concentrations in its natural habitat and has to protect itself, and especially the oxygen-sensitve enzymes of hydrogenosomal metabolism, from oxidative damage. We have identified two novel proteins in the hydrogenosomal proteome with strong similarity to two putative prokaryotic peroxidases, rubrerythrin and periplasmic thiol peroxidase. Both proteins have previously been found in many prokaryotes but were not known from eukaryotes, suggesting a significant prokaryotic component in the oxygen-detoxification system of trichomonad hydrogenosomes.},
}
@article {pmid15914576,
year = {2005},
author = {Jolly, RA and Goldstein, KM and Wei, T and Gao, H and Chen, P and Huang, S and Colet, JM and Ryan, TP and Thomas, CE and Estrem, ST},
title = {Pooling samples within microarray studies: a comparative analysis of rat liver transcription response to prototypical toxicants.},
journal = {Physiological genomics},
volume = {22},
number = {3},
pages = {346-355},
doi = {10.1152/physiolgenomics.00260.2004},
pmid = {15914576},
issn = {1531-2267},
mesh = {Animals ; Clofibrate/toxicity ; Cluster Analysis ; Diethylhexyl Phthalate/toxicity ; Fatty Acids/metabolism ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; Liver/*drug effects/*metabolism ; Liver Extracts/*metabolism ; Male ; Mitochondria/metabolism ; Models, Biological ; Models, Statistical ; Oligonucleotide Array Sequence Analysis/*methods ; Organ Size ; Phenotype ; Phylogeny ; Principal Component Analysis ; RNA/metabolism ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; Valproic Acid/toxicity ; },
abstract = {Combining or pooling individual samples when carrying out transcript profiling using microarrays is a fairly common means to reduce both the cost and complexity of data analysis. However, pooling does not allow for statistical comparison of changes between samples and can result in a loss of information. Because a rigorous comparison of the identified expression changes from the two approaches has not been reported, we compared the results for hepatic transcript profiles from pooled vs. individual samples. Hepatic transcript profiles from a single-dose time-course rat study in response to the prototypical toxicants clofibrate, diethylhexylphthalate, and valproic acid were evaluated. Approximately 50% more transcript expression changes were observed in the individual (statistical) analysis compared with the pooled analysis. While the majority of these changes were less than twofold in magnitude (approximately 80%), a substantial number were greater than twofold (approximately 20%). Transcript changes unique to the individual analysis were confirmed by quantitative RT-PCR, while all the changes unique to the pooled analysis did not confirm. The individual analysis identified more hits per biological pathway than the pooled approach. Many of the transcripts identified by the individual analysis were novel findings and may contribute to a better understanding of molecular mechanisms of these compounds. Furthermore, having individual animal data provided the opportunity to correlate changes in transcript expression to phenotypes (i.e., histology) observed in toxicology studies. The two approaches were similar when clustering methods were used despite the large difference in the absolute number of transcripts changed. In summary, pooling reduced resource requirements substantially, but the individual approach enabled statistical analysis that identified more gene expression changes to evaluate mechanisms of toxicity. An individual animal approach becomes more valuable when the overall expression response is subtle and/or when associating expression data to variable phenotypic responses.},
}
@article {pmid15923129,
year = {2005},
author = {Fischer, WM and Palmer, JD},
title = {Evidence from small-subunit ribosomal RNA sequences for a fungal origin of Microsporidia.},
journal = {Molecular phylogenetics and evolution},
volume = {36},
number = {3},
pages = {606-622},
doi = {10.1016/j.ympev.2005.03.031},
pmid = {15923129},
issn = {1055-7903},
support = {R01 GM-35087/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Fungi/*classification/*genetics ; Genes, Fungal/genetics ; Microsporidia/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {The phylum Microsporidia comprises a species-rich group of minute, single-celled, and intra-cellular parasites. Lacking normal mitochondria and with unique cytology, microsporidians have sometimes been thought to be a lineage of ancient eukaryotes. Although phylogenetic analyses using small-subunit ribosomal RNA (SSU-rRNA) genes almost invariably place the Microsporidia among the earliest branches on the eukaryotic tree, many other molecules suggest instead a relationship with fungi. Using maximum likelihood methods and a diverse SSU-rRNA data set, we have re-evaluated the phylogenetic affiliations of Microsporidia. We demonstrate that tree topologies used to estimate likelihood model parameters can materially affect phylogenetic searches. We present a procedure for reducing this bias: "tree-based site partitioning," in which a comprehensive set of alternative topologies is used to estimate sequence data partitions based on inferred evolutionary rates. This hypothesis-driven approach appears to be capable of utilizing phylogenetic information that is not available to standard likelihood implementations (e.g., approximation to a gamma distribution); we have employed it in maximum likelihood and Bayesian analysis. Applying our method to a phylogenetically diverse SSU-rRNA data set revealed that the early diverging ("deep") placement of Microsporidia typically found in SSU-rRNA trees is no better than a fungal placement, and that the likeliest placement of Microsporidia among non-long-branch eukaryotic taxa is actually within fungi. These results illustrate the importance of hypothesis testing in parameter estimation, provide a way to address certain problems in difficult data sets, and support a fungal origin for the Microsporidia.},
}
@article {pmid15926202,
year = {2005},
author = {Sato, S and Wilson, RJ},
title = {Organelle-specific cochaperonins in apicomplexan parasites.},
journal = {Molecular and biochemical parasitology},
volume = {141},
number = {2},
pages = {133-143},
doi = {10.1016/j.molbiopara.2005.01.010},
pmid = {15926202},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/chemistry/*genetics/metabolism ; Chaperonins/*analysis/chemistry/*genetics ; Cloning, Molecular ; DNA, Protozoan/chemistry ; Genes, Protozoan ; Green Fluorescent Proteins/analysis/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; Organelles/*chemistry ; Phylogeny ; Plasmodium falciparum/chemistry/*genetics/ultrastructure ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Protein maturation in eukaryotic organelles requires the type I chaperonin system; this comprises chaperonin 60 (Cpn60) and its cochaperonin. We have re-examined and revised the sequence of the nuclear genes specifying organellar cochaperonins in Plasmodium falciparum (Pf). One gene encodes a typical cochaperonin (PfCpn10) whereas the other (encoding PfCpn20) specifies two Cpn10 domains arranged in tandem as in plant chloroplasts. Transfection experiments using fluorescent reporters showed specific localization of PfCpn10 to the mitochondrion and PfCpn20 to the plastid. As P. falciparum also has two Cpn60s, one of which is targeted specifically to the mitochondrion and the other exclusively to the plastid, each organelle has a distinct type I chaperonin system. Comparative sequence analysis extended these findings to several other apicomplexan parasites that have both a mitochondrion and a plastid. Phylogenetic analysis suggests the Cpn10s and Cpn20s of apicomplexans are independently monophyletic. The apicomplexan Cpn10 is phylogenetically related to other mitochondrial versions but a significant relationship between apicomplexan Cpn20s and other cochaperonins was not established.},
}
@article {pmid15927004,
year = {2005},
author = {Williams, BA and Keeling, PJ},
title = {Microsporidian mitochondrial proteins: expression in Antonospora locustae spores and identification of genes coding for two further proteins.},
journal = {The Journal of eukaryotic microbiology},
volume = {52},
number = {3},
pages = {271-276},
doi = {10.1111/j.1550-7408.2005.05-00036.x},
pmid = {15927004},
issn = {1066-5234},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Blotting, Western ; Gene Expression ; Glycerolphosphate Dehydrogenase/isolation &amp; purification ; Membrane Transport Proteins/genetics ; Microsporidia/chemistry/*genetics ; Mitochondria/*chemistry ; Mitochondrial Proteins/biosynthesis/*genetics ; Monocarboxylic Acid Transporters ; Peptide Hydrolases/genetics ; Phylogeny ; Protozoan Proteins/biosynthesis/*genetics ; Pyruvate Dehydrogenase (Lipoamide)/isolation &amp; purification ; RNA, Messenger/analysis ; RNA, Protozoan/analysis ; Sequence Homology, Amino Acid ; Spores, Protozoan/genetics/*metabolism ; },
abstract = {Microsporidia are obligate intracellular parasites, phylogenetically allied to the fungi. Once considered amitochondriate, now a number of mitochondrion-derived genes have been described from various species, and the relict organelle was recently identified in Trachipleistophora hominis. We have investigated the expression of potential mitochondrial targeted proteins in the spore stage to determine whether the organelle is likely to have a role in the spore or early infection stage. To investigate whether the Antonospora locustae genome codes for a different complement of mitochondrial proteins than Encephalitozoon cuniculi an EST library was searched for putative mitochondrial genes that have not been identified in the E. cuniculi genome project. The spore is the infectious stage of microsporidia, but is generally considered to be metabolically dormant. Fourteen genes for putatively mitochondrion-targeted proteins were shown to be present in purified spore mRNA by 3'-rapid amplification of cDNA ends and EST sequencing. Pyruvate dehydrogenase E1alpha and mitochondrial glycerol-3-phosphate dehydrogenase proteins were also shown to be present in A. locustae and E. cuniculi spores, respectively, suggesting a role for these proteins in the early stages of infection, or within the spore itself. EST sequencing also revealed two mitochondrial protein-encoding genes in A. locustae that are not found in the genome of E. cuniculi. One encodes a possible pyruvate transporter, the other a subunit of the mitochondrial inner membrane peptidase. In yeast mitochondria, this protein is part of a trimeric complex that processes proteins targeted to the inner membrane and the intermembrane space, and its substrate in A. locustae is presently unknown.},
}
@article {pmid15936981,
year = {2005},
author = {Agatsuma, T and Iwagami, M and Uni, S and Takaoka, H and Katsumi, A and Kimura, E and Bain, O},
title = {Molecular phylogenetic relationships among seven Japanese species of Cercopithifilaria.},
journal = {Parasitology international},
volume = {54},
number = {3},
pages = {195-199},
doi = {10.1016/j.parint.2005.04.002},
pmid = {15936981},
issn = {1383-5769},
mesh = {Animals ; Antelopes/*parasitology ; DNA, Helminth/analysis ; DNA, Mitochondrial/analysis ; Deer/*parasitology ; Electron Transport Complex IV/genetics ; Filariasis/parasitology/*veterinary ; Filarioidea/*classification/*genetics/isolation &amp; purification/physiology ; Host-Parasite Interactions ; Japan ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {DNA sequences from a portion of the mitochondrial COI gene were used to clarify phylogenetic relationships among Japanese species in the genus Cercopithifilaria. Sequences were determined from seven Japanese species, five (C. shohoi, C. multicauda, C. minuta, C. tumidicervicata and C. bulboidea) from the serow (Capricornis crispus F. Bovidae) and two (C. longa and C. crassa) from the sika deer (Cervus nippon nippon F. Cervidae). No base substitutions were observed between C. bulboidea and C. longa, suggesting that recent host switching of a lineage of C. bulboidea between bovid and cervid hosts gave rise to C. longa. In phylogenetic trees inferred using a variety of methods, the morphologically ancestral type, C. bulboidea, appeared as a derived species. C. multicauda was found to be basal in the analyses. It seems therefore that C. multicauda is the most primitive out of the seven species.},
}
@article {pmid15967440,
year = {2005},
author = {Krause, K and Kilbienski, I and Mulisch, M and Rödiger, A and Schäfer, A and Krupinska, K},
title = {DNA-binding proteins of the Whirly family in Arabidopsis thaliana are targeted to the organelles.},
journal = {FEBS letters},
volume = {579},
number = {17},
pages = {3707-3712},
doi = {10.1016/j.febslet.2005.05.059},
pmid = {15967440},
issn = {0014-5793},
mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/analysis/classification/*metabolism ; Chloroplasts/chemistry/metabolism ; DNA-Binding Proteins/analysis/classification/*metabolism ; Mitochondria/chemistry/metabolism ; Organelles/chemistry/metabolism ; Phylogeny ; Protein Transport ; },
abstract = {Arabidopsis thaliana contains three genes with high homology to potato p24 which was described as a member of the Whirly family of nuclear transcriptional activators. Computer-based analysis revealed that all Arabidopsis Whirly (Why) proteins contain targeting sequences for either plastids or mitochondria. The functionality of these sequences was demonstrated by in vitro import assays into isolated organelles. Transient expression of GFP fusion proteins in protoplasts and onion epidermal cells confirmed the localisation of these proteins in plastids or mitochondria, respectively. The possession of organellar targeting sequences seems to be conserved among Why proteins of higher plant species, including potato p24.},
}
@article {pmid15967446,
year = {2005},
author = {Tang, WK and Chan, CB and Cheng, CH and Fong, WP},
title = {Seabream antiquitin: molecular cloning, tissue distribution, subcellular localization and functional expression.},
journal = {FEBS letters},
volume = {579},
number = {17},
pages = {3759-3764},
doi = {10.1016/j.febslet.2005.05.070},
pmid = {15967446},
issn = {0014-5793},
mesh = {Aldehyde Dehydrogenase/analysis/*genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Fish Proteins/analysis/*genetics/*metabolism ; Kidney/chemistry/metabolism ; Liver/chemistry/metabolism ; Mitochondria/chemistry ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/biosynthesis/genetics ; Sea Bream/genetics/*metabolism ; Tissue Distribution ; },
abstract = {Subsequent to our earlier report on the first purification of antiquitin protein from seabream liver and demonstration of its enzymatic activity [FEBS Letters 516 (2002) 183-186], we report herein the cloning of its full-length cDNA sequence. The open reading frame encodes a protein of 511 amino acids. Results of RT-PCR indicate that antiquitin is highly expressed in both the seabream liver and kidney. Transfection studies in cultured eukaryotic cells provided further evidence that it is a cytosolic protein. Bacterial expression of the enzyme was also performed. The purified recombinant protein was demonstrated to exhibit similar kinetic properties as the native enzyme.},
}
@article {pmid15979254,
year = {2005},
author = {Margeot, A and Garcia, M and Wang, W and Tetaud, E and di Rago, JP and Jacq, C},
title = {Why are many mRNAs translated to the vicinity of mitochondria: a role in protein complex assembly?.},
journal = {Gene},
volume = {354},
number = {},
pages = {64-71},
doi = {10.1016/j.gene.2005.04.022},
pmid = {15979254},
issn = {0378-1119},
mesh = {3' Untranslated Regions/chemistry/genetics ; Base Sequence ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/genetics/metabolism/*physiology ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polyribosomes/metabolism ; Protein Biosynthesis/*genetics ; Proton-Translocating ATPases/genetics/metabolism ; RNA, Messenger/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Signal Transduction/physiology ; },
abstract = {The longstanding question of the presence of mitochondria-bound polysomes has been recently revisited using new approaches. Genome-wide analyses provided evidence that many genes are actually translated on mitochondria-bound polysomes and GFP-labeling techniques have shown that, in vivo, the 3'UTR sequence of these genes contains signals which can target hybrid RNA molecules to the proximity of mitochondria. Evolutionary conservation of some of these signals will be presented. Interestingly, class I mRNA which are translated on free polysomes and class II mRNA which are translated on mitochondria-bound polysomes have, mostly, eukaryotic and prokaryotic origins respectively. Using ATP2, a typical prokaryotic-derived gene, as a model for class II mRNA, we showed that its 3'UTR sequence is essential both for a correct addressing of mRNA to mitochondria proximity and to a proper production of functional ATP synthases. These different observations suggest that prokaryotic-derived genes are, like the contemporary mitochondrial genes, translated near mitochondrial membranes. In both cases this locus specific translation process might be connected to a correct complex assembly program and the cases of ATP synthase and cytochrome c oxidase complexes will be considered in this respect.},
}
@article {pmid16007699,
year = {2005},
author = {Prado, M and Calo, P and Cepeda, A and Barros-Velázquez, J},
title = {Genetic evidence of an Asian background in heteroplasmic Iberian cattle (Bos taurus): effect on food authentication studies based on polymerase chain reaction-restriction fragment length polymorphism analysis.},
journal = {Electrophoresis},
volume = {26},
number = {15},
pages = {2918-2926},
doi = {10.1002/elps.200500011},
pmid = {16007699},
issn = {0173-0835},
mesh = {Animals ; Base Pair Mismatch ; Base Sequence ; Cattle/*genetics ; Cytochromes b/*genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; Genotype ; Mitochondria/genetics ; Muscle, Skeletal/enzymology ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; Species Specificity ; },
abstract = {This work was aimed at identifying nucleotide polymorphic sites in a 359 bp region of the cytochrome b (cytb) mitochondrial gene of Iberian cattle (Bos taurus). This region is widely used as target in polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) species identification studies in foodstuffs destined for human and animal consumption. Two different coexisting restriction patterns were observed in four of the six animals studied when the 359 bp DNA fragment was cleaved with PalI, HinfI, MvaI, RsaI, or MboI. The amplification of both genotypes with the mitochondrial-specific primers L14735 and H15149 revealed the absence of nuclear pseudo-cytb genes, confirming the existence of mitochondrial heteroplasmy. The two coexisting mtDNA fragments were selectively sequenced in PCR extracts in which one genotype predominated over the other, both exhibiting a sequence variation of 10.4%. From the 37 nucleotide mismatches observed between genotypes, 32 were transitions and five were transversions. While 31 of the nucleotide mismatches between genotypes resulted to be conservative at the amino acid level, six changes implied amino acid substitutions, five of them being located in the variable transmembrane region. Genetic analysis suggests the presence of an Asian background in the mitochondria of Iberian cattle: while one of the genotypes matched the published sequence for Bos taurus, the other genotype clustered with a B. primigenius indicus animal and close to an Asian Bos taurus animal. These results also suggest that a number of current PCR-RFLP species identification methods based on cytb sequences may not be reliable for the accurate detection and identification of bovine material: an alternative battery of enzymes consisting of MmeI, NlaIV, and AluI is proposed.},
}
@article {pmid16011000,
year = {2005},
author = {Smith, EJ and Shi, L and Tu, Z},
title = {Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups.},
journal = {Genetica},
volume = {124},
number = {1},
pages = {23-32},
doi = {10.1007/s10709-004-5184-4},
pmid = {16011000},
issn = {0016-6707},
mesh = {Aggrecans ; Animals ; Birds/*genetics ; Cell Nucleus ; Chickens/*genetics ; *Classification ; Extracellular Matrix Proteins/*genetics ; Lectins, C-Type ; *Phylogeny ; Proteoglycans/*genetics ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGCI) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1% among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39-48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.},
}
@article {pmid16021339,
year = {2005},
author = {Wong, CE and Li, Y and Whitty, BR and Díaz-Camino, C and Akhter, SR and Brandle, JE and Golding, GB and Weretilnyk, EA and Moffatt, BA and Griffith, M},
title = {Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap.},
journal = {Plant molecular biology},
volume = {58},
number = {4},
pages = {561-574},
pmid = {16021339},
issn = {0167-4412},
mesh = {Algorithms ; Arabidopsis/genetics ; Brassicaceae/*genetics ; Cold Temperature ; DNA, Complementary/chemistry/genetics ; Disasters ; *Expressed Sequence Tags ; *Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sodium Chloride/pharmacology ; Water/pharmacology ; },
abstract = {Thellungiella salsuginea (also known as T. halophila) is a close relative of Arabidopsis that is very tolerant of drought, freezing, and salinity and may be an appropriate model to identify the molecular mechanisms underlying abiotic stress tolerance in plants. We produced 6578 ESTs, which represented 3628 unique genes (unigenes), from cDNA libraries of cold-, drought-, and salinity-stressed plants from the Yukon ecotype of Thellungiella. Among the unigenes, 94.1% encoded products that were most similar in amino acid sequence to Arabidopsis and 1.5% had no match with a member of the family Brassicaceae. Unigenes from the cold library were more similar to Arabidopsis sequences than either drought- or salinity-induced sequences, indicating that latter responses may be more divergent between Thellungiella and Arabidopsis. Analysis of gene ontology using the best matched Arabidopsis locus showed that the Thellungiella unigenes represented all biological processes and all cellular components, with the highest number of sequences attributed to the chloroplast and mitochondria. Only 140 of the unigenes were found in all three abiotic stress cDNA libraries. Of these common unigenes, 70% have no known function, which demonstrates that Thellungiella can be a rich resource of genetic information about environmental responses. Some of the ESTs in this collection have low sequence similarity with those in Genbank suggesting that they may encode functions that may contribute to Thellungiella's high degree of stress tolerance when compared with Arabidopsis. Moreover, Thellungiella is a closer relative of agriculturally important Brassica spp. than Arabidopsis, which may prove valuable in transferring information to crop improvement programs.},
}
@article {pmid16040665,
year = {2005},
author = {Yu, F and Park, S and Rodermel, SR},
title = {Functional redundancy of AtFtsH metalloproteases in thylakoid membrane complexes.},
journal = {Plant physiology},
volume = {138},
number = {4},
pages = {1957-1966},
pmid = {16040665},
issn = {0032-0889},
mesh = {Arabidopsis/*enzymology/genetics ; Gene Duplication ; Gene Expression Regulation, Plant ; Metalloproteases/genetics/*metabolism ; Multigene Family ; Mutation ; Oryza/enzymology ; Pisum sativum/enzymology ; Phylogeny ; Plants, Genetically Modified ; Thylakoids/*enzymology ; },
abstract = {FtsH is an ATP-dependent metalloprotease found in bacteria, mitochondria, and plastids. Arabidopsis (Arabidopsis thaliana) contains 12 AtFtsH proteins, three in the mitochondrion and nine in the chloroplast. Four of the chloroplast FtsH proteins are encoded by paired members of closely related genes (AtFtsH1 and 5, and AtFtsH2 and 8). We have previously reported that AtFtsH2 and 8 are interchangeable components of AtFtsH complexes in the thylakoid membrane. In this article, we show that the var1 variegation mutant, which is defective in AtFtsH5, has a coordinate reduction in the AtFtsH2 and 8 pair, and that the levels of both pairs are restored to normal in var1 plants that overexpress AtFtsH1. Overexpression of AtFtsH1, but not AtFtsH2/VAR2, normalizes the pattern of var1 variegation, restoring a nonvariegated phenotype. We conclude that AtFtsH proteins within a pair, but not between pairs, are interchangeable and functionally redundant, at least in part. We further propose that the abundance of each pair is matched with that of the other pair, with excess subunits being turned over. The variegation phenotype of var1 (as well as var2, which is defective in AtFtsH2) suggests that a threshold concentration of subunits is required for normal chloroplast function. AtFtsH1, 2, 5, and 8 do not show evidence of tissue or developmental specific expression. Phylogenetic analyses revealed that rice (Oryza sativa) and Arabidopsis share a conserved core of seven FtsH subunit genes, including the AtFtsH1 and 5 and AtFtsH2 and 8 pairs, and that the structure of the present-day gene families can be explained by duplication events in each species following the monocot/dicot divergence.},
}
@article {pmid16050982,
year = {2005},
author = {Itoi, S and Misaki, R and Hirayama, M and Nakaniwa, M and Liang, CS and Kondo, H and Watabe, S},
title = {Identification of three isoforms for mitochondrial adenine nucleotide translocator in the pufferfish Takifugu rubripes.},
journal = {Mitochondrion},
volume = {5},
number = {3},
pages = {162-172},
doi = {10.1016/j.mito.2005.01.003},
pmid = {16050982},
issn = {1567-7249},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Computational Biology ; Conserved Sequence ; DNA, Complementary ; Genome ; Isoenzymes/*chemistry/*genetics/isolation &amp; purification ; Mitochondria, Heart/enzymology ; Mitochondria, Muscle/enzymology ; Mitochondrial ADP, ATP Translocases/*chemistry/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Takifugu/*genetics ; Tissue Distribution ; Transcription, Genetic ; },
abstract = {Three adenine nucleotide translocator (ANT) genes were identified through in silico data mining of the Fugu genome database along with isolation of their corresponding cDNAs in vivo from the pufferfish (Takifugu rubripes). As a result of phylogenetic analysis, the ANT gene on scaffold_254 corresponded to mammalian ANT1, whereas both of those on scaffold_6 and scaffold_598 to mammalian ANT3. The ANT gene encoded by scaffold_6 was expressed ubiquitously in various tissues, whereas the ANT genes encoded by scaffold_254 and scaffold_598 were predominantly expressed in skeletal muscle and heart, respectively.},
}
@article {pmid16055441,
year = {2005},
author = {Bedhomme, M and Hoffmann, M and McCarthy, EA and Gambonnet, B and Moran, RG and Rébeillé, F and Ravanel, S},
title = {Folate metabolism in plants: an Arabidopsis homolog of the mammalian mitochondrial folate transporter mediates folate import into chloroplasts.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {41},
pages = {34823-34831},
doi = {10.1074/jbc.M506045200},
pmid = {16055441},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/*metabolism ; Arabidopsis Proteins/*chemistry/physiology ; Blotting, Western ; CHO Cells ; Catalysis ; Chlorophyll/chemistry ; Chloroplasts/chemistry/*metabolism ; Cloning, Molecular ; Cricetinae ; DNA, Complementary/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Folic Acid/metabolism ; Genetic Complementation Test ; Glycine/chemistry ; Green Fluorescent Proteins/metabolism ; Immunoblotting ; Membrane Transport Proteins/*chemistry/metabolism/physiology ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Mutation ; Nucleic Acids/chemistry ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Time Factors ; Transfection ; },
abstract = {The distribution of folates in plant cells suggests a complex traffic of the vitamin between the organelles and the cytosol. The Arabidopsis thaliana protein AtFOLT1 encoded by the At5g66380 gene is the closest homolog of the mitochondrial folate transporters (MFTs) characterized in mammalian cells. AtFOLT1 belongs to the mitochondrial carrier family, but GFP-tagging experiments and Western blot analyses indicated that it is targeted to the envelope of chloroplasts. By using the glycine auxotroph Chinese hamster ovary glyB cell line, which lacks a functional MFT and is deficient in folates transport into mitochondria, we showed by complementation that AtFOLT1 functions as a folate transporter in a hamster background. Indeed, stable transfectants bearing the AtFOLT1 cDNA have enhanced levels of folates in mitochondria and can support growth in glycine-free medium. Also, the expression of AtFOLT1 in Escherichia coli allows bacterial cells to uptake exogenous folate. Disruption of the AtFOLT1 gene in Arabidopsis does not lead to phenotypic alterations in folate-sufficient or folate-deficient plants. Also, the atfolt1 null mutant contains wild-type levels of folates in chloroplasts and preserves the enzymatic capacity to catalyze folate-dependent reactions in this subcellular compartment. These findings suggest strongly that, despite many common features shared by chloroplasts and mitochondria from mammals regarding folate metabolism, the folate import mechanisms in these organelles are not equivalent: folate uptake by mammalian mitochondria is mediated by a unique transporter, whereas there are alternative routes for folate import into chloroplasts.},
}
@article {pmid16086405,
year = {2005},
author = {Liana, M and Witaliński, W},
title = {Sperm structure and phylogeny of Astigmata.},
journal = {Journal of morphology},
volume = {265},
number = {3},
pages = {318-324},
doi = {10.1002/jmor.10361},
pmid = {16086405},
issn = {0362-2525},
mesh = {Acari/*anatomy &amp; histology ; Animals ; Male ; Microscopy, Electron ; Models, Biological ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; },
abstract = {The Astigmata, a large and variable group, is still a subject of taxonomic dispute. Particularly, their origin from ancestors of the lower oribatid mites (e.g., Malaconothroidea) seems well documented by many lines of evidence. The structure of spermatozoa has been successfully applied to phylogenetic investigations in many animal groups. The aim of our study was to provide new data on spermatozoon structure in Astigmata and to consider its appropriateness in phylogenetic studies. The study reveals information on spermatozoa in 17 species of Astigmata (11 species studied for the first time) extending our knowledge to 18 species (one species known only from the literature) representing 12 families and 7 superfamilies. Spermatozoa have the same basic structure in all species: cells are multiform and the chromatin forms thin threads embedded directly in the cytoplasm; the acrosome is absent. The cytoplasm in most species contains electron-dense lamellae, varying in both number and arrangement within the cell. In Sarcoptoidea, electron-dense tubules in contact with lamellae margins were also observed in Psoroptidae (Psoroptes equi), whereas in two representatives of Sarcoptidae (Notoedres cati and Sarcoptes scabiei), only electron-dense tubules were found. In two species, Canestrinia sellnicki (Canestrinioidea: Canestriniidae) and Scutulanyssus obscurus (Analgoidea: Pteronyssidae), neither lamellae nor tubules were present. The mitochondria in a spermatozoon are usually gathered at the cell periphery and their structure is usually modified to form so-called mitochondrial derivatives. The chromatin threads are an autapomorphy strongly supporting the monophyly of Astigmata. As spermatozoa vary considerably between species in Astigmata, we deduce that sperm structure may be useful for phylogenetic analyses within the group. Several conclusions concerning the affinities within Astigmata are presented. Spermatology seems to be unhelpful, however, in questions on the origin of Astigmata (particularly for Astigmata-Oribatida relationships), since their sperm do not possess synapomorphies with sperm of the remaining groups of Acariformes, i.e., Endeostigmata, Prostigmata, and Oribatida.},
}
@article {pmid16112882,
year = {2005},
author = {Wiklund, H and Nygren, A and Pleijel, F and Sundberg, P},
title = {Phylogeny of Aphroditiformia (Polychaeta) based on molecular and morphological data.},
journal = {Molecular phylogenetics and evolution},
volume = {37},
number = {2},
pages = {494-502},
doi = {10.1016/j.ympev.2005.07.005},
pmid = {16112882},
issn = {1055-7903},
mesh = {Animals ; Cell Nucleus/genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Polychaeta/*anatomy &amp; histology/*classification/genetics ; RNA, Ribosomal, 18S/*genetics ; },
abstract = {The phylogeny of Aphroditiformia, benthic polychaetes carrying dorsal elytra, is assessed from nuclear 18S rDNA, mitochondrial cytochrome c oxidase subunit I (COI), and 31 morphological characters. Two non-elytrabearing taxa, Palmyra and Pisione, are included to assess their relationship to the elytrabearers. The data are analysed both separately and combined, with parsimony, maximum likelihood and Bayesian analyses. In total, 19 terminal taxa are examined, including 12 elytrabearing taxa from all scale-worm groups, Palmyra, Pisione, and five outgroup taxa. The results show that Palmyra and Pisione are nested within Aphroditiformia. Palmyra is sister to Aphrodita, and both Pisione and Pholoe are positioned within Sigalionidae, suggesting that both family names Pisionidae and Pholoidae should be treated as junior synonyms of Sigalionidae.},
}
@article {pmid16151221,
year = {2005},
author = {van der Giezen, M and León-Avila, G and Tovar, J},
title = {Characterization of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica.},
journal = {Microbiology (Reading, England)},
volume = {151},
number = {Pt 9},
pages = {3107-3115},
doi = {10.1099/mic.0.28068-0},
pmid = {16151221},
issn = {1350-0872},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Chaperonin 10/chemistry/genetics/*metabolism ; DNA, Protozoan/analysis ; Entamoeba histolytica/genetics/*metabolism ; Heat-Shock Response ; Humans ; Intestines/*parasitology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Entamoeba histolytica is the causative agent of amoebiasis, a poverty-related disease that kills an estimated 100 000 people each year. E. histolytica does not contain "standard mitochondria", but harbours mitochondrial remnant organelles called mitosomes. These organelles are characterized by the presence of mitochondrial chaperonin Cpn60, but little else is known about the functions and molecular composition of mitosomes. In this study, a gene encoding molecular chaperonin Cpn10--the functional partner of Cpn60--was cloned, and its structure and expression were characterized, as well as the cellular localization of its encoded protein. The 5' untranslated region of the gene contains all of the structural promoter elements required for transcription in this organism. The amoebic Cpn10, like Cpn60, is not significantly upregulated upon heat-shock treatment. Computer-assisted protein modelling, and specific antibodies against Cpn10 and Cpn60, suggest that both proteins interact with each other, and that they function in the same intracellular compartment. Thus, E. histolytica appears to have retained at least two of the key molecular components required for the refolding of imported mitosomal proteins.},
}
@article {pmid16162288,
year = {2005},
author = {Liang, P and Nair, JR and Song, L and McGuire, JJ and Dolnick, BJ},
title = {Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.},
journal = {BMC genomics},
volume = {6},
number = {},
pages = {125},
pmid = {16162288},
issn = {1471-2164},
support = {CA101515/CA/NCI NIH HHS/United States ; EB002116/EB/NIBIB NIH HHS/United States ; P30 CA016056/CA/NCI NIH HHS/United States ; CA16056/CA/NCI NIH HHS/United States ; R01 EB002116/EB/NIBIB NIH HHS/United States ; R03 CA101515/CA/NCI NIH HHS/United States ; CA43500/CA/NCI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cell Line ; Codon ; Computational Biology/*methods ; Genome ; Genomics/*methods ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms ; Protein Structure, Tertiary ; Subcellular Fractions ; Thymidylate Synthase/*genetics/metabolism ; },
abstract = {BACKGROUND: The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSalpha and rTSbeta. The rTSbeta isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown.<br><br>RESULTS: Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSbeta. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSgamma, which is absent in rTSbeta. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSgamma and rTSbeta proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events.<br><br>CONCLUSION: The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.},
}
@article {pmid16183216,
year = {2005},
author = {Dávila, S and Piñero, D and Bustos, P and Cevallos, MA and Dávila, G},
title = {The mitochondrial genome sequence of the scorpion Centruroides limpidus (Karsch 1879) (Chelicerata; Arachnida).},
journal = {Gene},
volume = {360},
number = {2},
pages = {92-102},
doi = {10.1016/j.gene.2005.06.008},
pmid = {16183216},
issn = {0378-1119},
mesh = {Animals ; Arachnida/*genetics ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Genome ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics/metabolism ; },
abstract = {The mitochondrial genome of the scorpion Centruroides limpidus (Chelicerata; Arachnida) has been completely sequenced and is 14519 bp long. The genome contains 13 protein-encoding genes, two ribosomal RNA genes, 21 transfer RNA genes and a large non-coding region related to the control region. The overall A+T composition is the lowest among the complete mitochondrial sequences published within the Chelicerata subphylum. Gene order and gene content differ slightly from that of Limulus polyphemus (Chelicerata: Xiphosura): i.e., the lack of the trnD gene, and the translocation-inversion of the trnI gene. Preliminary phylogenetic analysis of some Chelicerata shows that scorpions (C. limpidus and Mesobuthus gibbosus) make a tight cluster with the spiders (Arachnida; Araneae). Our analysis does not support that Scorpiones order is the sister group to all Arachnida Class, since it is closer to Araneae than to Acari orders.},
}
@article {pmid16187796,
year = {2005},
author = {Salas, A and Yao, YG and Macaulay, V and Vega, A and Carracedo, A and Bandelt, HJ},
title = {A critical reassessment of the role of mitochondria in tumorigenesis.},
journal = {PLoS medicine},
volume = {2},
number = {11},
pages = {e296},
pmid = {16187796},
issn = {1549-1676},
mesh = {Artifacts ; Biomarkers, Tumor/*genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics/metabolism ; Databases, Nucleic Acid ; Diagnostic Errors ; Genetics, Medical ; Haplotypes ; Humans ; Mutation/genetics ; Neoplasms/diagnosis/*genetics/metabolism ; Phylogeny ; Reproducibility of Results ; Research Design ; },
abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results.<br><br>METHODS AND FINDINGS: In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis.<br><br>CONCLUSION: The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.},
}
@article {pmid16188880,
year = {2005},
author = {Chen, W and Li, N and Chen, T and Han, Y and Li, C and Wang, Y and He, W and Zhang, L and Wan, T and Cao, X},
title = {The lysosome-associated apoptosis-inducing protein containing the pleckstrin homology (PH) and FYVE domains (LAPF), representative of a novel family of PH and FYVE domain-containing proteins, induces caspase-independent apoptosis via the lysosomal-mitochondrial pathway.},
journal = {The Journal of biological chemistry},
volume = {280},
number = {49},
pages = {40985-40995},
doi = {10.1074/jbc.M502190200},
pmid = {16188880},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*physiology ; Apoptosis Regulatory Proteins ; Blotting, Northern ; Caspases/*metabolism ; Cathepsin D/metabolism ; Cathepsin L ; Cathepsins/metabolism ; Cell Line, Tumor ; Cell Membrane Permeability ; Cloning, Molecular ; Cysteine Endopeptidases/metabolism ; DNA, Complementary/genetics ; Fibrosarcoma ; Gene Expression ; Humans ; Lysosomes/*metabolism ; Mice ; Microscopy, Electron ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Proteins/*chemistry/genetics/*physiology ; RNA, Messenger/antagonists &amp; inhibitors ; RNA, Small Interfering/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Transfection ; Tumor Necrosis Factor-alpha/pharmacology ; },
abstract = {Lysosomes have recently been identified as important apoptotic signal integrators in response to various stimuli. Here we report the functional characterization of LAPF, a novel lysosome-associated apoptosis-inducing protein containing PH and FYVE domains. LAPF is a representative of a new protein family, the Phafins (protein containing both PH and FYVE domains), which consists of 14 unidentified proteins from various species. Overexpression of LAPF in L929 cells induces apoptosis and also increases cell sensitivity to TNFalpha-induced apoptosis, concomitant with its translocation to lysosomes. Two mutants of LAPF, either lacking the PH or FYVE domain, failed to induce cell death and translocate to lysosomes, suggesting that both domains are required for its apoptosis-inducing activity and relocation. We demonstrate that LAPF may induce apoptosis via the following steps: LAPF translocation to lysosomes, lysosomal membrane permeabilization (LMP), release of cathepsin (cath) D and L, mitochondrial membrane permeabilization (MMP), release of apoptosis-inducing factor (AIF), and caspase-independent apoptosis. The cath D-specific inhibitor attenuates LAPF-induced apoptosis, indicating a pivotal role of lysosomes in LAPF-initiated apoptosis. We also demonstrate that the lysosomal pathway was employed in the typical apoptotic model in which high dose TNFalpha was used to stimulate L929 cells. Silencing of LAPF expression by small RNA interference protected L929 cells from hTNFalpha-induced apoptosis by impairing hTNFalpha-triggered LMP and MMP. Therefore, LAPF may launch caspase-independent apoptosis through the lysosomal-mitochondrial pathway.},
}
@article {pmid16197560,
year = {2005},
author = {Monti, MM and Nappo, AG and Giorgini, M},
title = {Molecular characterization of closely related species in the parasitic genus Encarsia (Hymenoptera: Aphelinidae) based on the mitochondrial cytochrome oxidase subunit I gene.},
journal = {Bulletin of entomological research},
volume = {95},
number = {5},
pages = {401-408},
doi = {10.1079/ber2005371},
pmid = {16197560},
issn = {0007-4853},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Hymenoptera/*classification/*genetics ; Mitochondria/*enzymology/*genetics ; Parasites/classification/genetics ; Phylogeny ; Protein Subunits ; },
abstract = {The genus Encarsia Förster includes parasitoid species that are effective natural enemies of whitefly and armoured scale insect agricultural pests. Within this genus, several species groups have been recognized on the basis of morphological similarity, although their monophyly appears uncertain. It is often difficult to separate morphologically similar species, and there is evidence that some species could in fact be complexes of cryptic species. Their correct identification is fundamental for biological control purposes. Recently, due to unreliability of morphological characters, molecular techniques have been investigated to identify markers that differentiate closely related species. In this study, DNA variation in an approximately 900 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene was examined by both sequencing and PCR-RFLP. Two pairs of species that are difficult to distinguish morphologically were analysed: Encarsia formosa Gahan and Encarsialuteola Howard, belonging to the luteola group, and two populations of Encarsiasophia (Girault &amp; Dodd) from Pakistan and Spain, belonging to the strenua group, recently characterized as cryptic species. High sequence divergence and species-specific restriction patterns clearly differentiate both species pairs. Parsimony analysis of the nucleotide sequences was also performed, including Encarsiahispida De Santis (luteola group) and Encarsia protransvena Viggiani (strenua group). Two monophyletic clades supporting the two groups of species considered were resolved. The results of this study support the use of the COI gene as a useful marker in separating species of Encarsia, for which morphological differences are subtle. Moreover, the COI gene appears potentially useful for understanding phylogenetic relationships in this genus.},
}
@article {pmid16207980,
year = {2005},
author = {Biswas, SK and Wang, L and Yokoyama, K and Nishimura, K},
title = {Molecular phylogenetics of the genus trichosporon inferred from mitochondrial cytochrome B gene sequences.},
journal = {Journal of clinical microbiology},
volume = {43},
number = {10},
pages = {5171-5178},
pmid = {16207980},
issn = {0095-1137},
mesh = {Amino Acid Sequence ; Cytochromes b/chemistry/*genetics ; DNA, Fungal/analysis ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mycological Typing Techniques ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Trichosporon/*classification/*genetics ; },
abstract = {Mitochondrial cytochrome b (cyt b) genes of 42 strains representing 23 species of the genus Trichosporon were partially sequenced to determine their molecular phylogenetic relationships. Almost half of the 22 strains investigated (from 11 different species) contained introns in their sequences. Analysis of a 396-bp coding sequence from each strain of Trichosporon under investigation showed a total of 141 (35.6%) variable nucleotide sites. A phylogenetic tree based on the cyt b gene sequences revealed that all species of Trichosporon except Trichosporon domesticum and Trichosporon montevideense had species-specific cyt b genes. Trichosporon sp. strain CBS 5581 was identified as Trichosporon pullulans, and one clinical isolate, IFM 48794, was identified as Trichosporon faecale. Analysis of 132-bp deduced amino acid sequences showed a total of 34 (25.75%) variable amino acid sites. T. domesticum and T. montevideense, Trichosporon asahii and Trichosporon asteroides, and Trichosporon gracile and Trichosporon guehoae had identical amino acid sequences. A phylogenetic tree constructed with the ascomycetes Saccharomyces douglasii and Candida glabrata taken as outgroup species and including representative species from closely related genera species of Trichosporon clustered with other basidiomycetous yeasts that contain xylose in their cell wall compositions. These results indicate the effectiveness of mitochondrial cyt b gene sequences for both species identification and the phylogenetic analysis of Trichosporon species.},
}
@article {pmid16247555,
year = {2005},
author = {Urantowka, A and Knorpp, C and Olczak, T and Kolodziejczak, M and Janska, H},
title = {Plant mitochondria contain at least two i-AAA-like complexes.},
journal = {Plant molecular biology},
volume = {59},
number = {2},
pages = {239-252},
pmid = {16247555},
issn = {0167-4412},
mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology ; Arabidopsis Proteins/chemistry/genetics/metabolism ; DNA, Bacterial/genetics ; Intracellular Membranes/metabolism ; Metalloproteases/*chemistry/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/chemistry/genetics/metabolism ; Mutagenesis, Insertional/genetics ; Mutation ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {The FtsH proteases, also called AAA proteases, are membrane-bound ATP-dependent metalloproteases. The Arabidopsis genome contains a total of 12 FtsH-like genes. Two of them, AtFtsH4 and AtFtsH11, encode proteins with a high similarity to Yme1p, a subunit of the i-AAA complex in yeast mitochondria. Phylogenetic analysis groups the AtFtsH4, AtFtsH11 and Yme1 proteins together, with AtFtsH4 being the most similar to Yme1. Using immunological method we demonstrate here that AtFtsH4 is an exclusively mitochondrial protein while AtFtsH11 is found in both chloroplasts and mitochondria. AtFtsH4 and AtFtsH11 proteases are integral parts of the inner mitochondrial membrane and expose their catalytic sites towards the intermembrane space, same as yeast i-AAA. Database searches revealed that orthologs of AtFtsH4 and AtFtsH11 are present in both monocotyledonous and dicotyledonous plants. The two plant i-AAA proteases differ significantly in their termini: the FtsH4 proteins have a characteristic alanine stretch at the C-terminal end while FtsH11s have long N-terminal extensions. Blue-native gel electrophoresis revealed that AtFtsH4 and AtFtsH11 form at least two complexes with apparent molecular masses of about 1500 kDa. This finding implies that plants, in contrast to fungi and metazoa, have more than one complex with a topology similar to that of yeast i-AAA.},
}
@article {pmid16252476,
year = {2005},
author = {Putignani, L},
title = {The unusual architecture and predicted function of the mitochondrion organelle in Cryptosporidium parvum and hominis species: the strong paradigm of the structure-function relationship.},
journal = {Parassitologia},
volume = {47},
number = {2},
pages = {217-225},
pmid = {16252476},
issn = {0048-2951},
mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Chaperonins/genetics ; Cryptophyta/ultrastructure ; Cryptosporidium/genetics/growth &amp; development/physiology/*ultrastructure ; Cryptosporidium parvum/genetics/growth &amp; development/physiology/*ultrastructure ; DNA, Mitochondrial/analysis ; DNA, Protozoan/analysis ; Eimeria tenella/ultrastructure ; Genomics ; Humans ; Mitochondria/*physiology/*ultrastructure ; Mitochondrial Membranes/ultrastructure ; Mitochondrial Proteins ; Models, Biological ; Oxidative Phosphorylation ; Oxidoreductases/genetics ; Phylogeny ; Plant Proteins ; Proteomics ; Protozoan Proteins/analysis/genetics ; Species Specificity ; Structure-Activity Relationship ; Superoxide Dismutase/genetics ; Toxoplasma/ultrastructure ; Alternative Oxidase ; },
abstract = {Cryptosporidium spp. is a protozoan parasite that causes widespread diarrhoeal disease in humans and other animals and is responsible for large waterborne outbreaks of cryptosporidiosis. Unlike many organisms belonging to the phylum Apicomplexa, such as Plasmodium spp. and Toxoplasma gondii, there is no clinically proven drug treatment against this parasite. Some aspects of the basic biology of Cryptosporidium spp. such as the understanding of key metabolic pathways or the full description of the organellar compartment are still lacking. Here I present evidence of the anomalous shape and substructure of the mitochondrion organelle in C. parvum and C. hominis, which is closer to the Guillardia theta nucleomorph structure rather than to the canonical mitochondrion of the proximate apicomplexan T gondii. The atypical architecture is accomplished by an altered organellar metabolone, inferred by in silico conceptual prediction and characterized by unusual, partial and/or reduced pathways. However, phylogeneticanalyses of the mitochondrion and mitochondrion-related loci hsp60, hsp70 (dnaK), alternative oxidase (AOX) and superoxide dismutase (SOD) in C. parvum show diversiform evolutionary pathways, suggesting a "chimera" derived organelle. Taken together these data depict peculiar and intriguing aspects of the C. parvum and C. hominis anomalous mitochondrion framework for further comparative analysis of the organelle within the Cryptosporidium spp. order.},
}
@article {pmid16269741,
year = {2005},
author = {Zhang, H and Lin, S},
title = {Development of a cob-18S rRNA gene real-time PCR assay for quantifying Pfiesteria shumwayae in the natural environment.},
journal = {Applied and environmental microbiology},
volume = {71},
number = {11},
pages = {7053-7063},
pmid = {16269741},
issn = {0099-2240},
mesh = {Animals ; Base Sequence ; Boston ; Chile ; Cytochromes b/*genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal/analysis ; Dinoflagellida/genetics/*isolation &amp; purification ; Genes, rRNA ; Maine ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 18S/*genetics ; Rivers/*parasitology ; Seawater/*parasitology ; },
abstract = {Despite the fact that the heterotrophic dinoflagellate Pfiesteria shumwayae is an organism of high interest due to alleged toxicity, its abundance in natural environments is poorly understood. To address this inadequacy, a real-time quantitative PCR assay based on mitochondrial cytochrome b (cob) and 18S rRNA gene was developed and P. shumwayae abundance was investigated in several geographic locations. First, cob and its 5'-end region were isolated from a P. shumwayae culture, revealing three different copies, each consisting of an identical cob coding region and an unidentified region (X) of variable length and sequence. The unique sequences in cob and the X region were then used to develop a P. shumwayae-specific primer set. This primer set was used with reported P. shumwayae-specific 18S primers in parallel real-time PCRs to investigate P. shumwayae abundance from Maine to North Carolina along the U.S. east coast and along coasts in Chile, Hawaii, and China. Both genes generally gave similar results, indicating that this species was present, but at low abundance (mostly <10 cells x ml(-1)), in all the American coast locations investigated (with the exception of Long Island Sound, where which both genes gave negative results). Genetic variation was detected by use of both genes in most of the locations, and while cob consistently detected P. shumwayae or close genetic variants, some of the 18S PCR products were unrelated to P. shumwayae. We conclude that (i) the real-time PCR assay developed is useful for specific quantification of P. shumwayae, and (ii) P. shumwayae is distributed widely at the American coasts, but normally only as a minor component of plankton even in high-risk estuaries (Neuse River and the Chesapeake Bay).},
}
@article {pmid16283554,
year = {2005},
author = {Nogueira, FT and Borecký, J and Vercesi, AE and Arruda, P},
title = {Genomic structure and regulation of mitochondrial uncoupling protein genes in mammals and plants.},
journal = {Bioscience reports},
volume = {25},
number = {3-4},
pages = {209-226},
doi = {10.1007/s10540-005-2886-5},
pmid = {16283554},
issn = {0144-8463},
mesh = {Animals ; Carrier Proteins/classification/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Membrane Proteins/classification/*genetics/metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Proteins/classification/*genetics/metabolism ; Protein Isoforms/classification/genetics/metabolism ; Transcription, Genetic ; },
abstract = {Uncoupling mitochondrial proteins (UCPs) belong to a discrete family within the mitochondrial anion carrier superfamily. Several uncoupling protein types have been found in mitochondria from mammals and plants, as well as in fishes, fungi, and protozoa. Mammalian UCPs and plant uncoupling proteins (PUMPs) form five distinct subfamilies. Only subfamily III contains both plant and animal uncoupling proteins, as well as UCPs from primitive eukaryotic organisms, which suggest that this group may represent an ancestral cluster from which other UCPs/PUMPs may have evolved. Genetic data indicate that UCPs/PUMPs are regulated at the transcriptional, post-transcriptional, and translational levels. Tissue/organ- and stress-specific gene expression suggests that UCPs/PUMPs are involved in the general balance of basic energy expenditure, protection against reactive oxygen species, and thermogenesis. Finally, the simultaneous occurrence of PUMP and alternative oxidase, another energy-dissipating system in plant mitochondria, raises the question of their response to biotic and abiotic stress at the transcriptional and functional levels.},
}
@article {pmid16283555,
year = {2005},
author = {Mozo, J and Emre, Y and Bouillaud, F and Ricquier, D and Criscuolo, F},
title = {Thermoregulation: what role for UCPs in mammals and birds?.},
journal = {Bioscience reports},
volume = {25},
number = {3-4},
pages = {227-249},
doi = {10.1007/s10540-005-2887-4},
pmid = {16283555},
issn = {0144-8463},
mesh = {Acclimatization ; Adipose Tissue, Brown/metabolism ; Animals ; Birds/*physiology ; Body Temperature Regulation/*physiology ; Carrier Proteins/chemistry/classification/genetics/*metabolism ; Cold Temperature ; Energy Metabolism/physiology ; Hormones/metabolism ; Humans ; Ion Channels ; Mammals/*physiology ; Membrane Proteins/chemistry/classification/genetics/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins ; Obesity/genetics/metabolism ; Phylogeny ; Protein Isoforms/chemistry/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; Uncoupling Protein 1 ; },
abstract = {Mammals and birds are endotherms and respond to cold exposure by the means of regulatory thermogenesis, either shivering or non-shivering. In this latter case, waste of cell energy as heat can be achieved by uncoupling of mitochondrial respiration. Uncoupling proteins, which belong to the mitochondrial carrier family, are able to transport protons and thus may assume a thermogenic function. The mammalian UCP1 physiological function is now well understood and gives to the brown adipose tissue the capacity for heat generation. But is it really the case for its more recently discovered isoforms UCP2 and UCP3? Additionally, whereas more and more evidence suggests that non-shivering also exists in birds, is the avian UCP also involved in response to cold exposure? In this review, we consider the latest advances in the field of UCP biology and present putative functions for UCP1 homologues.},
}
@article {pmid16286090,
year = {2005},
author = {Salducci, MD and Marty, C and Fouquet, A and Gilles, A},
title = {Phylogenetic relationships and biodiversity in Hylids (Anura: Hylidae) from French Guiana.},
journal = {Comptes rendus biologies},
volume = {328},
number = {10-11},
pages = {1009-1024},
doi = {10.1016/j.crvi.2005.07.005},
pmid = {16286090},
issn = {1631-0691},
mesh = {Animals ; Anura/classification/*physiology ; Biomarkers ; Cell Nucleus/genetics ; DNA/genetics ; DNA Primers ; DNA, Recombinant/genetics ; Databases, Genetic ; French Guiana ; Mitochondria/metabolism ; Monophenol Monooxygenase/genetics ; Phylogeny ; RNA/genetics ; RNA, Ribosomal, 18S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {We evaluated two biodiversity criteria, higher taxonomic diversity and phylogenetic diversity in French Guiana. For this, we used a recent assessment of the knowledge accumulated since 30 years of study on the amphibian species currently known in French Guiana. We focused on two well-represented genera, Hyla and Scinax, belonging to the subfamily Hylinae. We used partial sequences of two mitochondrial genes (16S rDNA and 12S rDNA, 813 bp) and two nuclear genes (tyrosinase and 18S rRNA, 1590 bp) covering a total of 2403 bp. According to the high bootstrap support in phylogenetic analysis of the complete dataset, the genus Scinax is a homophyletic clade formed by two species groups (rubra and rostrata) in French Guiana. The genus Hyla was confirmed to be a paraphyletic group formed by two species groups as well (30 chromosomes and the 'gladiator frogs'). We confirmed that these genera should be taxonomically reconsidered. Moreover, at the genus, subfamily and family levels, the use of only morphological characters or only molecular DNA markers would hamper estimations of biodiversity. Thus, we strongly advise the combined use of both morphology and molecular data (nuclear and mitochondrial markers).},
}
@article {pmid16306143,
year = {2005},
author = {van Lis, R and Atteia, A and Nogaj, LA and Beale, SI},
title = {Subcellular localization and light-regulated expression of protoporphyrinogen IX oxidase and ferrochelatase in Chlamydomonas reinhardtii.},
journal = {Plant physiology},
volume = {139},
number = {4},
pages = {1946-1958},
pmid = {16306143},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*enzymology/genetics/radiation effects ; DNA, Algal/genetics ; DNA, Complementary/genetics ; DNA, Protozoan/genetics ; Escherichia coli/genetics ; Ferrochelatase/genetics/*metabolism ; Gene Dosage ; Gene Expression Regulation, Enzymologic/radiation effects ; Genes, Protozoan ; Light ; Molecular Sequence Data ; Phylogeny ; Protoporphyrinogen Oxidase/genetics/*metabolism ; RNA, Algal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; },
abstract = {Protoporphyrinogen IX oxidase (PPO) catalyzes the last common step in chlorophyll and heme synthesis, and ferrochelatase (FeC) catalyzes the last step of the heme synthesis pathway. In plants, each of these two enzymes is encoded by two or more genes, and the enzymes have been reported to be located in the chloroplasts or in the mitochondria. We report that in the green alga Chlamydomonas reinhardtii, PPO and FeC are each encoded by a single gene. Phylogenetic analysis indicates that C. reinhardtii PPO and FeC are most closely related to plant counterparts that are located only in chloroplasts. Immunoblotting results suggest that C. reinhardtii PPO and FeC are targeted exclusively to the chloroplast, where they are associated with membranes. These results indicate that cellular needs for heme in this photosynthetic eukaryote can be met by heme that is synthesized in the chloroplast. It is proposed that the multiplicity of genes for PPO and FeC in higher plants could be related to differential expression in differently developing tissues rather than to targeting of different gene products to different organelles. The FeC content is higher in C. reinhardtii cells growing in continuous light than in cells growing in the dark, whereas the content of PPO does not significantly differ in light- and dark-grown cells. In cells synchronized to a light/dark cycle, the level of neither enzyme varied significantly with the phase of the cycle. These results indicate that heme synthesis is not directly regulated by the levels of PPO and FeC in C. reinhardtii.},
}
@article {pmid16307849,
year = {2006},
author = {Gissi, C and San Mauro, D and Pesole, G and Zardoya, R},
title = {Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters.},
journal = {Gene},
volume = {366},
number = {2},
pages = {228-237},
doi = {10.1016/j.gene.2005.07.034},
pmid = {16307849},
issn = {0378-1119},
mesh = {Amphibian Proteins/*genetics ; Animals ; Anura/*genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Analysis, Protein/methods ; },
abstract = {We explore whether phylogenetic analyses of the same sequence data set at the amino acid and nucleotide level are able to recover congruent topologies, as well as the advantages and limitations of both alternative approaches. As a case study, mitochondrial protein-coding genes were used to discern among competing hypotheses on the phylogenetic relationships of major anuran amphibian lineages. To properly address this phylogenetic question, the complete nucleotide sequences of the mitochondrial genomes of two archaeobatrachian species, Ascaphus truei and Pelobates cultripes, were determined anew. Bayesian and maximum likelihood phylogenetic inferences of the same sequence data set were performed based on both amino acid and nucleotide characters, with the latter analysed either as codons or as a reduced data set of first+second (P12) codon positions. In addition, likelihood-based ratio tests were performed to evaluate the support of alternative topologies. The different data sets arrived at congruent and highly supported topologies, suggesting a similar phylogenetic resolving power of the two character types provided that correctly selected sites and appropriate evolutionary models are used. The reconstructed anuran mitochondrial phylogeny supports the paraphyly of Archaeobatrachia, with Ascaphus as sister group to all the remaining anurans, and Pelobates as sister group of Neobatrachia. However, the employed tree reconstruction methods and likelihood-based ratio tests seemed to be negatively affected by the fast evolving sequences of neobatrachians, suggesting that the phylogeny of Anura here presented is not definitive, and needs further investigation using an extended taxon sampling.},
}
@article {pmid16313445,
year = {2005},
author = {Visvesvara, GS and De Jonckheere, JF and Marciano-Cabral, F and Schuster, FL},
title = {Morphologic and molecular identification of Naegleria dunnebackei n. sp. isolated from a water sample.},
journal = {The Journal of eukaryotic microbiology},
volume = {52},
number = {6},
pages = {523-531},
doi = {10.1111/j.1550-7408.2005.00061.x},
pmid = {16313445},
issn = {1066-5234},
mesh = {Animal Husbandry ; Animals ; Cattle ; DNA, Ribosomal Spacer/*analysis ; Fresh Water/*parasitology ; Mice ; Microscopy, Electron ; Molecular Sequence Data ; Naegleria/*classification/isolation &amp; purification/*ultrastructure/virology ; Phylogeny ; RNA, Ribosomal, 5.8S/*genetics ; Sequence Analysis, DNA ; *Water Supply ; },
abstract = {Naegleria dunnebackei n. sp., a new species of the free-living amoeboflagellate Naegleria, is described in this report. The organism was isolated from a water sample taken from drinking troughs associated with cases of primary amoebic meningoencephalitis in cattle at a ranch in southern California. The isolate grew at, but not above 37 degrees C, and did not kill young mice upon intranasal inoculation suggesting that it was not pathogenic. The new species combines morphological features of non-pathogenic Naegleria gruberi and pathogenic Naegleria fowleri. The trophic amoeba resembled other members of the genus, with a prominent vesicular nucleus and mitochondria with discoidal cristae; a Golgi apparatus was not observed by electron microscopy. The cyst stage had pores in the wall typical of those seen in pathogenic N. fowleri. Upon suspension in distilled water, amoebae transformed into temporary, non-feeding flagellates, mostly with two anterior flagella but occasionally with four. The rationale for its description as a new species was based upon sequencing of the 5.8S rDNA and internal transcribed spacers of the amoeba, which is similar to but not identical to that of Naegleria gallica, differing from that organism's DNA by six base pairs. Virus-like elements were found in the cytoplasm of trophic amoebae, often in association with crystalloids, and may be the cause of lysis of amoebae in culture.},
}
@article {pmid16313565,
year = {2005},
author = {van Opijnen, T and Baudry, E and Baldo, L and Bartos, J and Werren, JH},
title = {Genetic variability in the three genomes of Nasonia: nuclear, mitochondrial and Wolbachia.},
journal = {Insect molecular biology},
volume = {14},
number = {6},
pages = {653-663},
doi = {10.1111/j.1365-2583.2005.00595.x},
pmid = {16313565},
issn = {0962-1075},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genome, Bacterial ; *Genome, Insect ; Phylogeny ; Wasps/cytology/*genetics/microbiology ; Wolbachia/*genetics ; },
abstract = {Nasonia consists of three closely related species of parasitoid wasps that are all infected with the endosymbiotic bacteria Wolbachia, a reproductive parasite common in arthropods. This situation presents the opportunity to compare patterns of variation in three associated genomes, Wolbachia and the nuclear and mitochondrial genomes of its host. Furthermore, although Nasonia wasps are emerging as a model for evolutionary and genetic studies, little is known about their genetic variability. Using amplified fragment length polymorphisms (AFLPs), all three species present a relatively high level of nuclear polymorphism and have different patterns of variation, with one of the species, Nasonia giraulti, being divided into two divergent subgroups. In each species, the mitochondrial pattern of variation is different from the nuclear pattern, possibly due to genetic hitchhiking of the mitochondria during (cytoplasmically inherited) Wolbachia sweeps. Mitochondria in Nasonia show a synonymous substitution rate approximately 10-15-fold higher than nuclear genes, probably reflecting an elevated mitochondrial mutation rate that is among the highest found in insects. Finally, all three species are doubly infected with their own strains of Wolbachia, one each from the two major supergroups (A and B). Sequence analysis reveals that each of the three Nasonia species acquired their A and B bacteria independently by horizontal transfer events from other insects with the exception of B type Wolbachia in N. longicornis and N. giraulti, which were acquired prior to speciation and then codiverged with the host. This represents one of the few clear-cut examples of codivergence of Wolbachia during host speciation.},
}
@article {pmid16316982,
year = {2006},
author = {Kulikowicz, T and Shapiro, TA},
title = {Distinct genes encode type II Topoisomerases for the nucleus and mitochondrion in the protozoan parasite Trypanosoma brucei.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {6},
pages = {3048-3056},
doi = {10.1074/jbc.M505977200},
pmid = {16316982},
issn = {0021-9258},
support = {AI28855/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Blotting, Northern ; Blotting, Southern ; Blotting, Western ; Cell Nucleus/*enzymology/metabolism ; Crithidia/metabolism ; DNA Topoisomerases, Type II/*genetics ; DNA, Kinetoplast/genetics ; Escherichia coli/metabolism ; Flow Cytometry ; *Gene Expression Regulation, Enzymologic ; Immunoblotting ; Leishmania/metabolism ; Mitochondria/*enzymology ; Models, Genetic ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plasmids/metabolism ; RNA Interference ; RNA, Messenger/metabolism ; Transfection ; Trypanosoma brucei brucei/*enzymology ; },
abstract = {Topoisomerases are essential for orderly nucleic acid metabolism and cell survival and are proven targets for clinically useful antimicrobial and anticancer drugs. Interest in the topologically intricate mitochondrial DNA (kinetoplast or kDNA) of Trypanosoma brucei brucei and related kinetoplastid protozoan parasites has led to many reports of type II topoisomerases that participate in kDNA metabolism (we term the T. brucei brucei gene TbTOP2mt). We have now identified and characterized two new genes for type II topoisomerases in T. brucei brucei, termed TbTOP2alpha and TbTOP2beta. Phylogenetically, they share a common node with other nuclear topoisomerases, clearly distinct from a clade that includes the previously reported kinetoplastid genes, all of which are homologs of TbTOP2mt. Southern blot analysis reveals the new genes are single copy and positioned approximately 1.7 kb apart. Cognate mRNAs are expressed in African trypanosomes, but only a single message is detected in Leishmania or Crithidia. TbTOP2alpha encodes an ATP-dependent topoisomerase that appears as a single approximately 170-kDa band on immunoblots and localizes to the nucleus; RNA interference leads to pleomorphic nuclear (but not kDNA) abnormalities and early growth arrest. The role of TbTOP2beta is unclear. Although transcribed in trypanosomes, TbTOP2beta is not detected by beta-specific antiserum, and RNAi silencing results in no obvious phenotype. These studies indicate that African trypanosomes and related kinetoplastid human pathogens are unusual in having independent topoisomerase II genes to service their nuclear and mitochondrial genomes, and they highlight TbTOP2alpha as a promising target for the development of much-needed new therapies.},
}
@article {pmid16321390,
year = {2006},
author = {Aranda, A and Maugeri, D and Uttaro, AD and Opperdoes, F and Cazzulo, JJ and Nowicki, C},
title = {The malate dehydrogenase isoforms from Trypanosoma brucei: subcellular localization and differential expression in bloodstream and procyclic forms.},
journal = {International journal for parasitology},
volume = {36},
number = {3},
pages = {295-307},
doi = {10.1016/j.ijpara.2005.09.013},
pmid = {16321390},
issn = {0020-7519},
mesh = {Amino Acid Sequence ; Animals ; Chromatography, Agarose/methods ; Cross Reactions/immunology ; Cytosol/enzymology ; Gene Expression Regulation, Developmental/genetics ; Genes, Protozoan/genetics ; Isoenzymes/analysis/immunology ; Malate Dehydrogenase/*analysis/genetics/immunology ; Microbodies/enzymology/genetics/immunology ; Mitochondria/enzymology/genetics/immunology ; Oxaloacetic Acid/metabolism ; Phenylpyruvic Acids/metabolism ; Phylogeny ; Protozoan Proteins/metabolism ; Rabbits ; Recombinant Proteins/metabolism ; Sequence Alignment/methods ; Trypanosoma brucei brucei/*enzymology/immunology ; },
abstract = {Trypanosoma brucei procyclic forms possess three different malate dehydrogenase isozymes that could be separated by hydrophobic interaction chromatography and were recognized as the mitochondrial, glycosomal and cytosolic malate dehydrogenase isozymes. The latter is the only malate dehydrogenase expressed in the bloodstream forms, thus confirming that the expression of malate dehydrogenase isozymes is regulated during the T. brucei life cycle. To achieve further biochemical characterization, the genes encoding mitochondrial and glycosomal malate dehydrogenase were cloned on the basis of previously reported nucleotide sequences and the recombinant enzymes were functionally expressed in Escherichia coli cultures. Mitochondrial malate dehydrogenase showed to be more active than glycosomal malate dehydrogenase in the reduction of oxaloacetate; nearly 80% of the total activity in procyclic crude extracts corresponds to the former isozyme which also catalyzes, although less efficiently, the reduction of p-hydroxyphenyl-pyruvate. The rabbit antisera raised against each of the recombinant isozymes showed that the three malate dehydrogenases do not cross-react immunologically. Immunofluorescence experiments using these antisera confirmed the glycosomal and mitochondrial localization of glycosomal and mitochondrial malate dehydrogenase, as well as a cytosolic localization for the third malate dehydrogenase isozyme. These results clearly distinguish Trypanosoma brucei from Trypanosoma cruzi, since in the latter parasite a cytosolic malate dehydrogenase is not present and mitochondrial malate dehydrogenase specifically reduces oxaloacetate.},
}
@article {pmid16380372,
year = {2006},
author = {Guo, K and Lukacik, P and Papagrigoriou, E and Meier, M and Lee, WH and Adamski, J and Oppermann, U},
title = {Characterization of human DHRS6, an orphan short chain dehydrogenase/reductase enzyme: a novel, cytosolic type 2 R-beta-hydroxybutyrate dehydrogenase.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {15},
pages = {10291-10297},
doi = {10.1074/jbc.M511346200},
pmid = {16380372},
issn = {0021-9258},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Arginine/chemistry ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Cytosol/*enzymology/metabolism ; Dose-Response Relationship, Drug ; Exons ; Green Fluorescent Proteins/metabolism ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Hydroxybutyrate Dehydrogenase/*chemistry/genetics ; Kinetics ; Lipids/chemistry ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases/*chemistry ; Phylogeny ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; Sulfates/chemistry ; },
abstract = {Human DHRS6 is a previously uncharacterized member of the short chain dehydrogenases/reductase family and displays significant homologies to bacterial hydroxybutyrate dehydrogenases. Substrate screening reveals sole NAD(+)-dependent conversion of (R)-hydroxybutyrate to acetoacetate with K(m) values of about 10 mm, consistent with plasma levels of circulating ketone bodies in situations of starvation or ketoacidosis. The structure of human DHRS6 was determined at a resolution of 1.8 A in complex with NAD(H) and reveals a tetrameric organization with a short chain dehydrogenases/reductase-typical folding pattern. A highly conserved triad of Arg residues ("triple R" motif consisting of Arg(144), Arg(188), and Arg(205)) was found to bind a sulfate molecule at the active site. Docking analysis of R-beta-hydroxybutyrate into the active site reveals an experimentally consistent model of substrate carboxylate binding and catalytically competent orientation. GFP reporter gene analysis reveals a cytosolic localization upon transfection into mammalian cells. These data establish DHRS6 as a novel, cytosolic type 2 (R)-hydroxybutyrate dehydrogenase, distinct from its well characterized mitochondrial type 1 counterpart. The properties determined for DHRS6 suggest a possible physiological role in cytosolic ketone body utilization, either as a secondary system for energy supply in starvation or to generate precursors for lipid and sterol synthesis.},
}
@article {pmid16382169,
year = {2005},
author = {Marotta, R and Melone, G and Bright, M and Ferraguti, M},
title = {Spermatozoa and sperm aggregates in the vestimentiferan Lamellibrachia luymesi compared with those of Riftia pachyptila (Polychaeta: Siboglinidae: Vestimentifera).},
journal = {The Biological bulletin},
volume = {209},
number = {3},
pages = {215-226},
doi = {10.2307/3593111},
pmid = {16382169},
issn = {0006-3185},
mesh = {Acrosome/ultrastructure ; Anatomy, Comparative ; Animals ; Annelida/*ultrastructure ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/ultrastructure ; Phylogeny ; Spermatozoa/ultrastructure ; },
abstract = {The spermatozoa and the sperm bundles of the vestimentiferans Riftia pachyptila and Lamellibrachia luymesi (Annelida: Siboglinidae) were studied using several microscopical techniques (transmission and scanning electron microscopy, and confocal microscopy) and compared with some other annelid sperm. The spermatozoa and sperm bundles of both species show a similar structure, but they differ in the dimensions of the components of individual cells and in the number of spermatozoa forming each sperm bundle. The spermatozoa of R. pachyptila and L. luymesi are filiform cells composed, in sequence, by an acrosome in the form of a thread-like helical vesicle, an elongated coiled nucleus surrounded by two helical mitochondria, and a long flagellum. In the spermatozoa of both species, the apical portion of the nucleus is completely devoid of chromatin and is delimited by a thickened nuclear envelope with a fibrillar appearance. Both species have sperm bundles that resemble buds, having a calyx-like portion formed by the helical heads, and a stalk-like portion formed by the tightly packed flagella. A parsimony analysis based on spermatozoal characters showed monophyly of the Siboglinidae and the Vestimentifera. We propose a new set of autapomorphies characterizing vestimentiferan spermatozoa. Our analysis suggests that spermatozoal characters are useful to the understanding of the phylogeny of the group.},
}
@article {pmid16388691,
year = {2006},
author = {Paramá, A and Arranz, JA and Alvarez, MF and Sanmartín, ML and Leiro, J},
title = {Ultrastructure and phylogeny of Philasterides dicentrarchi (Ciliophora, Scuticociliatia) from farmed turbot in NW Spain.},
journal = {Parasitology},
volume = {132},
number = {Pt 4},
pages = {555-564},
doi = {10.1017/S0031182005009534},
pmid = {16388691},
issn = {0031-1820},
mesh = {Animals ; Ciliophora Infections/parasitology/*veterinary ; DNA Primers/chemistry ; DNA, Protozoan/chemistry ; DNA, Ribosomal/genetics ; Fish Diseases/*parasitology ; Fisheries ; Flatfishes/*parasitology ; Microscopy, Electron, Transmission/veterinary ; Molecular Sequence Data ; Oligohymenophorea/*classification/*ultrastructure ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; },
abstract = {Several species of opportunistic histophagous scuticociliates have been implicated in systemic infections of farmed fish. In turbot, scuticociliatosis is an emerging disease, and the identification of the parasite species involved is controversial. We have previously isolated Philasterides dicentrarchi from farmed turbot scuticociliatosis outbreaks in northwest Spain. In the present study, we report detailed ultrastructural studies of this parasite, and investigate phylogenetic relations with other members of the order Philasterida on the basis of sequence comparison of the small-subunit rRNA (SSUrRNA) gene. Ultrastructural study indicates the presence of dikinetids in the anterior two-thirds of the body; micronucleus closely associated with the macronucleus, though not physically connected; numerous mitochondria located below the cell cortex, parallel to the surface; numerous spherical and fusiform extrusomes located close to the plasma membrane. We consider that these characteristics are useful for diagnosis of infections by this parasite. A nested 350-bp nucleotide sequence of the SSUrRNA gene of the turbot P. dicentrachi isolate showed high identity with previously reported SSUrRNA gene sequences from 2 scuticociliates isolated from olive flounder Paralichthys olivaceus in Korea, namely P. dicentrarchi (98%) and Miamiensis avidus (99%); conversely, our P. dicentrarchi sequence showed low identity (86%) with that of Uronema marinum, a scuticociliate that has also been implicated in scuticociliatosis outbreaks in turbot in Europe and olive flounder in Asia. Phylogenetic tree construction on the basis of the SSUrRNA gene sequences, using the neighbour-joining method, confirm that the different P. dicentrarchi isolates and M. avidus are closely related and a possible synonymy between both ciliates species should be considered.},
}
@article {pmid16395585,
year = {2006},
author = {Dorion, S and Matton, DP and Rivoal, J},
title = {Characterization of a cytosolic nucleoside diphosphate kinase associated with cell division and growth in potato.},
journal = {Planta},
volume = {224},
number = {1},
pages = {108-124},
pmid = {16395585},
issn = {0032-0935},
mesh = {Amino Acid Sequence ; Cell Division/genetics ; Cell Enlargement ; Cells, Cultured ; DNA, Complementary/analysis ; Escherichia coli/genetics ; Kinetics ; Meristem/enzymology/growth &amp; development ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/genetics/metabolism/*physiology ; Plant Roots/cytology/enzymology/growth &amp; development ; Plant Shoots/cytology/enzymology/growth &amp; development ; Protein Isoforms/genetics/metabolism/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Solanum tuberosum/cytology/*enzymology/growth &amp; development ; Uridine Triphosphate/metabolism ; },
abstract = {A cDNA encoding Solanum chacoense cytosolic NDPK (NDPK1, EC 2.7.4.6) was isolated. The open reading frame encoded a 148 amino acid protein that shares homology with other cytosolic NDPKs including a conserved N-terminal domain. S. chacoense NDPK1 was expressed in Escherichia coli as a 6xHis-tagged protein and purified by affinity chromatography. The recombinant protein exhibited a pattern of abortive complex formation suggesting that the enzyme is strongly regulated by the NTP/NDP ratio. A polyclonal antibody generated against recombinant NDPK1 was specific for the cytosolic isoform in Solanum tuberosum as shown from immunoprecipitation experiments and immunoblot analysis of chloroplasts and mitochondria preparations. NDPK activity and NDPK1 protein were found at different levels in various vegetative and reproductive tissues. DEAE fractogel analyses of NDPK activity in root tips, leaves, tubers and cell cultures suggest that NDPK1 constitutes the bulk of extractable NDPK activity in all these organs. NDPK activity and NDPK1 protein levels raised during the exponential growth phase of potato cell cultures whereas no rise in activity or NDPK1 protein was observed when sucrose concentration in the culture was manipulated to limit growth. Activity measurements, immunoblot analysis as well as immunolocalization experiments performed on potato root tips and shoot apical buds demonstrated that NDPK1 was predominantly localized in the meristematic zones and provascular tissues of the apical regions. These data suggest that NDPK1 plays a specific role in the supply of UTP during early growth of plant meristematic and provascular tissues.},
}
@article {pmid16410965,
year = {2005},
author = {Giordano, R and Cortez, JC and Paulk, S and Stevens, L},
title = {Genetic diversity of Triatoma infestans (Hemiptera: Reduviidae) in Chuquisaca, Bolivia based on the mitochondrial cytochrome b gene.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {100},
number = {7},
pages = {753-760},
doi = {10.1590/s0074-02762005000700014},
pmid = {16410965},
issn = {0074-0276},
mesh = {Animals ; Bolivia ; Cytochromes b/analysis/*genetics ; DNA, Protozoan/genetics ; *Genetic Variation ; Haplotypes/*genetics ; Mitochondria/*chemistry ; Phylogeny ; Sequence Analysis, DNA ; Triatoma/chemistry/*genetics ; },
abstract = {Partial cytochrome b DNA sequences for 62 Triatoma infestans were analyzed to determine the degree of genetic variation present in populations of this insect in the northwest region of Chuquisaca, Bolivia. A total of seven haplotypes were detected in the localities sampled. The phylogenetic relationship and population genetic structure of the haplotypes found in this region, indicate that there is greater variation in this relatively small region of Bolivia than what has been previously reported by studies using the same gene fragment, for more distant geographic areas of this country. In addition, a comparison of rural and peri-urban localities, indicate that there is no difference in the genetic variation of T. infestans between these two environments.},
}
@article {pmid16436509,
year = {2006},
author = {Li, W and Sun, L and Liang, Q and Wang, J and Mo, W and Zhou, B},
title = {Yeast AMID homologue Ndi1p displays respiration-restricted apoptotic activity and is involved in chronological aging.},
journal = {Molecular biology of the cell},
volume = {17},
number = {4},
pages = {1802-1811},
pmid = {16436509},
issn = {1059-1524},
mesh = {*Apoptosis ; Electron Transport ; Electron Transport Complex I ; Gene Deletion ; Mitochondria/*metabolism ; NADH Dehydrogenase/classification/genetics/*metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Saccharomyces cerevisiae/enzymology/*growth &amp; development/ultrastructure ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; Superoxide Dismutase/genetics ; Time Factors ; Transcriptional Activation ; Superoxide Dismutase 2 ; },
abstract = {Apoptosis-inducing factor (AIF) and AIF-homologous mitochondrion-associated inducer of death (AMID) are both mitochondrial flavoproteins that trigger caspase-independent apoptosis. Phylogenetic analysis suggests that these two proteins evolutionarily diverge back from their common prokaryote ancestor. Compared with AIF, the proapoptotic nature of AMID and its mode of action are much less clarified. Here, we show that overexpression of yeast AMID homologue internal NADH dehydrogenase (NDI1), but not external NADH dehydrogenase (NDE1), can cause apoptosis-like cell death, and this effect can be repressed by increased respiration on glucose-limited media. This result indicates that the regulatory network of energy metabolism, in particular the cross-talk between mitochondria and the rest of the cell, is involved in Ndi1p-induced yeast cell apoptosis. The apoptotic effect of NDI1 overexpression is associated with increased production of reactive oxygen species (ROS) in mitochondria. In addition, NDI1 overexpression in sod2 background causes cell lethality in both fermentable and semifermentable media. Interruption of certain components in the electron transport chain can suppress the growth inhibition from Ndi1p overexpression. We finally show that disruption of NDI1 or NDE1 decreases ROS production and elongates the chronological life span of yeast, accompanied by the loss of survival fitness. Implication of these findings for Ndi1p-induced apoptosis is discussed.},
}
@article {pmid16452484,
year = {2006},
author = {Atteia, A and van Lis, R and Gelius-Dietrich, G and Adrait, A and Garin, J and Joyard, J and Rolland, N and Martin, W},
title = {Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {15},
pages = {9909-9918},
doi = {10.1074/jbc.M507862200},
pmid = {16452484},
issn = {0021-9258},
mesh = {Acetylesterase/metabolism ; Acetyltransferases/*physiology ; Adenosine Triphosphate/*chemistry ; Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*metabolism ; Chloroplasts/metabolism ; DNA, Complementary/metabolism ; Expressed Sequence Tags ; Gene Library ; Immunoblotting ; Mass Spectrometry ; Mitochondria/*metabolism ; Models, Biological ; Models, Chemical ; Molecular Sequence Data ; Peptides/chemistry ; Phylogeny ; Proteomics/methods ; Pyruvate Dehydrogenase Complex/chemistry ; Pyruvate Synthase/metabolism ; RNA/chemistry/metabolism ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Pyruvate formate-lyase (PFL) catalyzes the non-oxidative conversion of pyruvate to formate and acetyl-CoA. PFL and its activating enzyme (PFL-AE) are common among strict anaerobic and microaerophilic prokaryotes but are very rare among eukaryotes. In a proteome survey of isolated Chlamydomonas reinhardtii mitochondria, we found several PFL-specific peptides leading to the identification of cDNAs for PFL and PFL-AE, establishing the existence of a PFL system in this photosynthetic algae. Anaerobiosis and darkness led to increased PFL transcripts but had little effect on protein levels, as determined with antiserum raised against C. reinhardtii PFL. Protein blots revealed the occurrence of PFL in both chloroplast and mitochondria purified from aerobically grown cells. Mass spectrometry sequencing of C. reinhardtii mitochondrial proteins, furthermore, identified peptides for phosphotransacetylase and acetate kinase. The phosphotransacetylase-acetate kinase pathway is a common route of ATP synthesis or acetate assimilation among prokaryotes but is novel among eukaryotes. In addition to PFL and pyruvate dehydrogenase, the algae also expresses pyruvate:ferredoxin oxidoreductase and bifunctional aldehyde/alcohol dehydrogenase. Among eukaryotes, the oxygen producer C. reinhardtii has the broadest repertoire of pyruvate-, ethanol-, and acetate-metabolizing enzymes described to date, many of which were previously viewed as specific to anaerobic eukaryotic lineages.},
}
@article {pmid16464263,
year = {2006},
author = {Parham, JF and Feldman, CR and Boore, JL},
title = {The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA.},
journal = {BMC evolutionary biology},
volume = {6},
number = {},
pages = {11},
pmid = {16464263},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; DNA/chemistry ; DNA, Mitochondrial/*chemistry ; Gene Order ; *Genes, Mitochondrial ; Genome ; Genomics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Turtles/anatomy &amp; histology/*classification/genetics ; },
abstract = {BACKGROUND: The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.<br><br>RESULTS: We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.<br><br>CONCLUSION: Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.},
}
@article {pmid16467478,
year = {2006},
author = {Batista, WL and Matsuo, AL and Ganiko, L and Barros, TF and Veiga, TR and Freymüller, E and Puccia, R},
title = {The PbMDJ1 gene belongs to a conserved MDJ1/LON locus in thermodimorphic pathogenic fungi and encodes a heat shock protein that localizes to both the mitochondria and cell wall of Paracoccidioides brasiliensis.},
journal = {Eukaryotic cell},
volume = {5},
number = {2},
pages = {379-390},
pmid = {16467478},
issn = {1535-9778},
mesh = {Cell Wall/*metabolism/ultrastructure ; *Conserved Sequence ; Flow Cytometry ; Genome, Fungal ; HSP40 Heat-Shock Proteins/chemistry/*genetics/*metabolism ; Humans ; Introns/genetics ; Mitochondria/*metabolism/ultrastructure ; Paracoccidioides/*cytology/*genetics/metabolism/pathogenicity ; Paracoccidioidomycosis ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins ; },
abstract = {J-domain (DnaJ) proteins, of the Hsp40 family, are essential cofactors of their cognate Hsp70 chaperones, besides acting as independent chaperones. In the present study, we have demonstrated the presence of Mdj1, a mitochondrial DnaJ member, not only in the mitochondria, where it is apparently sorted, but also in the cell wall of Paracoccidioides brasiliensis, a thermodimorphic pathogenic fungus. The molecule (PbMdj1) was localized to fungal yeast cells using both confocal and electron microscopy and also flow cytometry. The anti-recombinant PbMdj1 antibodies used in the reactions specifically recognized a single 55-kDa mitochondrial and cell wall (alkaline beta-mercaptoethanol extract) component, compatible with the predicted size of the protein devoid of its matrix peptide-targeting signal. Labeling was abundant throughout the cell wall and especially in the budding regions; however, anti-PbMdj1 did not affect fungal growth in the concentrations tested in vitro, possibly due to the poor access of the antibodies to their target in growing cells. Labeled mitochondria stood preferentially close to the plasma membrane, and gold particles were detected in the thin space between them, toward the cell surface. We show that Mdj1 and the mitochondrial proteinase Lon homologues are heat shock proteins in P. brasiliensis and that their gene organizations are conserved among thermodimorphic fungi and Aspergillus, where the genes are adjacent and have a common 5' region. This is the first time a DnaJ member has been observed on the cell surface, where its function is speculative.},
}
@article {pmid16473895,
year = {2006},
author = {Borecky, J and Nogueira, FT and de Oliveira, KA and Maia, IG and Vercesi, AE and Arruda, P},
title = {The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots.},
journal = {Journal of experimental botany},
volume = {57},
number = {4},
pages = {849-864},
doi = {10.1093/jxb/erj070},
pmid = {16473895},
issn = {0022-0957},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Cold Temperature ; Computational Biology ; Gene Expression Profiling ; Genome, Plant ; Ion Channels ; Membrane Proteins/*genetics/metabolism ; Mitochondria/enzymology/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Multigene Family/*genetics/physiology ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharum/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Uncoupling Protein 1 ; Alternative Oxidase ; },
abstract = {The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved.},
}
@article {pmid16502095,
year = {2006},
author = {de Moraes-Barros, N and Silva, JA and Miyaki, CY and Morgante, JS},
title = {Comparative phylogeography of the Atlantic forest endemic sloth (Bradypus torquatus) and the widespread three-toed sloth (Bradypus variegatus) (Bradypodidae, Xenarthra).},
journal = {Genetica},
volume = {126},
number = {1-2},
pages = {189-198},
doi = {10.1007/s10709-005-1448-x},
pmid = {16502095},
issn = {0016-6707},
mesh = {Animals ; Brazil ; DNA, Mitochondrial ; Genetic Variation ; Geography ; Locus Control Region/genetics ; Mitochondria/genetics ; *Phylogeny ; Sloths/*genetics ; },
abstract = {The comparative phylogeographic study of the maned sloth (Bradypus torquatus) and the three-toed sloth (Bradypus variegatus) was performed using a segment of mitochondrial DNA (mtDNA) control region. We examined 19 B. torquatus from two regions and 47 B. variegatus from three distant regions of Atlantic forest. This first characterization of molecular diversity indicates a great diversity (B. torquatus: h = 0.901 +/- 0.039 and pi = 0.012 +/- 0.007; B. variegatus: h = 0.699 +/- 0.039 and pi = 0.010 +/- 0.006) and very divergent mitochondrial lineages within each sloth species. The different sampled regions carry distinct and non-overlapping sets of mtDNA haplotypes and are genetically divergent. This phylogeographic pattern may be characteristic of sloth species. In addition, we infer that two main phylogeographic groups exist in the Atlantic forest representing a north and south distinct divergence.},
}
@article {pmid16511496,
year = {2006},
author = {Shaw, GC and Cope, JJ and Li, L and Corson, K and Hersey, C and Ackermann, GE and Gwynn, B and Lambert, AJ and Wingert, RA and Traver, D and Trede, NS and Barut, BA and Zhou, Y and Minet, E and Donovan, A and Brownlie, A and Balzan, R and Weiss, MJ and Peters, LL and Kaplan, J and Zon, LI and Paw, BH},
title = {Mitoferrin is essential for erythroid iron assimilation.},
journal = {Nature},
volume = {440},
number = {7080},
pages = {96-100},
doi = {10.1038/nature04512},
pmid = {16511496},
issn = {1476-4687},
support = {P01 HL032262/HL/NHLBI NIH HHS/United States ; R01 DK070838/DK/NIDDK NIH HHS/United States ; R01 HL075714/HL/NHLBI NIH HHS/United States ; },
mesh = {Anemia/blood/metabolism ; Animals ; Cation Transport Proteins/genetics/metabolism ; Cell Differentiation ; Conserved Sequence ; Erythroblasts/cytology/*metabolism/pathology ; Gene Expression Regulation ; Genetic Complementation Test ; Heme/metabolism ; Homeostasis ; Humans ; Iron/*metabolism ; Iron Overload ; Iron-Sulfur Proteins/biosynthesis/genetics ; Membrane Transport Proteins/genetics/*metabolism ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Stem Cells/cytology/metabolism ; Zebrafish/genetics/metabolism ; Zebrafish Proteins/genetics/*metabolism ; },
abstract = {Iron has a fundamental role in many metabolic processes, including electron transport, deoxyribonucleotide synthesis, oxygen transport and many essential redox reactions involving haemoproteins and Fe-S cluster proteins. Defective iron homeostasis results in either iron deficiency or iron overload. Precise regulation of iron transport in mitochondria is essential for haem biosynthesis, haemoglobin production and Fe-S cluster protein assembly during red cell development. Here we describe a zebrafish mutant, frascati (frs), that shows profound hypochromic anaemia and erythroid maturation arrest owing to defects in mitochondrial iron uptake. Through positional cloning, we show that the gene mutated in the frs mutant is a member of the vertebrate mitochondrial solute carrier family (SLC25) that we call mitoferrin (mfrn). mfrn is highly expressed in fetal and adult haematopoietic tissues of zebrafish and mouse. Erythroblasts generated from murine embryonic stem cells null for Mfrn (also known as Slc25a37) show maturation arrest with severely impaired incorporation of 55Fe into haem. Disruption of the yeast mfrn orthologues, MRS3 and MRS4, causes defects in iron metabolism and mitochondrial Fe-S cluster biogenesis. Murine Mfrn rescues the defects in frs zebrafish, and zebrafish mfrn complements the yeast mutant, indicating that the function of the gene may be highly conserved. Our data show that mfrn functions as the principal mitochondrial iron importer essential for haem biosynthesis in vertebrate erythroblasts.},
}
@article {pmid16515731,
year = {2006},
author = {Höglund, J and Morrison, DA and Mattsson, JG and Engström, A},
title = {Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques.},
journal = {Parasitology},
volume = {133},
number = {Pt 1},
pages = {89-99},
doi = {10.1017/S0031182006009991},
pmid = {16515731},
issn = {0031-1820},
mesh = {Animals ; Base Sequence ; Cattle ; Cattle Diseases/*parasitology ; DNA, Helminth/*chemistry ; DNA, Mitochondrial/*chemistry ; Dictyocaulus/classification/*genetics ; Dictyocaulus Infections/*parasitology ; Genes, Helminth ; Genetic Markers ; Genetics, Population ; Genotype ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Sweden ; },
abstract = {Mitochondrial DNA (mtDNA) sequence data and amplified fragment length polymorphism (AFLP) patterns were compared for the lungworm Dictyocaulus viviparus, a nematode parasite of cattle. Eight individual D. viviparus samples from each of 8 herds in Sweden and 1 laboratory isolate were analysed, with the aim of describing the diversity and genetic structure in populations using different genetic markers on exactly the same DNA samples. There was qualitative agreement between the whole-genome AFLP data and the mtDNA sequence data, both indicating relatively strong genetic differentiation among the Swedish farms. However, the AFLP data detected much more genetic variation than did the mtDNA data, even after allowing for the different inheritance patterns of the markers, and indicated that there was much less differentiation among the populations. The mtDNA data therefore seemed to be more informative about the most recent history of the parasite populations, as the general patterns were less obscured by detailed inter-relationships among individual worms. The 4 mtDNA genes sequenced (1542 bp) showed consistent patterns, although there was more genetic variation in the protein-coding genes than in the structural RNA genes. Furthermore, there appeared to be at least 3 distinct genetic groups of D. viviparus infecting Swedish cattle, 1 of which was predominant and showed considerable differentiation between farms, but not necessarily within farms. Second, the 2 smaller genetic groups occurred on farms where the predominant group also occurred, suggesting that these farms have had multiple introductions of D. viviparus.},
}
@article {pmid16515848,
year = {2006},
author = {Dacks, JB and Dyal, PL and Embley, TM and van der Giezen, M},
title = {Hydrogenosomal succinyl-CoA synthetase from the rumen-dwelling fungus Neocallimastix patriciarum; an energy-producing enzyme of mitochondrial origin.},
journal = {Gene},
volume = {373},
number = {},
pages = {75-82},
doi = {10.1016/j.gene.2006.01.012},
pmid = {16515848},
issn = {0378-1119},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Mitochondria/*enzymology ; Models, Biological ; Molecular Sequence Data ; Neocallimastix/*enzymology/genetics ; Organelles/*enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; Succinate-CoA Ligases/*genetics ; },
abstract = {Hydrogenosomes are hydrogen-producing organelles that are related to mitochondria and found in a variety of evolutionarily unrelated anaerobic microbial eukaryotes. Similar to classic mitochondria, hydrogenosomes contain the enzyme catalyzing the only reaction of the citric acid cycle directly producing energy; succinyl-CoA synthetase. We have isolated and characterized the genes encoding both subunits of this enzyme from the anaerobic chytrid fungus Neocallimastix patriciarum, a model organism in hydrogenosome research. Both subunits contain all characteristic features of this enzyme, including predicted hydrogenosomal targeting signals. Phylogenetic analyses of succinyl-CoA synthetase clearly indicate its mitochondrial ancestry, both by affiliation with mitochondrially localized fungal homologues and by the sisterhood of the eukaryotic succinyl-CoA synthetase clade with alpha-proteobacteria. Our analyses of the Trichomonas vaginalis SCS sequences also confirmed the mitochondrial affiliation of these hydrogenosomal enzymes, in contrast to previous results. While both hydrogenosomal and mitochondrial succinyl-CoA synthetase homologues have been identified, no succinyl-CoA synthetase proteins were identifiable in taxa possessing another mitochondrially derived organelle, the mitosome. Our analyses further confirm the mitochondrial ancestry of the Neocallimastix hydrogenosome and sheds light upon the stepwise process by which mitochondria evolve into alternate forms of the organelle.},
}
@article {pmid16539155,
year = {2005},
author = {Otranto, D and Traversa, D and Milillo, P and De Luca, F and Stevens, J},
title = {Utility of mitochondrial and ribosomal genes for differentiation and phylogenesis of species of gastrointestinal bot flies.},
journal = {Journal of economic entomology},
volume = {98},
number = {6},
pages = {2235-2245},
doi = {10.1093/jee/98.6.2235},
pmid = {16539155},
issn = {0022-0493},
mesh = {Animals ; Base Sequence ; DNA/chemistry/*genetics ; Diptera/classification/*genetics ; *Genetic Variation ; Larva/genetics ; Mitochondria/*genetics ; Phylogeny ; Ribosomes/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Larvae of Gasterophilus spp. (Diptera: Oestridae) cause gastrointestinal myiasis of equids. However, their identification may be problematic due to morphological similarities between species infesting identical regions of the digestive tract. In this study, genes encoding for mitochondrial cytochrome oxidase I (COI) and for the 16S and 28S ribosomal subunits of the most commonly encountered Gasterophilinae subfamily species [i.e., Gasterophilus haemorrhoidalis (L.), Gasterophilus inermis (Brauer), Gasterophilus intestinalis (De Geer), Gasterophilus nasalis (L.), and Gasterophilus pecorum (F.)] were studied, together with Gyrostigma pavesii (Corti), a rhinoceros parasite, and Hypoderma lineatum (De Villers), as outgroup taxa. Analysis identified interspecific differences that allowed their unequivocal identification. The high genetic homology among the sequences of G. haemorrhoidalis and G. intestinalis (i.e., 100, 99.86, and 99.46% in the 28S, COI, and 16S genes, respectively) strongly support the hypothesis that they are morphotypes of the same species. Phylogenetic analyses (maximum-likelihood and parsimony) were performed using PAUP; all analyses supported monophyly of subfamily Gasterophilinae. This study confirms the utility of the COI and 16S and 28S rRNA genes to address diagnostic and phylogenetic questions in Gasterophilus species.},
}
@article {pmid16563428,
year = {2006},
author = {Azevedo, C and Balseiro, P and Casal, G and Gestal, C and Aranguren, R and Stokes, NA and Carnegie, RB and Novoa, B and Burreson, EM and Figueras, A},
title = {Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata.},
journal = {Journal of invertebrate pathology},
volume = {92},
number = {1},
pages = {23-32},
doi = {10.1016/j.jip.2006.02.002},
pmid = {16563428},
issn = {0022-2011},
mesh = {Animals ; Base Sequence ; Haplosporida/*genetics/*ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Mollusca/*parasitology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Spores, Protozoan/ultrastructure ; },
abstract = {A new member of the parasitic phylum Haplosporidia, which was found infecting the connective tissue, gill, digestive gland, and foot muscle of Haliotis tuberculata imported from Ireland and experimentally grown in Galicia (NW Spain), is described. Scanning electron microscopy, transmission electron microscopy, and molecular characterization of the small subunit ribosomal RNA (SSU rRNA) gene were carried out to confirm the description of this species. The ultrastructural morphology of the spores and their surrounding ornaments attached to the spore wall was described from light, scanning, and transmission electron microscopy observations. Systemic infection with uninucleated and multinucleated plasmodia containing spherical nuclei was observed among several sporocysts containing the different spore maturation stages. The spores were spherical to slightly ellipsoidal (2.42 +/- 0.5 x 2.31 +/- 0.6 microm). The apical zone of the spore wall was modified into a complex opercular system covering a circular orifice that measured about 0.5 microm in diameter. The operculum was connected to the spore wall by a hinge. The spore wall was about 110 nm thick, with 4 filaments (20-28 microm long). The filaments were composed of the same material that formed the wall. The cross-sections through the base of these filaments showed T-like and X-like sections. Internally, the uninucleated endosporoplasm contained typical haplosporidian structures, such as, haplosporosomes, a spherulosome, and mitochondria with vesicular cristae. The SSU rRNA gene sequence was different from previously reported haplosporidian SSU rRNA gene sequences, corroborating morphological data that this was an undescribed species. Based on differences from previously described haplosporidians in ultrastructural characteristics of the spore and SSU rRNA gene sequence, we describe the abalone haplosporidian as Haplosporidium montforti n. sp.},
}
@article {pmid16581267,
year = {2006},
author = {Yaakub, SM and Bellwood, DR and Herwerden, Lv and Walsh, FM},
title = {Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae).},
journal = {Molecular phylogenetics and evolution},
volume = {40},
number = {1},
pages = {84-100},
doi = {10.1016/j.ympev.2006.02.012},
pmid = {16581267},
issn = {1055-7903},
mesh = {Animals ; Anthozoa ; Asia ; Australia ; Cytochromes/genetics ; Ecology ; Female ; Fishes/*classification/*genetics ; *Hybridization, Genetic ; Inbreeding ; Introns/*genetics ; Male ; Mitochondria/genetics ; Oxidoreductases/genetics ; Phylogeny ; Ribosomes/genetics ; },
abstract = {Hybrids in coral reef fishes have traditionally been described based on external features using meristic characters and colouration to identify putative parental contributors. This study utilised molecular genetic techniques to verify hybrid status and identify putative parental species for five hybrid specimens (Labridae: Thalassoma) collected from Holmes Reef in the Coral Sea. Phylogenetic analyses support hybrid origins of the specimens. Mitochondrial COI gene, nuclear S7 (intron 1) and nuclear copy of mitochondrial (NUMT) D-loop region corroborate the identity of T. quinquevittatum as the maternal and T. jansenii as the paternal contributor. Backcrossing to parental species by hybrids and bi-directional gene exchange between the Holmes Reef populations of T. jansenii and T. quinquevittatum was detected, suggesting that hybrids are fertile and able to reproduce successfully. F(1) hybrids display a mixture of the colouration attributes of the two parental species, but subsequent backcrossed individuals were unrecognisable as hybrids and displayed colouration of either parental species. A large numerical imbalance exists between the putative parental species at Holmes Reef, with T. quinquevittatum outnumbering T. jansenii by approximately 25:1. In this case study, hybridization appears to be driven by ecological rather than evolutionary factors.},
}
@article {pmid16603388,
year = {2006},
author = {Domingues, VS and Santos, RS and Brito, A and Almada, VC},
title = {Historical population dynamics and demography of the Eastern Atlantic pomacentrid Chromis limbata (Valenciennes, 1833).},
journal = {Molecular phylogenetics and evolution},
volume = {40},
number = {1},
pages = {139-147},
doi = {10.1016/j.ympev.2006.02.009},
pmid = {16603388},
issn = {1055-7903},
mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; Geography ; History, Ancient ; Ice Cover ; Mitochondria/genetics ; Perciformes/classification/*genetics/*physiology ; *Phylogeny ; Population Dynamics ; },
abstract = {Recent studies have focused on the relationship between the marine fauna of the Eastern Atlantic and the Mediterranean Sea, but within the Atlantic, little is known about genetic relationships between populations of the Macaronesian islands. In this study, we tested whether the paleo-climatology and paleo-oceanography of the region could predict the genetic relationships among three Eastern Atlantic populations (Azores, Madeira, and Canaries) of a damselfish, Chromis limbata, and compared our results with its Mediterranean and adjacent Atlantic sister species, Chromis chromis. We combined phylogeographic and coalescent approaches using the fast evolving mitochondrial control region gene. No population structure was found for the three archipelagos. The coalescence time estimated for C. limbata (0.857-1.17 Mya) was much greater than that estimated for C. chromis. We propose that this difference reflects differences in glaciating extents in the Northeastern Atlantic and the Mediterranean. Diversity indexes (Hd and genetic distances) together with historical demographic parameters of C. limbata (Theta and g) revealed a more stable population history when compared to C. chromis. Our results suggest that the Macaronesian populations of C. limbata have probably been less affected by the last glaciation than the Mediterranean populations of C. chromis. Migration across the three archipelagos was estimated and a prevailing northwest trend was detected. This result supports the idea of a colonization of the Azores by warm water fish from Madeira or the westernmost Canary islands which acted as major glacial refugia for the tropical and subtropical marine fauna during the glaciations.},
}
@article {pmid16611603,
year = {2006},
author = {Sota, T and Sasabe, M},
title = {Utility of nuclear allele networks for the analysis of closely related species in the genus Carabus, subgenus Ohomopterus.},
journal = {Systematic biology},
volume = {55},
number = {2},
pages = {329-344},
doi = {10.1080/10635150500541607},
pmid = {16611603},
issn = {1063-5157},
mesh = {*Alleles ; Animals ; Coleoptera/anatomy &amp; histology/*classification/*genetics ; DNA/*genetics ; Genetic Speciation ; Genetic Variation ; Male ; Phylogeny ; Recombination, Genetic ; Species Specificity ; },
abstract = {Nuclear DNA sequence data for diploid organisms are potentially a rich source of phylogenetic information for disentangling the evolutionary relationships of closely related organisms, but present special phylogenetic problems owing to difficulties arising from heterozygosity and recombination. We analyzed allelic relationships for two nuclear gene regions (phosphoenolpyruvate carboxykinase and elongation factor-1a), along with a mitochondrial gene region (NADH dehydrogenase subunit 5), for an assemblage of closely related species of carabid beetles (Carabus subgenus Ohomopterus). We used a network approach to examine whether the nuclear gene sequences provide substantial phylogenetic information on species relationships and evolutionary history. The mitochondrial gene genealogy strongly contradicted the morphological species boundary as a result of introgression of heterospecific mitochondria. Two nuclear gene regions showed high allelic diversity within species, and this diversity was partially attributable to recombination between various alleles and high variability in the intron region. Shared nuclear alleles among species were rare and were considered to represent shared ancestral polymorphism. Despite the presence of recombination, nuclear allelic networks recovered species monophyly more often and presented genetic differentiation patterns (low to high) among species more clearly. Overall, nuclear gene networks provide clear evidence for separate biological species and information on the phylogenetic relationships among closely related carabid beetles.},
}
@article {pmid16621606,
year = {2006},
author = {Cheng, W and Tung, YH and Chiou, TT and Chen, JC},
title = {Cloning and characterisation of mitochondrial manganese superoxide dismutase (mtMnSOD) from the giant freshwater prawn Macrobrachium rosenbergii.},
journal = {Fish &amp; shellfish immunology},
volume = {21},
number = {4},
pages = {453-466},
doi = {10.1016/j.fsi.2006.02.005},
pmid = {16621606},
issn = {1050-4648},
mesh = {Actins/biosynthesis ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/chemistry ; Gene Expression Regulation, Enzymologic/*physiology ; Hemolymph/enzymology ; Hepatopancreas/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Palaemonidae/enzymology/*genetics ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*biosynthesis/*genetics ; Time Factors ; },
abstract = {A cDNA encoding a mitochondrial manganese superoxide dismutase (mtMnSOD) was cloned from the hepatopancreas of giant freshwater prawn Macrobrachium rosenbergii using reverse transcription polymerase chain reaction (RT-PCR) by degenerate primers. Both 3'- and 5'-regions were isolated by rapid amplification of cDNA end (RACE) PCR method. Analysis of nucleotide sequence revealed that the mtMnSOD full-length cDNA consists of 1202bp containing an open reading frame of 654bp, which encodes a protein consisting of 218 amino acids including a signal peptide of 16 amino acid residues. The calculated molecular mass of the mature proteins (202 amino acids) is 24kDa with an estimated pI of 7.12. Two putative N-glycosylation sites, NXT and NXS were observed in the mtMnSOD. Manganese superoxide dismutase signatures from 180 to 187 (DVWEHAYY), and four conserved amino acids responsible for binding manganese were observed (H48, H96, D180 and H184). Sequence comparison showed that the mtMnSOD deduced amino acid sequence of Macrobrachium rosenbergii has similarity of 88%, 78%, 56%, 54% and 46% to that of blue crab Callinectes sapidus, crucifix crab Charybdis feriatus, brown shrimp Farfantepenaeus aztecus, European lobster Palinurus vulgaris, and grass shrimp Palaemontes pugio, respectively, and has similarity of 45%, 44%, 43%, 26% and 25% to cytMnSOD (cytosolic MnSOD) deduced amino acid sequence of blue crab C. sapidus, prawn M. rosenbergii, tiger shrimp Penaeus monodon, grass shrimp P. pugio and brown shrimp F. aztecus, respectively. Quantitative real-time RT-PCR analysis showed that levels of mtMn-SOD transcripts in hepatopancreas and haemocytes were not significantly different between the M. rosenbergii injected with Lactococcus garvieae, and that injected with saline after 3h to 24h.},
}
@article {pmid16623392,
year = {2006},
author = {Hackstein, JH and Yarlett, N},
title = {Hydrogenosomes and symbiosis.},
journal = {Progress in molecular and subcellular biology},
volume = {41},
number = {},
pages = {117-142},
doi = {10.1007/3-540-28221-1_7},
pmid = {16623392},
issn = {0079-6484},
mesh = {Animals ; Hydrogen/*metabolism ; Mitochondria/metabolism/ultrastructure ; Organelles/*metabolism/ultrastructure ; Phylogeny ; *Symbiosis ; Trichomonas vaginalis/cytology/ultrastructure ; },
}
@article {pmid16636268,
year = {2006},
author = {Charrière, F and Helgadóttir, S and Horn, EK and Söll, D and Schneider, A},
title = {Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {18},
pages = {6847-6852},
pmid = {16636268},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Isoenzymes/classification/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Organisms, Genetically Modified ; Phylogeny ; RNA Interference ; RNA, Transfer, Trp/*metabolism ; Trypanosoma brucei brucei/cytology/*enzymology/genetics ; Tryptophan-tRNA Ligase/classification/genetics/*metabolism ; },
abstract = {The mitochondrion of Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by the import of a small fraction of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single-copy genes, suggesting the use of the same enzyme in the cytosol and mitochondrion. However, the T. brucei genome contains two distinct genes for eukaryotic tryptophanyl-tRNA synthetase (TrpRS). RNA interference analysis established that both TrpRS1 and TrpRS2 are essential for growth and required for cytosolic and mitochondrial tryptophanyl-tRNA formation, respectively. Decoding the mitochondrial tryptophan codon UGA requires mitochondria-specific C-->U RNA editing in the anticodon of the imported tRNA(Trp). In vitro charging assays with recombinant TrpRS enzymes demonstrated that the edited anticodon and the mitochondria-specific thiolation of U33 in the imported tRNA(Trp) act as antideterminants for the cytosolic TrpRS1. The existence of two TrpRS enzymes, therefore, can be explained by the need for a mitochondrial synthetase with extended substrate specificity to achieve aminoacylation of the imported thiolated and edited tRNA(Trp). Thus, the notion that, in an organism, all nuclear-encoded tRNAs assigned to a given amino acid are charged by a single aminoacyl-tRNA synthetase, is not universally valid.},
}
@article {pmid16640602,
year = {2006},
author = {Ahn, CS and Lee, JH and Reum Hwang, A and Kim, WT and Pai, HS},
title = {Prohibitin is involved in mitochondrial biogenesis in plants.},
journal = {The Plant journal : for cell and molecular biology},
volume = {46},
number = {4},
pages = {658-667},
doi = {10.1111/j.1365-313X.2006.02726.x},
pmid = {16640602},
issn = {0960-7412},
mesh = {DNA, Complementary ; Gene Silencing ; Homeostasis/genetics ; Membrane Potentials ; Mitochondria/chemistry/*metabolism/ultrastructure ; Mitochondrial Membranes/physiology ; Oxidative Stress ; Oxygen/metabolism ; Phylogeny ; Plant Proteins/analysis/genetics/*physiology ; Prohibitins ; Protein Subunits/analysis/genetics/physiology ; Reactive Oxygen Species/metabolism ; Repressor Proteins/analysis/genetics/*physiology ; Sequence Analysis, DNA ; Nicotiana/genetics/metabolism/ultrastructure ; },
abstract = {Prohibitin, which consists of two subunits PHB1 and PHB2, plays a role in cell-cycle progression, senescence, apoptosis, and maintenance of mitochondrial function in mammals and yeast. In this study, we examined the role of prohibitins in plants by using virus-induced gene silencing (VIGS) of two prohibitin subunit genes of Nicotiana benthamiana, designated NbPHB1 and NbPHB2. NbPHB1 and NbPHB2 were targeted to the mitochondria, and their gene expression was suppressed during senescence. VIGS of NbPHB2 caused severe growth inhibition, leaf yellowing and symptoms of cell death, whereas VIGS of NbPHB1 resulted in a milder phenotype. At the cellular level, depletion of these subunits affected mitochondria by severely reducing their number and/or mass, and by causing morphological and physiological abnormalities. Suppression of prohibitin function resulted in a 10- to 20-fold higher production of reactive oxygen species and induced premature leaf senescence. Finally, disruption of prohibitin function rendered the plants more susceptible to various oxidative stress-inducing reagents, including H(2)O(2), paraquat, antimycin A and salicylic acid. These results suggest that prohibitins play a crucial role in mitochondrial biogenesis and protection against stress and senescence in plant cells.},
}
@article {pmid16651558,
year = {2006},
author = {Shahsavarani, A and McNeill, B and Galvez, F and Wood, CM and Goss, GG and Hwang, PP and Perry, SF},
title = {Characterization of a branchial epithelial calcium channel (ECaC) in freshwater rainbow trout (Oncorhynchus mykiss).},
journal = {The Journal of experimental biology},
volume = {209},
number = {Pt 10},
pages = {1928-1943},
doi = {10.1242/jeb.02190},
pmid = {16651558},
issn = {0022-0949},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Calcium Channels/chemistry/genetics/*metabolism ; Epithelial Cells/cytology ; Epithelium/*metabolism ; Female ; Gills/*metabolism ; Immunohistochemistry ; Male ; Molecular Sequence Data ; Oncorhynchus mykiss/*metabolism ; Phylogeny ; },
abstract = {The entry of calcium (Ca2+) through an apical membrane epithelial calcium channel (ECaC) is thought to a key step in piscine branchial Ca2+ uptake. In mammals, ECaC is a member of the transient receptor potential (TRP) gene family of which two sub-families have been identified, TRPV5 and TPRV6. In the present study we have identified a single rainbow trout (Oncorhynchus mykiss) ECaC (rtECaC) that is similar to the mammalian TRPV5 and TRPV6. Phylogenetic analysis of the protein sequence suggests that an ancestral form of the mammalian genes diverged from those in the lower vertebrates prior to the gene duplication event that gave rise to TRPV5 and TRPV6. The putative model for Ca2+ uptake in fish proposes that the mitochondria-rich cell (also termed ionocyte or chloride cell) is the predominant or exclusive site of transcellular Ca2+ movements owing to preferential localisation of ECaC to the apical membrane of these cells. However, the results of real-time PCR performed on enriched gill cell populations as well as immunocytochemistry and in situ hybridisation analysis of enriched cells, cell cultures and whole gill sections strongly suggest that ECaC is not exclusive to mitochondria-rich cells but that it is also found in pavement cells. Not only was ECaC protein localized to areas of the gill normally having few mitochondria-rich cells, but there was also no consistent co-localization of ECaC- and Na+/K+-ATPase-positive (a marker of mitochondria rich cells) cells. Taken together, the results of the present study suggest that although ECaC (mRNA and protein) does exist in trout gill, its cellular distribution is more extensive than previously thought, thus suggesting that Ca2+ uptake may not be restricted to mitochondria-rich cells as was proposed in previous models.},
}
@article {pmid16710701,
year = {2007},
author = {Herget, M and Tampé, R},
title = {Intracellular peptide transporters in human--compartmentalization of the "peptidome".},
journal = {Pflugers Archiv : European journal of physiology},
volume = {453},
number = {5},
pages = {591-600},
pmid = {16710701},
issn = {0031-6768},
mesh = {ATP Binding Cassette Transporter 1 ; ATP Binding Cassette Transporter, Subfamily B, Member 2 ; ATP Binding Cassette Transporter, Subfamily B, Member 3 ; *ATP-Binding Cassette Transporters/antagonists &amp; inhibitors/genetics/physiology ; Antigen Presentation ; Humans ; Immediate-Early Proteins/physiology ; Lysosomes/physiology ; Models, Biological ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport/*physiology ; RNA-Binding Proteins/physiology ; Substrate Specificity ; Viral Proteins/physiology ; },
abstract = {In the human genome, the five adenosine triphosphate (ATP)-binding cassette (ABC) half transporters ABCB2 (TAP1), ABCB3 (TAP2), ABCB9 (TAP-like), and in part, also ABCB8 and ABCB10 are closely related with regard to their structural and functional properties. Although targeted to different cellular compartments such as the endoplasmic reticulum (ER), lysosomes, and mitochondria, they are involved in intracellular peptide trafficking across membranes. The transporter associated with antigen processing (TAP1 and TAP2) constitute a key machinery in the major histocompatibility complex (MHC) class I-mediated cellular immune defense against infected or malignantly transformed cells. TAP translocates the cellular "peptidome" derived primarily from cytosolic proteasomal degradation into the ER lumen for presentation by MHC class I molecules. The homodimeric ABCB9 (TAP-like) complex located in lysosomal compartments shares structural and functional similarities to TAP; however, its biological role seems to be different from the MHC I antigen processing. ABCB8 and ABCB10 are targeted to the inner mitochondrial membrane. MDL1, the yeast homologue of ABCB10, is involved in the export of peptides derived from proteolysis of inner-membrane proteins into the intermembrane space. As such peptides are presented as minor histocompatibility antigens on the surface of mammalian cells, a physiological role of ABCB10 in the antigen processing can be accounted.},
}
@article {pmid16757556,
year = {2006},
author = {Liu, Z and Lin, H and Ye, S and Liu, QY and Meng, Z and Zhang, CM and Xia, Y and Margoliash, E and Rao, Z and Liu, XJ},
title = {Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {24},
pages = {8965-8970},
pmid = {16757556},
issn = {0027-8424},
mesh = {Animals ; Apoptosis/*physiology ; Ascorbic Acid/metabolism ; Crystallography, X-Ray ; Cytochromes c/chemistry/classification/genetics/*metabolism ; DNA Damage ; Electron Transport Complex IV/metabolism ; Erythrocytes/cytology/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Male ; Mice ; Models, Molecular ; Oocytes/physiology ; Oxidants/metabolism ; Phylogeny ; Protein Conformation ; Protein Isoforms/*metabolism ; Reactive Oxygen Species/*metabolism ; Spermatozoa/physiology ; Testis/*enzymology/*metabolism ; Water/chemistry ; Xenopus laevis ; },
abstract = {Hydrogen peroxide (H(2)O(2)) is the major reactive oxygen species (ROS) produced in sperm. High concentrations of H(2)O(2) in sperm induce nuclear DNA fragmentation and lipid peroxidation and result in cell death. The respiratory chain of the mitochondrion is one of the most productive ROS generating systems in sperm, and thus the destruction of ROS in mitochondria is critical for the cell. It was recently reported that H(2)O(2) generated by the respiratory chain of the mitochondrion can be efficiently destroyed by the cytochrome c-mediated electron-leak pathway where the electron of ferrocytochrome c migrates directly to H(2)O(2) instead of to cytochrome c oxidase. In our studies, we found that mouse testis-specific cytochrome c (T-Cc) can catalyze the reduction of H(2)O(2) three times faster than its counterpart in somatic cells (S-Cc) and that the T-Cc heme has the greater resistance to being degraded by H(2)O(2). Together, these findings strongly imply that T-Cc can protect sperm from the damages caused by H(2)O(2). Moreover, the apoptotic activity of T-Cc is three to five times greater than that of S-Cc in a well established apoptosis measurement system using Xenopus egg extract. The dramatically stronger apoptotic activity of T-Cc might be important for the suicide of male germ cells, considered a physiological mechanism that regulates the number of sperm produced and eliminates those with damaged DNA. Thus, it is very likely that T-Cc has evolved to guarantee the biological integrity of sperm produced in mammalian testis.},
}
@article {pmid16762445,
year = {2006},
author = {Boore, JL},
title = {The use of genome-level characters for phylogenetic reconstruction.},
journal = {Trends in ecology &amp; evolution},
volume = {21},
number = {8},
pages = {439-446},
doi = {10.1016/j.tree.2006.05.009},
pmid = {16762445},
issn = {0169-5347},
mesh = {*Genome ; Mitochondria/genetics ; *Phylogeny ; },
abstract = {Now that large-scale genome-sequencing projects are sampling many organismal lineages, it is becoming possible to compare large data sets of not only DNA and protein sequences, but also genome-level features, such as gene arrangements and the positions of mobile genetic elements. Although it is unlikely that comparisons of such features will address a large number of evolutionary branch points across the broad tree of life owing to the infeasibility of such sampling, they have great potential for resolving many crucial, contested relationships for which no other data seem promising. Here, I discuss the advancements, advantages, methods, and problems of the use of genome-level characters for reconstructing evolutionary relationships.},
}
@article {pmid16769251,
year = {2006},
author = {Rewitz, KF and Styrishave, B and Løbner-Olsen, A and Andersen, O},
title = {Marine invertebrate cytochrome P450: emerging insights from vertebrate and insects analogies.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {143},
number = {4},
pages = {363-381},
doi = {10.1016/j.cbpc.2006.04.001},
pmid = {16769251},
issn = {1532-0456},
mesh = {Animals ; Annelida/enzymology ; Crustacea/enzymology ; *Cytochrome P-450 Enzyme System/genetics ; Echinodermata/enzymology ; Gene Expression Regulation ; Invertebrates/*enzymology/genetics ; Microsomes/enzymology ; Mitochondria/enzymology ; Mollusca/enzymology ; Phylogeny ; Tissue Distribution ; Xenobiotics/metabolism ; },
abstract = {Cytochrome P450 enzymes (P450s) are responsible for the oxidative metabolism of a plethora of endogenous and exogenous substrates. P450s and associated activities have been demonstrated in numerous marine invertebrates belonging to the phyla Cnidaria, Annelida (Polychaeta), Mollusca, Arthropoda (Crustacea) and Echinodermata. P450s of marine invertebrates and vertebrates show considerable sequence divergence and the few orthologs reveal the selective constraint on physiologically significant enzymes. P450s are present in virtually all tissues of marine invertebrates, although high levels usually are found in hepatic-like organs and steroidogenic tissues. High-throughput technologies result in the rapid acquisition of new marine invertebrate P450 sequences; however, the understanding of their function is poor. Based on analogy to vertebrates and insects, it is likely that P450s play a pivotal role in the physiology of marine invertebrates by catalyzing the biosynthesis of signal molecules including steroids such as 20-hydroxyecdysone (the molting hormone of crustaceans). The metabolism of many exogenous compounds including benzo(a)pyrene (BaP), pyrene, ethoxyresorufin, ethoxycoumarin and aniline is mediated by P450 enzymes in tissues of marine invertebrates. P450 gene expression, protein levels and P450 mediated metabolism of xenobiotics are induced by PAHs in some marine invertebrate species. Thus, regulation of P450 enzyme activity may play a central role in the adaptation of animals to environmental pollutants. Emphasis should be put on the elucidation of the function and regulation of the ever-increasing number of marine invertebrate P450s.},
}
@article {pmid16778769,
year = {2006},
author = {Crawford, MJ and Thomsen-Zieger, N and Ray, M and Schachtner, J and Roos, DS and Seeber, F},
title = {Toxoplasma gondii scavenges host-derived lipoic acid despite its de novo synthesis in the apicoplast.},
journal = {The EMBO journal},
volume = {25},
number = {13},
pages = {3214-3222},
pmid = {16778769},
issn = {0261-4189},
support = {F32 AI010482/AI/NIAID NIH HHS/United States ; AI05093/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Caprylates/pharmacology ; Cell Survival ; Mitochondria/metabolism ; Organelles/*metabolism ; Phylogeny ; Protozoan Proteins/*metabolism ; Thioctic Acid/*metabolism ; Toxoplasma/growth &amp; development/*metabolism/ultrastructure ; },
abstract = {In contrast to other eukaryotes, which manufacture lipoic acid, an essential cofactor for several vital dehydrogenase complexes, within the mitochondrion, we show that the plastid (apicoplast) of the obligate intracellular protozoan parasite Toxoplasma gondii is the only site of de novo lipoate synthesis. However, antibodies specific for protein-attached lipoate reveal the presence of lipoylated proteins in both, the apicoplast and the mitochondrion of T. gondii. Cultivation of T. gondii-infected cells in lipoate-deficient medium results in substantially reduced lipoylation of mitochondrial (but not apicoplast) proteins. Addition of exogenous lipoate to the medium can rescue this effect, showing that the parasite scavenges this cofactor from the host. Exposure of T. gondii to lipoate analogues in lipoate-deficient medium leads to growth inhibition, suggesting that T. gondii might be auxotrophic for this cofactor. Phylogenetic analyses reveal the secondary loss of the mitochondrial lipoate synthase gene after the acquisition of the plastid. Our studies thus reveal an unexpected metabolic deficiency in T. gondii and raise the question whether the close interaction of host mitochondria with the parasitophorous vacuole is connected to lipoate supply by the host.},
}
@article {pmid16788047,
year = {2006},
author = {Nomura, H and Athauda, SB and Wada, H and Maruyama, Y and Takahashi, K and Inoue, H},
title = {Identification and reverse genetic analysis of mitochondrial processing peptidase and the core protein of the cytochrome bc1 complex of Caenorhabditis elegans, a model parasitic nematode.},
journal = {Journal of biochemistry},
volume = {139},
number = {6},
pages = {967-979},
doi = {10.1093/jb/mvj114},
pmid = {16788047},
issn = {0021-924X},
mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Blotting, Western ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry/*genetics/metabolism ; DNA, Complementary/genetics ; Electron Transport Complex III/chemistry/*genetics/metabolism ; Humans ; Metalloendopeptidases/chemistry/*genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nematoda/genetics/metabolism ; Phylogeny ; Protein Structure, Quaternary ; RNA Interference ; Recombinant Proteins/chemistry/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Mitochondrial Processing Peptidase ; },
abstract = {Mitochondria could be a good target for anti-parasitic drugs. The alpha and beta subunits of mitochondrial processing peptidase (MPP) and the core subunits of the cytochrome bc1 complex, UCR-1 and UCR-2, are homologous to one another and are important for mitochondrial functions. However, our knowledge of these proteins in nematodes is very limited. Caenorhabditis elegans, a free-living nematode, has six genes coding for proteins homologous to these subunits. On primary structure comparison, and immunochemical and enzymological analyses, the gene products were assigned as follows: Y71G12B.24, alpha-MPP; ZC410.2, beta-MPP; F56D2.1, UCR-1; VW06B3R.1, T10B10.2; and T24C4.1, UCR-2. The primary structures of beta-MPP and UCR-1 from Brugia malayi, a parasitic nematode causing human filariasis, were deduced from their cDNA structures. Phylogenetic analysis showed that the UCR-1s from both C. elegans and B. malayi were less related to mammalian UCR-1s than to MPPs from various organisms. MPP and the bc1 complex are essential for the life cycle of C. elegans, because their reverse genetic inhibition is lethal. This suggests the possibility that these proteins are also essential for the viability of B. malayi and other parasitic nematodes, and are potential targets for anti-parasitic agents.},
}
@article {pmid16790414,
year = {2006},
author = {Fang, M and Andersson, L},
title = {Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication.},
journal = {Proceedings. Biological sciences},
volume = {273},
number = {1595},
pages = {1803-1810},
pmid = {16790414},
issn = {0962-8452},
mesh = {Animals ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*analysis ; Europe ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Swine/*genetics ; },
abstract = {Mitochondrial DNA (mtDNA) diversity in European and Asian pigs was assessed using 1536 samples representing 45 European and 21 Chinese breeds. Diagnostic nucleotide differences in the cytochrome b (Cytb) gene between the European and Asian mtDNA variants were determined by pyrosequencing as a rapid screening method. Subsequently, 637bp of the hypervariable control region was sequenced to further characterize mtDNA diversity. All sequences belonged to the D1 and D2 clusters of pig mtDNA originating from ancestral wild boar populations in Europe and Asia, respectively. The average frequency of Asian mtDNA haplotypes was 29% across European breeds, but varied from 0 to 100% within individual breeds. A neighbour-joining (NJ) tree of control region sequences showed that European and Asian haplotypes form distinct clusters consistent with the independent domestication of pigs in Asia and Europe. The Asian haplotypes found in the European pigs were identical or closely related to those found in domestic pigs from Southeast China. The star-like pattern detected by network analysis for both the European and Asian haplotypes was consistent with a previous demographic expansion. Mismatch analysis supported this notion and suggested that the expansion was initiated before domestication.},
}
@article {pmid16804921,
year = {2006},
author = {Tripepi, S and Jamieson, BG and Brunelli, E},
title = {Ultrastructure of the spermatid of Caprimulgus europaeus Linnaeus 1758, the European nightjar (Aves; Caprimulgidae), with phylogenetic implications.},
journal = {Journal of morphology},
volume = {267},
number = {10},
pages = {1157-1164},
doi = {10.1002/jmor.10466},
pmid = {16804921},
issn = {0362-2525},
mesh = {Acrosome/ultrastructure ; Animals ; Birds/*classification ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Europe ; Male ; *Phylogeny ; Sperm Midpiece/ultrastructure ; Spermatids/cytology/*ultrastructure ; Spermatogenesis/physiology ; },
abstract = {The sperm of Caprimulgus europaeus is typical of other nonpasserines in many respects. Features shared with Paleognathae and Galloanserae are the conical acrosome, shorter than the nucleus; the presence of a perforatorium and endonuclear canal; the presence of a proximal as well as distal centriole; the elongate midpiece with mitochondria grouped around a central axis (here maximally six mitochondria in approximately 10 tiers); and the presence of a fibrous or amorphous sheath around the principal piece of the axoneme. A major (apomorphic) difference from paleognaths and galloanserans is the short distal centriole, the midpiece being penetrated for most of its length by the axoneme and for only a very short proximal portion by the centriole. Nonpasserines differ from paleognaths in that the latter have a transversely ribbed fibrous sheath, whereas in nonpasserines it is amorphous, as in Caprimulgus, or absent. The absence of an annulus is an apomorphic feature of Caprimulgus, apodiform, psittaciform, gruiform, and passerine sperm, homoplastic in at least some of these. In contrast to passerines, in Caprimulgus the cytoplasmic microtubules in the spermatid are restricted to a transient longitudinal manchette. The structure of the spermatid and spermatozoon is consistent with placement of the Caprimulgidae near the Psittacidae, but is less supportive of close proximity to the Apodidae, from DNA-DNA hybridization and some other analyses.},
}
@article {pmid16817936,
year = {2006},
author = {Lo, N and Beninati, T and Sassera, D and Bouman, EA and Santagati, S and Gern, L and Sambri, V and Masuzawa, T and Gray, JS and Jaenson, TG and Bouattour, A and Kenny, MJ and Guner, ES and Kharitonenkov, IG and Bitam, I and Bandi, C},
title = {Widespread distribution and high prevalence of an alpha-proteobacterial symbiont in the tick Ixodes ricinus.},
journal = {Environmental microbiology},
volume = {8},
number = {7},
pages = {1280-1287},
doi = {10.1111/j.1462-2920.2006.01024.x},
pmid = {16817936},
issn = {1462-2912},
mesh = {Alphaproteobacteria/*genetics/growth &amp; development ; Animals ; Europe/epidemiology ; Female ; Infectious Disease Transmission, Vertical ; Ixodes/*microbiology ; Male ; Mitochondria/*microbiology ; Ovary/cytology/microbiology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; },
abstract = {The tick Ixodes ricinus is responsible for the transmission of a number of bacterial, protozoan and viral diseases to humans and animals in Europe and Northern Africa. Female I. ricinus from England, Switzerland and Italy have been found to harbour an intracellular alpha-proteobacterium, designated IricES1, within the cells of the ovary. IricES1 is the only prokaryote known to exist within the mitochondria of any animal or multicellular organism. To further examine the distribution, prevalence and mode of transmission of IricES1, we performed polymerase chain reaction screening of I. ricinus adults from 12 countries across its geographic distribution, including tick colonies that have been maintained in the laboratory for varying periods of time. IricES1 was detected in 100% of field-collected female ticks from all countries examined (n = 128), while 44% of males were found to be infected (n = 108). Those males that are infected appear to harbour fewer bacteria than females. Sequencing of fragments of the 16S rRNA and gyrB genes revealed very low nucleotide diversity among various populations of IricES1. Transmission of IricES1 from engorged adult females to eggs was found to be 100% (n = 31). In tick colonies that had been maintained in the laboratory for several years, a relatively low prevalence was found in females (32%; n = 25). To our knowledge, IricES1 is the most widespread and highly prevalent of any tick-associated symbiont.},
}
@article {pmid16835267,
year = {2006},
author = {Browman, DT and Resek, ME and Zajchowski, LD and Robbins, SM},
title = {Erlin-1 and erlin-2 are novel members of the prohibitin family of proteins that define lipid-raft-like domains of the ER.},
journal = {Journal of cell science},
volume = {119},
number = {Pt 15},
pages = {3149-3160},
doi = {10.1242/jcs.03060},
pmid = {16835267},
issn = {0021-9533},
mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Cholesterol/metabolism ; Endoplasmic Reticulum/chemistry/*metabolism ; Humans ; Membrane Microdomains/chemistry/*metabolism ; Membrane Proteins/classification/genetics/*metabolism ; Mice ; Molecular Sequence Data ; Monocytes/chemistry/cytology/metabolism ; Nerve Tissue Proteins/classification/genetics/*metabolism ; Phylogeny ; Prohibitins ; Recombinant Fusion Proteins/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; Sequence Alignment ; Subcellular Fractions/chemistry/metabolism ; },
abstract = {Our laboratory was interested in characterizing the molecular composition of non-caveolar lipid rafts. Thus, we generated monoclonal antibodies to lipid raft proteins of human myelomonocytic cells. Two of these proteins, KE04p and C8orf2, were found to be highly enriched in the detergent-insoluble, buoyant fraction of sucrose gradients in a cholesterol-dependent manner. They contain an evolutionarily conserved domain placing them in the prohibitin family of proteins. In contrast to other family members, these two proteins localized to the ER. Furthermore, the extreme N-termini of KE04p and C8orf2 were found to be sufficient for heterologous targeting of GFP to the ER in the absence of classical ER retrieval motifs. We also demonstrate that all prohibitin family members rely on sequences in their extreme N-termini for their distinctive subcellular distributions including the mitochondria, plasma membrane and Golgi vesicles. Owing to their subcellular localization and their presence in lipid rafts, we have named KE04p and C8orf2, ER lipid raft protein (erlin)-1 and erlin-2, respectively. Interestingly, the ER contains relatively low levels of cholesterol and sphingolipids compared with other organelles. Thus, our data support the existence of lipid-raft-like domains within the membranes of the ER.},
}
@article {pmid16842408,
year = {2006},
author = {Spaulding, AW and Mock, KE and Schroeder, MA and Warheit, KI},
title = {Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus).},
journal = {Molecular ecology},
volume = {15},
number = {9},
pages = {2317-2332},
doi = {10.1111/j.1365-294X.2006.02935.x},
pmid = {16842408},
issn = {0962-1083},
mesh = {Animals ; Canada ; Cell Nucleus/genetics ; Galliformes/*genetics/*physiology ; Genetic Variation/*genetics ; Mitochondria/genetics ; Phylogeny ; Population Dynamics ; United States ; },
abstract = {Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites. For historical context, we also analysed CR-I in all species of Tympanuchus. Within T. phasianellus, we found evidence for restricted gene flow between eastern and western portions of the species range, generally corresponding with the range boundary of T. p. columbianus and T. p. jamesi. The mismatch distribution and molecular clock estimates from the CR-I data suggested that all Tympanuchus underwent a range expansion prior to sorting of mitotypes among the species, and that sorting may have been delayed as a result of mutation-drift disequilibrium. This study illustrates the challenge of using genetic data to detect historical divergence in groups that are of relatively recent origin, or that have a history dominated by nonequilibrium conditions. We suggest that in such cases, morphological, ecological, and behavioural data may be particularly important adjuncts to molecular data for the recognition of historically or adaptively divergent groups.},
}
@article {pmid16844075,
year = {2006},
author = {Palmieri, F and Agrimi, G and Blanco, E and Castegna, A and Di Noia, MA and Iacobazzi, V and Lasorsa, FM and Marobbio, CM and Palmieri, L and Scarcia, P and Todisco, S and Vozza, A and Walker, J},
title = {Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins.},
journal = {Biochimica et biophysica acta},
volume = {1757},
number = {9-10},
pages = {1249-1262},
doi = {10.1016/j.bbabio.2006.05.023},
pmid = {16844075},
issn = {0006-3002},
support = {MC_U105663150/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Biological Transport ; Mitochondrial ADP, ATP Translocases/*metabolism ; Phylogeny ; Recombinant Proteins/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; },
abstract = {The inner membranes of mitochondria contain a family of carrier proteins that are responsible for the transport in and out of the mitochondrial matrix of substrates, products, co-factors and biosynthetic precursors that are essential for the function and activities of the organelle. This family of proteins is characterized by containing three tandem homologous sequence repeats of approximately 100 amino acids, each folded into two transmembrane alpha-helices linked by an extensive polar loop. Each repeat contains a characteristic conserved sequence. These features have been used to determine the extent of the family in genome sequences. The genome of Saccharomyces cerevisiae contains 34 members of the family. The identity of five of them was known before the determination of the genome sequence, but the functions of the remaining family members were not. This review describes how the functions of 15 of these previously unknown transport proteins have been determined by a strategy that consists of expressing the genes in Escherichia coli or Saccharomyces cerevisiae, reconstituting the gene products into liposomes and establishing their functions by transport assay. Genetic and biochemical evidence as well as phylogenetic considerations have guided the choice of substrates that were tested in the transport assays. The physiological roles of these carriers have been verified by genetic experiments. Various pieces of evidence point to the functions of six additional members of the family, but these proposals await confirmation by transport assay. The sequences of many of the newly identified yeast carriers have been used to characterize orthologs in other species, and in man five diseases are presently known to be caused by defects in specific mitochondrial carrier genes. The roles of eight yeast mitochondrial carriers remain to be established.},
}
@article {pmid16857679,
year = {2006},
author = {Coustou, V and Biran, M and Besteiro, S and Rivière, L and Baltz, T and Franconi, JM and Bringaud, F},
title = {Fumarate is an essential intermediary metabolite produced by the procyclic Trypanosoma brucei.},
journal = {The Journal of biological chemistry},
volume = {281},
number = {37},
pages = {26832-26846},
doi = {10.1074/jbc.M601377200},
pmid = {16857679},
issn = {0021-9258},
mesh = {Animals ; Cytosol/enzymology ; Electrons ; Fumarates/*chemistry ; Glucose/metabolism ; Green Fluorescent Proteins/metabolism ; Microbodies/metabolism ; Mitochondria/enzymology ; Mutation ; Phylogeny ; Protein Isoforms ; RNA Interference ; Time Factors ; Trypanosoma brucei brucei/*metabolism ; },
abstract = {The procyclic stage of Trypanosoma brucei, a parasitic protist responsible for sleeping sickness in humans, converts most of the consumed glucose into excreted succinate, by succinic fermentation. Succinate is produced by the glycosomal and mitochondrial NADH-dependent fumarate reductases, which are not essential for parasite viability. To further explore the role of the succinic fermentation pathways, we studied the trypanosome fumarases, the enzymes providing fumarate to fumarate reductases. The T. brucei genome contains two class I fumarase genes encoding cytosolic (FHc) and mitochondrial (FHm) enzymes, which account for total cellular fumarase activity as shown by RNA interference. The growth arrest of a double RNA interference mutant cell line showing no fumarase activity indicates that fumarases are essential for the parasite. Interestingly, addition of fumarate to the medium rescues the growth phenotype, indicating that fumarate is an essential intermediary metabolite of the insect stage trypanosomes. We propose that trypanosomes use fumarate as an essential electron acceptor, as exemplified by the fumarate dependence previously reported for an enzyme of the essential de novo pyrimidine synthesis (Takashima, E., Inaoka, D. K., Osanai, A., Nara, T., Odaka, M., Aoki, T., Inaka, K., Harada, S., and Kita, K. (2002) Mol. Biochem. Parasitol. 122, 189-200).},
}
@article {pmid16872296,
year = {2006},
author = {Leander, BS and Ramey, PA},
title = {Cellular identity of a novel small subunit rDNA sequence clade of apicomplexans: description of the marine parasite Rhytidocystis polygordiae n. sp. (host: Polygordius sp., Polychaeta).},
journal = {The Journal of eukaryotic microbiology},
volume = {53},
number = {4},
pages = {280-291},
doi = {10.1111/j.1550-7408.2006.00109.x},
pmid = {16872296},
issn = {1066-5234},
mesh = {Animals ; Apicomplexa/*classification/*cytology/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Genes, rRNA ; Intestines/parasitology ; Microscopy, Electron, Transmission ; Phylogeny ; Polychaeta/*parasitology ; RNA, Ribosomal/*genetics ; Seawater/*parasitology ; },
abstract = {A new species of Rhytidocystis (Apicomplexa) is characterized from North American waters of the Atlantic Ocean using electron microscopy and phylogenetic analyses of small subunit (SSU) rDNA sequences. Rhytidocystis polygordiae n. sp. is a parasite of the polychaete Polygordius sp. and becomes the fourth described species within this genus. The trophozoites of R. polygordiae were relatively small oblong cells (L=35-55 microm; W=20-25 microm) and distinctive in possessing subterminal indentations at both ends of the cell. The surface of the trophozoites had six to eight longitudinal series of small transverse folds and several micropores arranged in short linear rows. The trophozoites of R. polygordiae were positioned beneath the brush border of the intestinal epithelium but appeared to reside between the epithelial cells within the extracellular matrix rather than within the cells. The trophozoites possessed a uniform distribution of paraglycogen granules, putative apicoplasts, mitochondria with tubular cristae, and a centrally positioned nucleus. The trophozoites were non-motile and lacked a mucron and an apical complex. Intracellular sporozoites of R. polygordiae had a conoid, a few rhoptries, micronemes, dense granules, and a posteriorly positioned nucleus. Phylogenies inferred from SSU rDNA sequences demonstrated a close relationship between R. polygordiae and the poorly known parasite reported from the hemolymph of the giant clam Tridacna crocea. The rhytidocystid clade diverged early in the apicomplexan radiation and showed a weak affinity to a clade consisting of cryptosporidian parasites, monocystids, and neogregarines.},
}
@article {pmid16874468,
year = {2006},
author = {Park, JS and Cho, BC and Simpson, AG},
title = {Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern.},
journal = {Extremophiles : life under extreme conditions},
volume = {10},
number = {6},
pages = {493-504},
pmid = {16874468},
issn = {1431-0651},
mesh = {Animals ; *DNA, Protozoan ; Eukaryota/*classification/genetics/growth &amp; development/isolation &amp; purification/metabolism/ultrastructure ; Flagella/ultrastructure ; Korea ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Ribotyping ; Seawater/chemistry/*parasitology ; Sodium Chloride/analysis/*metabolism ; Temperature ; },
abstract = {Recently, heterotrophic nanoflagellates (HNF) have been reported to actively ingest prokaryotes in high salinity waters. We report the isolation and culture of an HNF from a Korean saltern pond of 300 per thousand salinity. The organism is biflagellated with an acronematic anterior flagellum and never glides on surfaces. The mitochondria have tubular cristae. Neither transitional helix nor spiral fiber were observed in the transition zones of the flagella. The cell has a cytostome supported by an arc of eight microtubules, suggesting that our isolate is a bicosoecid. Our isolate had neither mastigonemes, lorica, body scales, nor cytopharynx and thus could not be placed in any of the presently described bicosoecid genera. Phylogenetic analysis of 18S rRNA gene sequences from stramenopiles confirmed the bicosoecid affinities of our isolate, but did not place it within any established genus or family. Its closest relatives include Caecitellus and Cafeteria. The optimal range of growth temperature was 30-35 degrees C. The isolated HNF grew optimally at 150 per thousand salinity and tolerated up to 363 per thousand salinity, but it failed to grow below 75 per thousand salinity, indicating that it could be a borderline extreme halophile. On the basis of its morphological features and position in 18S rRNA trees we propose a novel genus for our isolate; Halocafeteria, n. gen. The species name Halocafeteria seosinensis sp. nov. is proposed.},
}
@article {pmid16884501,
year = {2006},
author = {Bernard, L and Desplats, C and Mus, F and Cuiné, S and Cournac, L and Peltier, G},
title = {Agrobacterium tumefaciens type II NADH dehydrogenase. Characterization and interactions with bacterial and thylakoid membranes.},
journal = {The FEBS journal},
volume = {273},
number = {15},
pages = {3625-3637},
doi = {10.1111/j.1742-4658.2006.05370.x},
pmid = {16884501},
issn = {1742-464X},
mesh = {Agrobacterium tumefaciens/*enzymology ; Amino Acid Sequence ; Bacteria/classification/*metabolism ; Cell Membrane/metabolism ; Electrophoresis, Polyacrylamide Gel ; Genetic Complementation Test ; Molecular Sequence Data ; Mutation ; NADH Dehydrogenase/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Thylakoids/*metabolism ; },
abstract = {Type II NADH dehydrogenases (NDH-2) are monomeric enzymes that catalyse quinone reduction and allow electrons to enter the respiratory chain in different organisms including higher plant mitochondria, bacteria and yeasts. In this study, an Agrobacterium tumefaciens gene encoding a putative alternative NADH dehydrogenase (AtuNDH-2) was isolated and expressed in Escherichia coli as a (His)6-tagged protein. The purified 46 kDa protein contains FAD as a prosthetic group and oxidizes both NADH and NADPH with similar Vmax values, but with a much higher affinity for NADH than for NADPH. AtuNDH-2 complements the growth (on a minimal medium) of an E. coli mutant strain deficient in both NDH-1 and NDH-2, and is shown to supply electrons to the respiratory chain when incubated with bacterial membranes prepared from this mutant. By measuring photosystem II chlorophyll fluorescence on thylakoid membranes prepared from the green alga Chlamydomonas reinhardtii, we show that AtuNDH-2 is able to stimulate NADH-dependent reduction of the plastoquinone pool. We discuss the possibility of using heterologous expression of NDH-2 enzymes to improve nonphotochemical reduction of plastoquinones and H2 production in C. reinhardtii.},
}
@article {pmid16896205,
year = {2006},
author = {Colasante, C and Alibu, VP and Kirchberger, S and Tjaden, J and Clayton, C and Voncken, F},
title = {Characterization and developmentally regulated localization of the mitochondrial carrier protein homologue MCP6 from Trypanosoma brucei.},
journal = {Eukaryotic cell},
volume = {5},
number = {8},
pages = {1194-1205},
pmid = {16896205},
issn = {1535-9778},
mesh = {Animals ; Base Sequence ; Escherichia coli/genetics ; Gene Expression Regulation, Developmental ; Humans ; Mitochondrial Membranes/*chemistry ; Mitochondrial Proteins/*chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*chemistry/*genetics ; RNA, Messenger/biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*genetics/growth &amp; development ; },
abstract = {Proteins of the mitochondrial carrier family (MCF) are located mainly in the inner mitochondrial membrane and mediate the transport of a large range of metabolic intermediates. The genome of Trypanosoma brucei harbors 29 genes encoding different MCF proteins. We describe here the characterization of MCP6, a novel T. brucei MCF protein. Sequence comparison and phylogenetic reconstruction revealed that MCP6 is closely related to different mitochondrial ADP/ATP and calcium-dependent solute carriers, including the ATP-Mg/Pi carrier of Homo sapiens. However, MCP6 lacks essential amino acids and sequence motifs conserved in these metabolite transporters, and functional reconstitution and transport assays with E. coli suggested that this protein indeed does not function as an ADP/ATP or ATP-Mg/Pi carrier. The subcellular localization of MCP6 is developmentally regulated: in bloodstream-form trypanosomes, the protein is predominantly glycosomal, whereas in the procyclic form, it is found mainly in the mitochondria. Depletion of MCP6 in procyclic trypanosomes resulted in growth inhibition, an increased cell size, aberrant numbers of nuclei and kinetoplasts, and abnormal kinetoplast morphology, suggesting that depletion of MCP6 inhibits division of the kinetoplast.},
}
@article {pmid16905872,
year = {2006},
author = {Munemasa, M and Nikaido, M and Donnellan, S and Austin, CC and Okada, N and Hasegawa, M},
title = {Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes.},
journal = {Genes &amp; genetic systems},
volume = {81},
number = {3},
pages = {181-191},
doi = {10.1266/ggs.81.181},
pmid = {16905872},
issn = {1341-7568},
mesh = {Animals ; *DNA, Mitochondrial ; *Genome ; Likelihood Functions ; Marsupialia/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; },
abstract = {Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.},
}
@article {pmid16911214,
year = {2006},
author = {Audzijonyte, A and Daneliya, ME and Väinölä, R},
title = {Comparative phylogeography of Ponto-Caspian mysid crustaceans: isolation and exchange among dynamic inland sea basins.},
journal = {Molecular ecology},
volume = {15},
number = {10},
pages = {2969-2984},
doi = {10.1111/j.1365-294X.2006.03018.x},
pmid = {16911214},
issn = {0962-1083},
mesh = {Animals ; Crustacea/*genetics ; Ecology ; Genetic Variation ; *Geography ; Haplotypes ; Mitochondria/metabolism ; Oceans and Seas ; *Phylogeny ; Species Specificity ; },
abstract = {The distributions of many endemic Ponto-Caspian brackish-water taxa are subdivided among the Black, Azov and Caspian Sea basins and further among river estuaries. Of the two alternative views to explain the distributions, the relict school has claimed Tertiary fragmentation of the once contiguous range by emerging geographical and salinity barriers, whereas the immigration view has suggested recolonization of the westerly populations from the Caspian Sea after extirpation during Late Pleistocene environmental perturbations. A study of mitochondrial (COI) phylogeography of seven mysid crustacean taxa from the genera Limnomysis and Paramysis showed that both scenarios can be valid for different species. Four taxa had distinct lineages related to the major basin subdivision, but the lineage distributions and depths of divergence were not concordant. The data do not support a hypothesis of Late Miocene (10-5 Myr) vicariance; rather, range subdivisions and dispersal from and to the Caspian Sea seem to have occurred at different times throughout the Pleistocene. For example, in Paramysis lacustris each basin had an endemic clade 2-5% diverged from the others, whereas Paramysis kessleri from the southern Caspian and the western Black Sea were nearly identical. Species-specific ecological characteristics such as vagility and salinity tolerance seem to have played important roles in shaping the phylogeographic patterns. The mitochondrial data also suggested recent, human-mediated cryptic invasions of P. lacustris and Limnomysis benedeni from the Caspian to the Sea of Azov basin via the Volga-Don canal. Cryptic species-level subdivisions were recorded in populations attributed to Paramysis baeri, and possibly in P. lacustris.},
}
@article {pmid16918441,
year = {2006},
author = {Salvioli, S and Capri, M and Valensin, S and Tieri, P and Monti, D and Ottaviani, E and Franceschi, C},
title = {Inflamm-aging, cytokines and aging: state of the art, new hypotheses on the role of mitochondria and new perspectives from systems biology.},
journal = {Current pharmaceutical design},
volume = {12},
number = {24},
pages = {3161-3171},
doi = {10.2174/138161206777947470},
pmid = {16918441},
issn = {1381-6128},
mesh = {Aging/*physiology ; Animals ; Cytokines/genetics/*physiology ; Humans ; Inflammation/genetics/*physiopathology ; Mitochondria/*physiology ; Phylogeny ; Polymorphism, Genetic/genetics ; Systems Biology/methods ; },
abstract = {In this article we summarise present knowledge on the role of pro-inflammatory cytokines on chronic inflammation leading to organismal aging, a phenomenon we proposed to call "inflamm-aging". In particular, we review genetic data regarding polymorphisms of genes encoding for cytokines and proteins involved in natural immunity (such as Toll-like Receptors and Heat Shock Proteins) obtained from large population studies including young, old and very old people in good health status or affected by age-related diseases such as Alzheimer's Disease and Type II Diabetes. On the whole, despite some controversial results, the available data are in favour of the hypothesis that pro-inflammatory cytokines play an important role in aging and longevity. Further, we present a possible hypothesis to reconcile energetic dysfunction, including mitochondria, and inflamm-aging. New perspectives for future studies, including phylogenetic studies in animal models and in silico studies on mathematical and bioinformatic models inspired by the systems biology approach, are also proposed.},
}
@article {pmid16923211,
year = {2006},
author = {Lo, N and Eldridge, RH and Lenz, M},
title = {Phylogeny of Australian Coptotermes (Isoptera: Rhinotermitidae) species inferred from mitochondrial COII sequences.},
journal = {Bulletin of entomological research},
volume = {96},
number = {4},
pages = {433-437},
pmid = {16923211},
issn = {0007-4853},
mesh = {Animals ; Australia ; Electron Transport Complex IV/*genetics ; Isoptera/*enzymology/*genetics ; Mitochondria/*enzymology ; *Phylogeny ; },
abstract = {Six Australian species of Coptotermes are traditionally recognized, but recent cuticular hydrocarbon studies suggest that some of these may represent more than one species. An understanding of the phylogenetic diversity of Australian Coptotermes, particularly the pest species, is likely to be important for the improvement of termite management strategies. A study of phylogenetic relationships among species of this genus was performed, based on the mitochondrial cytochrome oxidase (COII) gene, comparing the data with recent data from Asian species. Representatives of the species C. lacteus (Froggatt), C. frenchi Hill and C. michaelseni Silvestri were each found to form closely related monophyletic groups, however representatives of C. acinaciformis (Froggatt) were not. For C. acinaciformis, representatives from northern mound-building populations were found to form a distinct group to southern, tree-nesting forms. Among southern C. acinaciformis, two Western Australian representatives were found to be divergent from other populations. The results suggest that C. acinaciformis probably represents a complex of species rather than one, as has been suggested previously. One unidentified Coptotermes sp. taxon from Melbourne was found to be divergent from other taxa. Notably, some Australian species were more closely related to Asian species than other Australian species.},
}
@article {pmid16938841,
year = {2006},
author = {Margulis, L and Chapman, M and Guerrero, R and Hall, J},
title = {The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
number = {35},
pages = {13080-13085},
pmid = {16938841},
issn = {0027-8424},
mesh = {Cell Movement ; Cell Nucleus/physiology ; Cytoskeleton/*physiology ; Eukaryotic Cells/*cytology/*physiology ; History, Ancient ; Microtubules/metabolism ; Mitochondria/physiology ; *Models, Biological ; *Phylogeny ; Spirochaetales/*cytology/physiology ; Sulfides/metabolism ; Symbiosis ; Time Factors ; },
abstract = {We develop a symbiogenetic concept of the origin of eukaryotic intracellular motility systems from anaerobic but aerotolerant spirochetes in sulfide-rich environments. The last eukaryotic common ancestors (LECAs) have extant archaeprotist descendants: motile nucleated cells with Embden-Meyerhof glycolysis and substrate-level phosphorylation that lack the alpha-proteobacterial symbiont that became the mitochondrion. Swimming and regulated O(2)-tolerance via sulfide oxidation already had been acquired by sulfidogenic wall-less archaebacteria (thermoplasmas) after aerotolerant cytoplasmic-tubule-containing spirochetes (eubacteria) attached to them. Increasing stability of sulfide-oxidizing/sulfur-reducing consortia analogous to extant sulfur syntrophies (Thiodendron) led to fusion. The eubacteria-archaebacteria symbiosis became permanent as the nucleus evolved by prokaryotic recombination with membrane hypertrophy, analogous to Gemmata obscuriglobus and other delta-proteobacteria with membrane-bounded nucleoids. Histone-coated DNA, protein-synthetic RNAs, amino-acylating, and other enzymes were contributed by the sulfidogen whereas most intracellular motility derives from the spirochete. From this redox syntrophy in anoxic and microoxic Proterozoic habitats LECA evolved. The nucleus originated by recombination of eu- and archaebacterial DNA that remained attached to eubacterial motility structures and became the microtubular cytoskeleton, including the mitotic apparatus. Direct LECA descendants include free-living archaeprotists in anoxic environments: archamoebae, metamonads, parabasalids, and some mammalian symbionts with mitosomes. LECA later acquired the fully aerobic Krebs cycle-oxidative phosphorylation-mitochondrial metabolism by integration of the protomitochondrion, a third alpha-proteobacterial symbiont from which the ancestors to most protoctists, all fungi, plants, and animals evolved. Secondarily anaerobic eukaryotes descended from LECA after integration of this oxygen-respiring eubacterium. Explanatory power and experimental predictions for molecular biology of the LECA concept are stated.},
}
@article {pmid16949250,
year = {2006},
author = {Haitina, T and Lindblom, J and Renström, T and Fredriksson, R},
title = {Fourteen novel human members of mitochondrial solute carrier family 25 (SLC25) widely expressed in the central nervous system.},
journal = {Genomics},
volume = {88},
number = {6},
pages = {779-790},
doi = {10.1016/j.ygeno.2006.06.016},
pmid = {16949250},
issn = {0888-7543},
mesh = {Animals ; *Biological Transport ; Brain/metabolism ; Central Nervous System/*metabolism ; Computational Biology/methods ; Female ; Humans ; Male ; Markov Chains ; Membrane Transport Proteins/*genetics/*metabolism ; Mice ; Mitochondria/*metabolism ; *Multigene Family ; Phylogeny ; Polymerase Chain Reaction/methods ; Rats ; Rats, Sprague-Dawley ; Synteny ; },
abstract = {Members of the solute carrier family 25 (SLC25) are known to transport molecules over the mitochondrial membrane. In this paper we present 14 novel members of SLC25 family in human. These were provided with following gene symbols by the HGNC: SLC25A32, SLC25A33, SLC25A34, SLC25A35, SLC25A37, SLC25A38, SLC25A39, SLC25A40, SLC25A41, SLC25A42, SLC25A43, SLC25A44, SLC25A45, and SLC25A46. We also identified the orthologues for these genes in rat and mouse. Moreover, we found yeast orthologues for 9 of these genes and show that the predicted substrate binding residues are highly conserved in the human and yeast proteins. We performed a comprehensive tissue localization study for 9 of these genes on a panel of 30 rat tissues with quantitative real-time polymerse chain reaction. We detected their mRNA in a wide number of tissues, both in brain and in periphery. This study provides an overall roadmap of the repertoire of the SLC25 family in mammals, showing that there are at least 46 genes in the human genome coding for mitochondrial transporters.},
}
@article {pmid16949352,
year = {2006},
author = {Faure, E and Casanova, JP},
title = {Comparison of chaetognath mitochondrial genomes and phylogenetical implications.},
journal = {Mitochondrion},
volume = {6},
number = {5},
pages = {258-262},
doi = {10.1016/j.mito.2006.07.004},
pmid = {16949352},
issn = {1567-7249},
mesh = {Animals ; Base Sequence ; *DNA, Mitochondrial ; Genes, Mitochondrial ; *Genome ; Invertebrates/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; },
abstract = {Two complete mitochondrial genomes (mtDNAs) of chaetognaths, Spadella cephaloptera and Paraspadella gotoi, have been recently published. These genomes are highly unusual. They are the smallest metazoan mtDNAs so far known; atp6 and atp8 genes are missing; lastly, our reanalysis has evidenced that, contrarily to what has been previously published for one sequence, both contain a unique transfer RNA (tRNA(Met)) evidencing that both have the same gene content. Indeed, even if the gene order seems very different, two gene blocks are conserved. In addition, comparison of gene arrangement suggests phylogenetical relationships between chaetognaths and some lophotrochozoa like annelids and molluscs.},
}
@article {pmid16950266,
year = {2006},
author = {Troell, K and Engström, A and Morrison, DA and Mattsson, JG and Höglund, J},
title = {Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants.},
journal = {International journal for parasitology},
volume = {36},
number = {12},
pages = {1305-1316},
doi = {10.1016/j.ijpara.2006.06.015},
pmid = {16950266},
issn = {0020-7519},
mesh = {Animals ; Base Sequence ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Gene Amplification/genetics ; Genes, Helminth/genetics ; Genetic Markers/genetics ; Genetics, Population ; Genotype ; Goats/parasitology ; Haemonchus/classification/*genetics ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Polymorphism, Genetic/*genetics ; Ruminants/*parasitology ; Sheep/parasitology ; },
abstract = {We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.},
}
@article {pmid16968273,
year = {2006},
author = {Peijnenburg, KT and Fauvelot, C and Breeuwer, JA and Menken, SB},
title = {Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.},
journal = {Molecular ecology},
volume = {15},
number = {11},
pages = {3319-3338},
doi = {10.1111/j.1365-294X.2006.03002.x},
pmid = {16968273},
issn = {0962-1083},
mesh = {Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Ecosystem ; Electron Transport Complex IV/chemistry/genetics ; Europe ; Genetic Markers/genetics ; Genetic Variation ; Haplotypes ; Mediterranean Sea ; Microsatellite Repeats/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plankton/enzymology/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.},
}
@article {pmid16968450,
year = {2006},
author = {Hoppenrath, M and Leander, BS},
title = {Dinoflagellate, Euglenid, or Cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp.},
journal = {The Journal of eukaryotic microbiology},
volume = {53},
number = {5},
pages = {327-342},
doi = {10.1111/j.1550-7408.2006.00110.x},
pmid = {16968450},
issn = {1066-5234},
mesh = {Animals ; Cell Nucleus/ultrastructure ; Cell Wall/ultrastructure ; Cytoplasm/ultrastructure ; DNA, Ribosomal/genetics ; Dinoflagellida/classification/*genetics/ultrastructure ; Euglenida/classification/*genetics/ultrastructure ; Eukaryota/classification/genetics/ultrastructure ; Microscopy, Electron, Scanning/methods ; Microscopy, Electron, Transmission/methods ; *Phylogeny ; },
abstract = {Protaspis is an enigmatic genus of marine phagotrophic biflagellates that have been tentatively classified with several different groups of eukaryotes, including dinoflagellates, euglenids, and cercomonads. This uncertainty led us to investigate the phylogenetic position of Protaspis grandis n. sp. with ultrastructural and small subunit (SSU) rDNA sequence data. Our results demonstrated that the cells were dorsoventrally flattened, shaped like elongated ovals with parallel lateral sides, 32.5-55.0 mum long and 20.0-35.0 mum wide. Moreover, two heterodynamic flagella emerged through funnels that were positioned subapically, each within a depression and separated by a distinctive protrusion. A complex multilayered wall surrounded the cell. Like dinoflagellates and euglenids, the nucleus contained permanently condensed chromosomes and a large nucleolus throughout the cell cycle. Pseudopodia containing numerous mitochondria with tubular cristae emerged from a ventral furrow through a longitudinal slit that was positioned posterior to the protrusion and flagellar apparatus. Batteries of extrusomes were present within the cytoplasm and had ejection sites through pores in the cell wall. The SSU rDNA phylogeny demonstrated a very close relationship between the benthic P. grandis n. sp. and the planktonic Cryothecomonas longipes. These ultrastructural and molecular phylogenetic data for Protaspis indicated that the current taxonomy of Protaspis and Crythecomonas is in need of re-evaluation. The composition and identity of Protaspis is reviewed and suggestions for future taxonomic changes are presented. Problems within the genus Cryothecomonas are highlighted as well, and the missing data needed to resolve ambiguities between the two genera are clarified.},
}
@article {pmid16972986,
year = {2006},
author = {Rot, C and Goldfarb, I and Ilan, M and Huchon, D},
title = {Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria.},
journal = {BMC evolutionary biology},
volume = {6},
number = {},
pages = {71},
pmid = {16972986},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; Ecosystem ; Electron Transport Complex IV/genetics ; Fungi/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/classification/*genetics/*microbiology ; RNA/chemistry/genetics ; RNA, Mitochondrial ; Sequence Alignment ; Symbiosis/*genetics ; },
abstract = {BACKGROUND: The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera).<br><br>RESULTS: A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor.<br><br>CONCLUSION: Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.},
}
@article {pmid16978258,
year = {2006},
author = {Bouzenzana, J and Pelosi, L and Briolay, A and Briolay, J and Bulone, V},
title = {Identification of the first Oomycete annexin as a (1--&gt;3)-beta-D-glucan synthase activator.},
journal = {Molecular microbiology},
volume = {62},
number = {2},
pages = {552-565},
doi = {10.1111/j.1365-2958.2006.05389.x},
pmid = {16978258},
issn = {0950-382X},
mesh = {Amino Acid Sequence ; Annexins/analysis/genetics/*metabolism ; Blotting, Western/methods ; Calcium Chloride/pharmacology ; Catalysis/drug effects ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; Egtazic Acid/pharmacology ; Electrophoresis, Gel, Two-Dimensional/methods ; Electrophoresis, Polyacrylamide Gel/methods ; Glucosyltransferases/genetics/*metabolism ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Molecular Weight ; Oomycetes/enzymology/genetics ; Phylogeny ; Saprolegnia/*enzymology/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein/methods ; Sequence Homology, Amino Acid ; },
abstract = {(1-->3)-beta-D-Glucans are major components of the cell walls of Oomycetes and as such they play an essential role in the morphogenesis and growth of these microorganisms. Despite the biological importance of (1-->3)-beta-D-glucans, their mechanisms of biosynthesis are poorly understood. Previous studies on (1-->3)-beta-D-glucan synthases from Saprolegnia monoica have shown that three protein bands of an apparent molecular weight of 34, 48 and 50 kDa co-purify with enzyme activity. However, none of the corresponding proteins have been identified. Here we have identified, purified, sequenced and characterized a protein from the 34 kDa band and clearly shown that it has all the biochemical properties of proteins from the annexin family. In addition, we have unequivocally demonstrated that the purified protein is an activator of (1-->3)-beta-D-glucan synthase. This represents a new type of function for proteins belonging to the annexin family. Two other proteins from the 48 and 50 kDa bands were identified as ATP synthase subunits, which most likely arise from contaminations by mitochondria during membrane preparation. The results, which are discussed in relation with the possible regulation mechanisms of (1-->3)-beta-D-glucan synthases, represent a first step towards a better understanding of cell wall polysaccharide biosynthesis in Oomycetes.},
}
@article {pmid16990491,
year = {2007},
author = {Nishimoto, G and Sasaki, G and Yaoita, E and Nameta, M and Li, H and Furuse, K and Fujinaka, H and Yoshida, Y and Mitsudome, A and Yamamoto, T},
title = {Molecular characterization of water-selective AQP (EbAQP4) in hagfish: insight into ancestral origin of AQP4.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {292},
number = {1},
pages = {R644-51},
doi = {10.1152/ajpregu.00362.2006},
pmid = {16990491},
issn = {0363-6119},
mesh = {Amino Acid Sequence ; Animals ; Biological Transport, Active/physiology ; Blotting, Western ; Cell Membrane/metabolism ; DNA, Complementary/biosynthesis/genetics ; Freeze Fracturing ; Gills/metabolism ; Hagfishes/*metabolism ; Immunohistochemistry ; Mercury/pharmacology ; Microscopy, Electron ; Molecular Sequence Data ; Multigene Family/genetics ; Oocytes/metabolism ; Permeability ; Phylogeny ; RNA/biosynthesis/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Water/metabolism ; Xenopus ; },
abstract = {Hagfish (Eptatretus burgeri) are agnathous and are the earliest vertebrates still in existence. Pavement cells adjacent to the mitochondria-rich cells show orthogonal arrays of particles (OAPs) in the gill of hagfish, a known ultrastructural morphology of aquaporin (AQP) in mammalian freeze-replica studies, suggesting that an AQP homolog exists in pavement cells. We therefore cloned water channels from hagfish gill and examined their molecular characteristics. The cloned AQP [E. burgeri AQP4 (EbAQP4)] encodes 288 amino acids, including two NPA motifs and six transmembrane regions. The deduced amino acid sequence of EbAQP4 showed high homology to mammalian and avian AQP4 (rat, 44%; quail, 43%) and clustered with AQP4 subsets by the molecular phylogenetic tree. The osmotic water permeability of Xenopus oocytes injected with EbAQP4 cRNA increased eightfold compared with water-injected controls and was not reversibly inhibited by 0.3 mM HgCl(2). EbAQP4 mRNA expression in the gill was demonstrated by the RNase protection assay; antibody raised against the COOH terminus of EbAQP4 also detected (by Western blot analysis) a major approximately 31-kDa band in the gill. Immunohistochemistry and immunoelectron microscopy showed EbAQP4 localized along the basolateral membranes of gill pavement cells. In freeze-replica studies, OAPs were detected on the protoplasmic face of the split membrane comprising particles 5-6 nm long on the basolateral side of the pavement cells. These observations suggest that EbAQP4 is an ancestral water channel of mammalian AQP4 and plays a role in basolateral water transport in the gill pavement cells.},
}
@article {pmid17021930,
year = {2006},
author = {Ruiz-González, MX and Marín, I},
title = {Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes.},
journal = {Journal of molecular evolution},
volume = {63},
number = {4},
pages = {504-512},
pmid = {17021930},
issn = {0022-2844},
mesh = {ATP-Dependent Proteases/chemistry/genetics ; Amino Acid Sequence ; Bacteria/*genetics ; Cell Lineage ; Escherichia coli Proteins/chemistry/genetics ; Eukaryotic Cells/*metabolism ; Genes, Bacterial/*genetics ; Mitochondria ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Proteasome Endopeptidase Complex/*genetics ; Sequence Alignment ; },
abstract = {Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU complex has been envisaged as a precursor or ancestral type of proteasome. Here we show that species of most of the main eukaryotic lineages have HslU and HslV genes very similar to those found in proteobacteria. We have detected them in amoebozoa, plantae, chromoalveolata, rhizaria, and excavata species. Phylogenetic analyses suggest that these genes have been obtained by endosymbiosis from the proteobacterial ancestor that gave rise to eukaryotic mitochondria. The products encoded by these eukaryotic genes adopt, according to modeling based on the known crystal structures of prokaryotic HslU and HslV proteins, conformations that are compatible with their being fully active, suggesting that functional HslVU complexes may be present in many eukaryotic species.},
}
@article {pmid17035181,
year = {2006},
author = {Wang, HJ and Zhang, ZM and Liu, ZL and Xiong, GM},
title = {[A molecular phylogeny of Shennongjia white bear based on mitochondrial cytochrome b gene sequence].},
journal = {Yi chuan = Hereditas},
volume = {28},
number = {10},
pages = {1237-1241},
doi = {10.1360/yc-006-1237},
pmid = {17035181},
issn = {0253-9772},
mesh = {Animals ; Base Sequence ; China ; Cytochromes b/*genetics ; Databases, Genetic ; Mitochondria/*genetics ; Mutation ; *Phylogeny ; Ursidae/*classification/*genetics ; },
abstract = {The phylogenetic relationship of Shennongjia white bear has been an open question. Total DNA was extracted and sequenced from hair and feces of Shennongjia white bear. Based on the partial Cyt b gene sequence obtained from the samples, the authors aligned them using the Clustal W software program. The MEGA software was used to analyze the divergences and base substitutions of the partial Cyt b gene among the 11 species: Shennongjia white bear, Selenarctos thibetanus, Euarctos americanus, Helarctos malayanus, Ursus arctos, Thalarctos maritimus, Melursus ursinus, Procyon lotor, Ailuropoda melanoleuca, Ailurus fulgens and Tremarctos ornatus. The phylogenetic trees constructed by multiple methods (NJ and MP) supported nearly the same topology. Our molecular results show that the sequence divergence between Shennongjia white bear and Asiatic black bear (Selenarctos thibetanus) is lower than that between other species.},
}
@article {pmid17058107,
year = {2007},
author = {Luchetti, A and Trentini, M and Pampiglione, S and Fioravanti, ML and Mantovani, B},
title = {Genetic variability of Tunga penetrans (Siphonaptera, Tungidae) sand fleas across South America and Africa.},
journal = {Parasitology research},
volume = {100},
number = {3},
pages = {593-598},
pmid = {17058107},
issn = {0932-0113},
mesh = {Africa ; Animals ; Base Sequence ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Siphonaptera/*genetics ; South America ; },
abstract = {Tunga penetrans is a widely distributed sand flea, infecting men and domestic animals. It originated in South America, but it is now also endemic of Sub-Saharan Africa due to a recent accidental introduction. Previous genetic analyses indicated a very limited variability in the Ecuadorian populations; on the other hand, samples from Madagascar resulted to be genetically isolated. To better examine the genetic variability of T. penetrans, a wider sampling was analysed for mitochondrial (cytochrome oxidase II) and nuclear (ribosomal internal transcribed spacer [ITS] 2) DNA sequences. The mitochondrial marker confirms the low genetic variability, with few haplotypes characterizing the majority of individuals from different populations. Haplotype distribution is in agreement with a recent colonization of Africa and with a rapid spreading across this continent. Moreover, a consistent gene flow between the Pacific and Atlantic South American populations emerges, possibly due to human and/or animal cross-Andean dispersal. On the other hand, the ITS2 marker depicts a sharply diverging pattern with samples collected in Ecuador unequivocally distinguished from the Brazilian and African ones. On the whole, taking into account also the molecular features of the marker used, data here presented are better interpreted in the light of a high dispersal ability of T. penetrans, probably reducing the phylogeographic signal.},
}
@article {pmid17061145,
year = {2007},
author = {Canestrelli, D and Verardi, A and Nascetti, G},
title = {Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear markers.},
journal = {Genetica},
volume = {130},
number = {3},
pages = {241-255},
doi = {10.1007/s10709-006-9102-9},
pmid = {17061145},
issn = {0016-6707},
mesh = {Alleles ; Animals ; Anura/*genetics ; Cell Nucleus/*metabolism ; Cytochromes b/metabolism ; Cytoplasm/metabolism ; DNA, Mitochondrial/genetics ; Enzymes/chemistry ; Gene Frequency ; *Genetic Variation ; Geography ; Italy ; Mitochondria/*metabolism ; Models, Genetic ; Phylogeny ; },
abstract = {The genetic differentiation among 33 populations of the Italian treefrog, Hyla intermedia (Anura: Hylidae), was investigated using both biparentally (23 allozyme loci) and maternally (partial mitochondrial cytochrome b gene) inherited markers. Two main population groups were evidenced by both markers, located north and south of the northern Apennines. However, the pattern of differentiation between these two groups was much less pronounced at allozymes than at mtDNA, leading to gene flow estimates that were 25 times lower at mitochondrial than at nuclear level. Also, the mtDNA divergence between the two groups was particularly marked for two cospecific lineages of anuran amphibians (the P-distance being on average 9.04%), while their average genetic distance at allozymes was comparatively low (D (NEI) = 0.07). This contrasting pattern of nuclear versus mitochondrial genetic variation is discussed in the context of: (1) marker specific selection, (2) secondary contact and sex-biased gene flow and (3) ancestral polymorphism and colonization from north to south. Finally we emphasize how, for population genetic studies, the use of multiple markers having distinct evolutionary properties can help unravel the existence of more complex evolutionary histories.},
}
@article {pmid17071643,
year = {2006},
author = {Navrot, N and Collin, V and Gualberto, J and Gelhaye, E and Hirasawa, M and Rey, P and Knaff, DB and Issakidis, E and Jacquot, JP and Rouhier, N},
title = {Plant glutathione peroxidases are functional peroxiredoxins distributed in several subcellular compartments and regulated during biotic and abiotic stresses.},
journal = {Plant physiology},
volume = {142},
number = {4},
pages = {1364-1379},
pmid = {17071643},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Binding Sites ; Gene Expression Regulation, Plant ; Genome, Plant ; Glutathione Peroxidase/analysis/chemistry/*physiology ; Green Fluorescent Proteins/analysis ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Peroxides/metabolism ; Phylogeny ; Plant Proteins/analysis/chemistry/*physiology ; Populus/chemistry/*enzymology/genetics ; Protein Isoforms/analysis/chemistry/physiology ; Recombinant Fusion Proteins/analysis ; Sequence Alignment ; Substrate Specificity ; Thioredoxins/metabolism ; },
abstract = {We provide here an exhaustive overview of the glutathione (GSH) peroxidase (Gpx) family of poplar (Populus trichocarpa). Although these proteins were initially defined as GSH dependent, in fact they use only reduced thioredoxin (Trx) for their regeneration and do not react with GSH or glutaredoxin, constituting a fifth class of peroxiredoxins. The two chloroplastic Gpxs display a marked selectivity toward their electron donors, being exclusively specific for Trxs of the y type for their reduction. In contrast, poplar Gpxs are much less specific with regard to their electron-accepting substrates, reducing hydrogen peroxide and more complex hydroperoxides equally well. Site-directed mutagenesis indicates that the catalytic mechanism and the Trx-mediated recycling process involve only two (cysteine [Cys]-107 and Cys-155) of the three conserved Cys, which form a disulfide bridge with an oxidation-redox midpoint potential of -295 mV. The reduction/formation of this disulfide is detected both by a shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by measuring the intrinsic tryptophan fluorescence of the protein. The six genes identified coding for Gpxs are expressed in various poplar organs, and two of them are localized in the chloroplast, with one colocalizing in mitochondria, suggesting a broad distribution of Gpxs in plant cells. The abundance of some Gpxs is modified in plants subjected to environmental constraints, generally increasing during fungal infection, water deficit, and metal stress, and decreasing during photooxidative stress, showing that Gpx proteins are involved in the response to both biotic and abiotic stress conditions.},
}
@article {pmid17080938,
year = {2006},
author = {Li, WY and Wong, FL and Tsai, SN and Phang, TH and Shao, G and Lam, HM},
title = {Tonoplast-located GmCLC1 and GmNHX1 from soybean enhance NaCl tolerance in transgenic bright yellow (BY)-2 cells.},
journal = {Plant, cell &amp; environment},
volume = {29},
number = {6},
pages = {1122-1137},
doi = {10.1111/j.1365-3040.2005.01487.x},
pmid = {17080938},
issn = {0140-7791},
mesh = {Amino Acid Sequence ; Bacterial Proteins/analysis/genetics ; Chloride Channels/chemistry/*genetics/physiology ; Cloning, Molecular ; Intracellular Membranes/drug effects/*metabolism/ultrastructure ; Luminescent Proteins/analysis/genetics ; Mitochondria/drug effects/metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*genetics/physiology ; Plants, Genetically Modified/drug effects/metabolism ; Polyethylene Glycols/pharmacology ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/analysis ; Sequence Alignment ; Sodium Chloride/*pharmacology ; Sodium-Hydrogen Exchangers/chemistry/*genetics/physiology ; Glycine max/drug effects/*genetics/ultrastructure ; Surface-Active Agents/pharmacology ; Nicotiana/genetics ; Vacuoles/drug effects/metabolism/ultrastructure ; },
abstract = {Genes encoding ion transporters that regulate ion homeostasis in soybean have not been carefully investigated. Using degenerate primers, we cloned a putative chloride channel gene (GmCLC1) and a putative Na+/H+ antiporter gene (GmNHX1) from soybean. Confocal microscopic studies using yellow fluorescent fusion proteins revealed that GmCLC1 and GmNHX1 were both localized on tonoplast. The expressions of GmCLC1 and GmNHX1 were both induced by NaCl or dehydration stress imposed by polyethylene glycol (PEG). Using mitochondrial integrity and cell death as the damage indicators, a clear alleviation under NaCl stress (but not PEG stress) was observed in both GmCLC1 and GmNHX1 transgenic cells. Using fluorescent dye staining and quenching, respectively, a higher concentration of chloride ion (Cl-) or sodium ion (Na+) was observed in isolated vacuoles in the cells of GmCLC1 and of GmNHX1 transgenic lines. Our result suggested that these vacuolar-located ion transporters function to sequester ions from cytoplasm into vacuole to reduce its toxic effects.},
}
@article {pmid17082386,
year = {2006},
author = {Sassera, D and Beninati, T and Bandi, C and Bouman, EAP and Sacchi, L and Fabbi, M and Lo, N},
title = {'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {56},
number = {Pt 11},
pages = {2535-2540},
doi = {10.1099/ijs.0.64386-0},
pmid = {17082386},
issn = {1466-5026},
mesh = {Alphaproteobacteria/*classification/*isolation &amp; purification/physiology/ultrastructure ; Animals ; Cytoplasm/microbiology ; DNA Gyrase/genetics ; DNA, Bacterial/chemistry/genetics ; Female ; In Situ Hybridization ; Ixodes/*microbiology/ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Mitochondrial Membranes/microbiology ; Molecular Sequence Data ; Ovary/cytology/microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Symbiosis ; },
abstract = {An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name 'Candidatus Midichloria mitochondrii' for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44%). Based on EM and in situ hybridization studies, the presence of 'Candidatus M. mitochondrii' in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. 'Candidatus M. mitochondrii' is the first bacterium to be identified that resides within animal mitochondria.},
}
@article {pmid17086397,
year = {2007},
author = {Murayama, S and Handa, H},
title = {Genes for alkaline/neutral invertase in rice: alkaline/neutral invertases are located in plant mitochondria and also in plastids.},
journal = {Planta},
volume = {225},
number = {5},
pages = {1193-1203},
pmid = {17086397},
issn = {0032-0935},
mesh = {Arabidopsis/classification/genetics ; Cloning, Molecular ; DNA Primers ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Hydrogen-Ion Concentration ; Mitochondria/*enzymology ; Oryza/classification/*enzymology/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plastids/*enzymology ; Recombinant Fusion Proteins/metabolism ; beta-Fructofuranosidase/*genetics/metabolism ; },
abstract = {Two cDNA clones (OsNIN1 and OsNIN3) encoding an alkaline/neutral invertase localized in organelles were identified from rice. The deduced amino acid sequences of these cDNA clones showed high homology to other plant alkaline/neutral invertases. Semi-quantitative reverse transcription polymerase chain reaction revealed that the expression of OsNIN1 was constitutive and independent of organ difference, although its expression level was low. Analyses using five types of web software for the prediction of protein localization in the cell, Predotar, PSORT, Mitoprot, TargetP, and ChloroP, strongly supported the possibility that OsNIN1 is transported into the mitochondria and that OsNIN3 is transported into plastids. Transient expression of fusion proteins combining the amino terminal region of these two proteins with sGFP demonstrated that N-OsNIN1::GFP and N-OsNIN3::GFP fusion proteins were transported into the mitochondria and plastids, respectively. We expressed the OsNIN1 protein in vitro and revealed that the translated protein had an invertase activity. These results clearly indicate that some of alkaline/neutral invertases are located in plant organelles, mitochondria and plastids, and that they might have a novel physiological function in plant organelles.},
}
@article {pmid17092626,
year = {2007},
author = {Lopez, L and Picardi, E and Quagliariello, C},
title = {RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales.},
journal = {Biochimie},
volume = {89},
number = {1},
pages = {159-167},
doi = {10.1016/j.biochi.2006.09.011},
pmid = {17092626},
issn = {0300-9084},
mesh = {Amino Acid Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Liliaceae/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Polymerase Chain Reaction ; *RNA Editing ; RNA, Plant/*genetics ; Ribosomal Proteins/*genetics ; },
abstract = {RNA editing in plant mitochondria alters the RNA sequence by converting C-to-U or U-to-C at a specific site. We investigated the requirement for RNA editing in the complete genomic sequences of the gene encoding the cytochrome oxidase subunit III (cox3) and the ribosomal protein S13 (rps13) in 59 closely related species within the Asparagales and Liliales (monocots). To obtain a comprehensive picture of the degree of variation in editing we explored the non-synonymous RNA editing sites within the newly sequenced cox3 and rps13 genes by a comparative phylogenetic approach. RNA editing is predicted to occur in all the surveyed species, but to different extents. Zero to one non-synonymous editing site is inferred in the cox3 mRNA in species from Amaryllidaceae and Iridaceae. No RNA editing of rps13 mRNAs is required in Amaryllidaceae, because all respective genomic sequences resemble the edited version of the mRNAs of other analysed land plants. The observed absence of cox3 and rps13 RNA editing in Iridaceae and Amaryllidaceae and the striking RNA editing reduction of ccb2 in the latter family is likely generated by recombination and reverse transcription mediated events involving edited mitochondrial transcripts.},
}
@article {pmid17098851,
year = {2007},
author = {Murcha, MW and Elhafez, D and Lister, R and Tonti-Filippini, J and Baumgartner, M and Philippar, K and Carrie, C and Mokranjac, D and Soll, J and Whelan, J},
title = {Characterization of the preprotein and amino acid transporter gene family in Arabidopsis.},
journal = {Plant physiology},
volume = {143},
number = {1},
pages = {199-212},
pmid = {17098851},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/ultrastructure ; Arabidopsis Proteins/analysis/classification/*genetics ; Carrier Proteins/analysis/classification/*genetics ; Chloroplasts/metabolism ; Genetic Complementation Test ; Genome, Plant ; Membrane Transport Proteins/genetics ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; },
abstract = {Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic organisms, this family of proteins has greatly expanded in plants, with 24 loci in rice (Oryza sativa). Most of the Arabidopsis and rice genes are orthologous, indicating expansion of this family before monocot and dicot divergence. In vitro protein uptake assays, in vivo green fluorescent protein tagging, and immunological analyses of selected proteins determined either mitochondrial or plastidic localization for 10 and six proteins, respectively. The protein encoded by At5g24650 is targeted to both mitochondria and chloroplasts and, to our knowledge, is the first membrane protein reported to be targeted to mitochondria and chloroplasts. Three genes encoded translocase of the inner mitochondrial membrane (TIM)17-like proteins, three TIM23-like proteins, and three outer envelope protein16-like proteins in Arabidopsis. The identity of Arabidopsis TIM22-like proteins is most likely a protein encoded by At3g10110/At1g18320, based on phylogenetic analysis, subcellular localization, and complementation of a yeast (Saccharomyces cerevisiae) mutant and coexpression analysis. The lack of a preprotein and amino acid transporter domain in some proteins, localization in mitochondria, plastids, or both, variation in gene structure, and the differences in expression profiles indicate that the function of this family has diverged in plants beyond roles in protein translocation.},
}
@article {pmid17110332,
year = {2006},
author = {Qin, Y and Polacek, N and Vesper, O and Staub, E and Einfeldt, E and Wilson, DN and Nierhaus, KH},
title = {The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome.},
journal = {Cell},
volume = {127},
number = {4},
pages = {721-733},
doi = {10.1016/j.cell.2006.09.037},
pmid = {17110332},
issn = {0092-8674},
mesh = {Amino Acid Sequence ; Computational Biology ; *Conserved Sequence ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; GTP Phosphohydrolases/metabolism ; Green Fluorescent Proteins/metabolism ; Models, Genetic ; Molecular Sequence Data ; Peptide Elongation Factor G/chemistry ; Peptide Elongation Factors/*metabolism ; Peptide Initiation Factors ; Phylogeny ; Protein Biosynthesis/*genetics ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Ribosomes/*metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors/chemistry/*metabolism ; },
abstract = {The ribosomal elongation cycle describes a series of reactions prolonging the nascent polypeptide chain by one amino acid and driven by two universal elongation factors termed EF-Tu and EF-G in bacteria. Here we demonstrate that the extremely conserved LepA protein, present in all bacteria and mitochondria, is a third elongation factor required for accurate and efficient protein synthesis. LepA has the unique function of back-translocating posttranslocational ribosomes, and the results suggest that it recognizes ribosomes after a defective translocation reaction and induces a back-translocation, thus giving EF-G a second chance to translocate the tRNAs correctly. We suggest renaming LepA as elongation factor 4 (EF4).},
}
@article {pmid17120136,
year = {2007},
author = {Carrie, C and Murcha, MW and Millar, AH and Smith, SM and Whelan, J},
title = {Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria.},
journal = {Plant molecular biology},
volume = {63},
number = {1},
pages = {97-108},
pmid = {17120136},
issn = {0167-4412},
mesh = {Acetyl-CoA C-Acetyltransferase/genetics/*metabolism ; Acetyl-CoA C-Acyltransferase/genetics/*metabolism ; Amino Acid Sequence ; Arabidopsis Proteins/genetics/metabolism ; Cluster Analysis ; Cytosol/*metabolism ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peroxisomes/*metabolism ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; },
abstract = {The sub-cellular location of enzymes of fatty acid beta-oxidation in plants is controversial. In the current debate the role and location of particular thiolases in fatty acid degradation, fatty acid synthesis and isoleucine degradation are important. The aim of this research was to determine the sub-cellular location and hence provide information about possible functions of all the putative 3-ketoacyl-CoA thiolases (KAT) and acetoacetyl-CoA thiolases (ACAT) in Arabidopsis. Arabidopsis has three genes predicted to encode KATs, one of which encodes two polypeptides that differ at the N-terminal end. Expression in Arabidopsis cells of cDNAs encoding each of these KATs fused to green fluorescent protein (GFP) at their C-termini showed that three are targeted to peroxisomes while the fourth is apparently cytosolic. The four KATs are also predicted to have mitochondrial targeting sequences, but purified mitochondria were unable to import any of the proteins in vitro. Arabidopsis also has two genes encoding a total of five different putative ACATs. One isoform is targeted to peroxisomes as a fusion with GFP, while the others display no targeting in vivo as GFP fusions, or import into isolated mitochondria. Analysis of gene co-expression clusters in Arabidopsis suggests a role for peroxisomal KAT2 in beta-oxidation, while KAT5 co-expresses with genes of the flavonoid biosynthesis pathway and cytosolic ACAT2 clearly co-expresses with genes of the cytosolic mevalonate biosynthesis pathway. We conclude that KATs and ACATs are present in the cytosol and peroxisome, but are not found in mitochondria. The implications for fatty acid beta-oxidation and for isoleucine degradation in mitochondria are discussed.},
}
@article {pmid17123444,
year = {2006},
author = {Roy, V and Demanche, C and Livet, A and Harry, M},
title = {Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers.},
journal = {BMC evolutionary biology},
volume = {6},
number = {},
pages = {102},
pmid = {17123444},
issn = {1471-2148},
mesh = {Animals ; Base Sequence ; DNA, Intergenic/analysis ; DNA, Mitochondrial/analysis ; Gabon ; *Genetic Drift ; Genetic Markers ; *Genetic Variation ; Isoptera/*genetics ; Microsatellite Repeats ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {BACKGROUND: Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies.<br><br>RESULTS: Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve.<br><br>CONCLUSION: Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters.},
}
@article {pmid17148377,
year = {2006},
author = {Tokuda, G and Yamada, A and Nakano, K and Arita, N and Yamasaki, H},
title = {Occurrence and recent long-distance dispersal of deep-sea hydrothermal vent shrimps.},
journal = {Biology letters},
volume = {2},
number = {2},
pages = {257-260},
pmid = {17148377},
issn = {1744-9561},
mesh = {Animals ; Decapoda/*classification/genetics ; Electron Transport Complex IV/genetics ; *Environment ; Japan ; Mitochondria/enzymology ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 18S/genetics ; Seawater ; },
abstract = {Deep-sea hydrothermal vents and methane seeps are extreme environments that have a high concentration of hydrogen sulphide. However, abundant unique invertebrates including shrimps of the family Bresiliidae have been found in such environments. The bresiliid shrimps are believed to have radiated in the Miocene (less than 20 Myr); however, the period when and the mechanisms by which they dispersed across the hydrothermal vents and cold seeps in oceans worldwide have not been clarified. In the present study, we collected the deep-sea blind shrimp Alvinocaris longirostris from the hydrothermal vent site in the Okinawa Trough and carried out the first investigation of the 18S rRNA gene of a bresiliid shrimp. The phylogenetic analysis revealed that the bresiliid shrimp is situated at an intermediate lineage within the infraorder Caridea and shows monophyly with palaemonid shrimps, which live in shallow sea and freshwater. Furthermore, the mitochondrial cytochrome oxidase I (COI) gene sequences were analysed to determine the phylogenetic relationship with known bresiliid shrimps. A. longirostris of the Okinawa Trough had two haplotypes of the COI gene, one of which was identical to the Alvinocaris sp. of the cold seeps in Sagami Bay. These results indicate that a long-distance dispersal of A. longirostris occurred possibly within the last 100,000 years.},
}
@article {pmid17152948,
year = {2006},
author = {Kimura, M and Dhondt, AA and Irby J, L},
title = {Phylogeographic structuring of Plasmodium lineages across the North American range of the house finch (Carpodacus Mexicanus).},
journal = {The Journal of parasitology},
volume = {92},
number = {5},
pages = {1043-1049},
doi = {10.1645/GE-639R.1},
pmid = {17152948},
issn = {0022-3395},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Protozoan/blood/chemistry/isolation &amp; purification ; Finches/*parasitology ; Haplotypes ; Malaria, Avian/epidemiology/*parasitology ; Mitochondria/enzymology/genetics ; Phylogeny ; Plasmodium/*classification/genetics ; Polymerase Chain Reaction/veterinary ; Prevalence ; United States/epidemiology ; },
abstract = {The determinants of the geographic distribution of avian hematozoa are poorly understood. Sampling parasites from one avian host species across a wide geographic range is an accepted approach to separate the potential influence of host species distribution from geographic effects not directly related to host species biology. We used polymerase chain reaction to screen samples for hematozoan infection from 490 house finches (Carpodacus mexicanus) collected at 8 sites spanning continental North America. To explore geographic patterns of parasite lineage distributions, we sequenced a portion of the mitochondrial cytochrome b gene of Plasmodium species infecting 77 house finches. We identified 5 distinct Plasmodium haplotypes representing 3 lineages that likely represent 3 species. One lineage was common at all sites where we detected Plasmodium species. The second lineage contained 3 haplotypes that showed phylogeographic structuring on a continent-wide scale, with 1 haplotype common in eastern North America and 2 common in western North America. The third divergent lineage was recovered from 1 individual host. Considered together, the partial phylogeographic structuring of Plasmodium cytochrome b lineages over the range of the house finch suggests that parasite lineage distribution is not solely dependent on host species distribution, and other factors such as arthropod vector competence and distribution may be important.},
}
@article {pmid17158683,
year = {2007},
author = {Kitada, S and Uchiyama, T and Funatsu, T and Kitada, Y and Ogishima, T and Ito, A},
title = {A protein from a parasitic microorganism, Rickettsia prowazekii, can cleave the signal sequences of proteins targeting mitochondria.},
journal = {Journal of bacteriology},
volume = {189},
number = {3},
pages = {844-850},
pmid = {17158683},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Kinetics ; Metalloendopeptidases/chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Peptides/chemistry/metabolism ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Rickettsia prowazekii/genetics/*metabolism ; Sequence Alignment ; Mitochondrial Processing Peptidase ; },
abstract = {The obligate intracellular parasitic bacteria rickettsiae are more closely related to mitochondria than any other microbes investigated to date. A rickettsial putative peptidase (RPP) was found to resemble the alpha and beta subunits of mitochondrial processing peptidase (MPP), which cleaves the transport signal sequences of mitochondrial preproteins. RPP showed completely conserved zinc-binding and catalytic residues compared with beta-MPP but barely contained any of the glycine-rich loop region characteristic of alpha-MPP. When the biochemical activity of RPP purified from a recombinant source was analyzed, RPP specifically hydrolyzed basic peptides and presequence peptides with frequent cleavage at their MPP-processing sites. Moreover, RPP appeared to activate yeast beta-MPP so that it processed preproteins with shorter presequences. Thus, RPP behaves as a bifunctional protein that could act as a basic peptide peptidase and a somewhat regulatory protein for other protein activities in rickettsiae. These are the first biological and enzymological studies to report that a protein from a parasitic microorganism can cleave the signal sequences of proteins targeted to mitochondria.},
}
@article {pmid17158739,
year = {2006},
author = {Mukherjee, M and Brown, MT and McArthur, AG and Johnson, PJ},
title = {Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis.},
journal = {Eukaryotic cell},
volume = {5},
number = {12},
pages = {2062-2071},
pmid = {17158739},
issn = {1535-9778},
support = {/WT_/Wellcome Trust/United Kingdom ; T32 AI007323/AI/NIAID NIH HHS/United States ; 2-T32-AI-07323/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Dihydrolipoamide Dehydrogenase/genetics/metabolism ; Genes, Protozoan ; Glycine Decarboxylase Complex/genetics/*metabolism ; Glycine Decarboxylase Complex H-Protein/genetics/metabolism ; Kinetics ; Molecular Sequence Data ; Organelles/enzymology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/*enzymology/genetics ; },
abstract = {Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the identification of two glycine cleavage H proteins and a dihydrolipoamide dehydrogenase (L protein) of the glycine decarboxylase complex in T. vaginalis with predicted N-terminal hydrogenosomal presequences. Immunofluorescence analyses reveal that both H and L proteins are localized in hydrogenosomes, providing the first evidence for amino acid metabolism in this organelle. All three proteins were expressed in Escherichia coli and purified to homogeneity. The experimental Km of L protein for the two H proteins were 2.6 microM and 3.7 microM, consistent with both H proteins serving as substrates of L protein. Analyses using purified hydrogenosomes showed that endogenous H proteins exist as monomers and endogenous L protein as a homodimer in their native states. Phylogenetic analyses of L proteins revealed that the T. vaginalis homologue shares a common ancestry with dihydrolipoamide dehydrogenases from the firmicute bacteria, indicating its acquisition via a horizontal gene transfer event independent of the origins of mitochondria and hydrogenosomes.},
}
@article {pmid17161897,
year = {2007},
author = {Zhang, H and Meng, LH and Pommier, Y},
title = {Mitochondrial topoisomerases and alternative splicing of the human TOP1mt gene.},
journal = {Biochimie},
volume = {89},
number = {4},
pages = {474-481},
doi = {10.1016/j.biochi.2006.11.002},
pmid = {17161897},
issn = {0300-9084},
support = {//Intramural NIH HHS/United States ; },
mesh = {*Alternative Splicing ; Catalysis ; DNA Replication ; DNA Topoisomerases, Type I/chemistry/*genetics/*metabolism ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/*enzymology ; Phylogeny ; Transcription, Genetic ; },
abstract = {Mitochondria are the only organelles containing metabolically active DNA besides nuclei. By analogy with the nuclear topoisomerases, mitochondrial topoisomerase activities are probably critical for maintaining the topology of mitochondrial DNA during replication, transcription, and repair. Mitochondrial diseases include a wide range of defects including neurodegeneracies, myopathies, metabolic abnormalities and premature aging. Vertebrates only have one known specific mitochondrial topoisomerase gene (TOP1mt), coding for a type IB topoisomerase. Like the mitochondrial DNA and RNA polymerase, the TOP1mt gene is encoded in the nuclear genome. The TOP1mt gene possesses the 13 exon Top1B signature motif and codes for a mitochondrial targeting signals at the N-terminus of the Top1mt polypeptide. This review summarizes our current knowledge of mitochondrial topoisomerases (type IA, IB and type II) in eukaryotes including budding and fission yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and protozoan parasites (kinetoplastidiae and plasmodium). It also includes new data showing alternative splice variants of human TOP1mt.},
}
@article {pmid17185738,
year = {2007},
author = {Alkhalfioui, F and Renard, M and Montrichard, F},
title = {Unique properties of NADP-thioredoxin reductase C in legumes.},
journal = {Journal of experimental botany},
volume = {58},
number = {5},
pages = {969-978},
doi = {10.1093/jxb/erl248},
pmid = {17185738},
issn = {0022-0957},
mesh = {Amino Acid Sequence ; Gene Expression Regulation, Plant ; Medicago truncatula/*enzymology ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Thioredoxin-Disulfide Reductase/chemistry/genetics/*metabolism ; },
abstract = {NADP-thioredoxin reductases (NTRs) reduce thioredoxins (Trxs), using NADPH as a reductant, together constituting complete redox systems (NTS). Beside NTRA and NTRB targeted to both cytosol and mitochondria of plant cells, there is in chloroplasts an unusual NTR (NTRC) harbouring a Trx domain in a C-terminal extension, as recently reported in Oryza sativa. Although NTRC may constitute a complete NTS, it was described as a bifunctional enzyme. Because the gene is only present in photosynthetic organisms and the protein in green tissues, NTRC was thought to have a role restricted to photosynthetic cells. To determine whether NTRC from dicot plants is a bifunctional enzyme or a complete NTS, as well as to identify its putative target, NTRC from Medicago truncatula was cloned and NTRA was cloned for comparison. Here evidence is presented that MtNTRC (i) acts as an NTS and reduces dithiobisnitrobenzoate (DTNB) with a turnover (0.62 s(-1)) similar to that measured with MtNTRA in the presence of a Trxh (0.81 s(-1)); (ii) is able to use both NADPH (k(M)=2.4 microM) and NADH (k(M)=11 microM) as cofactors; (iii) efficiently reduces BAS1, a plastidial peroxiredoxin; and (iv) is expressed in both leaves and stems but unexpectedly is even more abundant in cotyledons from dry and germinating seeds. Because BAS1 is also present in both green tissues and seeds, NTRC/BAS1 may be involved in the scavenging of peroxides produced in green tissues during the day or the night and in seeds during germination. These results suggest different roles for NTRC in monocot and dicot plants.},
}
@article {pmid17216232,
year = {2007},
author = {Yang, KS and Kim, HS and Jin, UH and Lee, SS and Park, JA and Lim, YP and Pai, HS},
title = {Silencing of NbBTF3 results in developmental defects and disturbed gene expression in chloroplasts and mitochondria of higher plants.},
journal = {Planta},
volume = {225},
number = {6},
pages = {1459-1469},
pmid = {17216232},
issn = {0032-0935},
mesh = {Amino Acid Sequence ; Chloroplasts/*metabolism ; *Gene Expression Regulation, Plant ; *Gene Silencing ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*deficiency/genetics/metabolism ; Phenotype ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Nicotiana/*cytology/*genetics ; Transcription Factors/chemistry/*deficiency/genetics/metabolism ; },
abstract = {BTF3 (betaNAC) was originally isolated as a general transcription factor required for RNA polymerase II-dependent transcription, and later found to be a beta-subunit of nascent-polypeptide-associated complex that has been implicated in regulating protein localization during translation. In this study, virus-induced gene silencing of NbBTF3 encoding a Nicotiana benthamiana homolog of human BTF3 caused leaf yellowing and abnormal leaf morphology without altering the overall growth of the plant. The NbBTF3 gene is constitutively expressed and the NbBTF3-GFP fusion protein is primarily targeted to the nucleus. At the cellular level, downregulation of NbBTF3 expression reduced the chloroplast sizes and chlorophyll contents. The affected cells produced excessive amounts of reactive oxygen species. Furthermore, the transcript level of various plastid- and mitochondria-encoded genes was severely reduced in the NbBTF3-depleted leaf cells. These findings indicate that depletion of NbBTF3 activity preferentially affected development and/or physiology of chloroplasts and mitochondria in plants, possibly by hampering efficient translocation of the nascent organellar proteins into the organelles.},
}
@article {pmid17216240,
year = {2007},
author = {Hansen, H and Bakke, TA and Bachmann, L},
title = {Mitochondrial haplotype diversity of Gyrodactylus thymalli (Platyhelminthes; Monogenea): extended geographic sampling in United Kingdom, Poland, and Norway reveals further lineages.},
journal = {Parasitology research},
volume = {100},
number = {6},
pages = {1389-1394},
pmid = {17216240},
issn = {0932-0113},
mesh = {Animals ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Norway ; Phylogeny ; Platyhelminths/*classification/*genetics ; Poland ; Salmonidae/parasitology ; United Kingdom ; },
abstract = {In recent years, the mitochondrial haplotype diversity of the monogenean ectoparasites Gyrodactylus salaris Malmberg, 1957 on Atlantic salmon and G. thymalli Zitnan, 1960 on grayling has been studied intensively to understand the taxonomy and phylogeography of the two species. According to these studies, neither species can be considered monophyletic, but unfortunately, the geographic sampling has mostly been restricted to Fennoscandia. Only few samples from continental Europe have been analysed, and samples from the United Kingdom have not been included at all. Gyrodactylosis is a notifiable disease in Europe and is in the UK considered the most important exotic disease threat to wild Atlantic salmon populations. In this study, we report six new mitochondrial haplotypes of G. thymalli from England, Poland, and Norway detected by sequencing 745 bp of the cytochrome oxidase I gene. The six new haplotypes add five new clades to a neighbor-joining dendrogram deduced on the basis of the currently known 44 mitochondrial haplotypes for G. thymalli and G. salaris. We conclude that G. thymalli established in the UK along with the immigration of grayling. There is currently no reason to suspect that this parasite is a threat to Atlantic salmon in the UK, although its infectivity to salmon stocks in the UK has not been tested.},
}
@article {pmid17222063,
year = {2007},
author = {Signorovitch, AY and Buss, LW and Dellaporta, SL},
title = {Comparative genomics of large mitochondria in placozoans.},
journal = {PLoS genetics},
volume = {3},
number = {1},
pages = {e13},
pmid = {17222063},
issn = {1553-7404},
support = {R21 AI066242/AI/NIAID NIH HHS/United States ; T32 GM007499/GM/NIGMS NIH HHS/United States ; 5 T32 GM07499-28/GM/NIGMS NIH HHS/United States ; R21-AI066242-01A1/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Exons/genetics ; Genome/genetics ; *Genomics ; Introns/genetics ; Invertebrates/*cytology/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/chemistry ; },
abstract = {The first sequenced mitochondrial genome of a placozoan, Trichoplax adhaerens, challenged the conventional wisdom that a compact mitochondrial genome is a common feature among all animals. Three additional placozoan mitochondrial genomes representing highly divergent clades have been sequenced to determine whether the large Trichoplax mtDNA is a shared feature among members of the phylum Placozoa or a uniquely derived condition. All three mitochondrial genomes were found to be very large, 32- to 37-kb, circular molecules, having the typical 12 respiratory chain genes, 24 tRNAs, rnS, and rnL. They share with the Trichoplax mitochondrial genome the absence of atp8, atp9, and all ribosomal protein genes, the presence of several cox1 introns, and a large open reading frame containing an intron group I LAGLIDADG endonuclease domain. The differences in mtDNA size within Placozoa are due to variation in intergenic spacer regions and the presence or absence of long open reading frames of unknown function. Phylogenetic analyses of the 12 respiratory chain genes support the monophyly of Placozoa. The similarities in composition and structure between the three mitochondrial genomes reported here and that of Trichoplax's mtDNA suggest that their uncompacted state is a shared ancestral feature to other nonmetazoans while their gene content is a derived feature shared only among the Metazoa.},
}
@article {pmid17226040,
year = {2007},
author = {Rymaszewska, A},
title = {Symbiotic bacteria in oocyte and ovarian cell mitochondria of the tick Ixodes ricinus: biology and phylogenetic position.},
journal = {Parasitology research},
volume = {100},
number = {5},
pages = {917-920},
pmid = {17226040},
issn = {0932-0113},
mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Ixodes/*microbiology/physiology ; Mitochondria/*microbiology ; Oocytes/*microbiology ; Phylogeny ; Symbiosis ; },
abstract = {Under natural conditions, eukaryote cells may contain bacteria. Arthropods such as ticks, insects or mites are a group particularly favoured by the obligate intracellular bacteria. While arthropods are vectors for some of them, other bacteria inhabit invertebrate host cells having entered mutualistic interactions. Such endosymbionts dwell usually in the host cell vacuoles or cytoplasm but have been also reported from tick oocyte mitochondria. The microorganisms contribute to mitochondria degradation, but their colonies are not eliminated from the tick cells affected. So far, such bacteria have been detected in three research centres. The Italian centre has reported on results of microscope and molecular analyses, while the Polish centre published molecular data. The Danish centre registered a 16S rRNA gene fragment in GenBank. Independent comparisons of the 16S rRNA gene sequences, carried out in the Italian and Polish centres, confirmed that the nucleotide sequences of the Ixodes ricinus endosymbionts formed a single clade with certain non-identified tick bacterium species isolated from the tick Haemaphysalis wellingtoni. On the other hand, pathogenic species of the genera Anaplasma, Ehrlichia and Rickettsia detected in I. ricinus as well as symbionts of the genus Wolbachia present in Culex pipiens and Drosophila simulans have been placed at a different site on the phylogenetic tree.},
}
@article {pmid17235548,
year = {2007},
author = {Valkiūnas, G and Zehtindjiev, P and Hellgren, O and Ilieva, M and Iezhova, TA and Bensch, S},
title = {Linkage between mitochondrial cytochrome b lineages and morphospecies of two avian malaria parasites, with a description of Plasmodium (Novyella) ashfordi sp. nov.},
journal = {Parasitology research},
volume = {100},
number = {6},
pages = {1311-1322},
pmid = {17235548},
issn = {0932-0113},
mesh = {Animals ; Cytochromes b/*genetics ; Malaria, Avian/*parasitology ; Mitochondria/*enzymology ; Passeriformes/*parasitology ; Phylogeny ; Plasmodium/*classification/enzymology/*genetics ; },
abstract = {Numerous lineages of avian malaria parasites of the genus Plasmodium have been deposited in GenBank. However, only seven morphospecies have been linked to these lineages. This study linked two molecular sequences with morphospecies of malaria parasites. Two species of Plasmodium (mitochondrial cytochrome b gene lineages P-GRW2 and P-GRW4) were isolated from naturally infected adult great reed warblers (Acrocephalus arundinaceus) and inoculated to naive juvenile individuals of the same host species. Heavy parasitemia developed in the subinoculated birds, which enable identification of the species and deposition of their voucher specimens. Parasites of the lineage P-GRW2 were described as a new species, Plasmodium (Novyella) ashfordi, which is characterized primarily by the fan-like mature erythrocytic meronts containing seven to eight merozoites and the terminal position of clumped pigment granules in the gametocytes. Illustrations of the blood stages of the new species and Plasmodium (Haemamoeba) relictum (lineage P-GRW4) are given. The parasites of both lineages are transmitted in Africa and probably not in northern Europe. Other lineages closely related to P. ashfordi and P. relictum are identified. This study establishes the value of PCR-based identification of avian malaria parasites.},
}
@article {pmid17240176,
year = {2007},
author = {Miotto, G and Tessaro, S and Rotta, GA and Bonatto, D},
title = {In silico analyses of Fsf1 sequences, a new group of fungal proteins orthologous to the metazoan sideroblastic anemia-related sideroflexin family.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {44},
number = {8},
pages = {740-753},
doi = {10.1016/j.fgb.2006.12.004},
pmid = {17240176},
issn = {1087-1845},
mesh = {Amino Acid Sequence ; Cation Transport Proteins/*genetics ; Computational Biology ; Conserved Sequence ; Fungal Proteins/*genetics ; Fungi/*genetics ; Hydrophobic and Hydrophilic Interactions ; Iron/metabolism ; Membrane Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; *Sequence Homology, Amino Acid ; },
abstract = {Sideroblastic anemias are pathologies observed in metazoan species characterized by accumulation of iron in the mitochondria (sideroblasts), defective erythropoiesis, and iron overload. Some genes have been associated with sideroblastic anemia, e.g. delta-aminolevulinic acid synthase gene (e-ALAS2). Recently, a new sideroblastic-associated protein family was discovered in metazoans and termed sideroflexin (Sfxn). The metazoan Sfxn family comprises five groups of paralogous proteins, present in mitochondria and whose functions are unknown. Using an in silico approach, we have identified and characterized new sideroflexin sequences from the genomes of different fungal species. An in-depth phylogenetic analysis of these new fungal Sfxn sequences (termed Fsf1p) showed that they form a distinct clade within the metazoan Sfxn family. Hydrophobic cluster analysis and transmembrane topological mapping allowed us to compare conserved regions among Fsf1 and Sfxn proteins. The results indicate that Fsf1 probably belongs to an ancient, mitochondrial group of proteins, necessary to maintain the homeostasis of iron within this organelle.},
}
@article {pmid17251121,
year = {2007},
author = {Ujvari, B and Dowton, M and Madsen, T},
title = {Mitochondrial DNA recombination in a free-ranging Australian lizard.},
journal = {Biology letters},
volume = {3},
number = {2},
pages = {189-192},
pmid = {17251121},
issn = {1744-9561},
mesh = {Animals ; Australia ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Genes, Mitochondrial/genetics ; Geography ; Haplotypes/genetics ; Lizards/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic/*genetics ; },
abstract = {Mitochondrial DNA (mtDNA) is the traditional workhorse for reconstructing evolutionary events. The frequent use of mtDNA in such analyses derives from the apparent simplicity of its inheritance: maternal and lacking bi-parental recombination. However, in hybrid zones, the reproductive barriers are often not completely developed, resulting in the breakdown of male mitochondrial elimination mechanisms, leading to leakage of paternal mitochondria and transient heteroplasmy, resulting in an increased possibility of recombination. Despite the widespread occurrence of heteroplasmy and the presence of the molecular machinery necessary for recombination, we know of no documented example of recombination of mtDNA in any terrestrial wild vertebrate population. By sequencing the entire mitochondrial genome (16761bp), we present evidence for mitochondrial recombination in the hybrid zone of two mitochondrial haplotypes in the Australian frillneck lizard (Chlamydosaurus kingii).},
}
@article {pmid17265184,
year = {2007},
author = {Kirschning, J and Zachos, FE and Cirovic, D and Radovic, IT and Hmwe, SS and Hartl, GB},
title = {Population Genetic Analysis of Serbian Red Foxes (Vulpes vulpes) by Means of Mitochondrial Control Region Sequences.},
journal = {Biochemical genetics},
volume = {45},
number = {5-6},
pages = {409-420},
doi = {10.1007/s10528-007-9082-1},
pmid = {17265184},
issn = {0006-2928},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Foxes/*genetics ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Yugoslavia/epidemiology ; },
abstract = {A population genetic analysis based on sequences of the mitochondrial control region in 110 red foxes from five sampling localities in northern Serbia was carried out. The analysis yielded nine different haplotypes. Neither haplotype phylogeny nor their distribution was in accordance with the geographic location of the populations. In particular, the data failed to detect an unequivocal influence of the two big rivers, the Danube and the Tisza, separating the populations studied. Population differentiation was altogether low, without any relationship to the rivers as possible migration barriers. Although the possibility of foxes crossing the rivers over bridges or by swimming, thus keeping up gene flow, cannot be ruled out, it is most probable that the control region sequences are not sensitive enough to resolve small-scale population relationships but rather show patterns determined by stochastic processes such as genetic drift or lineage sorting.},
}
@article {pmid17292632,
year = {2007},
author = {Wood, AR and Apte, S and MacAvoy, ES and Gardner, JP},
title = {A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&amp;2) and mitochondrial (COI) DNA sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {44},
number = {2},
pages = {685-698},
doi = {10.1016/j.ympev.2006.12.019},
pmid = {17292632},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Bivalvia/classification/*genetics ; Cell Nucleus/*genetics ; DNA/*genetics ; DNA, Ribosomal Spacer/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Mitochondria/*genetics ; *Phylogeny ; },
abstract = {A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.},
}
@article {pmid17295027,
year = {2007},
author = {Schwacke, R and Fischer, K and Ketelsen, B and Krupinska, K and Krause, K},
title = {Comparative survey of plastid and mitochondrial targeting properties of transcription factors in Arabidopsis and rice.},
journal = {Molecular genetics and genomics : MGG},
volume = {277},
number = {6},
pages = {631-646},
pmid = {17295027},
issn = {1617-4615},
mesh = {Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Cell Nucleus/metabolism ; Chloroplasts/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/genetics ; Green Fluorescent Proteins/metabolism ; Mitochondria/chemistry/metabolism ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Sorting Signals ; Transcription Factors/chemistry/*metabolism ; },
abstract = {A group of nuclear transcription factors, the Whirly proteins, were recently shown to be targeted also to chloroplasts and mitochondria. In order to find out whether other proteins might share this feature, an in silico-based screening of transcription factors from Arabidopsis and rice was carried out with the aim of identifying putative N-terminal chloroplast and mitochondrial targeting sequences. For this, the individual predictions of several independent programs were combined to a consensus prediction using a naïve Bayes method. This consensus prediction shows a higher specificity at a given sensitivity value than each of the single programs. In both species, transcription factors from a variety of protein families that possess putative N-terminal plastid or mitochondrial target peptides as well as nuclear localization sequences, were found. A search for homologues within members of the AP2/EREBP protein family revealed that target peptide-containing proteins are conserved among monocotyledonous and dicotyledonous species. Fusion of one of these proteins to GFP revealed, indeed, a dual targeting activity of this protein. We propose that dually targeted transcription factors might be involved in the communication between the nucleus and the organelles in plant cells. We further discuss how recent results on the physical interaction between the organelles and the nucleus could have significance for the regulation of the localization of these proteins.},
}
@article {pmid17347008,
year = {2007},
author = {Li, X and Zhu, Z and Mo, D and Wang, H and Yang, S and Zhao, S and Li, K},
title = {Comparative molecular characterization of ADSS1 and ADSS2 genes in pig (Sus scrofa).},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {147},
number = {2},
pages = {271-277},
doi = {10.1016/j.cbpb.2007.01.013},
pmid = {17347008},
issn = {1096-4959},
mesh = {Adenylosuccinate Synthase/*genetics ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Cluster Analysis ; DNA Primers ; *Gene Expression ; Gene Expression Profiling ; Isoenzymes/genetics ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; *Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sus scrofa/*genetics ; },
abstract = {Adenylosuccinate synthetase (ADSS) catalyzes the key step of AMP synthesis. Vertebrates have two isozymes of ADSS, which are named ADSS1 and ADSS2, respectively. In this study, we cloned porcine ADSS1 and ADSS2 genes and comparatively analyzed their sequence, chromosome mapping, mRNA distribution and subcellular localization. According to our results, the ADSS1 gene was predominantly expressed in the striated muscle tissues, while ADSS2 gene distributed widely in all the tissues detected. Additionally, ADSS1 gene was up-regulated significantly along with porcine muscle growth, and ADSS2 gene expression was more constant during the muscle development. Porcine ADSS1 gene was assigned to SSC7q and the linked marker was SSC12B09, ADSS2 gene was mapped on SSC10p and the linked marker was SW497, and porcine ADSS2 protein was subcellular localized in mitochondria. Moreover, we found that one single nucleotide polymorphism (SNP, T/C(70)) in the ninth intron of ADSS2 gene was significantly associated with average daily gain trait (ADG, P<0.05) and loin muscle area trait (P<0.05).},
}
@article {pmid17349998,
year = {2007},
author = {Kimura, M and Okano, Y},
title = {Human Misato regulates mitochondrial distribution and morphology.},
journal = {Experimental cell research},
volume = {313},
number = {7},
pages = {1393-1404},
doi = {10.1016/j.yexcr.2007.02.004},
pmid = {17349998},
issn = {0014-4827},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; COS Cells ; Cell Cycle Proteins/genetics/*metabolism ; Cell Survival ; Chlorocebus aethiops ; Cytoskeletal Proteins/genetics/*metabolism ; Drosophila Proteins/genetics ; Extrachromosomal Inheritance ; Gene Expression Regulation ; HeLa Cells ; Humans ; Immunohistochemistry ; Mitochondria/genetics/*metabolism/physiology ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics/*metabolism/physiology ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; Sequence Homology, Amino Acid ; Transfection ; },
abstract = {Misato of Drosophila melanogaster and Saccharomyces cerevisiae DML1 are conserved proteins having a homologous region with a part of the GTPase family that includes eukaryotic tubulin and prokaryotic FtsZ. We characterized human Misato sharing homology with Misato of D. melanogaster and S. cerevisiae DML1. Tissue distribution of Misato exhibited ubiquitous distribution. Subcellular localization of the protein studied using anti-Misato antibody suggested that it is localized to the mitochondria. Further experiments of fractionating mitochondria revealed that Misato was localized to the outer membrane. The transfection of Misato siRNA led to growth deficiencies compared with control siRNA transfected HeLa cells, and the Misato-depleted HeLa cells showed apoptotic nuclear fragmentation resulting in cell death. After silencing of Misato, the filamentous mitochondrial network disappeared and fragmented mitochondria were observed, indicating human Misato has a role in mitochondrial fusion. To examine the effects of overexpression, COS-7 cells were transfected with cDNA encoding EGFP-Misato. Its overexpression resulted in the formation of perinuclear aggregations of mitochondria in these cells. The Misato-overexpressing cells showed low viability and had no nuclei or a small and structurally unusual ones. These results indicated that human Misato has a role(s) in mitochondrial distribution and morphology and that its unregulated expression leads to cell death.},
}
@article {pmid17374133,
year = {2007},
author = {Toro, N and Jiménez-Zurdo, JI and García-Rodríguez, FM},
title = {Bacterial group II introns: not just splicing.},
journal = {FEMS microbiology reviews},
volume = {31},
number = {3},
pages = {342-358},
doi = {10.1111/j.1574-6976.2007.00068.x},
pmid = {17374133},
issn = {0168-6445},
mesh = {Bacteria/classification/genetics ; Genes, Bacterial/genetics ; Introns/*genetics ; Phylogeny ; RNA Splicing/*genetics/physiology ; RNA, Catalytic/classification/*physiology ; Retroelements/physiology ; },
abstract = {Group II introns are both catalytic RNAs (ribozymes) and mobile retroelements that were discovered almost 14 years ago. It has been suggested that eukaryotic mRNA introns might have originated from the group II introns present in the alphaproteobacterial progenitor of the mitochondria. Bacterial group II introns are of considerable interest not only because of their evolutionary significance, but also because they could potentially be used as tools for genetic manipulation in biotechnology and for gene therapy. This review summarizes what is known about the splicing mechanisms and mobility of bacterial group II introns, and describes the recent development of group II intron-based gene-targetting methods. Bacterial group II intron diversity, evolutionary relationships, and behaviour in bacteria are also discussed.},
}
@article {pmid17390094,
year = {2007},
author = {Massey, SE and Garey, JR},
title = {A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs.},
journal = {Journal of molecular evolution},
volume = {64},
number = {4},
pages = {399-410},
pmid = {17390094},
issn = {0022-2844},
mesh = {Animals ; Codon/*genetics ; Codon, Nonsense/genetics ; Genetic Code/*genetics ; Genome/genetics ; *Genomics ; Mitochondria/*chemistry/*genetics ; Phylogeny ; Proteome/*genetics ; RNA, Transfer/*genetics ; },
abstract = {Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.},
}
@article {pmid17393186,
year = {2007},
author = {Hagner, SC and Misof, B and Maier, WA and Kampen, H},
title = {Bayesian analysis of new and old malaria parasite DNA sequence data demonstrates the need for more phylogenetic signal to clarify the descent of Plasmodium falciparum.},
journal = {Parasitology research},
volume = {101},
number = {3},
pages = {493-503},
pmid = {17393186},
issn = {0932-0113},
mesh = {Animals ; *Base Sequence ; *Bayes Theorem ; Computational Biology ; Cytochromes b/*genetics ; DNA, Protozoan/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptide Hydrolases/*genetics ; *Phylogeny ; Plasmodium/classification/enzymology/genetics ; Plasmodium falciparum/classification/enzymology/*genetics ; Plastids ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Software ; },
abstract = {Molecular systematic studies published during the last 15 years to clarify the phylogenetic relationships among the malaria parasites have led to two major hypotheses on the descent of Plasmodium falciparum: One supports an avian origin as a result of a relatively recent host switch, and another one favours the evolutionary development of P. falciparum together with its human host from primate ancestors. In this paper, we present phylogenetic analyses of three different Plasmodium genes, the nuclear 18 small sub-unit (SSU) ribosomal ribonucleic acid (rRNA), the mitochondrial cytochrome b (cyt b) and the plastid caseinolytic protease C (ClpC) gene, using numerous haemosporidian parasite DNA sequences obtained from the GenBank as well as several new sequences for major malaria parasites including the avian one Plasmodium cathemerium, which has never been considered in molecular phylogenetic analyses before. Most modern and sophisticated DNA substitution models based on Bayesian inference analysis were applied to estimate the cyt b and ClpC phylogenetic trees, whereas the 18 SSU rRNA gene was examined with regards to its secondary structure using PHASE software. Our results indicate that the data presently available are generally neither sufficient in number nor in information to solve the problem of the phylogenetic origin of P. falciparum.},
}
@article {pmid17396019,
year = {2007},
author = {Odahara, M and Inouye, T and Fujita, T and Hasebe, M and Sekine, Y},
title = {Involvement of mitochondrial-targeted RecA in the repair of mitochondrial DNA in the moss, Physcomitrella patens.},
journal = {Genes &amp; genetic systems},
volume = {82},
number = {1},
pages = {43-51},
doi = {10.1266/ggs.82.43},
pmid = {17396019},
issn = {1341-7568},
mesh = {Amino Acid Sequence ; Bryopsida/*enzymology/genetics ; *DNA Repair ; DNA, Mitochondrial/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/analysis/*metabolism ; Rec A Recombinases/analysis/*metabolism ; Recombination, Genetic ; Sequence Alignment ; Time Factors ; },
abstract = {Homologous recombination is a universal process that contributes to genetic diversity and genomic integrity. Bacterial-type RecA generally exists in all bacteria and plays a crucial role in homologous recombination. Although RecA homologues also exist in plant mitochondria, there have been few reports about the in vivo functions of these homologues. We identified a recA gene orthologue (named PprecA1) in a cDNA library of the moss, Physcomitrella patens. N-terminal fusion of the putative organellar targeting sequence of PpRecA1 to GFP caused a targeting of PpRecA1 to mitochondria. PprecA1 partially complemented the effects of a DNA damaging agent in an Escherichia coli recA deficient strain. Additionally, the expression of PprecA1 was induced by treating the plants with DNA damaging agents. Disruption of PprecA1 by targeted replacement resulted lower rate of the recovery of the mitochondrial DNA from methyl methan sulfonate damage. This is the first report about the characteristics of a null mutant of bacterial-type recA gene in plant. The data suggest that PprecA1 participates in the repair of mitochondrial DNA in P. patens.},
}
@article {pmid17403155,
year = {2007},
author = {Imanian, B and Carpenter, KJ and Keeling, PJ},
title = {Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins.},
journal = {The Journal of eukaryotic microbiology},
volume = {54},
number = {2},
pages = {146-153},
doi = {10.1111/j.1550-7408.2007.00245.x},
pmid = {17403155},
issn = {1066-5234},
mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/chemistry/genetics ; Dinoflagellida/classification/*genetics/*ultrastructure ; Electron Transport/genetics ; Electron Transport Complex IV/genetics ; Microscopy, Electron, Transmission ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; },
abstract = {Mitochondria and plastids originated through endosymbiosis, and subsequently became reduced and integrated with the host in similar ways. Plastids spread between lineages through further secondary or even tertiary endosymbioses, but mitochondria appear to have originated once and have not spread between lineages. Mitochondria are also generally lost in secondary and tertiary endosymbionts, with the single exception of the diatom tertiary endosymbiont of dinoflagellates like Kryptoperidinium foliaceum, where both host and endosymbiont are reported to contain mitochondria. Here we describe the first mitochondrial genes from this system: cytochrome c oxidase 1 (cox1), cytochrome oxidase 3 (cox3), and cytochrome b (cob). Phylogenetic analyses demonstrated that all characterized genes were derived from the pennate diatom endosymbiont, and not the host. We also demonstrated that all three genes are expressed, that cox1 contains spliced group II introns, and that cob and cox3 form an operon, all like their diatom relatives. The endosymbiont mitochondria not only retain a genome, but also express their genes, and are therefore likely involved in electron transport. Ultrastructural examination confirmed the endosymbiont mitochondria retain normal tubular cristae. Overall, these data suggest the endosymbiont mitochondria have not reduced at the genomic or functional level.},
}
@article {pmid17445713,
year = {2007},
author = {Pinkert, CA and Trounce, IA},
title = {Generation of transmitochondrial mice: development of xenomitochondrial mice to model neurodegenerative diseases.},
journal = {Methods in cell biology},
volume = {80},
number = {},
pages = {549-569},
doi = {10.1016/S0091-679X(06)80027-0},
pmid = {17445713},
issn = {0091-679X},
mesh = {Animals ; Cells, Cultured ; DNA, Mitochondrial/genetics ; *Disease Models, Animal ; Embryonic Stem Cells/transplantation ; Hybrid Cells/transplantation ; *Mice ; Mice, Transgenic ; Mitochondria/genetics/*transplantation ; Models, Biological ; Mutation ; Neurodegenerative Diseases/*pathology ; Phylogeny ; Transfection ; },
}
@article {pmid17450603,
year = {2007},
author = {Dagan, T and Martin, W},
title = {Testing hypotheses without considering predictions.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {29},
number = {5},
pages = {500-503},
doi = {10.1002/bies.20566},
pmid = {17450603},
issn = {0265-9247},
mesh = {Animals ; Mitochondria/metabolism ; Phylogeny ; *Research Design ; Symbiosis ; },
}
@article {pmid17472911,
year = {2007},
author = {Whitworth, TL and Dawson, RD and Magalon, H and Baudry, E},
title = {DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae).},
journal = {Proceedings. Biological sciences},
volume = {274},
number = {1619},
pages = {1731-1739},
pmid = {17472911},
issn = {0962-8452},
mesh = {Animals ; Classification/*methods ; Diptera/classification/*genetics/microbiology ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Hybridization, Genetic ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; United States ; Wolbachia/genetics ; },
abstract = {In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia-associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.},
}
@article {pmid17478060,
year = {2007},
author = {Nolan, DV and Carpenter, S and Barber, J and Mellor, PS and Dallas, JF and Mordue Luntz, AJ and Piertney, SB},
title = {Rapid diagnostic PCR assays for members of the Culicoides obsoletus and Culicoides pulicaris species complexes, implicated vectors of bluetongue virus in Europe.},
journal = {Veterinary microbiology},
volume = {124},
number = {1-2},
pages = {82-94},
doi = {10.1016/j.vetmic.2007.03.019},
pmid = {17478060},
issn = {0378-1135},
mesh = {Animals ; Bluetongue/*transmission ; Bluetongue virus ; Ceratopogonidae/*classification/genetics/virology ; Electron Transport Complex IV/*genetics ; Female ; Insect Vectors/*classification/genetics/virology ; Likelihood Functions ; Male ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods/veterinary ; Sequence Alignment/veterinary ; Species Specificity ; },
abstract = {Biting midges of the Culicoides obsoletus Meigen and Culicoides pulicaris L. species complexes (Diptera: Ceratopogonidae) are increasingly implicated as vectors of bluetongue virus in Palearctic regions. However, predicting epidemiological risk and the spread of disease is hampered because whilst vector competence of Culicoides is expressed only in adult females, morphological identification of constituent species is only readily applicable to adult males and some species distinguishing traits have overlapping character states. Furthermore, adult males are typically rare in field collections, making characterisation of Culicoides communities impossible. Here we highlight the utility of mitochondrial cytochrome oxidase subunit I (COI) DNA sequences for taxonomic resolution and species identification of all species within C. obsoletus and C. pulicarus complexes. Culicoides were collected from 18 sites in the UK and Continental Europe, and identified to species level, or species complex level, based on morphological characters. The sample comprised four species from the C. obsoletus complex (n = 88) and five species from the C. pulicaris complex (n = 39). The DNA sequence of the 5' end of the COI gene was obtained from all individuals. Each member species formed a well-supported reciprocally monophyletic clade in a maximum likelihood phylogeny. Levels of DNA sequence divergence were sufficiently high between species to allow the design of species-specific PCR primers that can be used in PCR for identification of members of the C. pulicaris complex or in a multiplex PCR to identify members of the C. obsoletus complex. This approach provides a valuable diagnostic tool for monitoring species composition in mixed field collections of Culicoides.},
}
@article {pmid17485854,
year = {2007},
author = {Lertwattanasakul, N and Sootsuwan, K and Limtong, S and Thanonkeo, P and Yamada, M},
title = {Comparison of the gene expression patterns of alcohol dehydrogenase isozymes in the thermotolerant yeast Kluyveromyces marxianus and their physiological functions.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {71},
number = {5},
pages = {1170-1182},
doi = {10.1271/bbb.60622},
pmid = {17485854},
issn = {0916-8451},
mesh = {Alcohol Dehydrogenase/genetics/isolation &amp; purification/*metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Blotting, Southern ; Carbon/metabolism ; Cloning, Molecular ; Conserved Sequence ; Cytoplasm/enzymology ; Ethanol/analysis ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Glucose/analysis ; Isoenzymes/genetics/metabolism ; Kluyveromyces/*enzymology/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; TATA Box ; Temperature ; },
abstract = {Four genes encoding alcohol dehydrogenase (Adh) isozymes in the thermotolerant yeast Kluyveromyces marxianus, a potent candidate for ethanol production at high temperatures, were investigated. Of these, KmADH3 and KmADH4 were cloned and sequenced, and their deduced amino acid sequences were compared with those of KmAdh1 and KmAdh2 and other Adhs of Kluyveromyces lactis and Saccharomyces cerevisiae. The four KmAdhs had high sequence similarity, though KmAdh3 and KmAdh4 possessed an amino-terminal extension as a mitochondrial targeting sequence, and appear to belong to the zinc-containing Adh family. These results and the results of Southern blot experiments suggest that there are at least four Adh isozymes in K. marxianus, two cytoplasmic enzymes and two mitochondrial enzymes. The expression profile revealed that KmADH genes are differently expressed depending on growth phase and carbon source, suggesting that these highly homologous Adhs play distinctive roles in cells.},
}
@article {pmid17498627,
year = {2007},
author = {Huo, G and Jiang, G and Sun, Z and Liu, D and Zhang, Y and Lu, L},
title = {Phylogenetic reconstruction of the family Acrypteridae (Orthoptera: Acridoidea) based on mitochondrial cytochrome B gene.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {34},
number = {4},
pages = {294-306},
doi = {10.1016/S1673-8527(07)60031-9},
pmid = {17498627},
issn = {1673-8527},
mesh = {Animals ; Codon ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Orthoptera/*classification/cytology/*genetics ; *Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {Sequences from the mitochondrial cytochrome b gene (Cyt b) were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony (MP) and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A + T and G + C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.},
}
@article {pmid17509845,
year = {2007},
author = {Kageyama, K and Senda, M and Asano, T and Suga, H and Ishiguro, K},
title = {Intra-isolate heterogeneity of the ITS region of rDNA in Pythium helicoides.},
journal = {Mycological research},
volume = {111},
number = {Pt 4},
pages = {416-423},
doi = {10.1016/j.mycres.2007.01.019},
pmid = {17509845},
issn = {0953-7562},
mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genes, Fungal ; Genetic Variation ; Phylogeny ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Pythium/*genetics ; Sequence Analysis, DNA ; },
abstract = {Heterogeneity of the rDNA ITS region in Pythium helicoides and the phylogenetic relationship between P. helicoides and closely related species were investigated. In PCR-RFLP analysis of the rDNA ITS region of six P. helicoides isolates investigated, including the type culture, intraspecific variation was found at the HhaI site. The total length of fragments was longer than before cutting, indicating sequence heterogeneity within isolates. Digestion of the cloned rDNA ITS region derived from seven isolates with HhaI revealed polymorphisms among and within single zoospore isolates, and variability of the region was also present among the clones derived from the same isolate. To test whether the rDNA ITS region of closely related species and other regions in the genome of P. helicoides are also variable, the rDNA ITS region of P. ultimum and the cytochrome oxydase II (cox II) gene encoded in mitochondria were sequenced. P. ultimum had little variation in the rDNA ITS region. The cox II gene sequences of both species revealed only a low intraspecific variability and no intra-isolate variation. In the phylogenic tree based on the rDNA ITS sequences, all clones of P. helicoides formed one large clade that was distinct from the clades comprising morphologically similar species, such as P. oedochilum and P. ostracodes, and was closely related to P. chamaehyphon rather than the other species.},
}
@article {pmid17514372,
year = {2008},
author = {Kerscher, S and Dröse, S and Zickermann, V and Brandt, U},
title = {The three families of respiratory NADH dehydrogenases.},
journal = {Results and problems in cell differentiation},
volume = {45},
number = {},
pages = {185-222},
doi = {10.1007/400_2007_028},
pmid = {17514372},
issn = {0080-1844},
mesh = {Amino Acid Sequence ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Catalysis ; *Electron Transport ; Electron Transport Complex I ; Mitochondria/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; NADH Dehydrogenase/*chemistry/*physiology ; Phylogeny ; Sequence Homology, Amino Acid ; Sodium/chemistry ; },
abstract = {Most reducing equivalents extracted from foodstuffs during oxidative metabolism are fed into the respiratory chains of aerobic bacteria and mitochondria by NADH:quinone oxidoreductases. Three families of enzymes can perform this task and differ remarkably in their complexity and role in energy conversion. Alternative or NDH-2-type NADH dehydrogenases are simple one subunit flavoenzymes that completely dissipate the redox energy of the NADH/quinone couple. Sodium-pumping NADH dehydrogenases (Nqr) that are only found in procaryotes contain several flavins and are integral membrane protein complexes composed of six different subunits. Proton-pumping NADH dehydrogenases (NDH-1 or complex I) are highly complicated membrane protein complexes, composed of up to 45 different subunits, that are found in bacteria and mitochondria. This review gives an overview of the origin, structural and functional properties and physiological significance of these three types of NADH dehydrogenase.},
}
@article {pmid17517886,
year = {2007},
author = {Chen, S and Sánchez-Fernández, R and Lyver, ER and Dancis, A and Rea, PA},
title = {Functional characterization of AtATM1, AtATM2, and AtATM3, a subfamily of Arabidopsis half-molecule ATP-binding cassette transporters implicated in iron homeostasis.},
journal = {The Journal of biological chemistry},
volume = {282},
number = {29},
pages = {21561-21571},
doi = {10.1074/jbc.M702383200},
pmid = {17517886},
issn = {0021-9258},
support = {DK53953/DK/NIDDK NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/chemistry/*physiology ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*physiology ; Cloning, Molecular ; Cytochromes c/metabolism ; Cytosol/metabolism ; Iron/chemistry/metabolism ; Microscopy, Fluorescence ; Models, Biological ; Models, Genetic ; Mutation ; Phenotype ; Phylogeny ; Plant Roots/metabolism ; Protein Transport ; },
abstract = {The functional capabilities of one of the smallest subfamilies of ATP-binding cassette transporters from Arabidopsis thaliana, the AtATMs, are described. Designated AtATM1, AtAATM2, and AtATM3, these half-molecule ABC proteins are homologous to the yeast mitochondrial membrane protein ATM1 (ScATM1), which is clearly implicated in the export of mitochondrially synthesized iron/sulfur clusters. Yeast ATM1-deficient (atm1) mutants grow very slowly (have a petite phenotype), are respiration-deficient, accumulate toxic levels of iron in their mitochondria, and show enhanced compensatory high affinity iron uptake. Of the three Arabidopsis ATMs, AtATM3 bears the closest functional resemblance to ScATM1. Heterologously expressed AtATM3 is not only able to complement the yeast atm1 petite phenotype but is also able to suppress the constitutively high capacity for high affinity iron uptake associated with loss of the chromosomal copy of ScATM1, abrogate intra-mitochondrial iron hyperaccumulation, and restore mitochondrial respiratory function and cytochrome c levels. By comparison, AtATM1 only weakly suppresses the atm1 phenotype, and AtATM2 exerts little or no suppressive action but instead is toxic when expressed in this system. The differences between AtATM3 and AtATM1 are maintained after exchanging their target peptides, and these proteins as well as AtATM2 colocalize with the mitochondrial fluor MitoTracker Red when expressed in yeast as GFP fusions. Although its toxicity when heterologously expressed in yeast, except when fused with GFP, precludes the functional analysis of native AtATM2, a common function, mitochondrial export of Fe/S clusters or their precursors for the assembly of cytosolic Fe/S proteins, is inferred for AtATM3 and AtATM1.},
}
@article {pmid17544704,
year = {2007},
author = {Lane, CE and Lindstrom, SC and Saunders, GW},
title = {A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding.},
journal = {Molecular phylogenetics and evolution},
volume = {44},
number = {2},
pages = {634-648},
doi = {10.1016/j.ympev.2007.03.016},
pmid = {17544704},
issn = {1055-7903},
mesh = {Base Sequence ; Chloroplasts/genetics ; Cloning, Molecular ; DNA/*classification/*genetics ; Databases, Nucleic Acid ; Genetic Markers ; Mitochondria/genetics ; Pacific Ocean ; Phaeophyceae/*classification/*genetics ; Phylogeny ; Transcription, Genetic/genetics ; },
abstract = {Despite their relatively complex morphologies, species in the genus Alaria Greville are notoriously difficult to identify with certainty. Morphological characters, often influenced by environmental factors, make individuals in similar habitats artificially appear related. Species identification would, therefore, benefit greatly from the application of molecular tools. We applied DNA barcoding, using the 5' end of the cytochrome c oxidase I (coxI-5') gene from the mitochondrial genome, to define species limits and relationships in northeast Pacific populations of Alaria. This emerging technique is being employed to catalogue species diversity worldwide, particularly among animals, and it has been shown to be sensitive enough to discriminate between closely related species. However, the utility of this marker for identifying or categorizing the majority of life remains unclear. We compared the resolution obtained with this marker to two other molecular systems commonly used in algal research: the nuclear internal transcribed spacer (ITS) of the ribosomal cistron, and the plastid Rubisco operon spacer (rbcSp). In agreement with previous results, Alaria fistulosa Postels &amp; Ruprecht, with its distinct morphological, ecological and molecular features, stands apart from the other species in the genus and we establish Druehlia gen. nov. to accommodate it. For the remaining isolates, distinct mitochondrial haplotypes resolved with the barcode data indicate a period of genetic isolation for at least three incipient species in the northeast Pacific, whereas unexpected levels and patterns of ITS variation, as well as the extreme morphological plasticity found among these isolates, have most probably resulted from a recent collapse in species barriers. The cloning of ITS amplicons revealed multiple ITS copies in several individuals, further supporting this hypothesis.},
}
@article {pmid17546088,
year = {2007},
author = {Handa, H},
title = {Investigation of the origin and transmission of linear mitochondrial plasmid based on phylogenetic analysis in Japanese rapeseed varieties.},
journal = {Genome},
volume = {50},
number = {2},
pages = {234-240},
doi = {10.1139/g06-150},
pmid = {17546088},
issn = {0831-2796},
mesh = {Brassica rapa/*genetics ; Cell Nucleus/metabolism ; Chromosomes, Plant/*genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Genome, Plant ; Models, Genetic ; Oligonucleotides/chemistry ; Phylogeny ; Plant Proteins/*genetics ; Plasmids/metabolism ; Polymerase Chain Reaction ; },
abstract = {A linear mitochondrial plasmid is present in some varieties of rapeseed. To elucidate its origin and transmission the author investigated types of mitochondrial genome and the presence of plasmid in 78 rapeseed varieties and landraces in Japan and carried out a comparative analysis using the breeding history of Japanese rapeseed varieties. The mitochondrial genome of rapeseed was classified roughly into 2 types, type I (nap) and type II (cam). Type II rapeseed mitochondria closely resembles that of Brassica rapa, which is a related species of rapeseed. In this study, the author found that all varieties with type II mitochondria originated from interspecific crosses between rapeseed (B. napus) and B. rapa. This indicates that type II cytoplasm was introduced to rapeseed through a breeding program. The presence of plasmid was limited to B. rapa landraces and rapeseed varieties that arose by interspecific crosses between B. napus and B. rapa. The results suggest that mitochondrial plasmid is of B. rapa origin and that it has been introduced into rapeseed by interspecific crosses in a modern breeding program, as in the case of the mitochondrial genome. Phylogenetic study of Japanese rapeseed varieties suggests the participation not of the mitochondrial genome but, rather, the nuclear genome for the perpetuation of plasmid in progeny varieties.},
}
@article {pmid17565672,
year = {2007},
author = {Kiraga, J and Mackiewicz, P and Mackiewicz, D and Kowalczuk, M and Biecek, P and Polak, N and Smolarczyk, K and Dudek, MR and Cebrat, S},
title = {The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms.},
journal = {BMC genomics},
volume = {8},
number = {},
pages = {163},
pmid = {17565672},
issn = {1471-2164},
mesh = {Base Composition/genetics ; Computational Biology ; *Ecosystem ; Isoelectric Point ; Mutation/genetics ; *Phylogeny ; Proteins/*chemistry ; Proteomics/*methods ; Species Specificity ; },
abstract = {BACKGROUND: The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.<br><br>RESULTS: We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes--positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.<br><br>CONCLUSION: The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.},
}
@article {pmid17569023,
year = {2007},
author = {Zhang, SC and Barclay, C and Alexander, LA and Geldenhuys, L and Porter, GA and Casson, AG and Murphy, PR},
title = {Alternative splicing of the FGF antisense gene: differential subcellular localization in human tissues and esophageal adenocarcinoma.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {85},
number = {11},
pages = {1215-1228},
pmid = {17569023},
issn = {0946-2716},
mesh = {Adenocarcinoma/*genetics/pathology ; Alternative Splicing/*genetics ; Amino Acid Sequence ; Animals ; COS Cells ; Cell Proliferation ; Chlorocebus aethiops ; Computational Biology ; Disease-Free Survival ; Esophageal Neoplasms/*genetics/pathology ; Fibroblast Growth Factor 2/chemistry/*genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genetic Complementation Test ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Protein Transport ; *RNA Transport ; RNA, Messenger/genetics/metabolism ; Sequence Deletion ; Subcellular Fractions/metabolism ; },
abstract = {Overexpression of FGF-2 is associated with tumor recurrence and reduced survival after surgical resection of esophageal cancer, and these risks are reduced in tumors co-expressing the FGF antisense (FGF-AS) RNA. The aim of this study was to characterize the expression of alternatively spliced FGF-AS transcripts and encoded nudix-motif proteins in normal human tissues and in esophageal adenocarcinoma, and to correlate their expression with clinicopathologic findings and outcome. Three alternatively spliced FGF-AS transcripts encoding GFG/NUDT6 isoforms with distinct N termini were detected in various human tissues including esophageal adenocarcinoma. Expression of each isoform as a fusion protein with enhanced green fluorescent protein revealed differential subcellular trafficking: hGFGa is localized to mitochondria by an N-terminal targeting sequence (MTS), whereas hGFGb and hGFGc were localized in the cytoplasm and nucleus. Mutation/deletion analysis confirmed that the predicted MTS was necessary and sufficient for mitochondrial compartmentalization. The predominant FGF-AS mRNA expressed in esophageal tumors was splice variant b. GFG immunoreactivity was detected in the cytoplasm of all esophageal adenocarcinomas and in 88% of tumor cell nuclei. Although we found a trend towards reduced disease-free survival in patients with FGF-2 overexpressing esophageal adenocarcinomas, significantly worse disease-free survival was noted among patients whose tumors did not also overexpress the FGF-AS b isoform (p = 0.03). Tetracycline-inducible FGF-AS b expression in stably transfected human Seg-1 esophageal adenocarcinoma cells resulted in a significant suppression of steady state FGF-2 mRNA content and cell proliferation. Our data implicate the FGF-AS b isoform in modulation of FGF-2 expression and clinical outcome in esophageal adenocarcinoma.},
}
@article {pmid17588779,
year = {2007},
author = {Makokha, JS and Bauer, AM and Mayer, W and Matthee, CA},
title = {Nuclear and mtDNA-based phylogeny of southern African sand lizards, Pedioplanis (Sauria: Lacertidae).},
journal = {Molecular phylogenetics and evolution},
volume = {44},
number = {2},
pages = {622-633},
doi = {10.1016/j.ympev.2007.04.021},
pmid = {17588779},
issn = {1055-7903},
mesh = {Africa ; Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; Databases, Nucleic Acid ; Lizards/*genetics ; Mitochondria/*genetics ; *Phylogeny ; *Silicon Dioxide ; Time Factors ; },
abstract = {The diversity of lacertid lizards in Africa is highest in the southern African subcontinent, where over two-thirds of the species are endemic. With eleven currently recognized species, Pedioplanis is the most diverse among the southern African genera. In this study we use 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) to (i) assess the phylogeny of Pedioplanis and (ii) estimate divergence time among lineages using the relaxed molecular clock method. Individual analyses of each gene separately supported different nodes in the phylogeny and the combined analysis yielded more well supported relationships. We present the first, well-resolved gene tree for the genus Pedioplanis and this is largely congruent with a phylogeny derived from morphology. Contrary to previous suggestions Heliobolus/Nucras are sister to Pedioplanis. The genus Pedioplanis is monophyletic, with P. burchelli/P. laticeps forming a clade that is sister to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The P. undata species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical clades that probably diverged during the mid-Miocene, after the development of the Benguella Current. This probably led to habitat changes associated with climate and, in conjunction with physical barriers (Great Escarpment), contributed towards speciation within the genus Pedioplanis.},
}
@article {pmid17594435,
year = {2007},
author = {Scheffer, SJ and Hawthorne, DJ},
title = {Molecular evidence of host-associated genetic divergence in the holly leafminer Phytomyza glabricola (Diptera: Agromyzidae): apparent discordance among marker systems.},
journal = {Molecular ecology},
volume = {16},
number = {13},
pages = {2627-2637},
doi = {10.1111/j.1365-294X.2007.03303.x},
pmid = {17594435},
issn = {0962-1083},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Ilex/classification/enzymology/*genetics ; Mitochondria/enzymology ; North Carolina ; Phylogeny ; Plant Leaves/*parasitology ; Plants/*parasitology ; South Carolina ; },
abstract = {Host races play a central part in understanding the role of host plant mediated divergence and speciation of phytophagous insects. Of greatest interest are host-associated populations that have recently diverged; however, finding genetic evidence for very recent divergences is difficult because initially only a few loci are expected to evolve diagnostic differences. The holly leafminer Phytomyza glabricola feeds on two hollies, Ilex glabra and I. coriacea, that are broadly sympatric throughout most of their ranges. The leafminer is often present on both host plants and exhibits a dramatic life history difference on the two hosts, suggesting that host races may be present. We collected 1393 bp of mitochondrial cytochrome oxidase I (COI) sequence and amplified fragment length polymorphism (AFLP) data (45 polymorphic bands) from sympatric populations of flies reared from the two hosts. Phylogenetic and frequency analysis of mitochondrial COI sequence data uncovered considerable variation but no structuring by the host plant, and only limited differentiation among geographical locations. In contrast, analysis of AFLP frequency data found a significant effect with host plant, and a much smaller effect with geographical location. Likewise, neighbour-joining analysis of AFLP data resulted in clustering by host plant. The AFLP data indicate that P. glabricola is most likely comprised of two host races. Because there were no fixed differences in mitochondrial or AFLP data, this host-associated divergence is likely to have occurred very recently. P. glabricola therefore provides a new sympatric system for exploring the role of geography and ecological specialization in the speciation of phytophagous insects.},
}
@article {pmid17626375,
year = {2007},
author = {Mitani, H and Takahashi, M and Masuyama, M and Fukunaga, M},
title = {Ixodes philipi (Acari: Ixodidae): phylogenetic status inferred from mitochondrial cytochrome oxidase subunit I gene sequence comparison.},
journal = {The Journal of parasitology},
volume = {93},
number = {3},
pages = {719-722},
doi = {10.1645/GE-953R.1},
pmid = {17626375},
issn = {0022-3395},
mesh = {Animals ; Base Sequence ; Bird Diseases/parasitology ; Birds ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Female ; *Genes, Mitochondrial ; Ixodes/*classification/enzymology/genetics ; Japan ; Male ; Mitochondria/enzymology ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; Sequence Alignment/veterinary ; Tick Infestations/parasitology/veterinary ; },
abstract = {Ixodes philipi ticks were collected from the nest burrows of streaked shearwaters, Calonectris luecomelas, on 3 different islands of Japan (Awashima: 38 degrees 45'N, 139 degrees 24'E; Mikurajima: 33 degrees 52'N, 139 degrees 36'E; and Omorijima: 36 degrees 8'N, 133 degrees 10'E). The mitochondrial cytochrome oxidase subunit I (COI) gene sequence was determined for each tick. The COI sequences of 9 other ixodid tick species also were determined, and they were used for taxonomic positioning of I. philipi. A metastriata tick, Amblyomma triguttatum, was used as an outgroup reference for the analysis. Phylogenetic examination indicated that the I. philipi ticks are on the branch with Ixodes turdus and Ixodes acutitarsus weakly, and the bootstrap value of this branching was low. Three different analyses, maximum parsimony, genetic distance, and maximum likelihood, support this conclusion. To further refine this analysis, 2761 base pairs (bp) of sequence, which included the genes for tRNA(Met), NADH dehydrogenase subunit 2 (ND2), tRNA(Trp), tRNA(Cys), tRNA(Tyr), and COI, were determined and compared for 6 I. philipi ticks from the 3 different collection sites. Although a base substitution (T to C in the ND2 gene for an Awashima tick) and 2 transitions (G to A in the COI gene for 1 Omorijima tick) have occurred, the overall sequences were highly conserved. Preserved mitochondrial sequences in the ticks from 3 widely separated locations suggest the possibility of gene flow, which was probably accomplished by migratory seabirds.},
}
@article {pmid17652520,
year = {2007},
author = {Wei, W and McCusker, JH and Hyman, RW and Jones, T and Ning, Y and Cao, Z and Gu, Z and Bruno, D and Miranda, M and Nguyen, M and Wilhelmy, J and Komp, C and Tamse, R and Wang, X and Jia, P and Luedi, P and Oefner, PJ and David, L and Dietrich, FS and Li, Y and Davis, RW and Steinmetz, LM},
title = {Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104},
number = {31},
pages = {12825-12830},
pmid = {17652520},
issn = {0027-8424},
support = {HG 000205/HG/NHGRI NIH HHS/United States ; GM 068717/GM/NIGMS NIH HHS/United States ; HG 02052/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM068717/GM/NIGMS NIH HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; Chromosome Inversion/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phenotype ; Phylogeny ; Polymorphism, Genetic/genetics ; Saccharomyces cerevisiae/*genetics ; Translocation, Genetic/genetics ; },
abstract = {We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the approximately 12-Mb genome of YJM789 contains approximately 60,000 SNPs and approximately 6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.},
}
@article {pmid17655652,
year = {2007},
author = {Aronsson, H and Boij, P and Patel, R and Wardle, A and Töpel, M and Jarvis, P},
title = {Toc64/OEP64 is not essential for the efficient import of proteins into chloroplasts in Arabidopsis thaliana.},
journal = {The Plant journal : for cell and molecular biology},
volume = {52},
number = {1},
pages = {53-68},
doi = {10.1111/j.1365-313X.2007.03207.x},
pmid = {17655652},
issn = {0960-7412},
mesh = {Arabidopsis/metabolism/*physiology ; Arabidopsis Proteins/genetics/*physiology ; Base Sequence ; Chloroplasts/*metabolism ; DNA Primers ; DNA, Bacterial/genetics ; Membrane Proteins/genetics/*physiology ; Microscopy, Electron, Transmission ; Mutagenesis, Insertional ; Phylogeny ; Protein Transport ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {Toc64/OEP64 was identified biochemically in pea as a putative component of the chloroplast protein import apparatus. In Arabidopsis, three paralogous genes (atTOC64-III, atTOC64-V and atTOC64-I) encode Toc64-related proteins, and these have been reported to localize in chloroplasts, mitochondria and the cytosol, respectively. To assess the role of the atToc64-III protein in chloroplast protein import in an in vivo context, we identified and characterized Arabidopsis knockout mutants. The absence of detectable defects in toc64-III single mutants raised the possibility of redundancy, and prompted us to also identify toc64-V and toc64-I mutants, cross them to toc64-III, and generate double- and triple-mutant combinations. The toc64 mutants were analysed carefully with respect to a variety of criteria, including chlorophyll accumulation, photosynthetic performance, organellar ultrastructure and chloroplast protein accumulation. In each case, the mutant plants were indistinguishable from wild type. Furthermore, the efficiency of chloroplast protein import was not affected by the toc64 mutations, even when a putative substrate of the atToc64-III protein (wheatgerm-translated precursor of the 33 kDa subunit of the oxygen-evolving complex, OE33) was examined. Moreover, under various stress conditions (high light, osmotic stress and cold), the toc64 triple-mutant plants were not significantly different from wild type. These results demonstrate that Toc64/OEP64 is not essential for the efficient import of proteins into chloroplasts in Arabidopsis, and draw into question the functional significance of this component.},
}
@article {pmid17662054,
year = {2007},
author = {Fekete, V and Cierna, M and Poláková, S and Piskur, J and Sulo, P},
title = {Transition of the ability to generate petites in the Saccharomyces/Kluyveromyces complex.},
journal = {FEMS yeast research},
volume = {7},
number = {8},
pages = {1237-1247},
doi = {10.1111/j.1567-1364.2007.00287.x},
pmid = {17662054},
issn = {1567-1356},
mesh = {DNA, Fungal/drug effects/genetics ; DNA, Mitochondrial/drug effects/genetics ; Ethidium/pharmacology ; Genome, Fungal/drug effects ; Kluyveromyces/classification/drug effects/*genetics/*growth &amp; development ; Mitochondria/drug effects/genetics ; Mutagenesis ; Mutagens/pharmacology ; Phenotype ; Phylogeny ; Saccharomyces/classification/drug effects/*genetics/*growth &amp; development ; },
abstract = {Petite-positivity - the ability to tolerate the loss of mtDNA - was examined after the treatment with ethidium bromide (EB) in over hundred isolates from the Saccharomyces/Kluyveromyces complex. The identity of petite mutants was confirmed by the loss of specific mtDNA DAPI staining patterns. Besides unequivocal petite-positive and petite-negative phenotypes, a few species exhibited temperature sensitive petite positive phenotype and petiteness of a few other species could be observed only at the elevated EB concentrations. Several yeast species displayed a mixed 'moot' phenotype, where a major part of the population did not tolerate the loss of mtDNA but several cells did. The genera from postwhole-genome duplication lineages (Saccharomyces, Kazachstania, Naumovia, Nakaseomyces) were invariably petite-positive. However, petite-positive traits could also be observed among the prewhole-genome duplication species.},
}
@article {pmid17674076,
year = {2007},
author = {Gibson, T and Blok, VC and Dowton, M},
title = {Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives.},
journal = {Journal of molecular evolution},
volume = {65},
number = {3},
pages = {308-315},
pmid = {17674076},
issn = {0022-2844},
mesh = {Animals ; Base Sequence ; *Conserved Sequence ; Cytochromes b/genetics ; DNA, Helminth/analysis ; *Genome, Mitochondrial ; Molecular Sequence Data ; Mosaicism ; Nematoda/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {Recently, a multipartite mitochondrial genome was characterized in the potato cyst nematode, Globodera pallida. Six subgenomic circles were detectable by PCR, while full-length genomes were not. We investigate here whether this subgenomic organization occurs in a close relative of G. pallida. We amplified and sequenced one entire mitochondrial subgenome from the cyst-forming nematode, Globodera rostochiensis. Comparison of the noncoding region of this subgenome with those reported previously for G. pallida facilitated the design of amplification primers for a range of subgenomes from G. rostochiensis. We then randomly sequenced five subgenomic fragments, each representative of a unique subgenome. This study indicates that the multipartite structure reported for G. pallida is conserved in G. rostochiensis. A comparison of subgenomic organization between these two Globodera species indicates a considerable degree of overlap between them. Indeed, we identify two subgenomes with an organization identical with that reported for G. pallida. However, other subgenomes are unique to G. rostochiensis, although some of these have blocks of genes comparable to those in G. pallida. Dot-plot comparisons of pairs of subgenomes from G. rostochiensis indicate that the different subgenomes share fragments with high sequence identity. We interpret this as evidence that recombination is operating in the mitochondria of G. rostochiensis.},
}
@article {pmid17676874,
year = {2007},
author = {Hemp, J and Han, H and Roh, JH and Kaplan, S and Martinez, TJ and Gennis, RB},
title = {Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb3 oxidase) of heme-copper oxygen reductases.},
journal = {Biochemistry},
volume = {46},
number = {35},
pages = {9963-9972},
doi = {10.1021/bi700659y},
pmid = {17676874},
issn = {0006-2960},
support = {R01 HL016101/HL/NHLBI NIH HHS/United States ; GM15590-37/GM/NIGMS NIH HHS/United States ; HL16101/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Amino Acid Substitution/genetics ; Copper/chemistry ; Electron Transport Complex IV/*genetics ; Heme/analogs &amp; derivatives/chemistry/*metabolism ; Ion Channels/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; *Mutagenesis, Site-Directed ; Oxidation-Reduction ; Phylogeny ; Proton Pumps/*genetics/metabolism ; *Protons ; Rhodobacter sphaeroides/*enzymology/genetics ; Sequence Analysis, DNA ; Vibrio cholerae/*enzymology/genetics ; },
abstract = {Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.},
}
@article {pmid17686885,
year = {2007},
author = {Nakada, T and Hoshijima, K and Esaki, M and Nagayoshi, S and Kawakami, K and Hirose, S},
title = {Localization of ammonia transporter Rhcg1 in mitochondrion-rich cells of yolk sac, gill, and kidney of zebrafish and its ionic strength-dependent expression.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {293},
number = {4},
pages = {R1743-53},
doi = {10.1152/ajpregu.00248.2007},
pmid = {17686885},
issn = {0363-6119},
support = {R01-GM-069382/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Base Sequence ; Cation Transport Proteins/chemistry/*genetics/*metabolism ; Gene Expression Regulation ; Gills/*cytology ; Green Fluorescent Proteins ; Kidney/*cytology ; Mitochondria/*metabolism ; Osmolar Concentration ; Phylogeny ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Water/chemistry ; Yolk Sac/*cytology ; Zebrafish ; Zebrafish Proteins/chemistry/*genetics/*metabolism ; },
abstract = {Members of the Rh glycoprotein family have been shown to be involved in ammonia transport in a variety of species. Here we show that zebrafish Rhcg1, a member of the Rh glycoprotein family, is highly expressed in the yolk sac, gill, and renal tubules. Molecular cloning and characterization indicate that zebrafish Rhcg1 shares 82% sequence identity with the pufferfish ortholog fRhcg1. RT-PCR, combined with in situ hybridization, revealed that Rhcg1 is first expressed in vacuolar-type H(+)-ATPase/mitochondrion-rich cells (vH-MRC) on the yolk sac of larvae at 3 days postfertilization (dpf) and later in vH-MRC-like cells in the gill at 4-5 dpf. Ammonia excretion from zebrafish larvae increased in parallel with the expression of Rhcg1. At larval stages, Rhcg1 mRNA was detected only on the yolk sac and gill; however, the kidney, as well as the gill, becomes a major site of Rhcg1 expression in adults. Using a zebrafish Tol2 transgenic line whose vH-MRC are labeled with green fluorescent protein (GFP) and an antibody against zebrafish Rhcg1, we demonstrate that Rhcg1 is located in the apical regions of 1) vH-MRC on the yolk sac and vH-MRC-like cells (cell population with the expression of Rhcg1 and GFP) in the gill and 2) cells in the renal distal tubule and intercalated cell-like cells in the collecting duct of the kidney. Remarkably, expression of Rhcg1 mRNA at the larval stage was changed by environmental ionic strength. These results suggest that roles of zebrafish Rhcg1 are not solely ammonia secretion to eliminate nitrogen from the gill.},
}
@article {pmid17765203,
year = {2007},
author = {Azuma, K and Kobayashi, M and Nakamura, M and Suzuki, N and Yashima, S and Iwamuro, S and Ikegame, M and Yamamoto, T and Hattori, A},
title = {Two osteoclastic markers expressed in multinucleate osteoclasts of goldfish scales.},
journal = {Biochemical and biophysical research communications},
volume = {362},
number = {3},
pages = {594-600},
doi = {10.1016/j.bbrc.2007.08.010},
pmid = {17765203},
issn = {0006-291X},
mesh = {Acid Phosphatase/*biosynthesis ; Amino Acid Sequence ; Animals ; Bone and Bones/metabolism ; Cathepsin K ; Cathepsins/*biosynthesis/metabolism ; Cloning, Molecular ; DNA, Complementary/metabolism ; Gene Expression Regulation ; Goldfish ; In Situ Hybridization ; Isoenzymes/*biosynthesis ; Molecular Sequence Data ; Osteoclasts/*metabolism ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; Tartrate-Resistant Acid Phosphatase ; },
abstract = {Complementary DNAs encoding two major osteoclastic markers, tartrate-resistant acid phosphatase (TRAP) and cathepsin K (Cath K) were cloned from the scales of a teleost, the goldfish. This is the first report of the full coding sequence of TRAP and Cath K molecules in fish. In the goldfish scale both TRAP and Cath K mRNAs were expressed in the multinucleate osteoclasts, which showed large numbers of mitochondria and lysosomes, and a well developed ruffled border. These characteristic features of osteoclasts in the scales are similar to those in mammals. Most teleosts use the scale as an internal calcium reservoir during the reproductive season. The expression of TRAP and Cath K mRNAs in the scale significantly increased in April, which is a reproductive season, compared with that in October, a non-reproductive season. Thus, both of these molecular markers should be useful for the study of osteoclasts in the teleost scale.},
}
@article {pmid17868468,
year = {2007},
author = {Chu, Z and Li, J and Eshaghi, M and Karuturi, RK and Lin, K and Liu, J},
title = {Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome.},
journal = {BMC genomics},
volume = {8},
number = {},
pages = {323},
pmid = {17868468},
issn = {1471-2164},
mesh = {Aniline Compounds/metabolism ; Cell Wall/metabolism ; DNA Polymerase gamma ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*genetics ; Fluorescent Dyes/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; Indoles/metabolism ; Models, Genetic ; Phylogeny ; Schizosaccharomyces/*genetics/metabolism/ultrastructure ; },
abstract = {BACKGROUND: DNA polymerase gamma(Pol-gamma) has been shown to be essential for maintenance of the mitochondrial genome (mtDNA) in the petite-positive budding yeast Saccharomyces cerevisiae. Budding yeast cells lacking mitochondria exhibit a slow-growing or petite-colony phenotype. Petite strains fail to grow on non-fermentable carbon sources. However, it is not clear whether the Pol-gamma is required for mtDNA maintenance in the petite-negative fission yeast Schizosaccharomyces pombe.<br><br>RESULTS: We show that disruption of the nuclear gene pog1+ that encodes Pol-gamma is sufficient to deplete mtDNA in S. pombe. Cells bearing pog1Delta allele require substantial growth periods to form petite colonies. Mitotracker assays indicate that pog1Delta cells are defective in mitochondrial function and EM analyses suggest that pog1Delta cells lack normal mitochondrial structures. Depletion of mtDNA in pog1Delta cells is evident from quantitative real-time PCR assays. Genome-wide expression profiles of pog1Delta and other mtDNA-less cells reveal that many genes involved in response to stimulus, energy derivation by oxidation of organic compounds, cellular carbohydrate metabolism, and energy reserve metabolism are induced. Conversely, many genes encoding proteins involved in amino acid metabolism and oxidative phosphorylation are repressed.<br><br>CONCLUSION: By showing that Pol-gamma is essential for mtDNA maintenance and disruption of pog1+ alters the genome-wide expression profiles, we demonstrated that cells lacking mtDNA exhibit adaptive nuclear gene expression responses in the petite-negative S. pombe.},
}
@article {pmid17880942,
year = {2008},
author = {Aguilera, P and Barry, T and Tovar, J},
title = {Entamoeba histolytica mitosomes: organelles in search of a function.},
journal = {Experimental parasitology},
volume = {118},
number = {1},
pages = {10-16},
doi = {10.1016/j.exppara.2007.08.004},
pmid = {17880942},
issn = {0014-4894},
support = {BB/C507145/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Entamoeba histolytica/classification/physiology/*ultrastructure ; Entamoebiasis/parasitology ; Genome, Protozoan ; Humans ; Intestine, Large/parasitology ; Iron-Sulfur Proteins/biosynthesis/physiology ; Mitochondria/physiology ; Organelles/genetics/*physiology/ultrastructure ; Oxygen Consumption ; Phylogeny ; Protozoan Proteins/metabolism ; Pyruvic Acid/metabolism ; Symbiosis ; },
abstract = {It has been more than eight years since the discovery of mitosomes (mitochondrial remnant organelles) in the intestinal human pathogen Entamoeba histolytica. Despite detailed knowledge about the biochemistry of this parasite and the completion of the E. histolytica genome sequencing project no physiological function has yet been unequivocally assigned to these organelles. Entamoeba mitosomes seem to be the most degenerate of all endosymbiosis-derived organelles studied to date. They do not appear to participate in energy metabolism and may have dispensed completely with the proteins required for iron-sulphur cluster biosynthesis. However, the large number of mitosomes found in E. histolytica trophozoites hints at a significant biological role for these organelles in their natural environment. Identifying the protein complement of mitosomes will provide answers as to their biological significance and the reason(s) for their retention in this parasite.},
}
@article {pmid17892581,
year = {2007},
author = {Imanian, B and Keeling, PJ},
title = {The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages.},
journal = {BMC evolutionary biology},
volume = {7},
number = {},
pages = {172},
pmid = {17892581},
issn = {1471-2148},
mesh = {Animals ; DNA Primers ; DNA, Complementary ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Dinoflagellida/classification/enzymology/*genetics/ultrastructure ; Electron Transport Complex IV/genetics ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/*ultrastructure ; Phylogeny ; RNA, Protozoan ; Sequence Analysis, DNA ; Symbiosis ; Transcription, Genetic ; },
abstract = {BACKGROUND: The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them.<br><br>RESULTS: We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate.<br><br>CONCLUSION: Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport.},
}
@article {pmid17897476,
year = {2007},
author = {Jackson, CJ and Norman, JE and Schnare, MN and Gray, MW and Keeling, PJ and Waller, RF},
title = {Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria.},
journal = {BMC biology},
volume = {5},
number = {},
pages = {41},
pmid = {17897476},
issn = {1741-7007},
mesh = {Animals ; Blotting, Southern ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/genetics ; Dinoflagellida/*genetics ; *Genome, Mitochondrial ; Genome, Protozoan ; Phylogeny ; Polymerase Chain Reaction ; RNA Editing ; RNA, Ribosomal/genetics ; Terminal Repeat Sequences ; Trans-Splicing ; *Transcription, Genetic ; },
abstract = {BACKGROUND: Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs) within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes.<br><br>RESULTS: From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression.<br><br>CONCLUSION: The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements within the genome, RNA editing, loss of stop codons, and use of trans-splicing.},
}
@article {pmid17898086,
year = {2008},
author = {Autio, KJ and Kastaniotis, AJ and Pospiech, H and Miinalainen, IJ and Schonauer, MS and Dieckmann, CL and Hiltunen, JK},
title = {An ancient genetic link between vertebrate mitochondrial fatty acid synthesis and RNA processing.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {22},
number = {2},
pages = {569-578},
doi = {10.1096/fj.07-8986},
pmid = {17898086},
issn = {1530-6860},
mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; DNA, Complementary/genetics ; Fatty Acids/*biosynthesis ; Gene Expression Regulation, Enzymologic ; Genome/genetics ; Humans ; Hydro-Lyases/chemistry/genetics/isolation &amp; purification/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutation/genetics ; Open Reading Frames/genetics ; Phylogeny ; RNA/*genetics ; Ribonuclease P/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; Transcription, Genetic/genetics ; Vertebrates/*genetics/*metabolism ; },
abstract = {In bacteria, functionally related gene products are often encoded by a common transcript. Such polycistronic transcripts are rare in eukaryotes. Here we isolated several clones from human cDNA libraries, which rescued the respiratory-deficient phenotype of a yeast mitochondrial 3-hydroxyacyl thioester dehydratase 2 (htd2) mutant strain. All complementing cDNAs were derived from the RPP14 transcript previously described to encode the RPP14 subunit of the human ribonuclease P (RNase P) complex. We identified a second, 3' open reading frame (ORF) on the RPP14 transcript encoding a protein showing similarity to known dehydratases and hydratase 2 enzymes. The protein was localized in mitochondria, and the recombinant enzyme exhibited (3R)-specific hydratase 2 activity. Based on our results, we named the protein human 3-hydroxyacyl-thioester dehydratase 2 (HsHTD2), which is involved in mitochondrial fatty acid synthesis. The bicistronic arrangement of RPP14 and HsHTD2, as well as the general exon structure of the gene, is conserved in vertebrates from fish to humans, indicating a genetic link conserved for 400 million years between RNA processing and mitochondrial fatty acid synthesis.},
}
@article {pmid17916323,
year = {2007},
author = {Yount, NY and Andrés, MT and Fierro, JF and Yeaman, MR},
title = {The gamma-core motif correlates with antimicrobial activity in cysteine-containing kaliocin-1 originating from transferrins.},
journal = {Biochimica et biophysica acta},
volume = {1768},
number = {11},
pages = {2862-2872},
doi = {10.1016/j.bbamem.2007.07.024},
pmid = {17916323},
issn = {0006-3002},
support = {AI39001/AI/NIAID NIH HHS/United States ; AI48031/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Antimicrobial Cationic Peptides/*chemistry/pharmacology ; Lactoferrin/*chemistry/*pharmacology ; Models, Molecular ; Models, Theoretical ; Molecular Sequence Data ; Phylogeny ; Transferrin/*chemistry ; Two-Hybrid System Techniques ; },
abstract = {Kaliocin-1 is a 31-residue peptide derived from human lactoferrin, and with antimicrobial properties that recapitulate those of its 611 amino acid parent holoprotein. As kaliocin-1 is a cysteine-stabilized peptide, it was of interest to determine whether it contained a multidimensional gamma-core signature recently identified as common to virtually all classes of disulfide-stabilized antimicrobial peptides. Importantly, sequence and structural analyses identified an iteration of this multidimensional antimicrobial signature in kaliocin-1. Further, the gamma-core motif was found to be highly conserved in the transferrin family of proteins across the phylogenetic spectrum. Previous studies suggested that the mechanism by which kaliocin-1 exerts anti-candidal efficacy depends on mitochondrial perturbation without cell membrane permeabilization. Interestingly, results of a yeast two-hybrid screening analysis identified an interaction between kaliocin-1 and mitochondrial initiation factor 2 in a Saccharomyces cerevisiae model system. Taken together, these data extend the repertoire of antimicrobial peptides that contain gamma-core motifs, and suggest that the motif is conserved within large native as well as antimicrobial peptide subcomponents of transferrin family proteins. Finally, these results substantiate the hypothesis that antimicrobial activity associated with host defense effector proteins containing a gamma-core motif may correspond to targets common to fungal mitochondria or their bacterial ancestors.},
}
@article {pmid17918371,
year = {2007},
author = {Hellgren, O and Krizanauskiene, A and Valkĭunas, G and Bensch, S},
title = {Diversity and phylogeny of mitochondrial cytochrome B lineages from six morphospecies of avian Haemoproteus (Haemosporida: Haemoproteidae).},
journal = {The Journal of parasitology},
volume = {93},
number = {4},
pages = {889-896},
doi = {10.1645/GE-1051R1.1},
pmid = {17918371},
issn = {0022-3395},
mesh = {Animals ; Bird Diseases/*parasitology ; Birds ; Cytochromes b/*genetics ; *Genetic Variation ; Haemosporida/classification/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Protozoan Infections, Animal/*parasitology ; },
abstract = {Species of Haemoproteus (Haemosporida: Haemoproteidae), avian haemosporidians, have traditionally been described based on morphology of their gametocytes and on limited experimental information on their vertebrate host specificity. We investigated to what extent the morphological species are represented by monophyletic groups based on DNA sequence data using 2 different fragment lengths of the cytochrome b (cyt. b) gene. Phylogenetic reconstructions of obtained cyt. b lineages from 6 morphospecies of Haemoproteus showed that all lineages formed monophyletic clusters matching the morphospecies. Comparing our data with a recently published study showed that this is not always the case; the morphospecies H. belopolskyi consists of 2 distinct clusters of lineages that apparently have converged in morphology. However, the overall broad congruence between the molecular and morphological clustering of lineages will facilitate the integration of the knowledge obtained by traditional and molecular parasitology. Mean between morphospecies variation was 10-fold higher than the within species variation (5.5% vs. 0.54%), suggesting that Haemoproteus lineages with a genetic differentiation >5% are expected to be morphologically differentiated in most cases. When investigate the utility of 2 different fragment sizes of the cyt. b gene, the partial, 479-bp, cyt. b protocol picked up all mitochondrial (mt)DNA lineages that are found when using the full cyt. b gene, 1073 bp, suggesting that this protocol is sufficient for identification of most mtDNA lineages. All of the mtDNA lineages were associated with unique alleles when amplification was possible at a nuclear locus, strengthening the hypothesis that the designation of lineages based on mtDNA is largely genome-wide representative. We, therefore, propose the use of a cyt. b fragment of this length as a standard gene fragment for a DNA bar-coding system for avian Haemoproteus species.},
}
@article {pmid17920299,
year = {2007},
author = {Boumans, L and Vieites, DR and Glaw, F and Vences, M},
title = {Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles.},
journal = {Molecular phylogenetics and evolution},
volume = {45},
number = {3},
pages = {822-839},
doi = {10.1016/j.ympev.2007.05.028},
pmid = {17920299},
issn = {1055-7903},
mesh = {Animals ; Madagascar ; Mitochondria/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reptiles/classification/*genetics ; },
abstract = {Using sequences of the mitochondrial 16S rRNA gene, we reconstructed the phylogeography of six widely distributed Malagasy reptiles: two gekkonid lizard species, Phelsuma lineata and Hemidactylus mercatorius; two chameleons, the Calumma brevicorne complex, and Furcifer lateralis; and two skinks, Trachylepis gravenhorstii and Trachylepis elegans. Genetic differentiation among major haplotype lineages was high and in some cases indicates or confirms species status of the divergent populations. Maximum uncorrected sequence divergences were between 2.2% and 8.3% within the various species or species complexes. Haplotype lineages were exclusive to geographic regions, except in the commensal H. mercatorius where in three anthropogenic habitats coexistence of haplotype lineages was observed, possibly due to human translocation. The eastward flowing rivers Mangoro and Mananara may represent barriers to gene flow in the case of three species each. Some species sampled from humid eastern and arid western Madagascar showed no differentiation between populations from these two regions; instead the pattern observed was in several cases more concordant with a differentiation along a north-south axis.},
}
@article {pmid17942449,
year = {2007},
author = {Ono, Y and Sakai, A and Takechi, K and Takio, S and Takusagawa, M and Takano, H},
title = {NtPolI-like1 and NtPolI-like2, bacterial DNA polymerase I homologs isolated from BY-2 cultured tobacco cells, encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.},
journal = {Plant &amp; cell physiology},
volume = {48},
number = {12},
pages = {1679-1692},
doi = {10.1093/pcp/pcm140},
pmid = {17942449},
issn = {0032-0781},
mesh = {Amino Acid Sequence ; Base Sequence ; Cells, Cultured ; DNA Polymerase I/chemistry/isolation &amp; purification/*metabolism ; DNA Primers ; *DNA Replication ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*enzymology ; },
abstract = {Two cDNAs encoding homologs of bacterial DNA polymerase I were isolated from cultured tobacco (Nicotiana tabacum) BY-2 cells, and the corresponding genes were named NtPolI-like1 and NtPolI-like2. High sequence similarity suggested that they are orthologous genes each derived from respective parental species of N. tabacum, an allotetraploid plant. Each of the NtPolI-like1/2 gene products had a putative transit peptide for plastid localization at the N-terminus, followed by a 3'-5' exonuclease domain in the internal region, and a DNA polymerase domain in the C-terminal region. Among family A DNA polymerases, NtPolI-like proteins formed, together with other plant DNA polymerase I homologs, a phylogenetic group distinct from mitochondrial DNA polymerase gamma in animals and fungi, as well as eukaryotic cell nuclear-localized repair enzymes. In contrast to computer predictions, experiments with green fluorescent protein (GFP) fusion protein and Western blotting analysis suggested dual targeting of the gene products to both plastids and mitochondria. The recombinant NtPolI-like2 protein exhibited DNA polymerase activity in vitro. Their biochemical character roughly coincided with those of the 116 kDa DNA polymerases found in the plastid and mitochondrial nuclei (nucleoids) isolated from BY-2 cells. Pre-treatment of the organelle nuclear extracts with anti-NtPolI-like antibody removed most of the DNA polymerase activity. Reverse transcription-PCR (RT-PCR) and Western blotting analyses demonstrated transient activation of NtPolI-like gene expression in the initial phase of cell proliferation, exactly when the 116 kDa DNA polymerases in the isolated organelle nuclei were activated and preferential synthesis of organelle DNAs occurred. Taken together, our results suggest that NtPolI-like1/2 genes encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.},
}
@article {pmid17961221,
year = {2007},
author = {Fahrein, K and Talarico, G and Braband, A and Podsiadlowski, L},
title = {The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida.},
journal = {BMC genomics},
volume = {8},
number = {},
pages = {386},
pmid = {17961221},
issn = {1471-2164},
mesh = {Animals ; Arachnida/classification/*genetics ; DNA, Mitochondrial/genetics ; *Gene Order ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; },
abstract = {BACKGROUND: Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in phylogenetic analyses. Arachnid phylogeny is still highly debated and there is a lack of sufficient sequence data for many taxa. Ricinulei (hooded tickspiders) are a morphologically distinct clade of arachnids with uncertain phylogenetic affinities.<br><br>RESULTS: The first complete mitochondrial DNA genome of a member of the Ricinulei, Pseudocellus pearsei (Arachnida: Ricinulei) was sequenced using a PCR-based approach. The mitochondrial genome is a typical circular duplex DNA molecule with a size of 15,099 bp, showing the complete set of genes usually present in bilaterian mitochondrial genomes. Five tRNA genes (trnW, trnY, trnN, trnL(CUN), trnV) show different relative positions compared to other Chelicerata (e.g. Limulus polyphemus, Ixodes spp.). We propose that two events led to this derived gene order: (1) a tandem duplication followed by random deletion and (2) an independent translocation of trnN. Most of the inferred tRNA secondary structures show the common cloverleaf pattern except tRNA-Glu where the TpsiC-arm is missing. In phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference) using concatenated amino acid and nucleotide sequences of protein-coding genes the basal relationships of arachnid orders remain unresolved.<br><br>CONCLUSION: Phylogenetic analyses (ML, MP, BI) of arachnid mitochondrial genomes fail to resolve interordinal relationships of Arachnida and remain in a preliminary stage because there is still a lack of mitogenomic data from important taxa such as Opiliones and Pseudoscorpiones. Gene order varies considerably within Arachnida - only eight out of 23 species have retained the putative arthropod ground pattern. Some gene order changes are valuable characters in phylogenetic analysis of intraordinal relationships, e.g. in Acari.},
}
@article {pmid17967180,
year = {2007},
author = {Shen, YQ and Burger, G},
title = {'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools.},
journal = {BMC bioinformatics},
volume = {8},
number = {},
pages = {420},
pmid = {17967180},
issn = {1471-2105},
mesh = {Algorithms ; Amino Acid Motifs ; Arabidopsis Proteins/chemistry ; Computational Biology/*instrumentation/*methods ; Databases, Protein ; False Positive Reactions ; Internet ; Mitochondria/metabolism ; Peptides/chemistry ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; Proteins/*chemistry ; Reproducibility of Results ; Sequence Alignment ; Sequence Analysis, Protein ; Software ; },
abstract = {BACKGROUND: Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for a given protein. Since the individual tools each have particular strengths, we set out to integrate them in a way that optimally exploits their potential. The method we present here is applicable to various subcellular locations, but tailored for predicting whether or not a protein is localized in mitochondria. Knowledge of the mitochondrial proteome is relevant to understanding the role of this organelle in global cellular processes.<br><br>RESULTS: In order to develop a method for enhanced prediction of subcellular localization, we integrated the outputs of available localization prediction tools by several strategies, and tested the performance of each strategy with known mitochondrial proteins. The accuracy obtained (up to 92%) surpasses by far the individual tools. The method of integration proved crucial to the performance. For the prediction of mitochondrion-located proteins, integration via a two-layer decision tree clearly outperforms simpler methods, as it allows emphasis of biologically relevant features such as the mitochondrial targeting peptide and transmembrane domains.<br><br>CONCLUSION: We developed an approach that enhances the prediction accuracy of mitochondrial proteins by uniting the strength of specialized tools. The combination of machine-learning based integration with biological expert knowledge leads to improved performance. This approach also alleviates the conundrum of how to choose between conflicting predictions. Our approach is easy to implement, and applicable to predicting subcellular locations other than mitochondria, as well as other biological features. For a trial of our approach, we provide a webservice for mitochondrial protein prediction (named YimLOC), which can be accessed through the AnaBench suite at http://anabench.bcm.umontreal.ca/anabench/. The source code is provided in the Additional File 2.},
}
@article {pmid17999954,
year = {2008},
author = {Xu, Y and Johansson, M and Karlsson, A},
title = {Human UMP-CMP kinase 2, a novel nucleoside monophosphate kinase localized in mitochondria.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {3},
pages = {1563-1571},
doi = {10.1074/jbc.M707997200},
pmid = {17999954},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Cloning, Molecular ; DNA, Complementary ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Neoplastic ; HeLa Cells ; Humans ; Isoelectric Point ; Kinetics ; Mitochondria/*enzymology ; Models, Biological ; Molecular Sequence Data ; Neoplasms/enzymology/genetics ; Nucleoside-Phosphate Kinase/chemistry/genetics/*isolation &amp; purification/*metabolism ; Nucleotides/metabolism ; Phylogeny ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Subcellular Fractions/enzymology ; Substrate Specificity ; },
abstract = {Enzyme deficiency in the salvage pathway of deoxyribonucleotide synthesis in mitochondria can cause mtDNA depletion syndromes. We have identified a human mitochondrial UMP-CMP kinase (UMP-CMPK, cytidylate kinase; EC 2.7.4.14), designated as UMP-CMP kinase 2 (UMP-CMPK2). The C-terminal domain of this 449-amino acid protein contains all consensus motifs of a nucleoside monophosphate kinase. Phylogenetic analysis showed that UMP-CMPK2 belonged to a novel nucleoside monophosphate kinase family, which was closer to thymidylate kinase than to cytosolic UMP-CMP kinase. Subcellular localization with green fluorescent protein fusion proteins illustrated that UMP-CMPK2 was localized in the mitochondria of HeLa cells and that the mitochondrial targeting signal was included in the N-terminal 22 amino acids. The enzyme was able to phosphorylate dUMP, dCMP, CMP, and UMP with ATP as phosphate donor, but the kinetic properties were different compared with the cytosolic UMP-CMPK. Its efficacy to convert dUMP was highest, followed by dCMP, whereas CMP and UMP were the poorest substrates. It also phosphorylated the monophosphate forms of the nucleoside analogs ddC, dFdC, araC, BVDU, and FdUrd, which suggests that UMP-CMPK2 may be involved in mtDNA depletion caused by long term treatment with ddC or other pyrimidine analogs. UMP-CMPK2 mRNA expression was exclusively detected in chronic myelogenous leukemia K-562 and lymphoblastic leukemia MOLT-4 among eight studied cancer cell lines. Particular high expression in leukemia cells, dominant expression in bone marrow, and tight correlation with macrophage activation and inflammatory response suggest that UMP-CMPK2 may have other functions in addition to the supply of substrates for mtDNA synthesis.},
}
@article {pmid18007659,
year = {2007},
author = {Bos, MP and Robert, V and Tommassen, J},
title = {Functioning of outer membrane protein assembly factor Omp85 requires a single POTRA domain.},
journal = {EMBO reports},
volume = {8},
number = {12},
pages = {1149-1154},
pmid = {18007659},
issn = {1469-221X},
mesh = {Bacterial Outer Membrane Proteins/classification/genetics/*metabolism ; Binding Sites/genetics ; Cell Membrane/metabolism ; Electrophoresis, Polyacrylamide Gel ; Immunoblotting ; Mutation ; Neisseria meningitidis/genetics/*metabolism ; Phylogeny ; },
abstract = {beta-Barrel proteins are present in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. The central component of their assembly machinery is called Omp85 in bacteria. Omp85 is predicted to consist of an integral membrane domain and an amino-terminal periplasmic extension containing five polypeptide-transport-associated (POTRA) domains. We have addressed the function of these domains by creating POTRA domain deletions in Omp85 of Neisseria meningitidis. Four POTRA domains could be deleted with only slight defects in Omp85 function. Only the most carboxy-terminal POTRA domain was essential, as was the membrane domain. Thus, similar to the mitochondrial Omp85 homologue, the functional core of bacterial Omp85 consists of its membrane domain and a single POTRA domain, that is, POTRA5.},
}
@article {pmid18028257,
year = {2008},
author = {Moosmann, B and Behl, C},
title = {Mitochondrially encoded cysteine predicts animal lifespan.},
journal = {Aging cell},
volume = {7},
number = {1},
pages = {32-46},
doi = {10.1111/j.1474-9726.2007.00349.x},
pmid = {18028257},
issn = {1474-9726},
mesh = {Aging ; Animals ; Computational Biology ; Cysteine/*analysis/genetics/metabolism ; DNA, Mitochondrial/genetics ; Free Radicals/metabolism ; Humans ; Longevity/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*chemistry/genetics ; Models, Molecular ; Phylogeny ; },
abstract = {The role of genetic factors in the determination of lifespan is undisputed. However, numerous successful efforts to identify individual genetic modulators of longevity have not yielded yet a quantitative measure to estimate the lifespan of a species from scratch, merely based on its genomic constitution. Here, we report on a meta-examination of genome sequences from 248 animal species with known maximum lifespan, including mammals, birds, fish, insects, and helminths. Our analysis reveals that the frequency with which cysteine is encoded by mitochondrial DNA is a specific and phylogenetically ubiquitous molecular indicator of aerobic longevity: long-lived species synthesize respiratory chain complexes which are depleted of cysteine. Cysteine depletion was also found on a proteome-wide scale in aerobic versus anaerobic bacteria, archaea, and unicellular eukaryotes; in mitochondrial versus hydrogenosomal sequences; and in the mitochondria of free-living, aerobic versus anaerobic-parasitic worms. The association of longevity with mitochondrial cysteine depletion persisted after correction for body mass and phylogenetic interdependence, but it was uncoupled in helminthic species with predominantly anaerobic lifestyle. We conclude that protein-coding genes on mitochondrial DNA constitute a quantitative trait locus for aerobic longevity, wherein the oxidation of mitochondrially translated cysteine mediates the coupling of trait and locus. These results provide distinct support for the free radical theory of aging.},
}
@article {pmid18045382,
year = {2007},
author = {Gill, EE and Diaz-Triviño, S and Barberà, MJ and Silberman, JD and Stechmann, A and Gaston, D and Tamas, I and Roger, AJ},
title = {Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi.},
journal = {Molecular microbiology},
volume = {66},
number = {6},
pages = {1306-1320},
doi = {10.1111/j.1365-2958.2007.05979.x},
pmid = {18045382},
issn = {0950-382X},
mesh = {Amoeba/genetics/*metabolism/ultrastructure ; Anaerobiosis ; Animals ; Chaperonin 60/genetics/metabolism ; Cloning, Molecular ; Electrophoresis, Gel, Two-Dimensional ; Immunoblotting ; Iron-Sulfur Proteins/metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/*metabolism/ultrastructure ; Organelles/*metabolism/ultrastructure ; Phylogeny ; Protozoan Proteins/classification/genetics/metabolism ; },
abstract = {Unicellular eukaryotes that lack mitochondria typically contain related organelles such as hydrogenosomes or mitosomes. To characterize the evolutionary diversity of these organelles, we conducted an expressed sequence tag (EST) survey on the free-living amoeba Mastigamoeba balamuthi, a relative of the human parasite Entamoeba histolytica. From 19 182 ESTs, we identified 21 putative mitochondrial proteins implicated in protein import, amino acid interconversion and carbohydrate metabolism, two components of the iron-sulphur cluster (Fe-S) assembly apparatus as well as two enzymes characteristic of hydrogenosomes. By immunofluorescence microscopy and subcellular fractionation, we show that mitochondrial chaperonin 60 is targeted to small abundant organelles within Mastigamoeba. In transmission electron micrographs, we identified double-membraned compartments that likely correspond to these mitochondrion-derived organelles, The predicted organellar proteome of the Mastigamoeba organelle indicates a unique spectrum of functions that collectively have never been observed in mitochondrion-related organelles. However, like Entamoeba, the Fe-S cluster assembly proteins in Mastigamoeba were acquired by lateral gene transfer from epsilon-proteobacteria and do not possess obvious organellar targeting peptides. These data indicate that the loss of classical aerobic mitochondrial functions and acquisition of anaerobic enzymes and Fe-S cluster assembly proteins occurred in a free-living member of the eukaryote super-kingdom Amoebozoa.},
}
@article {pmid18047017,
year = {2007},
author = {Chelomina, GN and Atopkin, DM and Bogdanov, AS},
title = {Phylogenetic relationships between species and intraspecific forms of forest mice from the genus Sylvaemus as determined by partial sequencing of the cytochrome b gene of mitochondrial DNA.},
journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections},
volume = {416},
number = {},
pages = {356-359},
pmid = {18047017},
issn = {0012-4966},
mesh = {Animals ; Cluster Analysis ; Cytochromes b/*genetics ; DNA/metabolism ; *DNA, Mitochondrial ; Genetic Variation ; Karyotyping ; Mice ; Mitochondria/metabolism ; Models, Biological ; Models, Statistical ; Phylogeny ; Species Specificity ; },
}
@article {pmid18047198,
year = {2007},
author = {Marquez, JG and Cummings, MA and Krafsur, ES},
title = {Phylogeography of stable fly (Diptera: Muscidae) estimated by diversity at ribosomal 16S and cytochrome oxidase I mitochondrial genes.},
journal = {Journal of medical entomology},
volume = {44},
number = {6},
pages = {998-1008},
doi = {10.1603/0022-2585(2007)44[998:posfdm]2.0.co;2},
pmid = {18047198},
issn = {0022-2585},
mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/*enzymology ; Muscidae/*genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The blood-feeding cosmopolitan stable fly, Stomoxys calcitrans L. (Diptera: Muscidae), is thought to disperse rapidly and widely, and earlier studies of allozyme variation were consistent with high vagility in this species. The geographic origins of New World populations are unknown. Diversity at mitochondrial loci r16S and cytochrome oxidase I was examined in 277 stable flies from 11 countries, including five zoogeographical regions. Of 809 nucleotides, 174 were polymorphic and 133 were parsimony informative. Seventy-six haplotypes were found in frequencies consistent with the Wright-Fisher infinite allele model. None were shared among four or more zoogeographical regions. The null hypothesis of mutation neutrality was not rejected, thereby validating the observed distribution. Fifty-nine haplotypes were singular, eight were private and confined to the Old World, and three of 76 haplotypes were shared between the Old and New World. Only 19 haplotypes were found in the New World, 14 of which were singletons. Haplotype and nucleotide diversities were heterogeneous among countries and regions. The most diversity was observed in sub-Saharan Africa. Regional differentiation indices were C(RT) = 0.26 and N(RT) = 0.31, indicating populations were highly structured macrogeographically. Palearctic and New World flies were the least differentiated from each other. There were strong genetic similarities among populations in the Nearctic, Neotropical, and Palearctic regions, and it is most likely that New World populations were derived from the Palearctic after 1492 CE, in the colonial era.},
}
@article {pmid18054044,
year = {2008},
author = {Uyttewaal, M and Mireau, H and Rurek, M and Hammani, K and Arnal, N and Quadrado, M and Giegé, P},
title = {PPR336 is associated with polysomes in plant mitochondria.},
journal = {Journal of molecular biology},
volume = {375},
number = {3},
pages = {626-636},
doi = {10.1016/j.jmb.2007.11.011},
pmid = {18054044},
issn = {1089-8638},
mesh = {Amino Acid Motifs ; Amino Acid Substitution ; Arabidopsis/cytology/genetics/metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Escherichia coli/genetics ; Homozygote ; Mitochondria/*metabolism ; Mitochondrial Membranes/chemistry ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Weight ; Phylogeny ; Plant Proteins/*metabolism ; Polyribosomes/*metabolism ; Protein Binding ; Repetitive Sequences, Amino Acid/genetics ; },
abstract = {The function of pentatricopeptide repeat (PPR) proteins has been associated with various post-transcriptional steps of organelle gene expression. Among them, translation and its regulation are essential processes. However, in plant mitochondria, they are also the steps of gene expression that are the least understood. In this study, PPR336 was identified as part of a high-molecular-weight complex in Arabidopsis mitochondria. PPR336 is an unusual representative of the large PPR family because it is relatively short and is characterised by a high expression level compared with other PPR proteins. PPR336 defines a small subgroup of eight class P PPR proteins that are similar in terms of motif organization. Among them, PPR336-like is the closest homolog of PPR336. Biochemical analysis has indicated that PPR336 is a strictly mitochondrial protein, extrinsically attached to the inner mitochondrial membrane and part of an RNase-sensitive complex. Sucrose gradients and polysome destabilisation experiments show that PPR336 is associated with ribosomes in plant mitochondria. Moreover, in Ppr336/336-like mutants, mitochondrial polysomes of lower molecular weight accumulate compared with wild-type plants. Polysome association and these unusual features suggest that PPR336 could be involved in a distinctive process, possibly translation in plant mitochondria.},
}
@article {pmid18075112,
year = {2007},
author = {Iwahashi, H and Ishidou, E and Kitagawa, E and Momose, Y},
title = {Combined cadmium and thiuram show synergistic toxicity and induce mitochondrial petite mutants.},
journal = {Environmental science &amp; technology},
volume = {41},
number = {22},
pages = {7941-7946},
doi = {10.1021/es071313y},
pmid = {18075112},
issn = {0013-936X},
mesh = {Biological Assay ; Cadmium/*analysis/chemistry ; Cluster Analysis ; DNA, Mitochondrial/chemistry ; Dose-Response Relationship, Drug ; *Gene Expression Profiling ; Mitochondria/*metabolism ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Phylogeny ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Thiram/*analysis ; },
abstract = {A bioassay is a system for monitoring toxicity of chemicals in the environment via the biological responses of experimental organisms. These responses can be detected by analysis of genome-wide changes in mRNA expression levels using DNA microarrays. We applied this system for evaluation of synergistic toxicity by cadmium and thiuram, as this combination showed mutual growth inhibition in yeast. Hierarchical cluster analysis using mRNA expression profiles suggested the response of yeast to this combination is similar to that seen with cadmium treatment alone. Functional characterization of genes induced by this combinational treatment also suggests that the toxicity of cadmium was enhanced. This toxicity was observed as the damage to mitochondrial functions, which were not observed with either cadmium or thiuram treatments alone. The potential toxicity to mitochondria by this combinational treatment was confirmed as the result of deletion of mitochondria with petite colony formation frequency. We could evaluate synergistic toxicity by cadmium and thiuram and show the possible use of transcriptome bioassay for synergistic toxicity.},
}
@article {pmid18078956,
year = {2008},
author = {Williams, BA and Haferkamp, I and Keeling, PJ},
title = {An ADP/ATP-specific mitochondrial carrier protein in the microsporidian Antonospora locustae.},
journal = {Journal of molecular biology},
volume = {375},
number = {5},
pages = {1249-1257},
doi = {10.1016/j.jmb.2007.11.005},
pmid = {18078956},
issn = {1089-8638},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Sequence ; Escherichia coli/genetics ; Green Fluorescent Proteins/metabolism ; Membrane Transport Proteins/*genetics/metabolism ; Microsporidia/*genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {The mitochondrion is one of the defining characteristics of eukaryotic cells, and to date, no eukaryotic lineage has been shown to have lost mitochondria entirely. In certain anaerobic or microaerophilic lineages, however, the mitochondrion has become severely reduced that it lacks a genome and no longer synthesizes ATP. One example of such a reduced organelle, called the mitosome, is found in microsporidian parasites. Only a handful of potential mitosomal proteins were found to be encoded in the complete genome of the microsporidian Encephalitozoon cuniculi, and significantly no proteins of the mitochondrial carrier family were identified. These carriers facilitate the transport of solutes across the inner mitochondrial membrane, are a means of communication between the mitochondrion and cytosol, and are abundant in organisms with aerobic mitochondria. Here, we report the characterization of a mitochondrial carrier protein in the microsporidian Antonospora locustae and demonstrate that the protein is heterologously targeted to mitochondria in Saccharomyces cerevisiae. The protein is phylogenetically allied to the NAD(+) transporter of S. cerevisiae, but we show that it has high specificity for ATP and ADP when expressed in Escherichia coli. An ADP/ATP carrier may provide ATP for essential ATP-dependent mitosomal processes such as Hsp70-dependent protein import and export of iron-sulfur clusters to the cytosol.},
}
@article {pmid18097445,
year = {2008},
author = {Youle, RJ and Strasser, A},
title = {The BCL-2 protein family: opposing activities that mediate cell death.},
journal = {Nature reviews. Molecular cell biology},
volume = {9},
number = {1},
pages = {47-59},
doi = {10.1038/nrm2308},
pmid = {18097445},
issn = {1471-0080},
mesh = {Animals ; Apoptosis/*physiology ; Humans ; Mitochondria/physiology ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary/physiology ; Proto-Oncogene Proteins c-bcl-2/*physiology ; },
abstract = {BCL-2 family proteins, which have either pro- or anti-apoptotic activities, have been studied intensively for the past decade owing to their importance in the regulation of apoptosis, tumorigenesis and cellular responses to anti-cancer therapy. They control the point of no return for clonogenic cell survival and thereby affect tumorigenesis and host-pathogen interactions and regulate animal development. Recent structural, phylogenetic and biological analyses, however, suggest the need for some reconsideration of the accepted organizational principles of the family and how the family members interact with one another during programmed cell death. Although these insights into interactions among BCL-2 family proteins reveal how these proteins are regulated, a unifying hypothesis for the mechanisms they use to activate caspases remains elusive.},
}
@article {pmid18160177,
year = {2008},
author = {Röhlk, C and Rohlfs, M and Leier, S and Schliwa, M and Liu, X and Parsch, J and Woehlke, G},
title = {Properties of the Kinesin-1 motor DdKif3 from Dictyostelium discoideum.},
journal = {European journal of cell biology},
volume = {87},
number = {4},
pages = {237-249},
doi = {10.1016/j.ejcb.2007.11.001},
pmid = {18160177},
issn = {0171-9335},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Dictyostelium/genetics/*metabolism ; Escherichia coli ; Kinesins/chemistry/genetics/*metabolism ; Microtubules/metabolism ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {The amoeba Dictyostelium discoideum possesses genes for 13 different kinesins. Here we characterize DdKif3, a member of the Kinesin-1 family. Kinesin-1 motors form homodimers that can move micrometer-long distances on microtubules using the energy derived from ATP hydrolysis. We expressed recombinant motors in Escherichia coli and tested them in different in vitro assays. Full-length and truncated Kif3 motors were active in gliding and ATPase assays. They showed a strong dependence on ionic strength. Like the full-length motor, the truncated DdKif3-592 motor (aa 1-592; comprising motor domain, neck, and partial stalk) reached its maximum speed of around 2.0micrcom s(-1) at a potassium acetate concentration of 200mM. The shortened DdKif3-342 motor (aa 1-342; comprising motor domain, partial neck) showed a high ATP turnover, comparable to that of the fungal Kinesin-1, Nkin. Results from the duty cycle calculations and gliding assays indicate that DdKif3 is a processive motor. A GFP-fusion protein revealed a mainly cytoplasmic localization of DdKif3. Immunofluorescence staining makes an association with the endoplasmic reticulum or mitochondria unlikely. Despite a similar phylogenetic distance to both metazoa and fungi, in terms of its biochemical properties DdKif3 revealed a closer similarity to fungal than animal kinesins.},
}
@article {pmid18167542,
year = {2008},
author = {Hampl, V and Silberman, JD and Stechmann, A and Diaz-Triviño, S and Johnson, PJ and Roger, AJ},
title = {Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis.},
journal = {PloS one},
volume = {3},
number = {1},
pages = {e1383},
pmid = {18167542},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Animals ; DNA, Mitochondrial/*genetics ; Energy Metabolism ; Eukaryota/classification/*genetics/metabolism ; Expressed Sequence Tags ; Molecular Sequence Data ; Phylogeny ; Protein Transport ; Sequence Homology, Amino Acid ; },
abstract = {Most modern eukaryotes diverged from a common ancestor that contained the alpha-proteobacterial endosymbiont that gave rise to mitochondria. The 'amitochondriate' anaerobic protist parasites that have been studied to date, such as Giardia and Trichomonas harbor mitochondrion-related organelles, such as mitosomes or hydrogenosomes. Yet there is one remaining group of mitochondrion-lacking flagellates known as the Preaxostyla that could represent a primitive 'pre-mitochondrial' lineage of eukaryotes. To test this hypothesis, we conducted an expressed sequence tag (EST) survey on the preaxostylid flagellate Trimastix pyriformis, a poorly-studied free-living anaerobe. Among the ESTs we detected 19 proteins that, in other eukaryotes, typically function in mitochondria, hydrogenosomes or mitosomes, 12 of which are found exclusively within these organelles. Interestingly, one of the proteins, aconitase, functions in the tricarboxylic acid cycle typical of aerobic mitochondria, whereas others, such as pyruvate:ferredoxin oxidoreductase and [FeFe] hydrogenase, are characteristic of anaerobic hydrogenosomes. Since Trimastix retains genetic evidence of a mitochondriate ancestry, we can now say definitively that all known living eukaryote lineages descend from a common ancestor that had mitochondria.},
}
@article {pmid18178670,
year = {2008},
author = {Avisar, D and Prokhnevsky, AI and Makarova, KS and Koonin, EV and Dolja, VV},
title = {Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana.},
journal = {Plant physiology},
volume = {146},
number = {3},
pages = {1098-1108},
pmid = {18178670},
issn = {0032-0889},
support = {GM 053190/GM/NIGMS NIH HHS/United States ; },
mesh = {Actins/metabolism ; DNA, Complementary ; Eukaryota/genetics ; Light ; Molecular Sequence Data ; Movement/*physiology ; Myosins/genetics/*metabolism ; Organelles/*physiology ; Phylogeny ; Plant Leaves/*physiology ; RNA Interference ; Nicotiana/*metabolism/physiology ; },
abstract = {A prominent feature of plant cells is the rapid, incessant movement of the organelles traditionally defined as cytoplasmic streaming and attributed to actomyosin motility. We sequenced six complete Nicotiana benthamiana cDNAs that encode class XI and class VIII myosins. Phylogenetic analysis indicates that these two classes of myosins diverged prior to the radiation of green algae and land plants from a common ancestor and that the common ancestor of land plants likely possessed at least seven myosins. We further report here that movement of Golgi stacks, mitochondria, and peroxisomes in the leaf cells of N. benthamiana is mediated mainly by myosin XI-K. Suppression of myosin XI-K function using dominant negative inhibition or RNA interference dramatically reduced movement of each of these organelles. When similar approaches were used to inhibit functions of myosin XI-2 or XI-F, only moderate to marginal effects were observed. Organelle trafficking was virtually unaffected in response to inhibition of each of the three class VIII myosins. Interestingly, none of the tested six myosins appears to be involved in light-induced movements of chloroplasts. Taken together, these data strongly suggest that myosin XI-K has a major role in trafficking of Golgi stacks, mitochondria, and peroxisomes, whereas myosins XI-2 and XI-F might perform accessory functions in this process. In addition, our analysis of thousands of individual organelles revealed independent movement patterns for Golgi stacks, mitochondria, and peroxisomes, indicating that the notion of coordinated cytoplasmic streaming is not generally applicable to higher plants.},
}
@article {pmid18179422,
year = {2008},
author = {Scocca, JR and Shapiro, TA},
title = {A mitochondrial topoisomerase IA essential for late theta structure resolution in African trypanosomes.},
journal = {Molecular microbiology},
volume = {67},
number = {4},
pages = {820-829},
doi = {10.1111/j.1365-2958.2007.06087.x},
pmid = {18179422},
issn = {0950-382X},
support = {R01 AI028855/AI/NIAID NIH HHS/United States ; R01AI28855/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; DNA Topoisomerases, Type I/genetics/*metabolism ; DNA, Kinetoplast/*chemistry/*metabolism ; Mitochondria/*enzymology/metabolism ; Phylogeny ; RNA Interference ; Trypanosoma brucei brucei/cytology/enzymology/*genetics/metabolism ; },
abstract = {Trypanosomes and Leishmania, protozoans that cause major human diseases, have a topologically intricate mitochondrial DNA (kinetoplast or kDNA) in the form of a network of thousands of interlocked circles. This unusual system provides a useful reporter for studying topoisomerase functions in vivo. We now find that these organisms have three type IA topoisomerases, one of which is phylogenetically distinctive and which we designate topoisomerase IA(mt). In Trypanosoma brucei topoisomerase IA(mt) immunolocalizes within the mitochondrion close to the kDNA disk in patterns that vary with the cell cycle. When expression of TOPIA(mt) is silenced by RNAi there is a striking accumulation of kDNA late theta structure replication intermediates, with subsequent loss of kDNA networks and halt in cell growth. This essential enzyme provides clear molecular evidence for the obligatory role of a type IA enzyme in the resolution of late theta structures in vivo. With no close orthologue in humans it also offers a target for the rational development of selectively toxic new antiprotozoal therapies.},
}
@article {pmid18205982,
year = {2008},
author = {Epis, S and Sassera, D and Beninati, T and Lo, N and Beati, L and Piesman, J and Rinaldi, L and McCoy, KD and Torina, A and Sacchi, L and Clementi, E and Genchi, M and Magnino, S and Bandi, C},
title = {Midichloria mitochondrii is widespread in hard ticks (Ixodidae) and resides in the mitochondria of phylogenetically diverse species.},
journal = {Parasitology},
volume = {135},
number = {4},
pages = {485-494},
doi = {10.1017/S0031182007004052},
pmid = {18205982},
issn = {1469-8161},
mesh = {Alphaproteobacteria/genetics/*isolation &amp; purification/ultrastructure ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Ixodes/*microbiology ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Symbiosis ; },
abstract = {The hard tick Ixodes ricinus (Ixodidae) is the sole animal thus far shown to harbour an intra-mitochondrial bacterium, which has recently been named Midichloria mitochondrii. The objectives of this work were (i) to screen ixodid ticks for Midichloria-related bacteria and (ii) to determine whether these bacteria exploit the intra-mitochondrial niche in other tick species. Our main goal was to discover further models of this peculiar form of symbiosis. We have thus performed a PCR screening for Midichloria-related bacteria in samples of ixodid ticks collected in Italy, North America and Iceland. A total of 7 newly examined species from 5 genera were found positive for bacteria closely related to M. mitochondrii. Samples of the tick species Rhipicephalus bursa, found positive in the PCR screening, were analysed with transmission electron microscopy, which revealed the presence of bacteria both in the cytoplasm and in the mitochondria of the oocytes. There is thus evidence that bacteria invade mitochondria in at least 2 tick species. Phylogenetic analysis on the bacterial 16S rRNA gene sequences generated from positive specimens revealed that the bacteria form a monophyletic group within the order Rickettsiales. The phylogeny of Midichloria symbionts and related bacteria does not appear completely congruent with the phylogeny of the hosts.},
}
@article {pmid18219313,
year = {2008},
author = {Tattoli, I and Carneiro, LA and Jéhanno, M and Magalhaes, JG and Shu, Y and Philpott, DJ and Arnoult, D and Girardin, SE},
title = {NLRX1 is a mitochondrial NOD-like receptor that amplifies NF-kappaB and JNK pathways by inducing reactive oxygen species production.},
journal = {EMBO reports},
volume = {9},
number = {3},
pages = {293-300},
pmid = {18219313},
issn = {1469-221X},
mesh = {Amino Acid Sequence ; HeLa Cells ; Humans ; JNK Mitogen-Activated Protein Kinases/*metabolism ; Mitochondria/drug effects/*enzymology ; Mitochondrial Proteins/chemistry/*metabolism ; Molecular Sequence Data ; NF-kappa B/*metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Shigella/drug effects/physiology ; Signal Transduction/drug effects ; Tumor Necrosis Factor-alpha/pharmacology ; },
abstract = {NOD-like receptors (NLRs) are a family of intracellular sensors of microbial- or danger-associated molecular patterns. Here, we report the identification of NLRX1, which is a new member of the NLR family that localizes to the mitochondria. NLRX1 alone failed to trigger most of the common signalling pathways, including nuclear factor-kappaB (NF)-kappaB- and type I interferon-dependent cascades, but could potently trigger the generation of reactive oxygen species (ROS). Importantly, NLRX1 synergistically potentiated ROS production induced by tumour necrosis factor alpha, Shigella infection and double-stranded RNA, resulting in amplified NF-kappaB-dependent and JUN amino-terminal kinases-dependent signalling. Together, these results identify NLRX1 as a NLR that contributes to the link between ROS generation at the mitochondria and innate immune responses.},
}
@article {pmid18227871,
year = {2008},
author = {Khrapko, K},
title = {Two ways to make an mtDNA bottleneck.},
journal = {Nature genetics},
volume = {40},
number = {2},
pages = {134-135},
pmid = {18227871},
issn = {1546-1718},
support = {R01 AG019787/AG/NIA NIH HHS/United States ; },
mesh = {Alleles ; Animals ; Cell Lineage ; Chromosomal Proteins, Non-Histone ; Computer Simulation ; DNA Replication ; DNA, Mitochondrial/*chemistry/*genetics ; Female ; Gene Dosage ; Gene Frequency ; Genetic Drift ; Green Fluorescent Proteins/metabolism ; Mice ; Mice, Inbred Strains ; Mitochondria/*chemistry ; Models, Biological ; Models, Genetic ; Mutation ; Oocytes/chemistry ; Oogenesis ; Repressor Proteins/metabolism ; Time Factors ; },
abstract = {Rapid changes in mitochondrial DNA allele frequency between generations have been explained by an ‘mtDNA bottleneck’ in the germ line, and mtDNA aggregates, or nucleoids have been recently proposed to drive such a bottleneck. Now, a new study finds a sharp reduction in mtDNA content in the germ line and suggests that such reduction alone may account for the bottleneck effect.},
}
@article {pmid18231851,
year = {2008},
author = {Suzuki, H and Filippucci, MG and Chelomina, GN and Sato, JJ and Serizawa, K and Nevo, E},
title = {A biogeographic view of Apodemus in Asia and Europe inferred from nuclear and mitochondrial gene sequences.},
journal = {Biochemical genetics},
volume = {46},
number = {5-6},
pages = {329-346},
doi = {10.1007/s10528-008-9149-7},
pmid = {18231851},
issn = {0006-2928},
mesh = {Animals ; Asia ; Cell Nucleus/*genetics ; Cytochromes b/*genetics ; Europe ; Eye Proteins/*genetics ; Homeodomain Proteins/*genetics ; Mitochondria/*genetics ; Murinae/classification/*genetics ; Phylogeny ; Receptors, Odorant/*genetics ; Retinol-Binding Proteins/*genetics ; von Willebrand Factor/*genetics ; Retinol-Binding Proteins, Interstitial ; },
abstract = {Sequences of the mitochondrial cyt b gene and nuclear IRBP, RAGI, 17, and vWF genes were used to assess the evolutionary history of major lineages of Apodemus, in particular to better understand dispersal between Asia and Europe. Our data show eight extant lineages of Late Tertiary origin: Apodemus agrarius, A. semotus, A. peninsulae, A. speciosus, A. argenteus, A. gurkha, A. mystacinus, and A. sylvaticus. Monophyly of two European lineages (A. mystacinus and A. sylvaticus) and four Asian lineages (A. agrarius, A. semotus, A. peninsulae, and A. speciosus) was confirmed with high bootstrap support. Together with literature data, the available molecular data depict three crucial evolutionary events: (1) initial wide dispersal and subsequent radiation around 6 million years ago, (2) region-specific radiations in Europe and southern China around 2 million years ago, and (3) westward dispersal of A. agrarius to Europe in the Late Quaternary.},
}
@article {pmid18241806,
year = {2008},
author = {Gérard, K and Roby, C and Chevalier, N and Thomassin, B and Chenuil, A and Féral, JP},
title = {Assessment of three mitochondrial loci variability for the crown-of-thorns starfish: a first insight into Acanthaster phylogeography.},
journal = {Comptes rendus biologies},
volume = {331},
number = {2},
pages = {137-143},
doi = {10.1016/j.crvi.2007.11.005},
pmid = {18241806},
issn = {1768-3238},
mesh = {Animals ; Australia ; Ecosystem ; Genetics, Population ; Geography ; Indian Ocean ; Kenya ; Madagascar ; Mitochondria/*genetics ; Phylogeny ; Population Density ; Starfish/classification/*genetics/ultrastructure ; },
abstract = {Acanthaster planci (L.) is one of the major threats to coral reefs, whose genetic diversity has been mainly studied with allozymes. Allozymes revealed the low genetic differentiation between A. planci populations in the Indo-Pacific area. We obtained sequences of A. planci from Kenya, Mayotte and Madagascar at the three loci cytochrome oxydase subunit I (COI), 16S rDNA (16S) and five tRNAs, analysed together with available sequences of Acanthaster from the Pacific Ocean. The level of genetic diversity varied among the three loci, tRNAs being on average three times less divergent than COI and 16S genes. The genus Acanthaster appeared monophyletic, the two species A. brevispinus (Fisher) and A. planci forming distinct clades in agreement with data from morphology and systematics. The A. planci clade split into a West Indian Ocean group and a Pacific group, in agreement with allozyme data on population differentiation.},
}
@article {pmid18244907,
year = {2008},
author = {Niu, BL and Weng, HB and He, LH and Shen, WF and Qi, XP and Liu, Y and Meng, ZQ},
title = {[Cloning and analysis of adenine nucleotide translocase gene in Helicoverpa armigera].},
journal = {Yi chuan = Hereditas},
volume = {30},
number = {1},
pages = {81-86},
doi = {10.3724/sp.j.1005.2008.00081},
pmid = {18244907},
issn = {0253-9772},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary/genetics ; Lepidoptera/classification/*enzymology/*genetics ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {A cDNA clone encoding the ADP/ATP translocase in Helicoverpa armigera has been identified by RT-PCR, 5'and 3'RACE methods. Sequence analysis shows that it is 1,190 bp long and contains a single open reading frame (ORF, 133-1,033 bp) encoding a protein of 300 amino acids (GenBank submission number, AY253868). The protein has a 22 aa signal peptide on its N-terminal, which leads the protein locating onto the inner membrane of the mitochondria. It also has three conserved domains of the mitochondrial carrier protein forming a channel to exchange ATP and ADP energy molecule through the inner membrane of the mitochondria. It shows extensive similarities to the known ADP/ATP translocase poly-peptides. The ADP/ATP translocase similarity was up to 90% in the Lepidoptera.},
}
@article {pmid18248575,
year = {2008},
author = {Chen, G and Hare, MP},
title = {Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa.},
journal = {Molecular ecology},
volume = {17},
number = {6},
pages = {1451-1468},
doi = {10.1111/j.1365-294X.2007.03657.x},
pmid = {18248575},
issn = {1365-294X},
mesh = {Animals ; Base Sequence ; *Biodiversity ; Cell Nucleus/genetics ; Copepoda/cytology/genetics/*physiology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Ecology ; Electron Transport Complex IV/genetics ; Geography ; Haplotypes ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plankton/genetics/*physiology ; Polymorphism, Restriction Fragment Length ; *Rivers ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The recent discovery of cryptic species in marine holoplankton, organisms that 'drift' in oceanic currents throughout their life cycle, contrasts with their potential for long-distance passive dispersal and presumably high gene flow. These observations suggest that holoplankton species are adapting to surprisingly small-scale oceanographic features and imply either limited dispersal or strong selection gradients. Acartia tonsa is a widespread and numerically dominant estuarine copepod containing deep mitochondrial lineages within and among populations along the northwestern Atlantic coast. In this study, we intensively investigated A. tonsa populations in Chesapeake Bay with the goals of testing species status for the deep lineages and testing for their association with environmental features over space and time. Phylogenetic analyses of DNA sequences from mitochondrial cytochrome c oxidase I (mtCOI) and the nuclear ribosomal internal transcribed spacer (nITS) resolved two concordant monophyletic clades. Deep divergence between the two clades (13.7% uncorrected sequence divergence for mtCOI and 32.2% for nITS) and genealogical concordance within sympatric populations strongly suggest that the two clades represent reproductively isolated cryptic species. Based on restriction fragment length polymorphisms of mtCOI, representatives from the two clades were found consistently associated with contrasting salinity regimes (oligohaline vs. meso-polyhaline) with an overlap between 2 and 12 PSU in samples from 1995 to 2005. Finding these patterns in one of the best-known estuarine copepods reinforces the conclusion that marine biodiversity is underestimated, not only in terms of species numbers, but also with respect to niche partitioning and the potential importance of ecological divergence in marine holoplankton.},
}
@article {pmid18255328,
year = {2008},
author = {De Zoysa, M and Pushpamali, WA and Whang, I and Kim, SJ and Lee, J},
title = {Mitochondrial thioredoxin-2 from disk abalone (Haliotis discus discus): molecular characterization, tissue expression and DNA protection activity of its recombinant protein.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {149},
number = {4},
pages = {630-639},
doi = {10.1016/j.cbpb.2007.12.009},
pmid = {18255328},
issn = {1096-4959},
mesh = {Amino Acid Sequence ; Animals ; Antioxidants/chemistry/isolation &amp; purification/metabolism ; Cloning, Molecular ; *DNA Damage ; DNA, Complementary/genetics ; DNA, Superhelical/genetics/metabolism ; Gastropoda/*genetics/metabolism ; *Gene Expression Regulation ; Hydrogen Peroxide/pharmacology ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Organ Specificity ; *Oxidative Stress ; Phylogeny ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Thioredoxins/chemistry/*genetics/isolation &amp; purification/*metabolism ; Up-Regulation/drug effects ; },
abstract = {Thioredoxin-2 is a mitochondria-specific member of the thioredoxin (TRx) super-family that plays an important role as a component of the mitochondrial antioxidant system. The gene coding mitochondrial TRx-2 was isolated from the disk abalone (Haliotis discus discus) cDNA library, denoted as AbTRx-2. It contains 1214-bp full length with 519-bp open reading frame, encoding 173 amino acids. AbTRx-2 showed characteristic TRx active site at (96)WCGPC(100) and mitochondrial targeting peptide at the N-terminal amino acid sequence. The deduced amino acid comparison showed that AbTRx-2 shares 43 and 42% identity with Xenopus laevis and human TRx-2, respectively. Purified recombinant AbTRx-2 fusion protein was shown to catalyze insulin reduction and protect supercoiled plasmid DNA from damages induced by metal-catalyzed generation of reactive oxygen species. Constitutive AbTRx-2 mRNA was detected in gill, mantle, gonad, abductor muscle, digestive tract, and hemocytes, in a tissue specific manner. The AbTRx-2 mRNA was up-regulated in gill and digestive tract tissues initially at 3 h post-injection of H(2)O(2) and maintained higher level at 6 h. Our results suggest that abalone TRx-2 may play an important role in regulating oxidative stress in mitochondria by catalyzing protein disulfide reduction, scavenging of ROS, and minimizing the DNA damage.},
}
@article {pmid18266623,
year = {2008},
author = {Hellgren, O and Bensch, S and Malmqvist, B},
title = {Bird hosts, blood parasites and their vectors--associations uncovered by molecular analyses of blackfly blood meals.},
journal = {Molecular ecology},
volume = {17},
number = {6},
pages = {1605-1613},
doi = {10.1111/j.1365-294X.2007.03680.x},
pmid = {18266623},
issn = {1365-294X},
mesh = {Animals ; Birds/*blood/genetics/*parasitology ; DNA, Mitochondrial/genetics ; Disease Vectors ; Electron Transport Complex IV/genetics ; Eukaryota/*genetics/*physiology ; Feeding Behavior ; Geography ; *Host-Parasite Interactions ; Mitochondria/enzymology/genetics ; Parasites/genetics/*physiology ; Phylogeny ; Simuliidae/*physiology ; Species Specificity ; Sweden ; },
abstract = {The level of host specificity of blood-sucking invertebrates may have both ecological and evolutionary implications for the parasites they are transmitting. We used blood meals from wild-caught blackflies for molecular identification of parasites and hosts to examine patterns of host specificity and how these may affect the transmission of avian blood parasites of the genus Leucocytozoon. We found that five different species of ornithophilic blackflies preferred different species of birds when taking their blood meals. Of the blackflies that contained avian blood meals, 62% were infected with Leucocytozoon parasites, consisting of 15 different parasite lineages. For the blackfly species, there was a significant association between the host width (measured as the genetic differentiation between the used hosts) and the genetic similarity of the parasites in their blood meals. The absence of similar parasite in blood meals from blackflies with different host preferences is interpreted as a result of the vector-host associations. The observed associations between blackfly species and host species are therefore likely to hinder parasites to be transmitted between different host-groups, resulting in ecologically driven associations between certain parasite lineages and hosts species.},
}
@article {pmid18287522,
year = {2008},
author = {Nakamura, N and Hirose, S},
title = {Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane.},
journal = {Molecular biology of the cell},
volume = {19},
number = {5},
pages = {1903-1911},
pmid = {18287522},
issn = {1939-4586},
mesh = {Amino Acid Sequence ; Animals ; COS Cells ; Chlorocebus aethiops ; Endopeptidases/chemistry/genetics/*metabolism ; Gene Expression Profiling ; HeLa Cells ; Humans ; Membrane Proteins/chemistry/metabolism ; Mice ; Mitochondria/*enzymology ; Mitochondrial Membranes/*enzymology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; *Organelle Shape ; Phylogeny ; Protein Sorting Signals ; Protein Transport ; Rats ; Subcellular Fractions/enzymology ; Thiolester Hydrolases/chemistry/genetics/*metabolism ; },
abstract = {Recent studies have suggested that ubiquitination of mitochondrial proteins participates in regulating mitochondrial dynamics in mammalian cells, but it is unclear whether deubiquitination is involved in this process. Here, we identify human ubiquitin-specific protease 30 (USP30) as a deubiquitinating enzyme that is embedded in the mitochondrial outer membrane. Depletion of USP30 expression by RNA interference induced elongated and interconnected mitochondria, depending on the activities of the mitochondrial fusion factors mitofusins, without changing the expression levels of the key regulators for mitochondrial dynamics. Mitochondria were rescued from this abnormal phenotype by ectopic expression of USP30 in a manner dependent on its enzymatic activity. Our findings reveal that USP30 participates in the maintenance of mitochondrial morphology, a finding that provides new insight into the cellular function of deubiquitination.},
}
@article {pmid18295512,
year = {2008},
author = {Albre, J and Gers, C and Legal, L},
title = {Molecular phylogeny of the Erebia tyndarus (Lepidoptera, Rhopalocera, Nymphalidae, Satyrinae) species group combining CoxII and ND5 mitochondrial genes: a case study of a recent radiation.},
journal = {Molecular phylogenetics and evolution},
volume = {47},
number = {1},
pages = {196-210},
doi = {10.1016/j.ympev.2008.01.009},
pmid = {18295512},
issn = {1055-7903},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cyclooxygenase 2/chemistry/*genetics ; DNA Primers ; Insect Proteins/chemistry/*genetics ; Lepidoptera/*classification/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; },
abstract = {The genus Erebia is one of the more controversial groups among the Holarctic Lepidoptera. In this genus, composed of around 100 mountain species, the Erebia tyndarus complex has certainly been a major source of debate for more than a century. According to the literature, between 2 and 11 species, and at least 45 subspecies or semi-species have been recognized. For the first time, we provide a complete molecular study, based on the ND5 and CoxII mitochondrial gene sequences, including all the recognized species and 60% of the subspecies of the entire group, with European, Caucasian, Siberian and North-American taxa. Our analyses led us to recognize 11 species even though there was some poor discrimination between Western Europe species. A complete study of the events of speciation is presented in the light of glacial and interglacial cycles during the Pleistocene.},
}
@article {pmid18302691,
year = {2008},
author = {Good, JM and Hird, S and Reid, N and Demboski, JR and Steppan, SJ and Martin-Nims, TR and Sullivan, J},
title = {Ancient hybridization and mitochondrial capture between two species of chipmunks.},
journal = {Molecular ecology},
volume = {17},
number = {5},
pages = {1313-1327},
doi = {10.1111/j.1365-294X.2007.03640.x},
pmid = {18302691},
issn = {1365-294X},
support = {1P20RRO16448-01//PHS HHS/United States ; },
mesh = {Animals ; Base Sequence ; Gene Flow ; *Genetic Speciation ; Geography ; Haplotypes ; *Hybridization, Genetic ; Likelihood Functions ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; Sciuridae/*genetics ; Sequence Analysis, DNA ; },
abstract = {Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks (Tamias ruficaudus and T. amoenus). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus, T. a. canicaudus, with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus. Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.},
}
@article {pmid18309660,
year = {2007},
author = {Kong, JQ and Wang, W and Zheng, XD and Zhu, P and Cheng, KD},
title = {[Cloning and bioinformatics analysis of P450 cDNA in Artemisia annua].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {32},
number = {21},
pages = {2227-2231},
pmid = {18309660},
issn = {1001-5302},
mesh = {Amino Acid Sequence ; Artemisia annua/enzymology/*genetics ; Base Sequence ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/classification/*genetics ; DNA, Complementary/chemistry/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Plant Proteins/*genetics ; Plants, Medicinal/enzymology/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {OBJECTIVE: Cloning and bioinformatics analysis of P450 cDNA in Artemisia annua.<br><br>METHOD: A P450 cDNA gene was cloned from A. annua by RT-PCR. The bioinformatics analysis of the P450 gene was performed.<br><br>RESULT: The complete ORF of this P450 cDNA is 1 464 bp and encodes 488 aa. The sequence was reported to GenBank and coded as DQ667171. Bioinformatics analysis of the P450 cDNA showed it encoded an A-type P450 protein with 54. 992 kDa, it's isoelectric point was 8.83 and the possibility of export to mitochondria was 0.893 2.<br><br>CONCLUSION: The comparable analysis of the P450 with CYP71AV1 revealed that the two proteins probably performed the same function because of the similar character.},
}
@article {pmid18326043,
year = {2008},
author = {Saito, T and Nishi, M and Lim, MI and Wu, B and Maeda, T and Hashimoto, H and Takeuchi, T and Roos, DS and Asai, T},
title = {A novel GDP-dependent pyruvate kinase isozyme from Toxoplasma gondii localizes to both the apicoplast and the mitochondrion.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {20},
pages = {14041-14052},
pmid = {18326043},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Guanosine Diphosphate/*chemistry ; Kinetics ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Binding ; Protein Isoforms ; Pyruvate Kinase/*chemistry ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; Toxoplasma/*metabolism ; },
abstract = {We previously reported a cytosolic pyruvate kinase (EC 2.7.1.40) from Toxoplasma gondii (TgPyKI) that differs from most eukaryotic pyruvate kinases in being regulated by glucose 6-phosphate rather than fructose 1,6-diphosphate. Another putative pyruvate kinase (TgPyKII) was identified from parasite genome, which exhibits 32% amino acid sequence identity to TgPyKI and retains pyruvate kinase signature motifs and amino acids essential for substrate binding and catalysis. Whereas TgPyKI is most closely related to plant/algal enzymes, phylogenetic analysis suggests a proteobacterial origin for TgPyKII. Enzymatic characterization of recombinant TgPyKII shows a high pH optimum at 8.5, and a preference for GDP as a phosphate recipient. Catalytic activity is independent of K+, and no allosteric or regulatory effects were observed in the presence of fructose 1,6-diphosphate, fructose 2,6-diphosphate, glucose 6-phosphate, ribose 5-phosphate, AMP, or ATP. Unlike TgPyKI, native TgPyKII activity was exclusively associated with the membranous fraction of a T. gondii tachyzoite lysate. TgPyKII possesses a long N-terminal extension containing five putative start codons before the conserved region and localizes to both apicoplast and mitochondrion by immunofluorescence assay using native antibody and fluorescent protein fusion to the N-terminal extension. Further deletional and site-directed mutagenesis suggests that a translation product from 1st Met is responsible for the localization to the apicoplast, whereas one from 3rd Met is for the mitochondrion. This is the first study of a potential mitochondrial pyruvate kinase in any system.},
}
@article {pmid18366542,
year = {2008},
author = {Salakij, C and Salakij, J and Narkkong, NA and Sirinarumitr, T and Pattanarangsan, R},
title = {Hematologic, cytochemical, ultrastructural, and molecular findings of Hepatozoon-infected flat-headed cats (Prionailurus planiceps).},
journal = {Veterinary clinical pathology},
volume = {37},
number = {1},
pages = {31-41},
doi = {10.1111/j.1939-165X.2008.00011.x},
pmid = {18366542},
issn = {0275-6382},
mesh = {Animal Diseases/blood/*parasitology ; Animals ; Blood Cell Count/veterinary ; Blood Chemical Analysis/veterinary ; Blood Platelets/ultrastructure ; Coccidia/genetics/isolation &amp; purification ; Coccidiosis/blood/*veterinary ; Erythrocytes/ultrastructure ; Felidae/*blood ; Female ; Leukocytes/ultrastructure ; Phylogeny ; },
abstract = {BACKGROUND: The flat-headed cat (Prionailurus planiceps) is a small wild cat of Southeast Asia and is considered extremely endangered. Little is known about the hematologic values, blood cell morphology, or hemoparasites of this species in relation to other Felidae.<br><br>OBJECTIVES: The objective of this study was to report basic hematologic values and describe the light microscopic, cytochemical, and ultrastructural characteristics of blood cells in 2 wild-caught flat-headed cats. In addition, molecular analysis was done of a Hepatozoon organism found in the neutrophils of both cats.<br><br>METHODS: Blood samples were collected into EDTA from the cephalic vein. A CBC, manual differential count, manual reticulocyte count, cytochemical stains (Sudan black B [SBB], alpha-naphthyl acetate esterase [ANAE], and beta-glucuronidase), and scanning and transmission electron microscopy were done using standard methods.<br><br>RESULTS: HCT was slightly lower and reticulocyte counts and red cell distribution width were higher than the expected values for other species of cats. Hepatozoon organisms were found in the cytoplasm of neutrophils in both cats, but the number of infected neutrophils was very low (1%-2%). Neutrophils stained strongly positive for SBB, but were negative for ANAE and beta-glucuronidase. Hepatozoon-infected neutrophils were negative for SBB, but focally positive for ANAE and beta-glucuronidase. By transmission electron microscopy, gamonts of Hepatozoon sp were observed in neutrophils, and rarely free in plasma. Infected neutrophils had fewer specific granules and more mitochondria compared with noninfected neutrophils. PCR products of partial 18S rRNA revealed that the isolate of Hepatozoon in the flat-headed cats was closely related to that of the frog Hepatozoon sp.<br><br>CONCLUSIONS: These results add to our understanding of hematologic values and blood cell morphology in Hepatozoon-infected flat-headed cats as well as the molecular analysis of the Hepatozoon organism, and may be useful for the health management and evaluation of hemoparasitic disease in this species.},
}
@article {pmid18369739,
year = {2008},
author = {Siddique, M and Gernhard, S and von Koskull-Döring, P and Vierling, E and Scharf, KD},
title = {The plant sHSP superfamily: five new members in Arabidopsis thaliana with unexpected properties.},
journal = {Cell stress &amp; chaperones},
volume = {13},
number = {2},
pages = {183-197},
pmid = {18369739},
issn = {1466-1268},
support = {R01 GM042762/GM/NIGMS NIH HHS/United States ; GM 42762/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Arabidopsis Proteins/*classification/genetics/isolation &amp; purification/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genes, Reporter ; Heat-Shock Proteins/*classification/genetics/isolation &amp; purification/physiology ; Hot Temperature ; Mitochondria/metabolism ; Molecular Sequence Data ; *Multigene Family ; Multiprotein Complexes/chemistry ; Open Reading Frames/genetics ; Phylogeny ; Protein Folding ; Protoplasts ; Recombinant Fusion Proteins/biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; Stress, Physiological/genetics ; Subcellular Fractions/metabolism ; Nicotiana ; },
abstract = {The small heat shock proteins (sHsps), which are ubiquitous stress proteins proposed to act as chaperones, are encoded by an unusually complex gene family in plants. Plant sHsps are classified into different subfamilies according to amino acid sequence similarity and localization to distinct subcellular compartments. In the whole Arabidopsis thaliana genome, 19 genes were annotated to encode sHsps, of which 14 belong to previously defined plant sHsp families. In this paper, we report studies of the five additional sHsp genes in A. thaliana, which can now be shown to represent evolutionarily distinct sHsp subfamilies also found in other plant species. While two of these five sHsps show expression patterns typical of the other 14 genes, three have unusual tissue specific and developmental profiles and do not respond to heat induction. Analysis of intracellular targeting indicates that one sHsp represents a new class of mitochondrion-targeted sHsps, while the others are cytosolic/nuclear, some of which may cooperate with other sHsps in formation of heat stress granules. Three of the five new proteins were purified and tested for chaperone activity in vitro. Altogether, these studies complete our basic understanding of the sHsp chaperone family in plants.},
}
@article {pmid18378601,
year = {2008},
author = {Ljungdahl, LG},
title = {The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.},
journal = {Annals of the New York Academy of Sciences},
volume = {1125},
number = {},
pages = {308-321},
doi = {10.1196/annals.1419.030},
pmid = {18378601},
issn = {0077-8923},
mesh = {Anaerobiosis ; Cellulase/*metabolism ; Fungal Proteins/metabolism ; Glycoside Hydrolases/*metabolism ; Neocallimastigales/classification/*enzymology ; Phylogeny ; },
abstract = {Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.},
}
@article {pmid18380652,
year = {2008},
author = {Otranto, D and Stevens, JR and Testini, G and Cantacessi, C and Máca, J},
title = {Molecular characterization and phylogenesis of Steganinae (Diptera, Drosophilidae) inferred by the mitochondrial cytochrome c oxidase subunit 1.},
journal = {Medical and veterinary entomology},
volume = {22},
number = {1},
pages = {37-47},
doi = {10.1111/j.1365-2915.2008.00714.x},
pmid = {18380652},
issn = {0269-283X},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA/chemistry/genetics ; Drosophilidae/*classification/*enzymology ; Electron Transport Complex IV/classification/*genetics ; *Genetic Variation ; Likelihood Functions ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Species Specificity ; },
abstract = {The subfamily Steganinae (Diptera, Drosophilidae) includes flies which display zoophilic feeding behaviour in the larval and/or adult stages, some of which act as vectors of Spirurida eyeworms, which infect both carnivores and humans. To date, the taxonomy and phylogeny of the subfamily Steganinae has been studied only superficially and many aspects of their systematics remain unresolved. Thus, the present study aimed to provide a molecular dataset to facilitate the identification and phylogenetic analysis of Steganinae species based on partial (approximately 700 basepairs) mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. A total of 134 flies belonging to 13 species and eight genera of Steganinae were subjected to molecular and phylogenetic analyses. The mean nucleotide variation within the Steganinae subfamily was 8.1%, with a variation within genera for which more than one species was examined ranging from 1.6% (in Phortica spp.) to 21.8% (in Amiota spp.). Interspecific pairwise divergence ranged from 1.6% (Phortica variegata vs. Phortica semivirgo) to 24.8% (Cacoxenus indagator vs. Amiota alboguttata) and intraspecific variation ranged from 0% to 1%. Seventy of the 233 amino acids were variable, including 26 parsimony informative sites and 44 singleton sites, with some highly conserved residues identified within the genera Stegana and Amiota. Parsimony and maximum likelihood-based phylogenetic analyses provided strong support for the genus Phortica, phylogenetically distinct from the genus Amiota. Gitona distigma was placed in an unresolved position adjacent to the outgroup taxa, Drosophila yakuba and Drosophila melanogaster. The molecular data reported here represent the first molecular dataset based on cox1 of Steganinae flies and provide a base for further investigations into the evolutionary relationships among this little-studied subfamily.},
}
@article {pmid18390807,
year = {2008},
author = {Jasinski, M and Sudre, D and Schansker, G and Schellenberg, M and Constant, S and Martinoia, E and Bovet, L},
title = {AtOSA1, a member of the Abc1-like family, as a new factor in cadmium and oxidative stress response.},
journal = {Plant physiology},
volume = {147},
number = {2},
pages = {719-731},
pmid = {18390807},
issn = {0032-0889},
mesh = {Arabidopsis/enzymology/genetics/*physiology ; Arabidopsis Proteins/classification/genetics/metabolism/*physiology ; Base Sequence ; Cadmium/*pharmacology ; Chloroplasts/metabolism ; DNA Primers ; DNA, Bacterial ; *Oxidative Stress ; Phylogeny ; Polymerase Chain Reaction ; Superoxide Dismutase/genetics/metabolism ; },
abstract = {The analysis of gene expression in Arabidopsis (Arabidopsis thaliana) using cDNA microarrays and reverse transcription-polymerase chain reaction showed that AtOSA1 (A. thaliana oxidative stress-related Abc1-like protein) transcript levels are influenced by Cd2+ treatment. The comparison of protein sequences revealed that AtOSA1 belongs to the family of Abc1 proteins. Up to now, Abc1-like proteins have been identified in prokaryotes and in the mitochondria of eukaryotes. AtOSA1 is the first member of this family to be localized in the chloroplasts. However, despite sharing homology to the mitochondrial ABC1 of Saccharomyces cerevisiae, AtOSA1 was not able to complement yeast strains deleted in the endogenous ABC1 gene, thereby suggesting different function between AtOSA1 and the yeast ABC1. The atosa1-1 and atosa1-2 T-DNA insertion mutants were more affected than wild-type plants by Cd2+ and revealed an increased sensitivity toward oxidative stress (hydrogen peroxide) and high light. The mutants exhibited higher superoxide dismutase activities and differences in the expression of genes involved in the antioxidant pathway. In addition to the conserved Abc1 region in the AtOSA1 protein sequence, putative kinase domains were found. Protein kinase assays in gelo using myelin basic protein as a kinase substrate revealed that chloroplast envelope membrane fractions from the AtOSA1 mutant lacked a 70-kD phosphorylated protein compared to the wild type. Our data suggest that the chloroplast AtOSA1 protein is a new factor playing a role in the balance of oxidative stress.},
}
@article {pmid18406119,
year = {2008},
author = {Sethuraman, J and Okoli, CV and Majer, A and Corkery, TL and Hausner, G},
title = {The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana.},
journal = {Mycological research},
volume = {112},
number = {Pt 5},
pages = {564-582},
doi = {10.1016/j.mycres.2007.11.017},
pmid = {18406119},
issn = {0953-7562},
mesh = {Amino Acid Sequence ; Ascomycota/chemistry/classification/*genetics/isolation &amp; purification ; Base Pairing ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Fungal Proteins/chemistry/genetics ; *Introns ; Mitochondria/chemistry/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Phylogeny ; Plant Diseases/microbiology ; Sequence Alignment ; Ulmus/microbiology ; },
abstract = {The presence of group I intron-like elements within the U7 region of the mtDNA large ribosomal subunit RNA gene (rnl) was investigated in strains of Ophiostoma novo-ulmi subsp. americana from Canada, Europe and Eurasia, and in selected strains of O. ips, O. minus, O. piceae, O. ulmi, and O. himal-ulmi. This insertion is of interest as it has been linked previously to the generation of plasmid-like mtDNA elements in diseased strains of O. novo-ulmi. Among 197 O. novo-ulmi subsp. americana strains tested, 61 contained a 1.6kb insertion within the rnl-U7 region and DNA sequence analysis suggests the presence of a group I intron (IA1 type) that encodes a potential double motif LAGLIDADG homing endonuclease-like gene (HEG). Phylogenetic analysis of rnl-U7 intron encoded HEG-like elements supports the view that double motif HEGs originated from a duplication event of a single-motif HEG followed by a fusion event that combined the two copies into one open reading frame (ORF). The data also show that rnl-U7 intron encoded ORFs belong to a clade that includes ORFs inserted into different types of group I introns, e.g. IB, ID, IC3, IA1, present within a variety of different mtDNA genes, such as the small ribosomal subunit RNA gene (rns), apo-cytochrome b gene (cob), NADH dehydrogenase subunit 5 (nad5), cytochrome oxidase subunit 1 gene (coxI), and ATPase subunit 9 gene (atp9). We also compared the occurrence of the rnl-U7 intron in our collection of 227 strains with the presence of the rnl-U11 group I intron and concluded that the U7 intron appears to be an optional element and the U11 intron is probably essential among the strains tested.},
}
@article {pmid18430024,
year = {2008},
author = {Moriyama, T and Terasawa, K and Fujiwara, M and Sato, N},
title = {Purification and characterization of organellar DNA polymerases in the red alga Cyanidioschyzon merolae.},
journal = {The FEBS journal},
volume = {275},
number = {11},
pages = {2899-2918},
doi = {10.1111/j.1742-4658.2008.06426.x},
pmid = {18430024},
issn = {1742-464X},
mesh = {Algal Proteins/*chemistry ; Amino Acid Sequence ; DNA Polymerase II/*chemistry/*isolation &amp; purification ; *Gene Expression Regulation, Plant ; Green Fluorescent Proteins/metabolism ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plastids/metabolism ; Recombinant Fusion Proteins/chemistry ; Recombinant Proteins/chemistry ; Rhodophyta/*enzymology ; Sequence Homology, Amino Acid ; Temperature ; },
abstract = {DNA polymerase gamma, a mitochondrial replication enzyme of yeasts and animals, is not present in photosynthetic eukaryotes. Recently, DNA polymerases with distant homology to bacterial DNA polymerase I were reported in rice, Arabidopsis, and tobacco, and they were localized to both plastids and mitochondria. We call them plant organellar DNA polymerases (POPs). However, POPs have never been purified in the native form from plant tissues. The unicellular thermotrophic red alga Cyanidioschyzon merolae contains two genes encoding proteins related to Escherichia coli DNA polymerase I (PolA and PolB). Phylogenetic analysis revealed that PolB is an ortholog of POPs. Nonphotosynthetic eukaryotes also have POPs, which suggested that POPs have an ancient origin before eukaryotic photosynthesis. PolA is a homolog of bacterial DNA polymerase I and is distinct from POPs. PolB was purified from the C. merolae cells by a series of column chromatography steps. Recombinant protein of PolA was also purified. Sensitivity to inhibitors of DNA synthesis was different in PolA, PolB, and E. coli DNA polymerase I. Immunoblot analysis and targeting studies with green fluorescent protein fusion proteins demonstrated that PolA was localized in the plastids, whereas PolB was present in both plastids and mitochondria. The expression of PolB was regulated by the cell cycle. The available results suggest that PolB is involved in the replication of plastids and mitochondria.},
}
@article {pmid18442968,
year = {2008},
author = {Bauerschmitt, H and Funes, S and Herrmann, JM},
title = {The membrane-bound GTPase Guf1 promotes mitochondrial protein synthesis under suboptimal conditions.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {25},
pages = {17139-17146},
doi = {10.1074/jbc.M710037200},
pmid = {18442968},
issn = {0021-9258},
mesh = {Cell Membrane/*enzymology ; Electron Transport Complex IV/metabolism ; Escherichia coli Proteins/metabolism ; GTP Phosphohydrolases/chemistry/*metabolism/physiology ; *Gene Expression Regulation, Fungal ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Models, Biological ; Nuclear Proteins/metabolism ; Peptide Initiation Factors ; Peptides/chemistry ; Phylogeny ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*physiology ; Species Specificity ; Temperature ; Transcriptional Elongation Factors/metabolism ; },
abstract = {Recently, the bacterial elongation factor LepA was identified as critical for the accuracy of in vitro translation reactions. Extremely well conserved homologues of LepA are present throughout bacteria and eukaryotes, but the physiological relevance of these proteins is unclear. Here we show that the yeast counterpart of LepA, Guf1, is located in the mitochondrial matrix and tightly associated with the inner membrane. It binds to mitochondrial ribosomes in a GTP-dependent manner. Mutants lacking Guf1 show cold- and heat-sensitive growth defects on non-fermentable carbon sources that are especially pronounced under nutrient-limiting conditions. The cold sensitivity is explained by diminished rates of protein synthesis at low temperatures. At elevated temperatures, Guf1-deficient mutants exhibit defects in the assembly of cytochrome oxidase, suggesting that the polypeptides produced are not functional. Moreover, Guf1 mutants exhibit synthetic growth defects with mutations of the protein insertase Oxa1. These observations show a critical role for Guf1 in vivo. The observed defects in Guf1-deficient mitochondria are consistent with a function of Guf1 as a fidelity factor of mitochondrial protein synthesis.},
}
@article {pmid18452298,
year = {2008},
author = {Jérôme, M and Martinsohn, JT and Ortega, D and Carreau, P and Verrez-Bagnis, V and Mouchel, O},
title = {Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database.},
journal = {Journal of agricultural and food chemistry},
volume = {56},
number = {10},
pages = {3460-3469},
doi = {10.1021/jf703704m},
pmid = {18452298},
issn = {0021-8561},
mesh = {Animals ; DNA/*analysis ; Databases, Nucleic Acid ; Fish Products/*analysis ; Fishes/*classification/*genetics ; Food Preservation ; Genetic Markers/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; },
abstract = {Traceability in the fish food sector plays an increasingly important role for consumer protection and confidence building. This is reflected by the introduction of legislation and rules covering traceability on national and international levels. Although traceability through labeling is well established and supported by respective regulations, monitoring and enforcement of these rules are still hampered by the lack of efficient diagnostic tools. We describe protocols using a direct sequencing method based on 212-274-bp diagnostic sequences derived from species-specific mitochondria DNA cytochrome b, 16S rRNA, and cytochrome oxidase subunit I sequences which can efficiently be applied to unambiguously determine even closely related fish species in processed food products labeled "anchovy". Traceability of anchovy-labeled products is supported by the public online database AnchovyID (http://anchovyid.jrc.ec.europa.eu), which provided data obtained during our study and tools for analytical purposes.},
}
@article {pmid18452512,
year = {2008},
author = {Hamblin, K and Standley, DM and Rogers, MB and Stechmann, A and Roger, AJ and Maytum, R and van der Giezen, M},
title = {Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.},
journal = {Molecular microbiology},
volume = {68},
number = {6},
pages = {1395-1405},
pmid = {18452512},
issn = {1365-2958},
support = {078566/WT_/Wellcome Trust/United Kingdom ; 078566/A/05/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Base Sequence ; Blastocystis/chemistry/*cytology/*enzymology/genetics ; Blastocystis Infections/parasitology ; Cytoplasmic Structures/chemistry/enzymology/genetics ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/chemistry/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; Purine Nucleotides/*metabolism ; Sequence Alignment ; Substrate Specificity ; Succinate-CoA Ligases/*chemistry/genetics/metabolism ; Swine/genetics ; },
abstract = {The anaerobic lifestyle of the intestinal parasite Blastocystis raises questions about the biochemistry and function of its mitochondria-like organelles. We have characterized the Blastocystis succinyl-CoA synthetase (SCS), a tricarboxylic acid cycle enzyme that conserves energy by substrate-level phosphorylation. We show that SCS localizes to the enigmatic Blastocystis organelles, indicating that these organelles might play a similar role in energy metabolism as classic mitochondria. Although analysis of residues inside the nucleotide-binding site suggests that Blastocystis SCS is GTP-specific, we demonstrate that it is ATP-specific. Homology modelling, followed by flexible docking and molecular dynamics simulations, indicates that while both ATP and GTP fit into the Blastocystis SCS active site, GTP is destabilized by electrostatic dipole interactions with Lys 42 and Lys 110, the side-chains of which lie outside the nucleotide-binding cavity. It has been proposed that residues in direct contact with the substrate determine nucleotide specificity in SCS. However, our results indicate that, in Blastocystis, an electrostatic gatekeeper controls which ligands can enter the binding site.},
}
@article {pmid18455442,
year = {2008},
author = {Veith, M and Lipscher, E and Oz, M and Kiefer, A and Baran, I and Polymeni, RM and Steinfartz, S},
title = {Cracking the nut: geographical adjacency of sister taxa supports vicariance in a polytomic salamander clade in the absence of node support.},
journal = {Molecular phylogenetics and evolution},
volume = {47},
number = {3},
pages = {916-931},
doi = {10.1016/j.ympev.2007.11.017},
pmid = {18455442},
issn = {1055-7903},
mesh = {Adenosine Triphosphatases/genetics ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Geography ; Haplotypes ; Inbreeding ; Mitochondria/genetics ; *Phylogeny ; Caudata/*classification/*genetics ; },
abstract = {The urodelan genus Lyciasalamandra, which inhabits a relatively small area along the southern Turkish coast and some Aegean islands, provides an outstanding example of a diverse but phylogenetically unresolved taxon. Molecular trees contain a single basal polytomy that could be either soft or hard. We here use the information of nuclear (allozymes) and mitochondrial (fractions of the 16S rRNA and ATPase genes) datasets in combination with area relationships of lineages to resolve the phylogenetic relationships among Lyciasalamandra species in the absence of sufficient node support. We can show that neither random processes nor introgressive hybridization can be invoked to explain that the majority of pairs of sister taxa form geographically adjacent units and interpret that this pattern has been shaped by vicariant events. Topology discordance between mitochondrial and nuclear trees mainly refers to an affiliation of L. helverseni, a taxon restricted to the Karpathos archipelago, to the western-most and geographically proximate mainland taxon in the nuclear tree, while in the organelle tree it turns out to be the sister lineage to the geographically most distant eastern clade. As this discordance cannot be explained by long-branch attraction in either dataset we suppose that oversea dispersal may have accounted for a second colonization of the Karpathos archipelago. It may have initiated introgression and selection driven manifestation of alien eastern mitochondrial genomes on a western nuclear background. Our approach of testing for area relationships of sister taxa against the null hypothesis of random distribution of these taxa seems to be especially helpful in phylogenetic studies where traditional measures of phylogenetic branch support fail to reject the null hypothesis of a hard polytomy.},
}
@article {pmid18490179,
year = {2008},
author = {Matsui, M and Yoshikawa, N and Tominaga, A and Sato, T and Takenaka, S and Tanabe, S and Nishikawa, K and Nakabayashi, S},
title = {Phylogenetic relationships of two Salamandrella species as revealed by mitochondrial DNA and allozyme variation (Amphibia: Caudata: Hynobiidae).},
journal = {Molecular phylogenetics and evolution},
volume = {48},
number = {1},
pages = {84-93},
doi = {10.1016/j.ympev.2008.04.010},
pmid = {18490179},
issn = {1095-9513},
mesh = {Amphibians/*classification/*genetics ; Animals ; DNA, Mitochondrial/genetics ; Enzymes/chemistry/genetics ; Liver/enzymology ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We conducted molecular phylogenetic analyses to confirm taxonomic relationships and to delimit distributional ranges of Siberian salamanders, Salamandrella keyserlingii and Salamandrella schrenckii, and to elucidate the origin of the isolated population of this species complex on Hokkaido, Japan. Phylogenetic trees constructed by MP, NJ, ML, and Bayesian methods, using complete sequences of mitochondrial cytochrome b genes, all indicated monophyly of Salamandrella and of each of the two species. Identical relationships were found on UPGMA, NJ, and CONTML trees derived from electrophoretic analysis of variation in 18 inferred allozyme loci. Populations from Hokkaido and northeastern China proved to be S. keyserlingii, while populations from Khabarovsk and Lazovsky are S. schrenckii. Genetic differentiations of S. keyserlingii within Sakhalin, and between Sakhalin and Hokkaido, are substantial. The Hokkaido population is hypothesized to have been isolated on the island since early Pleistocene, much earlier than isolation of sympatric anuran populations from their Sakhalin relatives. In contrast, the continental populations of S. keyserlingii are only slightly differentiated from some Sakhalin populations, and are thought to have expanded their ranges in the late Pleistocene.},
}
@article {pmid18497740,
year = {2008},
author = {Bych, K and Kerscher, S and Netz, DJ and Pierik, AJ and Zwicker, K and Huynen, MA and Lill, R and Brandt, U and Balk, J},
title = {The iron-sulphur protein Ind1 is required for effective complex I assembly.},
journal = {The EMBO journal},
volume = {27},
number = {12},
pages = {1736-1746},
pmid = {18497740},
issn = {1460-2075},
mesh = {Cysteine/metabolism ; Electron Spin Resonance Spectroscopy ; Electron Transport Complex I/*metabolism ; Fungal Proteins/*metabolism ; Gene Deletion ; Iron/metabolism ; Iron-Sulfur Proteins/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Mutant Proteins/metabolism ; Mutation/genetics ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Yarrowia/*metabolism ; },
abstract = {NADH:ubiquinone oxidoreductase (complex I) of the mitochondrial inner membrane is a multi-subunit protein complex containing eight iron-sulphur (Fe-S) clusters. Little is known about the assembly of complex I and its Fe-S clusters. Here, we report the identification of a mitochondrial protein with a nucleotide-binding domain, named Ind1, that is required specifically for the effective assembly of complex I. Deletion of the IND1 open reading frame in the yeast Yarrowia lipolytica carrying an internal alternative NADH dehydrogenase resulted in slower growth and strongly decreased complex I activity, whereas the activities of other mitochondrial Fe-S enzymes, including aconitase and succinate dehydrogenase, were not affected. Two-dimensional gel electrophoresis, in vitro activity tests and electron paramagnetic resonance signals of Fe-S clusters showed that only a minor fraction (approximately 20%) of complex I was assembled in the ind1 deletion mutant. Using in vivo and in vitro approaches, we found that Ind1 can bind a [4Fe-4S] cluster that was readily transferred to an acceptor Fe-S protein. Our data suggest that Ind1 facilitates the assembly of Fe-S cofactors and subunits of complex I.},
}
@article {pmid18498001,
year = {2008},
author = {Vilar, MG and Kaneko, A and Hombhanje, FW and Tsukahara, T and Hwaihwanje, I and Lum, JK},
title = {Reconstructing the origin of the Lapita Cultural Complex: mtDNA analyses of East Sepik Province, PNG.},
journal = {Journal of human genetics},
volume = {53},
number = {8},
pages = {698-708},
pmid = {18498001},
issn = {1434-5161},
mesh = {DNA, Mitochondrial/*genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; Mitochondria/*genetics ; Papua New Guinea ; Phylogeny ; },
abstract = {The colonization of Oceania occurred in two waves. By 32,000 BP, humans had reached New Guinea and settled all intervisible islands east to the Solomon Islands. Around 3,500 BP, a distinct intrusive group from Southeast Asia reached coastal New Guinea, integrated their components with indigenous resources, and gave rise to the Lapita Cultural Complex. Within 2,500 years, Lapita and its descendant cultures colonized the Pacific. To uncover the origin of the Lapita Cultural Complex, we analyzed the hypervariable region I of the mitochondrial deoxyribonucleic acid (mtDNA) in 219 individuals from eight East Sepik Province villages: two villages in each of four environmental zones. Same-zone villages spoke different languages: one Austronesian and three Papuan (Arapesh, Abelam, and Boiken). Our analysis examined whether language or geography better predicted gene flow. In general, language better predicted genetic affinities. Boiken villages across all four zones showed no significant genetic difference (F(ST) P value > 0.05). In contrast, the Austronesian village was significantly different to most other villages (P < 0.05). Only the mountains and coast showed zonal gene flow (P > 0.05). We interpret the data to reflect limited gene flow inland by Austronesians overshadowed by a regional displacement by inland Boiken speakers migrating seaward. These results are consistent with oral histories and ethnographic accounts.},
}
@article {pmid18504541,
year = {2008},
author = {McDermott, P and Connolly, V and Kavanagh, TA},
title = {The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {117},
number = {3},
pages = {459-470},
pmid = {18504541},
issn = {0040-5752},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Pairing ; Base Sequence ; Chromosomes, Plant/genetics ; Cytoplasm/*genetics ; Extrachromosomal Inheritance ; Fungi/genetics ; Gene Expression Regulation, Plant ; Genome, Mitochondrial/*genetics ; Lolium/*genetics ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Plant Infertility/*genetics ; Plant Proteins/chemistry/genetics ; Plasmids/*genetics ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) was shown to contain a 9.6 kb element, LpCMSi, that is absent in the mitochondrial genome of fertile lines. LpCMSi contains the previously described chimeric gene orfC9, and three additional open reading frames (orfs) encoding a unique 45 kDa predicted protein of unknown function, a family B-like DNA polymerase (LpDpo), and a phage-type single subunit RNA polymerase (LpRpo). The latter two proteins shared significant similarity with DNA and RNA polymerases encoded by extrachromosomal linear mitochondrial plasmids of plants and fungi, and also to integrated plasmid-like sequences found in various plant and fungal mitochondrial genomes. Transcripts for both LpDpo and LpRpo were detected by RT-PCR in mitochondria of the CMS line. PCR-based investigations further revealed the presence of LpCMSi-like sequences in fertile L. perenne lines that are likely maintained as low-copy number extrachromosomal replicons. The absence of integrated forms of LpCMSi in the mitochondrial genome of fertile lines suggests that LpCMSi integration adjacent to the atp9 gene may be responsible, directly or indirectly, for the sterility phenotype of the CMS line.},
}
@article {pmid18508749,
year = {2008},
author = {Alves, PC and Melo-Ferreira, J and Freitas, H and Boursot, P},
title = {The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {363},
number = {1505},
pages = {2831-2839},
pmid = {18508749},
issn = {0962-8436},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Demography ; Ecosystem ; Hares/*genetics ; Hybridization, Genetic/*genetics ; Phylogeny ; Portugal ; Spain ; },
abstract = {Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis, Lepus europaeus and Lepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genus Lepus. The phylogenetic inference reveals the presence of L. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.},
}
@article {pmid18539524,
year = {2008},
author = {Alverson, AJ},
title = {Molecular systematics and the diatom species.},
journal = {Protist},
volume = {159},
number = {3},
pages = {339-353},
pmid = {18539524},
issn = {1434-4610},
support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; 1F32GM080079-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA, Algal/genetics ; DNA, Ribosomal/genetics ; Diatoms/*classification/*genetics ; Mitochondria/genetics ; Phylogeny ; },
}
@article {pmid18543065,
year = {2008},
author = {Kmiec-Wisniewska, B and Krumpe, K and Urantowka, A and Sakamoto, W and Pratje, E and Janska, H},
title = {Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart.},
journal = {Plant molecular biology},
volume = {68},
number = {1-2},
pages = {159-171},
pmid = {18543065},
issn = {0167-4412},
mesh = {Arabidopsis/enzymology/*metabolism ; Arabidopsis Proteins/classification/genetics/*metabolism ; Chloroplasts/metabolism ; Fungal Proteins/genetics/metabolism ; GTP Phosphohydrolases/genetics/metabolism ; Green Fluorescent Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; Serine Endopeptidases/genetics/*metabolism ; Substrate Specificity ; Yeasts/enzymology/*metabolism ; },
abstract = {Rhomboid proteins comprise a class of serine proteases that are conserved in all kingdoms of organisms. They contain six or seven transmembrane helices and control a wide range of cellular functions and developmental processes by intramembrane proteolysis. This paper provides experimental evidence for the existence of rhomboid proteases in plant mitochondria and chloroplasts. Among 15 putative rhomboid-like proteins in Arabidopsis thaliana, we selected five predicted as mitochondrially targeted. For these proteins we performed the GFP transient assay, and identified two homologues, AtRBL11 (At5g25752) and AtRBL12 (At1g18600) to be targeted into plastids and mitochondria, respectively. Phylogenetic analysis reveals that AtRBL12 or AtRBL11 have only one clear orthologue in plant species with completely sequenced genomes. Complementation of the yeast lacking a functional copy of mitochondrial rhomboid with AtRBL12 indicates that this plant protease, in contrast to the human orthologue, does not recognize the yeast substrates, cytochrome c peroxidase (Ccp1) or dynamin-like GTPase (Mgm1). In agreement with this, we did not observe processing of Mgm1 when labeled precursor of this protein was incubated in vitro with Arabidopsis mitochondrial extract. Our results imply that plant mitochondrial rhomboids function in a specific manner and thus differ from their yeast and mammal counterparts.},
}
@article {pmid18558096,
year = {2009},
author = {Merkwirth, C and Langer, T},
title = {Prohibitin function within mitochondria: essential roles for cell proliferation and cristae morphogenesis.},
journal = {Biochimica et biophysica acta},
volume = {1793},
number = {1},
pages = {27-32},
doi = {10.1016/j.bbamcr.2008.05.013},
pmid = {18558096},
issn = {0006-3002},
mesh = {Animals ; *Cell Proliferation ; Electron Transport/physiology ; Humans ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membranes/*physiology ; Models, Biological ; Morphogenesis ; Phylogeny ; Prohibitins ; Repressor Proteins/analysis/*physiology ; },
abstract = {Prohibitins comprise an evolutionary conserved and ubiquitously expressed family of membrane proteins. Various roles in different cellular compartments have been proposed for prohibitin proteins. Recent experiments, however, identify large assemblies of two homologous prohibitin subunits, PHB1 and PHB2, in the inner membrane of mitochondria as the physiologically active structure. Mitochondrial prohibitin complexes control cell proliferation, cristae morphogenesis and the functional integrity of mitochondria. The processing of the dynamin-like GTPase OPA1, a core component of the mitochondrial fusion machinery, has been defined as a key process affected by prohibitins. The molecular mechanism of prohibitin function, however, remained elusive. The ring-like assembly of prohibitins and their sequence similarity with lipid raft-associated SPFH-family members suggests a scaffolding function of prohibitins, which may lead to functional compartmentalization in the inner membrane of mitochondria.},
}
@article {pmid18566830,
year = {2008},
author = {Huang, X and Zhu, W and Dai, S and Gai, S and Zheng, G and Zheng, C},
title = {The involvement of mitochondrial phosphate transporter in accelerating bud dormancy release during chilling treatment of tree peony (Paeonia suffruticosa).},
journal = {Planta},
volume = {228},
number = {4},
pages = {545-552},
pmid = {18566830},
issn = {0032-0935},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Arabidopsis/genetics ; *Cold Temperature ; DNA, Complementary ; DNA, Plant ; Flowers/anatomy &amp; histology/*growth &amp; development ; Gene Expression Regulation, Plant ; Mitochondria/*physiology ; Mitochondrial Membrane Transport Proteins/*physiology ; Molecular Sequence Data ; Paeonia/classification/metabolism/*physiology ; Phosphate Transport Proteins/chemistry/*physiology ; Phylogeny ; Plant Proteins/chemistry/*physiology ; Plants, Genetically Modified ; Up-Regulation ; },
abstract = {A cDNA clone was isolated from tree peony (Paeonia suffruticosa) subtractive cDNA library of burst buds and characterized with regard to its sequence, expression in response to chilling treatment during the release of bud dormancy, and its function in transgenic Arabidopsis thaliana. The clone, designated as PsMPT, contains 1,615 nucleotides with an open reading frame of 1,119 nucleotides, and the deduced amino acid sequence shows high homology with mitochondrial phosphate transporters (MPTs) from various organisms. The mRNA accumulation of PsMPT in tree peony was strongly induced by chilling treatment during the release of bud dormancy. When the treated plants were transferred to normal growth conditions, the level of PsMPT transcripts induced by sufficient chilling could be maintained high, whereas that induced by insufficient chilling decreased sharply. The transgenic Arabidopsis plants that overexpress PsMPT showed rapid growth and earlier flowering than wild-type plants. ATP contents in the transgenic plants were much higher than that in wild-type plants through various developmental stages. Together, these results suggest that the product of PsMPT is a MPT and might play an important role during the release of bud dormancy in tree peony.},
}
@article {pmid18579173,
year = {2008},
author = {Vignoli, V and Klann, AE and Michalik, P},
title = {Spermatozoa and sperm packages of the European troglophylous scorpion Belisarius xambeui Simon, 1879 (Troglotayosicidae, Scorpiones).},
journal = {Tissue &amp; cell},
volume = {40},
number = {6},
pages = {411-416},
doi = {10.1016/j.tice.2008.04.002},
pmid = {18579173},
issn = {0040-8166},
mesh = {Acrosome/ultrastructure ; Animals ; Axoneme/ultrastructure ; Cell Nucleus/ultrastructure ; Classification ; Europe ; Genitalia, Male/*cytology ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Reproduction ; Scorpions/*classification/*cytology ; Spermatozoa/*ultrastructure ; Vacuoles/ultrastructure ; },
abstract = {Studies on the sperm morphology in scorpions are rare, but the existing investigations already revealed a remarkable interfamiliar diversity. The present study reports for the first time on the spermatozoa and sperm packages of a representative of the family Troglotayosicidae, the troglophylous species Belisarius xambeui. The spermatozoa are characterized by (1) a thread-like nucleus, which is slightly bent anteriorly; (2) an asymmetrical cap-like acrosomal vacuole, which encloses the anterior tip of the nucleus; an acrosomal filament is absent; (3) an axoneme with a 9+0 microtubular pattern; (4) a midpiece consisting of elongated mitochondria coiling around the axoneme; the number can vary between 3 and 6 (mostly 4). At the end of spermiogenesis, the spermatozoa aggregate in order to form oval-shaped sperm packages in which all sperm cells show the same orientation. A single package consists of approximately 150 sperms. A secretion sheath is always absent. The present results might provide new characters for further systematic studies and their phylogenetic implications are briefly discussed.},
}
@article {pmid18579651,
year = {2008},
author = {Richards, JG and Sardella, BA and Schulte, PM},
title = {Regulation of pyruvate dehydrogenase in the common killifish, Fundulus heteroclitus, during hypoxia exposure.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {295},
number = {3},
pages = {R979-90},
doi = {10.1152/ajpregu.00192.2008},
pmid = {18579651},
issn = {0363-6119},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cytosol/metabolism ; Energy Metabolism/physiology ; Fundulidae/genetics/*metabolism ; Hypoxia/*metabolism/*physiopathology ; Isoenzymes/genetics/metabolism ; Mitochondria/metabolism ; Muscle, Skeletal/enzymology ; NAD/metabolism ; Oxygen/metabolism ; Phylogeny ; Protein Serine-Threonine Kinases/genetics/metabolism ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Pyruvate Dehydrogenase Complex/*metabolism ; Pyruvic Acid/metabolism ; },
abstract = {We examined the metabolic responses of the hypoxia-tolerant killifish (Fundulus heteroclitus) to 15 h of severe hypoxia and recovery with emphasis on muscle substrate usage and the regulation of the mitochondrial protein pyruvate dehydrogenase (PDH), which controls carbohydrate oxidation. Hypoxia survival involved a transient activation of substrate-level phosphorylation in muscle (decreases in [creatine phospate] and increases in [lactate]) during which time mechanisms to reduce overall ATP consumption were initiated. This metabolic transition did not affect total cellular [ATP], but had an impact on cellular energy status as indicated by large decreases in [ATP]/[ADP(free)] and [ATP]/[AMP(free)] and a significant loss of phosphorylation potential and Gibbs free energy of ATP hydrolysis (DeltafG'). The activity of PDH was rapidly (within 3 h) decreased by approximately 50% upon hypoxia exposure and remained depressed relative to normoxic samples throughout. Inactivation of PDH was primarily mediated via posttranslational modification following the accumulation of acetyl-CoA and subsequent activation of pyruvate dehydrogenase kinase (PDK). Estimated changes in cytoplasmic and mitochondrial [NAD(+)]/[NADH] did not parallel one another, suggesting the mitochondrial NADH shuttles do not function during hypoxia exposure. Large increases in the expression of PDK (PDK isoform 2) were consistent with decreased PDH activity; however, these changes in mRNA were not associated with changes in total PDK-2 protein content assessed using mammalian antibodies. No other changes in the expression of other known hypoxia-responsive genes (e.g., lactate dehydrogenase-A or -B) were observed in either muscle or liver.},
}
@article {pmid18602174,
year = {2008},
author = {Marciano, D and Llorente, C and Maugeri, DA and de la Fuente, C and Opperdoes, F and Cazzulo, JJ and Nowicki, C},
title = {Biochemical characterization of stage-specific isoforms of aspartate aminotransferases from Trypanosoma cruzi and Trypanosoma brucei.},
journal = {Molecular and biochemical parasitology},
volume = {161},
number = {1},
pages = {12-20},
doi = {10.1016/j.molbiopara.2008.05.005},
pmid = {18602174},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics/isolation &amp; purification/*metabolism ; Aspartic Acid/metabolism ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Isoenzymes/genetics/isolation &amp; purification/metabolism ; Ketoglutaric Acids/metabolism ; Kinetics ; Malate Dehydrogenase/biosynthesis ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Substrate Specificity ; Succinic Acid/metabolism ; Trypanosoma brucei brucei/*enzymology ; Trypanosoma cruzi/*enzymology ; },
abstract = {Three genes encoding putative aspartate aminotransferases (ASATs) were identified in the Trypanosoma cruzi genome. Two of these ASAT genes, presumably corresponding to a cytosolic and mitochondrial isoform, were cloned and expressed as soluble His-tagged proteins in Escherichia coli. The specific activities determined for both T. cruzi isozymes were notably higher than the values previously reported for Trypanosoma brucei orthologues. To confirm these differences, T. brucei mASAT and cASAT were also expressed as His-tagged enzymes. The kinetic analysis showed that the catalytic parameters of the new recombinant T. brucei ASATs were very similar to those determined for T. cruzi orthologues. The cASATs from both parasites displayed equally broad substrate specificities, while mASATs were highly specific towards aspartate/2-oxoglutarate. The subcellular localization of the mASAT was confirmed by digitonin extraction of intact epimastigotes. At the protein level, cASAT is constitutively expressed in T. brucei, whereas mASAT is down-regulated in the bloodstream forms. By contrast in T. cruzi, mASAT is expressed along the whole life cycle, whereas cASAT is specifically induced in the mammalian stages. Similarly, the expression of malate dehydrogenases (MDHs) is developmentally regulated in T. cruzi: while glycosomal MDH is only expressed in epimastigotes and mitochondrial MDH is present in the insect and mammalian stages. Taken together, these findings provide evidence for a metabolically active mitochondrion in the mammalian stages of T. cruzi, and suggest that the succinate excreted by amastigotes more likely represents a side product of an at least partially operative Krebs cycle, than an end product of glycosomal catabolism.},
}
@article {pmid18608923,
year = {2008},
author = {Jacobsen, MD and Rattray, AM and Gow, NA and Odds, FC and Shaw, DJ},
title = {Mitochondrial haplotypes and recombination in Candida albicans.},
journal = {Medical mycology},
volume = {46},
number = {7},
pages = {647-654},
doi = {10.1080/13693780801986631},
pmid = {18608923},
issn = {1369-3786},
support = {074898//Wellcome Trust/United Kingdom ; },
mesh = {Base Sequence ; Candida albicans/*genetics/isolation &amp; purification ; Candidiasis/microbiology ; Gene Frequency ; Geography ; Haplotypes/*genetics ; Linkage Disequilibrium ; Mitochondria/*genetics ; Mycological Typing Techniques ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic/*genetics ; Sequence Alignment ; },
abstract = {Candida albicans is a common commensal and opportunistic pathogenic fungus. Although it normally reproduces clonally, several lines of evidence exist for genetic recombination and some form of sexual reproduction. We have sequenced seven regions of its mitochondrial genome in 36 strains and constructed haplotypes for the 66 polymorphic sites, which include single-nucleotide polymorphisms and insertion/deletions. Nineteen different haplotypes were observed. Strains with the same mitochondrial haplotype were found in different clades defined by nuclear multilocus sequence typing (MLST) and the UPGMA dendrograms constructed using either set of data were different in topology. There was no apparent correlation between mitochondrial haplotype and the source of the strain (geographical or anatomical). Examination of the mitochondrial haplotypes revealed substantial evidence for recombination between polymorphic sites. This suggests that the use of mitochondrial haplotypes in phylogenetic studies should be approached with caution. These results provide further evidence for recombination and genetic exchange in the biology of C. albicans.},
}
@article {pmid18626081,
year = {2008},
author = {Ivanis, G and Esbaugh, AJ and Perry, SF},
title = {Branchial expression and localization of SLC9A2 and SLC9A3 sodium/hydrogen exchangers and their possible role in acid-base regulation in freshwater rainbow trout (Oncorhynchus mykiss).},
journal = {The Journal of experimental biology},
volume = {211},
number = {Pt 15},
pages = {2467-2477},
doi = {10.1242/jeb.017491},
pmid = {18626081},
issn = {0022-0949},
mesh = {*Acid-Base Equilibrium ; Animals ; Branchial Region/*metabolism ; Cloning, Molecular ; Fish Diseases/metabolism ; *Fresh Water ; Gene Expression Profiling ; Gene Expression Regulation ; Gills/cytology/metabolism ; Hydrocortisone/blood ; Hypercapnia/metabolism/veterinary ; Molecular Sequence Data ; Oncorhynchus mykiss/genetics/*metabolism ; Peanut Agglutinin/metabolism ; Phylogeny ; Protein Transport ; RNA, Messenger ; Sodium-Hydrogen Exchangers/genetics/*metabolism ; },
abstract = {Experiments were conducted on adult rainbow trout (Oncorhynchus mykiss) to test the hypothesis that SLC9 Na+/H+ exchangers (SLC9A2, NHE2; and SLC9A3, NHE3) on the gill epithelium are localized specifically to a subset of mitochondria-rich cells (MRCs) that are unable to bind peanut lectin agglutinin (PNA). This cell type, termed the PNA- MRC, is a sub-type of MRC believed to function in Na+ uptake and acid excretion. A technique using biotinylated PNA was used to distinguish between the PNA- and PNA+ MRCs on fixed gill sections. In contrast to expectations, both NHE2 (mRNA) and NHE3 (protein) were confined to cells enriched with Na+/K+-ATPase and capable of binding PNA. Thus, in trout, NHE2 and NHE3 are localized to PNA+ MRCs, the cells previously believed to be responsible for Cl- uptake and base excretion. Levels of mRNA for NHE2, the predominant isoform in the gill, were increased during 72 h of hypercapnic acidosis; NHE3 mRNA and protein levels were unaffected. Because plasma cortisol levels were increased during hypercapnia (from 35.3+/-9.4 to 100.1+/-30.9 ng ml(-1)), the effects of experimentally elevated cortisol levels on NHE expression were investigated. The elevation of plasma cortisol using intraperitoneal implants caused a significant increase in NHE2 mRNA expression without affecting NHE3 mRNA or protein abundance. Thus, we suggest that NHE2 contributes to acid-base regulation during hypercapnia owing to its transcriptional regulation by cortisol. The finding of NHE expression in PNA+ MRCs is discussed with reference to current models of ionic and acid-base regulation in teleost fish.},
}
@article {pmid18655725,
year = {2008},
author = {Voigt, O and Erpenbeck, D and Wörheide, G},
title = {A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata.},
journal = {BMC genomics},
volume = {9},
number = {},
pages = {350},
pmid = {18655725},
issn = {1471-2164},
mesh = {Animals ; Base Composition ; Base Sequence ; Chromosomes/*genetics/*metabolism ; Codon/metabolism ; DNA, Mitochondrial/genetics ; Gene Order ; Genome, Mitochondrial/*genetics ; Hydra/*cytology/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Terminal Repeat Sequences ; },
abstract = {BACKGROUND: Animal mitochondrial (mt) genomes are characteristically circular molecules of approximately 16-20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2).<br><br>RESULTS: The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp).<br><br>CONCLUSION: ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.},
}
@article {pmid18676618,
year = {2008},
author = {Simon, DM and Clarke, NA and McNeil, BA and Johnson, I and Pantuso, D and Dai, L and Chai, D and Zimmerly, S},
title = {Group II introns in eubacteria and archaea: ORF-less introns and new varieties.},
journal = {RNA (New York, N.Y.)},
volume = {14},
number = {9},
pages = {1704-1713},
pmid = {18676618},
issn = {1469-9001},
mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Introns/genetics ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Catalytic/*chemistry/*classification/genetics ; *Retroelements ; },
abstract = {Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.},
}
@article {pmid18689412,
year = {2008},
author = {Hiroi, J and Yasumasu, S and McCormick, SD and Hwang, PP and Kaneko, T},
title = {Evidence for an apical Na-Cl cotransporter involved in ion uptake in a teleost fish.},
journal = {The Journal of experimental biology},
volume = {211},
number = {Pt 16},
pages = {2584-2599},
doi = {10.1242/jeb.018663},
pmid = {18689412},
issn = {0022-0949},
mesh = {Acclimatization ; Amino Acid Sequence ; Animals ; Blotting, Western ; Cell Count ; *Cell Polarity ; Embryo, Nonmammalian/cytology/metabolism ; Fresh Water ; Gene Expression Profiling ; Gene Expression Regulation ; Gills/cytology/enzymology/metabolism ; Humans ; Ion Transport ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Proton-Translocating ATPases/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Seawater ; Sequence Alignment ; Sodium Chloride Symporters/chemistry/genetics/isolation &amp; purification/*metabolism ; Tilapia/*metabolism ; Time Factors ; Yolk Sac/cytology/metabolism ; },
abstract = {Cation-chloride cotransporters, such as the Na(+)/K(+)/2Cl(-) cotransporter (NKCC) and Na(+)/Cl(-) cotransporter (NCC), are localized to the apical or basolateral plasma membranes of epithelial cells and are involved in active ion absorption or secretion. The objectives of this study were to clone and identify ;freshwater-type' and ;seawater-type' cation-chloride cotransporters of euryhaline Mozambique tilapia (Oreochromis mossambicus) and to determine their intracellular localization patterns within mitochondria-rich cells (MRCs). From tilapia gills, we cloned four full-length cDNAs homologous to human cation-chloride cotransporters and designated them as tilapia NKCC1a, NKCC1b, NKCC2 and NCC. Out of the four candidates, the mRNA encoding NKCC1a was highly expressed in the yolk-sac membrane and gills (sites of the MRC localization) of seawater-acclimatized fish, whereas the mRNA encoding NCC was exclusively expressed in the yolk-sac membrane and gills of freshwater-acclimatized fish. We then generated antibodies specific for tilapia NKCC1a and NCC and conducted whole-mount immunofluorescence staining for NKCC1a and NCC, together with Na(+)/K(+)-ATPase, cystic fibrosis transmembrane conductance regulator (CFTR) and Na(+)/H(+) exchanger 3 (NHE3), on the yolk-sac membrane of tilapia embryos acclimatized to freshwater or seawater. The simultaneous quintuple-color immunofluorescence staining allowed us to classify MRCs clearly into four types: types I, II, III and IV. The NKCC1a immunoreactivity was localized to the basolateral membrane of seawater-specific type-IV MRCs, whereas the NCC immunoreactivity was restricted to the apical membrane of freshwater-specific type-II MRCs. Taking account of these data at the level of both mRNA and protein, we deduce that NKCC1a is the seawater-type cotransporter involved in ion secretion by type-IV MRCs and that NCC is the freshwater-type cotransporter involved in ion absorption by type-II MRCs. We propose a novel ion-uptake model by MRCs in freshwater that incorporates apically located NCC. We also reevaluate a traditional ion-uptake model incorporating NHE3; the mRNA was highly expressed in freshwater, and the immunoreactivity was found at the apical membrane of other freshwater-specific MRCs.},
}
@article {pmid18692147,
year = {2008},
author = {Dyer, NA and Lawton, SP and Ravel, S and Choi, KS and Lehane, MJ and Robinson, AS and Okedi, LM and Hall, MJ and Solano, P and Donnelly, MJ},
title = {Molecular phylogenetics of tsetse flies (Diptera: Glossinidae) based on mitochondrial (COI, 16S, ND2) and nuclear ribosomal DNA sequences, with an emphasis on the palpalis group.},
journal = {Molecular phylogenetics and evolution},
volume = {49},
number = {1},
pages = {227-239},
doi = {10.1016/j.ympev.2008.07.011},
pmid = {18692147},
issn = {1095-9513},
mesh = {Algorithms ; Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Female ; Genes, Insect ; Genes, Mitochondrial ; Genetic Markers ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tsetse Flies/anatomy &amp; histology/*classification/*genetics ; },
abstract = {Relationships of 13 species of the genus Glossina (tsetse flies) were inferred from mitochondrial (cytochrome oxidase 1, NADH dehydrogenase 2 and 16S) and nuclear (internal transcribed spacer 1 of rDNA) sequences. The resulting phylogeny confirms the monophyly of the morphologically defined fusca, morsitans and palpalis subgenera. Genetic distances between palpalis and morsitans subspecies suggest that their status needs revision. In particular, cytochrome oxidase 1 sequences showed large geographical differences within G. palpalis palpalis, suggesting the existence of cryptic species within this subspecies. The morphology of palpalis group female genital plates was examined, and individuals were found varying outside the ranges specified by the standard identification keys, making definitive morphological classification impossible. A diagnostic PCR to distinguish G. palpalis palpalis, G. tachinoides and G. palpalis gambiensis based on length differences of internal transcribed spacer 1 sequences is presented.},
}
@article {pmid18703057,
year = {2008},
author = {Carrie, C and Murcha, MW and Kuehn, K and Duncan, O and Barthet, M and Smith, PM and Eubel, H and Meyer, E and Day, DA and Millar, AH and Whelan, J},
title = {Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana.},
journal = {FEBS letters},
volume = {582},
number = {20},
pages = {3073-3079},
doi = {10.1016/j.febslet.2008.07.061},
pmid = {18703057},
issn = {0014-5793},
mesh = {Arabidopsis/*metabolism ; Chloroplasts/*enzymology ; Green Fluorescent Proteins/genetics ; Mitochondria/*enzymology ; NADPH Dehydrogenase/classification/genetics/*metabolism ; Peroxisomes/*metabolism ; Phylogeny ; Plant Proteins/classification/*metabolism ; Sequence Analysis, Protein ; },
abstract = {We found that four type II NAD(P)H dehydrogenases (ND) in Arabidopsis are targeted to two locations in the cell; NDC1 was targeted to mitochondria and chloroplasts, while NDA1, NDA2 and NDB1 were targeted to mitochondria and peroxisomes. Targeting of NDC1 to chloroplasts as well as mitochondria was shown using in vitro and in vivo uptake assays and dual targeting of NDC1 to plastids relies on regions in the mature part of the protein. Accumulation of NDA type dehydrogenases to peroxisomes and mitochondria was confirmed using Western blot analysis on highly purified organelle fractions. Targeting of ND proteins to mitochondria and peroxisomes is achieved by two separate signals, a C-terminal signal for peroxisomes and an N-terminal signal for mitochondria.},
}
@article {pmid18722554,
year = {2008},
author = {Luo, Y and Gao, W and Gao, Y and Tang, S and Huang, Q and Tan, X and Chen, J and Huang, T},
title = {Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation.},
journal = {Mitochondrion},
volume = {8},
number = {5-6},
pages = {352-357},
doi = {10.1016/j.mito.2008.07.005},
pmid = {18722554},
issn = {1567-7249},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {*Adaptation, Physiological ; Amino Acid Substitution ; Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Genome ; Hypoxia/*metabolism ; Lagomorpha/*genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Pikas originated in Asia and are small lagomorphs native to cold climates. The plateau pika, Ochotona curzoniae is a keystone species on the Qinghai-Tibet Plateau and an ideal animal model for hypoxic adaptation studies. Altered mitochondrial function, especially cytochrome c oxidase activity, is an important factor in modulation of energy generation and expenditure during cold and hypoxia adaptation. In this study, we determined the complete nucleotide sequence of the O. curzoniae mitochondrial genome. The plateau pika mitochondrial DNA is 17,131bp long and encodes the complete set of 37 proteins typical for vertebrates. Phylogenetic analysis based on concatenated heavy-strand encoded protein-coding genes revealed that pikas are closer to rabbit and hare than to rat. This suggests that rabbit or hare would be a good control animal for pikas in cold and hypoxia adaptation studies. Fifteen novel mitochondrial DNA-encoded amino acid changes were identified in the pikas, including three in the subunits of cytochrome c oxidase. These amino acid substitutions potentially function in modulation of mitochondrial complexes and electron transport efficiency during cold and hypoxia adaptation.},
}
@article {pmid18755281,
year = {2008},
author = {Kawazoe, K and Kawakita, A and Kameda, Y and Kato, M},
title = {Redundant species, cryptic host-associated divergence, and secondary shift in Sennertia mites (Acari: Chaetodactylidae) associated with four large carpenter bees (Hymenoptera: Apidae: Xylocopa) in the Japanese island arc.},
journal = {Molecular phylogenetics and evolution},
volume = {49},
number = {2},
pages = {503-513},
doi = {10.1016/j.ympev.2008.07.024},
pmid = {18755281},
issn = {1095-9513},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Bayes Theorem ; Bees/*classification/genetics/*parasitology ; DNA, Mitochondrial/genetics ; Genes, Insect ; Genes, Mitochondrial ; *Genetic Speciation ; Host-Parasite Interactions/*genetics ; Japan ; Likelihood Functions ; Markov Chains ; Mites/*classification/genetics ; Mitochondria/genetics ; Monte Carlo Method ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sennertia mites live as inquilines in the nests of carpenter bees and disperse as deutonymphs on newly emerged adult bees. Because their life cycle is tightly linked to that of the host bees, Sennertia may diverge in response to speciation in the hosts. However, the majority of Sennertia species are associated with several closely related carpenter bees, suggesting that host speciation may not be reflected in mite genetic structure. Here we investigate the extent of host-associated genetic differentiation in two Sennertia mites (S. alfkeni and S. japonica) that share four closely related, strictly allopatric large carpenter bees (Xylocopa). Analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene in Sennertia unexpectedly indicates that the two species represent morphological variants of a single species, and they collectively group into four distinct, allopatric clades that are uniquely associated with a single Xylocopa host. An exception is the mites associated with X. amamensis of the northernmost populations, which have genotypes typical of those associated with neighboring X. appendiculatacircumvolans. Additional analysis using amplified fragment length polymorphism (AFLP) further corroborates the presence of four mite clades but contrary to the COI data, suggests that the mites of the southernmost population of X. appendiculatacircumvolans have genetic profiles typical of those associated with X. amamensis. These results indicate that some mites have undergone secondary host switch after the formation of the four mite lineages and further experienced mitochondrial introgression during period of lineage coexistence. Overall, our results strongly urge reappraisal of deutonymph-based mite taxonomy and illuminate the importance of host-associated divergence during incipient stage of speciation in chaetodactylid mites. Furthermore, the occurrence of host switch and introgression between genetically differentiated mites entails that two host species have co-occurred in the past, thus providing a unique source of evidence for migration and competitive exclusion between the presently allopatric Xylocopa hosts.},
}
@article {pmid18792899,
year = {2008},
author = {Gochhait, S and Bhatt, A and Sharma, S and Singh, YP and Gupta, P and Bamezai, RN},
title = {Concomitant presence of mutations in mitochondrial genome and p53 in cancer development - a study in north Indian sporadic breast and esophageal cancer patients.},
journal = {International journal of cancer},
volume = {123},
number = {11},
pages = {2580-2586},
doi = {10.1002/ijc.23817},
pmid = {18792899},
issn = {1097-0215},
mesh = {Breast Neoplasms/epidemiology/*genetics/pathology ; Esophageal Neoplasms/epidemiology/*genetics/pathology ; Genome, Mitochondrial/*genetics ; Humans ; India/epidemiology ; Mutation/genetics ; Neoplasm Staging ; Phylogeny ; Tumor Suppressor Protein p53/*genetics ; },
abstract = {Mitochondrial DNA alterations in recent years have been suggested as modifier events, providing a possible proliferative advantage to the tumor cells. In order to provide further insight into the process of tumorigenesis, a study of whole mitochondria genome was conducted in 134 tissue samples obtained from 2 unrelated cancers (tumor and adjacent normal tissues from 36 breast cancer and 31 esophageal squamous cell carcinoma (ESCC) patients) with known p53 somatic mutation background. Fifteen of 36 (41.66%) breast and 12 of 31 (38.71%) ESCC tumors were found to contain at least 1 mtDNA somatic mutation, which correlated significantly with the concomitant presence of somatic mutation in DNA binding domain of the p53 gene (Breast cancer, p = 0.006; ESCC, p = 0.002). Interestingly, mutations in the non D-loop region of the mtDNA contributed significantly (Breast cancer, p = 0.004; ESCC, p = 0.032) in comparison to the hotspot-D-Loop-region. The concomitant presence of mutations in p53 and mtDNA were also predominant in breast cancer tumors with poor prognosis, that is, with the advanced stage, grade and the ER/PR negativity. Also, the observation made was apparently well explained in 10398A bearing N haplogroup genetic background with increased presence of novel and pathogenic germline mutation in mtDNA. Our study suggests that the concomitant presence of somatic alteration in mtDNA and the DNA binding domain of the p53 gene facilitates cell survival and tumorigenesis, requiring specialized therapeutic intervention because of a possible resistance to conventional chemotherapy.},
}
@article {pmid18794174,
year = {2008},
author = {Zhu, Y and Saraike, T and Yamamoto, Y and Hagita, H and Takumi, S and Murai, K},
title = {orf260cra, a novel mitochondrial gene, is associated with the homeotic transformation of stamens into pistil-like structures (pistillody) in alloplasmic wheat.},
journal = {Plant &amp; cell physiology},
volume = {49},
number = {11},
pages = {1723-1733},
doi = {10.1093/pcp/pcn143},
pmid = {18794174},
issn = {1471-9053},
mesh = {Amino Acid Sequence ; Cytoplasm/genetics/metabolism ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; Flowers/genetics/*growth &amp; development ; Gene Expression Regulation, Plant ; Genes, Mitochondrial ; Genes, Plant ; Mitochondria/genetics ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Proteins/genetics/*metabolism ; RNA, Plant/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, Protein ; Triticum/*genetics/growth &amp; development ; },
abstract = {Homeotic transformation of stamens into pistil-like structures (pistillody) can occur in cytoplasmic substitution (alloplasmic) lines of bread wheat (Triticum aestivum) that have the cytoplasm of the related species, Aegilops crassa. Previously we showed that pistillody results from altered patterns of expression of class B MADS-box genes mediated by mitochondrial gene(s) in the Ae. crassa cytoplasm. The wheat cultivar Chinese Spring does not show pistillody when Ae. crassa cytoplasm is introduced. The absence of an effect is due to a single dominant gene (designated Rfd1) located on the long arm of chromosome 7B. To identify the mitochondrial gene involved in pistillody induction, we performed a subtraction analysis using cDNAs derived from young spikes of a pistillody line and a normal line. We found that mitochondrial cDNA clone R04 was abundant in the young spikes of the pistillody line but was down-regulated in the normal line that carried nuclear Rfd1. Sequencing of the full-length cDNA corresponding to clone R04 showed that two genes were present, cox I (cytochrome c oxidase subunit I) and orf260(cra). orf260(cra) shows high sequence similarity to orf256, the T. timopheevii mitochondrial gene responsible for cytoplasmic male sterility (CMS). orf260(cra) was also present in the cytoplasms of Ae. juvenalis and Ae. vavilovii, which induce pistillody, but not in the cytoplasms of other species not associated with pistillody. Furthermore, Western blot analysis revealed that the ORF260cra protein was more abundant in the pistillody line than in the normal line. We suggest therefore that orf260(cra) is associated with pistillody induction.},
}
@article {pmid18805497,
year = {2008},
author = {Kodama, Y and Yanagimoto, T and Shinohara, G and Hayashi, I and Kojima, S},
title = {Deviation age of a deep-sea demersal fish, Bothrocara hollandi, between the Japan Sea and the Okhotsk Sea.},
journal = {Molecular phylogenetics and evolution},
volume = {49},
number = {2},
pages = {682-687},
doi = {10.1016/j.ympev.2008.08.022},
pmid = {18805497},
issn = {1095-9513},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Genetics, Population ; Haplotypes ; Japan ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
}
@article {pmid18819574,
year = {2008},
author = {Ling, H},
title = {Sequence analysis of GDSL lipase gene family in Arabidopsis thaliana.},
journal = {Pakistan journal of biological sciences : PJBS},
volume = {11},
number = {5},
pages = {763-767},
doi = {10.3923/pjbs.2008.763.767},
pmid = {18819574},
issn = {1028-8880},
mesh = {Amino Acid Motifs ; Arabidopsis/*enzymology/*genetics ; Arabidopsis Proteins/genetics ; DNA, Complementary/metabolism ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Introns ; Lipase/chemistry/*genetics ; Models, Genetic ; Multigene Family ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; },
abstract = {To analyze sequence characters of GDSL lipase gene family in Arabidopsis thaliana, 108 members of GDSL lipases were analyzed using data mining. The gene structures display remarkable diversity, consisting of zero to 13 introns. And the genes are asymmetrically distributed in chromosome 1-5, some of which are arranged in tandem. Phylogenetically, they were classified into three groups. Lipase-GDSL domain (PF00478) is housed at or close to N-terminus, or in the middle of amino acid sequences, additionally in which other domains and replicates were also found. Most GDSL lipases contain a signal peptide for conducting the secretary pathway. They are predicted to be extracellularly secreted, or target to mitochondria, chloroplast or any other parts of the cells. Functionally, these lipases are potentially involved in multiple physiological roles including seed germination, flowering and defense reactions. This study will help further understand the sequences and functions of Arabidopsis GDSL lipases.},
}
@article {pmid18822791,
year = {2008},
author = {Menzorov, AG and Matveeva, NM and Larkin, DM and Zaykin, DV and Serov, OL},
title = {[Fate of parental mitochondria in embryonic stem hybrid cells].},
journal = {Tsitologiia},
volume = {50},
number = {8},
pages = {711-718},
pmid = {18822791},
issn = {0041-3771},
support = {/WT_/Wellcome Trust/United Kingdom ; Z01 ES101866/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Animals ; Cell Fusion ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Embryonic Stem Cells/metabolism/*ultrastructure ; Fibroblasts/metabolism/ultrastructure ; Genetic Drift ; Genetic Markers ; Hybrid Cells/metabolism/*ultrastructure ; Mice ; *Mitochondria/genetics/metabolism ; Polymorphism, Restriction Fragment Length ; Species Specificity ; Spleen/metabolism/ultrastructure ; },
abstract = {When hybrid cells are created, not only the nuclear genomes of parental cells unite but their cytoplasm as well. Mitochondrial DNA (mtDNA) is a convenient marker of cytoplasm allowing one to gain insight into the organization of hybrid cell cytoplasm. We analyzed the parental mtDNAs in hybrid cells resulting from fusion of Mus musculus embryonic stem (ES) cells with splenocytes and fetal fibroblasts of DD/c mice or with splenocytes of M. caroli. Identification of the parental mtDNAs in hybrid cells was based on polymorphism among the parental mtDNAs for certain restrictases. We found that intra- and inter-specific ES cell-splenocyte hybrid cells lost entirely or partially mtDNA derived from the somatic partner, whereas ES cell-fibroblast hybrids retained mtDNAs from both parents in similar ratios with a slight bias. The lost of the “somatic” mitochondria by ES-splenocyte hybrids implies non-random segregation of the parental mitochondria as supported by a computer simulation of genetic drift. In contrast, ES cell-fibroblast hybrids show bilateral random segregation of the parental mitochondria judging from analysis of mtDNA in single cells. Preferential segregation of “somatic” mitochondria does not depend on the differences in sequences of the parental mtDNAs but depends on replicative state of the parental cells.},
}
@article {pmid18826668,
year = {2008},
author = {Hoshizaki, S and Washimori, R and Kubota, S and Ohno, S and Huang, Y and Tatsuki, S and Ishikawa, Y},
title = {Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan.},
journal = {Bulletin of entomological research},
volume = {98},
number = {5},
pages = {519-526},
doi = {10.1017/S0007485308005841},
pmid = {18826668},
issn = {0007-4853},
mesh = {Animals ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*chemistry/genetics ; Haplotypes ; Japan ; Moths/classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population harboring the lineage A mitochondria expanded in the recent past, while lineage B showed weak signals of a population expansion. It is not clear whether the two lineages of mtDNA evolved in separate or identical geographical regions. We discuss two hypotheses regarding the two lineages of mtDNA: a cryptic race/species hypothesis and a selective sweep hypothesis.},
}
@article {pmid18833571,
year = {2009},
author = {Torriani, SF and Brunner, PC and McDonald, BA and Sierotzki, H},
title = {QoI resistance emerged independently at least 4 times in European populations of Mycosphaerella graminicola.},
journal = {Pest management science},
volume = {65},
number = {2},
pages = {155-162},
doi = {10.1002/ps.1662},
pmid = {18833571},
issn = {1526-498X},
mesh = {Ascomycota/classification/drug effects/*genetics/physiology ; Cytochromes b/genetics/metabolism ; DNA, Mitochondrial/genetics ; *Drug Resistance, Fungal ; Europe ; Fungal Proteins/genetics/metabolism ; Fungicides, Industrial/*pharmacology ; Haplotypes ; Mutation, Missense ; Phylogeny ; Plant Diseases/*microbiology ; },
abstract = {BACKGROUND: QoI fungicides or quinone outside inhibitors (also called strobilurins) have been widely used to control agriculturally important fungal pathogens since their introduction in 1996. Strobilurins block the respiration pathway by inhibiting the cytochrome bc1 complex in mitochondria. Several plant pathogenic fungi have developed field resistance. The first QoI resistance in Mycosphaerella graminicola (Fuckel) Schroter was detected retrospectively in UK in 2001 at a low frequency in QoI-treated plots. During the following seasons, resistance reached high frequencies across northern Europe. The aim of this study was to identify the main evolutionary forces driving the rapid emergence and spread of QoI resistance in M. graminicola populations.<br><br>RESULTS: The G143A mutation causing QoI resistance was first detected during 2002 in all tested populations and in eight distinct mtDNA sequence haplotypes. By 2004, 24 different mtDNA haplotypes contained the G143A mutation. Phylogenetic analysis showed that strobilurin resistance was acquired independently through at least four recurrent mutations at the same site of cytochrome b. Estimates of directional migration rates showed that the majority of gene flow in Europe had occurred in a west-to-east direction.<br><br>CONCLUSION: This study demonstrated that recurring mutations independently introduced the QoI resistance allele into different genetic and geographic backgrounds. The resistant haplotypes then increased in frequency owing to the strong fungicide selection and spread eastward through wind dispersal of ascospores.},
}
@article {pmid18845277,
year = {2009},
author = {Nakazawa, F and Alev, C and Shin, M and Nakaya, Y and Jakt, LM and Sheng, G},
title = {PBRL, a putative peripheral benzodiazepine receptor, in primitive erythropoiesis.},
journal = {Gene expression patterns : GEP},
volume = {9},
number = {2},
pages = {114-121},
doi = {10.1016/j.gep.2008.09.005},
pmid = {18845277},
issn = {1567-133X},
mesh = {Amino Acid Sequence ; Animals ; COS Cells ; Cells, Cultured ; Chick Embryo ; Chickens/genetics ; Chlorocebus aethiops ; Erythropoiesis/*genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Heme/biosynthesis ; Models, Biological ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Receptors, GABA-A/*genetics/isolation &amp; purification/metabolism ; Sequence Homology ; },
abstract = {Benzodiazepines are a class of psychoactive drugs widely used for their anxiolytic, anticonvulsant, muscle relaxant and hypnotic properties. Although the benzodiazepine receptor in the central nervous system has been well studied, the role of peripheral type benzodiazepine receptor, PBR, remains elusive. Here, we show that there are two PBR homologous genes in amniotes, PBR and PBRL, based on phylogenetic analysis. In chickens, PBRL is exclusively expressed during early development in differentiating primitive erythrocytes and this expression is tightly correlated with that of hemoglobin genes. PBR is not expressed in hematopoietic system during this period and is weakly expressed in developing central nervous system. Because one of PBRs' known functions is to regulate heme transport between the mitochondria and cytoplasm, we investigated expression profiles of heme biosynthesis genes. Seven of the eight enzymes involved in heme biosynthesis, with the exception of protoporphyrinogen oxidase, are present in chicken genome. Five of them, delta-aminolevulinate synthase, delta-aminolevulinic acid dehydrogenase, porphobilinogen deaminase, coproporphyrinogen decarboxylase and ferrochelatase, show stage-specific increase in gene expression correlated with primitive hematopoiesis, but not with primitive erythrocyte differentiation. PBRL protein is localized to the mitochondria in culture cells, and pharmacological inhibition of PBRL activity results in a decrease in globin protein levels during primitive erythropoiesis. Our data suggest a developmental role of PBRs in erythropoiesis in chickens, possibly via the regulation of heme availability for the assembly of functional hemoglobins.},
}
@article {pmid18928449,
year = {2009},
author = {Traba, J and Satrústegui, J and del Arco, A},
title = {Characterization of SCaMC-3-like/slc25a41, a novel calcium-independent mitochondrial ATP-Mg/Pi carrier.},
journal = {The Biochemical journal},
volume = {418},
number = {1},
pages = {125-133},
doi = {10.1042/BJ20081262},
pmid = {18928449},
issn = {1470-8728},
mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Brain/metabolism ; Calcium/metabolism ; Cell Line ; Chlorocebus aethiops ; Gene Expression Regulation ; Humans ; Magnesium/*metabolism ; Male ; Mice ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Organ Specificity ; Phosphorus/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Testis/metabolism ; },
abstract = {The SCaMCs (small calcium-binding mitochondrial carriers) constitute a subfamily of mitochondrial carriers responsible for the ATP-Mg/P(i) exchange with at least three paralogues in vertebrates. SCaMC members are proteins with two functional domains, the C-terminal transporter domain and the N-terminal domain which harbours calcium-binding EF-hands and faces the intermembrane space. In the present study, we have characterized a shortened fourth paralogue, SCaMC-3L (SCaMC-3-like; also named slc25a41), which lacks the calcium-binding N-terminal extension. SCaMC-3L orthologues are found exclusively in mammals, showing approx. 60% identity to the C-terminal half of SCaMC-3, its closest paralogue. In mammalian genomes, SCaMC-3 and SCaMC-3L genes are adjacent on the same chromosome, forming a head-to-tail tandem array, and show identical exon-intron boundaries, indicating that SCaMC-3L could have arisen from an SCaMC-3 ancestor by a partial duplication event which occurred prior to mammalian radiation. Expression and functional data suggest that, following the duplication event, SCaMC-3L has acquired more restrictive functions. Unlike the broadly expressed longer SCaMCs, mouse SCaMC-3L shows a limited expression pattern; it is preferentially expressed in testis and, at lower levels, in brain. SCaMC-3L transport activity was studied in yeast deficient in Sal1p, the calcium-dependent mitochondrial ATP-Mg/P(i) carrier, co-expressing SCaMC-3L and mitochondrial-targeted luciferase, and it was found to perform ATP-Mg/P(i) exchange, in a similar manner to Sal1p or other ATP-Mg/P(i) carriers. However, metabolite transport through SCaMC-3L is calcium-independent, representing a novel mechanism involved in adenine nucleotide transport across the inner mitochondrial membrane, different to ADP/ATP translocases or long SCaMC paralogues.},
}
@article {pmid18930705,
year = {2009},
author = {Bandeiras, TM and Refojo, PN and Todorovic, S and Murgida, DH and Hildebrandt, P and Bauer, C and Pereira, MM and Kletzin, A and Teixeira, M},
title = {The cytochrome ba complex from the thermoacidophilic crenarchaeote Acidianus ambivalens is an analog of bc(1) complexes.},
journal = {Biochimica et biophysica acta},
volume = {1787},
number = {1},
pages = {37-45},
doi = {10.1016/j.bbabio.2008.09.009},
pmid = {18930705},
issn = {0006-3002},
mesh = {Acidianus/*metabolism ; Archaeal Proteins/*chemistry/genetics ; Cytochrome b Group/*chemistry/genetics ; Cytochromes c1/*chemistry ; Electron Transport Complex III/*chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Operon ; Oxidation-Reduction ; Phylogeny ; Spectrum Analysis, Raman ; },
abstract = {A novel cytochrome ba complex was isolated from aerobically grown cells of the thermoacidophilic archaeon Acidianus ambivalens. The complex was purified with two subunits, which are encoded by the cbsA and soxN genes. These genes are part of the pentacistronic cbsAB-soxLN-odsN locus. The spectroscopic characterization revealed the presence of three low-spin hemes, two of the b and one of the a(s)-type with reduction potentials of +200, +400 and +160 mV, respectively. The SoxN protein is proposed to harbor the heme b of lower reduction potential and the heme a(s), and CbsA the other heme b. The soxL gene encodes a Rieske protein, which was expressed in E. coli; its reduction potential was determined to be +320 mV. Topology predictions showed that SoxN, CbsB and CbsA should contain 12, 9 and one transmembrane alpha-helices, respectively, with SoxN having a predicted fold very similar to those of the cytochromes b in bc(1) complexes. The presence of two quinol binding motifs was also predicted in SoxN. Based on these findings, we propose that the A. ambivalens cytochrome ba complex is analogous to the bc(1) complexes of bacteria and mitochondria, however with distinct subunits and heme types.},
}
@article {pmid18976726,
year = {2008},
author = {Wonnapinij, P and Chinnery, PF and Samuels, DC},
title = {The distribution of mitochondrial DNA heteroplasmy due to random genetic drift.},
journal = {American journal of human genetics},
volume = {83},
number = {5},
pages = {582-593},
pmid = {18976726},
issn = {1537-6605},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila ; *Genetic Drift ; Humans ; Mice ; Mitochondria/*genetics ; Physiological Phenomena/*genetics ; },
abstract = {Cells containing pathogenic mutations in mitochondrial DNA (mtDNA) generally also contain the wild-type mtDNA, a condition called heteroplasmy. The amount of mutant mtDNA in a cell, called the heteroplasmy level, is an important factor in determining the amount of mitochondrial dysfunction and therefore the disease severity. mtDNA is inherited maternally, and there are large random shifts in heteroplasmy level between mother and offspring. Understanding the distribution in heteroplasmy levels across a group of offspring is an important step in understanding the inheritance of diseases caused by mtDNA mutations. Previously, our understanding of the heteroplasmy distribution has been limited to just the mean and variance of the distribution. Here we give equations, adapted from the work of Kimura on random genetic drift, for the full mtDNA heteroplasmy distribution. We describe how to use the Kimura distribution in mitochondrial genetics, and we test the Kimura distribution against human, mouse, and Drosophila data sets.},
}
@article {pmid18986973,
year = {2009},
author = {Krosby, M and Rohwer, S},
title = {A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds.},
journal = {Proceedings. Biological sciences},
volume = {276},
number = {1657},
pages = {615-621},
pmid = {18986973},
issn = {0962-8452},
mesh = {Animals ; California ; DNA, Mitochondrial/chemistry ; Extinction, Biological ; Female ; Genetic Speciation ; Geography ; Haplotypes ; *Hybridization, Genetic ; Male ; Population Dynamics ; Sequence Analysis, DNA ; *Sexual Behavior, Animal ; Songbirds/classification/genetics/*physiology ; Washington ; },
abstract = {Hybrid zones are natural experiments that expose the forces maintaining species differences. But for cases where a trait of one of the hybridizing pair appears shifted into the range of the other, the underlying mechanism can be difficult to infer. For example, hybridization between hermit warbler (Dendroica occidentalis) and Townsend's warbler (Dendroica townsendi) is restricted to narrow hybrid zones in Washington and Oregon, yet hermit mtDNA can be found in phenotypically pure Townsend's populations up to 2000 km north along the Pacific coast. This could reflect introgression of selectively favoured hermit mitochondria north across the hybrid zones, or a neutral genetic wake left behind following southern zone movement. Hermit mitochondrial haplotypes in populations of coastal Townsend's exhibit relatively high genetic diversity and significant divergence from those found in populations of hermit warblers. This contradicts the predictions of selective introgression, but is consistent with a northern population of hermits diverging in a glacial refugium before being replaced by Townsend's via aggressive hybridization. Previous field studies showing Townsend's males to be competitively superior to hermit males support this scenario, and suggest that the extreme hybrid zone movement evidenced by the hermit mitochondrial wake represents an extinction in progress.},
}
@article {pmid18991723,
year = {2008},
author = {Santos, C and Martínez, M and Lima, M and Hao, YJ and Simões, N and Montiel, R},
title = {Mitochondrial DNA mutations in cancer: a review.},
journal = {Current topics in medicinal chemistry},
volume = {8},
number = {15},
pages = {1351-1366},
doi = {10.2174/156802608786141151},
pmid = {18991723},
issn = {1873-4294},
mesh = {Aging/genetics/physiology ; Animals ; Apoptosis/genetics/physiology ; Base Sequence ; DNA, Mitochondrial/*genetics ; Humans ; Hybrid Cells/pathology ; Mutation/*genetics ; Neoplasms/*genetics/pathology ; Phylogeny ; },
abstract = {As mitochondria participate in fundamental process of the cellular metabolism, recent research has addressed the role of mitochondria, and of mitochondrial DNA (mtDNA), in apoptosis, aging, and complex diseases. The association between mtDNA and cancer has been discussed since the beginning of the last century, and more recently, it has gained attention due to the observation of many somatic mutations in several types of cancers. In this review we describe those germinal mutations that have been associated to cancer, and present a compilation of somatic mutations that have been observed in different cancer tissues, describing relevant characteristics among them in a phylogenetic context. We also summarize the drawbacks and criticisms made towards the studies that report an association between mtDNA mutations and cancer, and discuss the experimental models used to analyse this relationship. Although many reported somatic mutations may actually be the outcome of laboratory artefacts, a considerable number could be authentic and may have a relationship with cancer development. In our compilation, we have observed 271 cancer mutations occurring in conserved positions of mtDNA, 70 of them appearing in more than one tumour. These mutations may be candidates to be used as cancer biomarkers, and deserve further investigation, perhaps through the use of experimental models and by an analysis of tumours of distinct grade to determine if the mutations arose early during tumourigenesis. Experiments with cybrids have been successfully used; however, models are needed in which specific mtDNA variants may be introduced into the same mitochondrial and cellular background.},
}
@article {pmid18998587,
year = {2008},
author = {Rodríguez, F and Feist, SW and Guillou, L and Harkestad, LS and Bateman, K and Renault, T and Mortensen, S},
title = {Phylogenetic and morphological characterisation of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic oceans.},
journal = {Diseases of aquatic organisms},
volume = {81},
number = {3},
pages = {231-240},
doi = {10.3354/dao01956},
pmid = {18998587},
issn = {0177-5103},
mesh = {Animals ; Atlantic Ocean ; Chlorophyta/*classification/cytology/physiology/*ultrastructure ; Microscopy, Electron, Transmission ; Mytilus edulis/*parasitology ; *Phylogeny ; Pigments, Biological/chemistry ; },
abstract = {Blue mussels Mytilus edulis with shell deformations and green pustules containing parasitic algae were collected at 3 coastal sites (Burøy, Norway; Bockholm, Denmark; Goose Green, Falkland Islands). A comparative study, including mussel histopathology, algal morphology, ultrastructure and phylogenetic position was performed. Green pustules were mainly located in the posterior portion of the mantle and gonad tissues and the posterior adductor muscle. Electron microscopy confirmed the presence of algal cells with similar morphology to Coccomyxa parasitica. Algae were oval shaped with a single nucleus and chloroplast, 1 or 2 mitochondria and a dense granular cytoplasm with a lipid inclusion body, Golgi apparatus and small vesicles. Partial small subunit (SSU) rRNA phylogeny confirmed the inclusion of parasitic algae into the Coccomyxa clade. However, the sequence identity between almost full SSU rRNA sequences of parasitic algae and others in this clade yielded an unexpected result. Green algae from mussels were distant from C. parasitica Culture Collection of Algae and Protozoa (CCAP) strain 216/18 (94% identity), but very similar (99% identity) to C. glaronensis (a lichen endosymbiont) and green endophytes from the tree Ginkgo biloba. The CCAP strain 216/18 was a sister sequence to Nannochloris algae, far from the Coccomyxa clade. These results suggest a misidentification or outgrowth of the original CCAP strain 216/18 by a different 'Nannochloris-like' trebouxiophycean organism. In contrast, our sequences directly obtained from infested mussels could represent the true C. parasitica responsible for the green pustules in blue mussels.},
}
@article {pmid19002206,
year = {2009},
author = {Pérez-Espona, S and Pérez-Barbería, FJ and Goodall-Copestake, WP and Jiggins, CD and Gordon, IJ and Pemberton, JM},
title = {Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.},
journal = {Heredity},
volume = {102},
number = {2},
pages = {199-210},
doi = {10.1038/hdy.2008.111},
pmid = {19002206},
issn = {1365-2540},
mesh = {Animal Migration ; Animal Population Groups/*genetics ; Animals ; DNA, Mitochondrial/genetics ; Deer/classification/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Scotland ; },
abstract = {The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.},
}
@article {pmid19013103,
year = {2009},
author = {Ota, S and Vaulot, D and Le Gall, F and Yabuki, A and Ishida, K},
title = {Partenskyella glossopodia gen. et sp. nov., the first report of a Chlorarachniophyte that lacks a pyrenoid.},
journal = {Protist},
volume = {160},
number = {1},
pages = {137-150},
doi = {10.1016/j.protis.2008.09.003},
pmid = {19013103},
issn = {1434-4610},
mesh = {Chloroplasts/ultrastructure ; DNA, Algal/genetics ; DNA, Ribosomal/genetics ; Eukaryota/*genetics/*ultrastructure ; Flagella/ultrastructure ; Mediterranean Sea ; Phylogeny ; Plankton/*ultrastructure ; },
abstract = {A new chlorarachniophyte, Partenskyella glossopodia gen. et sp. nov., is described from a culture isolated from the Mediterranean Sea pelagic waters and maintained as strain RCC365 at the Roscoff Culture Collection (France). Vegetative cells of P. glossopodia are non-motile naked spherical cells. However, flagellate and amoeboid stages are also present in its life cycle. The cells are 2-4mum in diameter containing a pale-green, cup-shaped chloroplast, 1-2 mitochondria, a nucleus, and a Golgi apparatus. Vesicles containing storage product-like material are also present. The chloroplast is surrounded by four membranes possessing a nucleomorph in the periplastidal compartment. The minute cell size and the absence of a pyrenoid at any stage of the life cycle are unique characteristics among the chlorarachniophytes, which justifies our proposition for a new genus for strain RCC365.},
}
@article {pmid19030769,
year = {2008},
author = {Russell, RD and Beckenbach, AT},
title = {Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.},
journal = {Journal of molecular evolution},
volume = {67},
number = {6},
pages = {682-695},
pmid = {19030769},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Conserved Sequence ; Electron Transport Complex I/chemistry/genetics/metabolism ; Frameshift Mutation/*genetics ; Genetic Code/*genetics ; Genome, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; Protein Biosynthesis/*genetics ; Sequence Alignment ; Turtles/*genetics/metabolism ; },
abstract = {A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker's snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria.},
}
@article {pmid19037013,
year = {2009},
author = {Yu, X and Gimsa, U and Wester-Rosenlöf, L and Kanitz, E and Otten, W and Kunz, M and Ibrahim, SM},
title = {Dissecting the effects of mtDNA variations on complex traits using mouse conplastic strains.},
journal = {Genome research},
volume = {19},
number = {1},
pages = {159-165},
pmid = {19037013},
issn = {1088-9051},
mesh = {Animals ; Anxiety/genetics ; Behavior, Animal ; DNA, Mitochondrial/*genetics ; Encephalomyelitis, Autoimmune, Experimental/genetics ; Female ; *Genetic Variation ; Mice ; Mice, Congenic ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Mutation ; Phenotype ; Phylogeny ; },
abstract = {Previous reports have demonstrated that the mtDNA of mouse common inbred strains (CIS) originated from a single female ancestor and that mtDNA mutations occurred during CIS establishment. This situation provides a unique opportunity to investigate the impact of individual mtDNA variations on complex traits in mammals. In this study, we compiled the complete mtDNA sequences of 52 mouse CIS. Phylogenetic analysis demonstrated that 50 of the 52 CIS descended from a single female Mus musculus domesticus mouse, and mtDNA mutations have accumulated in 26 of the CIS. We then generated conplastic strains on the C57BL/6J background for 12 mtDNA variants with one to three functional mtDNA mutations. We also generated conplastic strains for mtDNA variants of the four M. musculus subspecies, each of which contains hundreds of mtDNA variations. In total, a panel of conplastic strains was generated for 16 mtDNA variants. Phenotypic analysis of the conplastic strains demonstrated that mtDNA variations affect susceptibility to experimental autoimmune encephalomyelitis and anxiety-related behavior, which confirms that mtDNA variations affect complex traits. Thus, we have developed a unique genetic resource that will facilitate exploration of the biochemical and physiological roles of mitochondria in complex traits.},
}
@article {pmid19048493,
year = {2008},
author = {Khan, HA and Arif, IA and Al Farhan, AH and Al Homaidan, AA},
title = {Phylogenetic analysis of oryx species using partial sequences of mitochondrial rRNA genes.},
journal = {Genetics and molecular research : GMR},
volume = {7},
number = {4},
pages = {1150-1155},
doi = {10.4238/vol7-4gmr490},
pmid = {19048493},
issn = {1676-5680},
mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ruminants/classification/*genetics ; Species Specificity ; },
abstract = {We conducted a comparative evaluation of 12S rRNA and 16S rRNA genes of the mitochondrial genome for molecular differentiation among three oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) with respect to two closely related outgroups, addax and roan. Our findings showed the failure of 12S rRNA gene to differentiate between the genus Oryx and addax, whereas a 342-bp partial sequence of 16S rRNA accurately grouped all five taxa studied, suggesting the utility of 16S rRNA segment for molecular phylogeny of oryx at the genus and possibly species levels.},
}
@article {pmid19057927,
year = {2009},
author = {Iorio, R and Slapeta, J and Otranto, D and Paoletti, B and Giangaspero, A and Traversa, D},
title = {Phylogenetic relationships of Habronema microstoma and Habronema muscae (Spirurida: Habronematidae) within the order Spirurida inferred using mitochondrial cytochrome c oxidase subunit 1 (cox1) gene analysis.},
journal = {Parasitology research},
volume = {104},
number = {5},
pages = {979-984},
pmid = {19057927},
issn = {1432-1955},
mesh = {Amino Acid Substitution/genetics ; Animals ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; Horse Diseases/parasitology ; Horses ; Italy ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Spirurida Infections/veterinary ; Spiruroidea/*classification/*genetics/isolation &amp; purification ; },
abstract = {The present study investigated genetic variability within a population of Habronema microstoma and Habronema muscae (Spirurida: Habronematidae) affecting horses in an endemic area of central Italy using polymerase chain reaction (PCR)-coupled sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). No different cox1 sequences were detected in any of the H. muscae individual, while two haplotypes representing H. microstoma individuals differed for one substitution. The pairwise distance between the H. muscae and H. microstoma was 11%, coding for five amino acid changes. The sequence of an informative region within the cox1 gene of H. microstoma and H. muscae was analyzed by Maximum Likelihood and Bayesian phylogenetic methods using available mitochondrial sequences spirurid taxa belonging to Filarioidea, Thelazioidea, and Habronematoidea. Phylogenetic analysis supported the split of the tree into two sister spirurid groups, Habronematoidea and Filarioidea + Thelazioidea. The phylogenetic and evolutionary implications of Habronema with Filaroidea and Thelazioidea are discussed.},
}
@article {pmid19070577,
year = {2008},
author = {Lee, HY and Chou, JY and Cheong, L and Chang, NH and Yang, SY and Leu, JY},
title = {Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species.},
journal = {Cell},
volume = {135},
number = {6},
pages = {1065-1073},
doi = {10.1016/j.cell.2008.10.047},
pmid = {19070577},
issn = {1097-4172},
mesh = {Carbon/metabolism ; Chimera ; Fungal Proteins/genetics ; Genetic Speciation ; Genome, Fungal ; Genome, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proton-Translocating ATPases/genetics ; Protein Biosynthesis ; Saccharomyces/*genetics ; Saccharomyces cerevisiae/*genetics/growth &amp; development/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {Hybrids between species are usually unviable or sterile. One possible mechanism causing reproductive isolation is incompatibility between genes from different species. These "speciation" genes are interacting components that cannot function properly when mixed with alleles from other species. To test whether such genes exist in two closely related yeast species, we constructed hybrid lines in which one or two chromosomes were derived from Saccharomyces bayanus, and the rest were from Saccharomyces cerevisiae. We found that the hybrid line with Chromosome 13 substitution was completely sterile and identified Aep2, a mitochondrial protein encoded on Chromosome 13, to cause the sporulation defect as S. bayanus AEP2 is incompatible with S. cerevisiae mitochondria. This is caused by the inability of S. bayanus Aep2 protein to regulate the translation of the S. cerevisiae OLI1 mRNA. We speculate that AEP2 and OLI1 have evolved during the adaptation of S. bayanus to nonfermentable carbon sources, thereby driving speciation.},
}
@article {pmid19070685,
year = {2009},
author = {Harrison, SP and Turrion-Gomez, JL},
title = {Mitochondrial DNA: an important female contribution to thoroughbred racehorse performance: amendments to nomenclature.},
journal = {Mitochondrion},
volume = {9},
number = {1},
pages = {58-9; discussion 60},
doi = {10.1016/j.mito.2008.11.002},
pmid = {19070685},
issn = {1567-7249},
mesh = {Animals ; DNA, Mitochondrial/*metabolism ; Female ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes ; Horses/*genetics/*physiology ; Mitochondria/metabolism ; Pedigree ; Phylogeny ; Running ; Sex Factors ; Terminology as Topic ; },
}
@article {pmid19103153,
year = {2009},
author = {Houstek, J and Kmoch, S and Zeman, J},
title = {TMEM70 protein - a novel ancillary factor of mammalian ATP synthase.},
journal = {Biochimica et biophysica acta},
volume = {1787},
number = {5},
pages = {529-532},
doi = {10.1016/j.bbabio.2008.11.013},
pmid = {19103153},
issn = {0006-3002},
mesh = {Animals ; Brain Diseases/genetics/metabolism ; Cardiomyopathy, Hypertrophic, Familial/genetics/metabolism ; Cell Nucleus/genetics/pathology ; Electron Transport Complex IV/genetics/metabolism ; Genetic Complementation Test ; Humans ; Mammals ; Membrane Proteins/*genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics ; Mitochondrial Proton-Translocating ATPases/genetics/*metabolism ; Mutation ; Oxidative Phosphorylation ; Phylogeny ; Species Specificity ; },
abstract = {An increasing number of patients with nuclear genetic defects of mitochondrial ATP synthase have been identified in recent years. They are characterized by early onset, lactic acidosis, 3-methylglutaconic aciduria, hypertrophic cardiomyopathy and encephalopathy and most cases have a fatal outcome. Patient tissues show isolated defect of the ATP synthase complex and its content decreases to > or =30% of normal due to altered enzyme biosynthesis and assembly. Gene mapping and complementation studies have identified mutations in TMEM70 gene encoding a 30kD mitochondrial protein of unknown function as the cause of the disease. An altered synthesis of this new ancillary factor in ATP synthase biogenesis was found in most of the known patients with decreased ATP synthase content. As revealed by phylogenetic analysis, TMEM70 is specific for higher eukaryotes.},
}
@article {pmid19127329,
year = {2008},
author = {Jeon, HK and Kim, KH and Chai, JY and Yang, HJ and Rim, HJ and Eom, KS},
title = {Sympatric distribution of three human Taenia tapeworms collected between 1935 and 2005 in Korea.},
journal = {The Korean journal of parasitology},
volume = {46},
number = {4},
pages = {235-241},
pmid = {19127329},
issn = {0023-4001},
mesh = {Animals ; Base Sequence ; Cestode Infections/epidemiology/parasitology ; Cyclooxygenase 1/genetics/metabolism ; DNA, Ribosomal Spacer/genetics ; Gene Expression Regulation ; Humans ; Korea/epidemiology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Taenia/*classification/*genetics ; Time Factors ; },
abstract = {Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium.},
}
@article {pmid19144713,
year = {2009},
author = {Van Wynsberghe, PM and Ahlquist, P},
title = {5' cis elements direct nodavirus RNA1 recruitment to mitochondrial sites of replication complex formation.},
journal = {Journal of virology},
volume = {83},
number = {7},
pages = {2976-2988},
pmid = {19144713},
issn = {1098-5514},
support = {R01 GM035072/GM/NIGMS NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; GM35072/GM/NIGMS NIH HHS/United States ; R37 GM035072/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM07215/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cell Line ; Drosophila ; Mitochondria/*virology ; Nodaviridae/*physiology ; Nucleic Acid Conformation ; Phylogeny ; RNA, Viral/*genetics/*metabolism ; Saccharomyces cerevisiae/virology ; Sequence Homology, Nucleic Acid ; Viral Proteins/metabolism ; *Virus Replication ; },
abstract = {Positive-strand RNA viruses replicate their genomes on intracellular membranes, usually in conjunction with virus-induced membrane rearrangements. For the nodavirus flock house virus (FHV), we recently showed that multifunctional FHV replicase protein A induces viral RNA template recruitment to a membrane-associated state, but the site(s) and function of this recruitment were not determined. By tagging viral RNA with green fluorescent protein, we show here in Drosophila cells that protein A recruits FHV RNA specifically to the outer mitochondrial membrane sites of RNA replication complex formation. Using Drosophila cells and yeast cells, which also support FHV replication, we also defined the cis-acting regions that direct replication and template recruitment for FHV genomic RNA1. RNA1 nucleotides 68 to 205 were required for RNA replication and directed efficient protein A-mediated RNA recruitment in both cell types. RNA secondary structure prediction, structure probing, and phylogenetic comparisons in this region identified two stable, conserved stem-loops with nearly identical loop sequences. Further mutational analysis showed that both stem-loops and certain flanking sequences were required for RNA1 recruitment, negative-strand synthesis, and subsequent positive-strand amplification in yeast and Drosophila cells. Thus, we have shown that protein A recruits RNA1 templates to mitochondria, as expected for RNA replication, and identified a new RNA1 cis element that is necessary and sufficient for RNA1 template recognition and recruitment to these mitochondrial membranes for negative-strand RNA1 synthesis. These results establish RNA recruitment to the sites of replication complex formation as an essential, distinct, and selective early step in nodavirus replication.},
}
@article {pmid19157810,
year = {2009},
author = {Yoshida, M and Nakayama, T and Inouye, I},
title = {Nuclearia thermophila sp. nov. (Nucleariidae), a new nucleariid species isolated from Yunoko Lake in Nikko (Japan).},
journal = {European journal of protistology},
volume = {45},
number = {2},
pages = {147-155},
doi = {10.1016/j.ejop.2008.09.004},
pmid = {19157810},
issn = {1618-0429},
mesh = {Animals ; DNA, Ribosomal/genetics ; Eukaryota/*classification/cytology/*physiology/ultrastructure ; *Fresh Water ; Japan ; Molecular Sequence Data ; Phagocytosis/physiology ; Phylogeny ; },
abstract = {A new species of unicellular opisthokont protist, Nuclearia thermophila sp. nov., was isolated from the warm spring water of Yunoko Lake, Japan, and has been described using light and electron microscopy. It exists as a spherical floating form and a flattened amoeboid form showing various shapes. The cells occasionally extended as branches or knobbed filopodia. The spherical form when suspended in medium measured 20-40microm in diameter (excluding filopodia). The amoeboid form may exceed 65microm along the longest axis. A nucleus with an obvious spherical nucleolus, dictyosomes, mitochondria with flat cristae, food vacuoles, and lipid droplet-like vacuoles with homogeneous contents were observed; no extracellular matrix or bacterial endosymbionts were present. The cells ingested flour particles. No cysts were seen. The molecular phylogenetic tree constructed on the basis of the small subunit ribosomal DNA revealed the novelty of N. thermophila and its relationships with previously known nucleariids.},
}
@article {pmid19165886,
year = {2009},
author = {Schuiki, I and Daum, G},
title = {Phosphatidylserine decarboxylases, key enzymes of lipid metabolism.},
journal = {IUBMB life},
volume = {61},
number = {2},
pages = {151-162},
doi = {10.1002/iub.159},
pmid = {19165886},
issn = {1521-6551},
support = {P 21429/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Biological Transport/genetics ; Carboxy-Lyases/chemistry/genetics/*metabolism ; Conserved Sequence ; Decarboxylation ; Eukaryotic Cells/metabolism ; Forecasting ; Lipid Metabolism/*genetics ; Molecular Sequence Data ; Phosphatidylethanolamines/biosynthesis/genetics ; Phylogeny ; Prokaryotic Cells/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity/genetics ; },
abstract = {Phosphatidylserine decarboxylases (PSDs) (E.C. 4.1.1.65) are enzymes which catalyze the formation of phosphatidylethanolamine (PtdEtn) by decarboxylation of phosphatidylserine (PtdSer). This enzymatic activity has been identified in both prokaryotic and eukaryotic organisms. PSDs occur as two types of proteins depending on their localization and the sequence of a conserved motif. Type I PSDs include enzymes of eukaryotic mitochondria and bacterial origin which contain the amino acid sequence LGST as a characteristic motif. Type II PSDs are found in the endomembrane system of eukaryotes and contain a typical GGST motif. These characteristic motifs are considered as autocatalytic cleavage sites where proenzymes are split into alpha- and beta-subunits. The S-residue set free by this cleavage serves as an attachment site of a pyruvoyl group which is required for the activity of the enzymes. Moreover, PSDs harbor characteristic binding sites for the substrate PtdSer. Substrate supply to eukaryotic PSDs requires lipid transport because PtdSer synthesis and decarboxylation are spatially separated. Targeting of PSDs to their proper locations requires additional intramolecular domains. Mitochondrially localized type I PSDs are directed to the inner mitochondrial membrane by N-terminal targeting sequences. Type II PSDs also contain sequences in their N-terminal extensions which might be required for subcellular targeting. Lack of PSDs causes various defects in different cell types. The physiological relevance of these findings and the central role of PSDs in lipid metabolism will be discussed in this review.},
}
@article {pmid19173734,
year = {2009},
author = {Yubuki, N and Edgcomb, VP and Bernhard, JM and Leander, BS},
title = {Ultrastructure and molecular phylogeny of Calkinsia aureus: cellular identity of a novel clade of deep-sea euglenozoans with epibiotic bacteria.},
journal = {BMC microbiology},
volume = {9},
number = {},
pages = {16},
pmid = {19173734},
issn = {1471-2180},
mesh = {Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Euglenida/classification/*genetics/*ultrastructure ; Microscopy, Electron, Transmission ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {BACKGROUND: The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades - euglenids, kinetoplastids and diplonemids--that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond.<br><br>RESULTS: We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 - 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world.<br><br>CONCLUSION: Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".},
}
@article {pmid19184408,
year = {2009},
author = {Jeong, HC and Kim, JA and Im, HH and Jeong, HU and Hong, MY and Lee, JE and Han, YS and Kim, I},
title = {Mitochondrial DNA sequence variation of the swallowtail butterfly, Papilio xuthus, and the cabbage butterfly, Pieris rapae.},
journal = {Biochemical genetics},
volume = {47},
number = {3-4},
pages = {165-178},
doi = {10.1007/s10528-008-9214-2},
pmid = {19184408},
issn = {1573-4927},
mesh = {Animals ; Butterflies/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Genetics, Population ; Korea ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilio xuthus L. (Lepidoptera: Papilionidae), and the cabbage butterfly, Pieris rapae L. (Lepidoptera: Pieridae). Papilio xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas Pi. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise: a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seem to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.},
}
@article {pmid19207245,
year = {2009},
author = {Kanbe, T and Akimoto, S},
title = {Allelic and genotypic diversity in long-term asexual populations of the pea aphid, Acyrthosiphon pisum in comparison with sexual populations.},
journal = {Molecular ecology},
volume = {18},
number = {5},
pages = {801-816},
doi = {10.1111/j.1365-294X.2008.04077.x},
pmid = {19207245},
issn = {1365-294X},
mesh = {*Alleles ; Animals ; Aphids/*genetics ; Electron Transport Complex IV/genetics ; Female ; Genetic Loci/genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; Geography ; Japan ; Male ; Microsatellite Repeats/genetics ; Mitochondria/enzymology ; Oviparity/genetics ; Pisum sativum/*parasitology ; Phylogeny ; Reproduction, Asexual/*genetics ; Sample Size ; Time Factors ; Viviparity, Nonmammalian/genetics ; },
abstract = {Many aphid species exhibit geographical variation in the mode of reproduction that ranges from cyclical parthenogenesis with a sexual phase to obligate parthenogenesis (asexual reproduction). Theoretical studies predict that organisms reproducing asexually should maintain higher allelic diversity per locus but lower genotypic diversity than organisms reproducing sexually. To corroborate this hypothesis, we evaluated genotypic and allelic diversities in the sexual and asexual populations of the pea aphid, Acyrthosiphon pisum (Harris). Microsatellite analysis revealed that populations in central Japan are asexual, whereas populations in northern Japan are obligatorily sexual. No mixed populations were detected in our study sites. Phylogenetic analysis using microsatellite data and mitochondrial cytochrome oxidase subunit I (COI) gene sequences revealed a long history of asexuality in central Japan and negated the possibility of the recent origin of the asexual populations from the sexual populations. Asexual populations exhibited much lower genotypic diversity but higher allelic richness per locus than did sexual populations. Asexual populations consisted of a few predominant clones that were considerably differentiated from one another. Sexual populations on alfalfa, an exotic plant in Japan, were most closely related to asexual populations associated with Vicia sativa L. The alfalfa-associated sexual populations harboured one COI haplotype that was included in the haplotype clade of the asexual populations. Available evidence suggests that the sexuality of the alfalfa-associated populations has recently been restored through the northward migration and colonization of alfalfa by V. sativa-associated lineages. Therefore, our results support the theoretical predictions and provide a new perspective on the origin of sexual populations.},
}
@article {pmid19207251,
year = {2009},
author = {Cardoso, YP and Montoya-Burgos, JI},
title = {Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: the Guyanas Region.},
journal = {Molecular ecology},
volume = {18},
number = {5},
pages = {947-964},
doi = {10.1111/j.1365-294X.2008.04068.x},
pmid = {19207251},
issn = {1365-294X},
mesh = {*Animal Migration ; Animals ; Catfishes/*genetics ; Cell Nucleus/genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Guyana ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; *Tropical Climate ; },
abstract = {Neotropical freshwater fishes have reached an unrivalled diversity, organized into several areas of endemism, yet the underlying processes are still largely unknown. The topographical and ecological characteristics of the Guyanas Region make it an ideal area of endemism in which to investigate the forces that have shaped this great diversity. This region is thought to be inhabited by species descending from Amazonian ancestors, which would have used two documented routes that, however, hardly explain the entrance of species adapted to running waters. Here, we investigate the evolutionary history of Pseudancistrus brevispinis, a catfish endemic to this region and exclusively found in running waters, thus making it an ideal model for investigating colonization routes and dispersal in such habitats. Our analyses, based on mitochondrial and nuclear markers, revealed an unexpected diversity consisting of six monophyletic lineages within P. brevispinis, showing a disjoint distribution pattern. The lineages endemic to Guyanas coastal rivers form a monophyletic group that originated via an ancestral colonization event from the Amazon basin. Evidence given favours a colonization pathway through river capture between an Amazonian tributary and the Upper Maroni River. Population genetic analyses of the most widespread species indicate that subsequent dispersal among Guyanas coastal rivers occurred principally by temporary connections between adjacent rivers during periods of lower sea level, yet instances of dispersal via interbasin river captures are not excluded. During high sea level intervals, the isolated populations would have diverged leading to the observed allopatric species. This evolutionary process is named the sea level fluctuation (SLF) hypothesis of diversification.},
}
@article {pmid19214710,
year = {2009},
author = {Yamaguchi, M},
title = {Novel protein RGPR-p117: its role as the regucalcin gene transcription factor.},
journal = {Molecular and cellular biochemistry},
volume = {327},
number = {1-2},
pages = {53-63},
pmid = {19214710},
issn = {1573-4919},
mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Gene Expression ; Humans ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Transcription Factors/*genetics/*metabolism ; },
abstract = {RGPR-p117 was originally discovered as a novel protein that binds to a nuclear factor I (NFI) consensus motif TTGGC(N)(6)CC, which is present in the 5'-flanking region of the regucalcin gene (rgn). RGPR-p117 has been identified in human, rat, mouse, bovine, rabbit, and chicken livers. Phylogenetic analysis of six vertebrates shows that RGPR-p117 appears to form a single cluster, indicating a common evolutionary relationship of the RGPR-p117 family. The RGPR-p117 gene consists of at least 26 exons spanning approximately 4.1 kbp and is localized on human chromosome 1q25.2. RGPR-p117 mRNA is expressed in the liver, kidney, heart, spleen, and brain of rats. RGPR-p117 mRNA expression is stimulated through signaling mechanisms. Mammalian RGPR-p117 conserves a leucine zipper motif, which is present in many gene regulatory proteins. RGPR-p117 has been shown to translocate from the cytoplasm to the nucleus in NRK52E cells, a process which is mediated through protein kinase C signaling following hormonal stimulation. The phosphorylated RGPR-p117 binds to the TTGGC motif in the promoter region of the regucalcin gene and enhances regucalcin mRNA expression in the cells, indicating a role as a transcriptional factor. RGPR-p117 is also localized in the plasma membranes, nucleus, mitochondria, microsomes, and cytoplasm. Overexpression of RGPR-p117 has been found to induce a significant decrease in protein and DNA contents in cells, suggesting that RGPR-p117 may regulate the gene expression of other related proteins as well as the transcription factor. Also, overexpression of RGPR-p117 has a suppressive effect on cell death by inhibiting the gene expression of caspase-3, caspase-8, and Fas-associating death domain protein whose TTGGC motif is present in the promoter region of their genes. The novel protein RGPR-p117 has been shown to play an important role as a transcription factor.},
}
@article {pmid19219673,
year = {2009},
author = {Yamaguchi, T and Prabowo, RE and Ohshiro, Y and Shimono, T and Jones, D and Kawai, H and Otani, M and Oshino, A and Inagawa, S and Akaya, T and Tamura, I},
title = {The introduction to Japan of the Titan barnacle, Megabalanus coccopoma (Darwin, 1854) (Cirripedia: Balanomorpha) and the role of shipping in its translocation.},
journal = {Biofouling},
volume = {25},
number = {4},
pages = {325-333},
doi = {10.1080/08927010902738048},
pmid = {19219673},
issn = {1029-2454},
mesh = {Animals ; Australia ; Biofilms/growth &amp; development ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetics, Population ; Haplotypes ; Japan ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; *Ships ; Species Specificity ; Thoracica/*classification/genetics/*physiology ; },
abstract = {The Titan Acorn barnacle, Megabalanus coccopoma, a native of the tropical eastern Pacific, has become established in the western Atlantic (Brazil and the northern Gulf of Mexico to the Carolinas), northwestern Europe and the western Indian Ocean (Mauritius), and therefore its dispersal capabilities are well known. This study reports its introduction to Japan and confirms its occurrence in Australia. In an attempt to determine the source of this introduction, phylogeographic techniques, involving cytochrome c oxidase I sequences of various widely separate populations of M. rosa and M. volcano, were utilized. No significant genetic differentiation or haplotype patterns between widely separated populations of each of the three species were found. Lack of such differentiation indicates recent geographical isolation and thus negates a null hypothesis predicting that the occurrence of one of more of these species in Australia was natural.},
}
@article {pmid19248758,
year = {2009},
author = {Zutz, A and Gompf, S and Schägger, H and Tampé, R},
title = {Mitochondrial ABC proteins in health and disease.},
journal = {Biochimica et biophysica acta},
volume = {1787},
number = {6},
pages = {681-690},
doi = {10.1016/j.bbabio.2009.02.009},
pmid = {19248758},
issn = {0006-3002},
mesh = {ATP-Binding Cassette Transporters/*chemistry/genetics/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Heme/biosynthesis ; Homeostasis ; Humans ; Hydrolysis ; Iron/metabolism ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Phylogeny ; Protein Processing, Post-Translational ; },
abstract = {ABC transporters represent one of the largest families of membrane proteins that are found in all three phyla of life. Mitochondria comprise up to four ABC systems, ABCB7/ATM1, ABCB10/MDL1, ABCB8 and ABCB6. These half-transporters, which assemble into homodimeric complexes, are involved in a number of key cellular processes, e.g. biogenesis of cytosolic iron-sulfur clusters, heme biosynthesis, iron homeostasis, multidrug resistance, and protection against oxidative stress. Here, we summarize recent advances and emerging themes in our understanding of how these ABC systems in the inner and outer mitochondrial membrane fulfill their functions in important (patho) physiological processes, including neurodegenerative and hematological disorders.},
}
@article {pmid19249364,
year = {2009},
author = {López-Calcagno, PE and Moreno, J and Cedeño, L and Labrador, L and Concepción, JL and Avilán, L},
title = {Cloning, expression and biochemical characterization of mitochondrial and cytosolic malate dehydrogenase from Phytophthora infestans.},
journal = {Mycological research},
volume = {113},
number = {Pt 6-7},
pages = {771-781},
doi = {10.1016/j.mycres.2009.02.012},
pmid = {19249364},
issn = {1469-8102},
mesh = {Amino Acid Sequence ; *Cloning, Molecular ; Cytosol/chemistry/*enzymology ; Escherichia coli/genetics/metabolism ; *Gene Expression ; Kinetics ; Malate Dehydrogenase/*chemistry/genetics/metabolism ; Mitochondria/chemistry/*enzymology/genetics ; Molecular Sequence Data ; Oomycetes/chemistry/classification/genetics ; Phylogeny ; Phytophthora infestans/chemistry/classification/*enzymology/genetics ; Sequence Alignment ; },
abstract = {The genes of the mitochondrial and cytosolic malate dehydrogenase (mMDH and cMDH) of Phytophthora infestans were cloned and overexpressed in Escherichia coli as active enzymes. The catalytic properties of these proteins were determined: both enzymes have a similar specific activity. In addition, the natural mitochondrial isoenzyme was semi-purified from mycelia and its catalytic properties determined: the recombinant mitochondrial isoform behaved as the natural enzyme. A phylogenetic analysis indicated that mMDH, present in all stramenopiles studied, can be useful to study the relationships between these organisms. MDH with the conserved domain MDH_cytoplasmic_cytosolic is absent in some stramenopiles as well as in fungi. This enzyme seems to be less related within the stramenopile group. The Phytophthora cMDHs have an insertion of six amino acids that is also present in the stramenopile cMDHs studied, with the exception of Thalassiosira pseudonana cMDH, and is absent in other known eukaryotic cMDHs.},
}
@article {pmid19268697,
year = {2009},
author = {Shen, X and Sun, M and Wu, Z and Tian, M and Cheng, H and Zhao, F and Meng, X},
title = {The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes.},
journal = {Gene},
volume = {437},
number = {1-2},
pages = {1-8},
doi = {10.1016/j.gene.2009.02.014},
pmid = {19268697},
issn = {1879-0038},
mesh = {Animals ; Chromosome Mapping ; Codon ; *Genome, Mitochondrial ; Palaemonidae/*genetics ; Phylogeny ; RNA, Transfer/*genetics ; },
abstract = {The complete mitochondrial (mt) DNA sequence was determined for a ridgetail white prawn, Exopalaemon carinicauda Holthuis, 1950 (Crustacea: Decopoda: Palaemonidae). The mt genome is 15,730 bp in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which is typical for metazoans. The majority-strand consists of 33.6% A, 23.0% C, 13.4% G, and 30.0% T bases (AT skew=0.057; GC skew=-0.264). A total of 1045 bp of non-coding nucleotides were observed in 16 intergenic regions, including a major A+T rich (79.7%) noncoding region (886 bp). A novel translocation of tRNA(Pro) and tRNA(Thr) was found when comparing this genome with the pancrustacean ground pattern indicating that gene order is not conserved among caridean mitochondria. Furthermore, the rate of Ka/Ks in 13 protein-coding genes between three caridean species is much less than 1, which indicates a strong purifying selection within this group. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based on currently available malacostracan complete mitochondrial sequences were built with the maximum likelihood and Bayesian models. All analyses based on nucleotide and amino acid data strongly support the monophyly of Decapoda. The Penaeidae, Reptantia, Caridea, and Meiura clades were also recovered as monophyletic groups with strong statistical support. However, the phylogenetic relationships within Pleocyemata are unstable, as represented by the inclusion or exclusion of Caridea.},
}
@article {pmid19281475,
year = {2009},
author = {Bovers, M and Hagen, F and Kuramae, EE and Boekhout, T},
title = {Promiscuous mitochondria in Cryptococcus gattii.},
journal = {FEMS yeast research},
volume = {9},
number = {3},
pages = {489-503},
doi = {10.1111/j.1567-1364.2009.00494.x},
pmid = {19281475},
issn = {1567-1364},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Cluster Analysis ; Cryptococcosis/microbiology/veterinary ; Cryptococcus/classification/*genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Fungal/*genetics ; DNA, Mitochondrial/*genetics ; Environmental Microbiology ; Genotype ; Mitochondria/classification/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Recombination, Genetic ; },
abstract = {Cryptococcus gattii is a primary pathogenic basidiomycetous yeast comprising four genotypic groups. Here we present data on two mitochondrial loci (MtLrRNA and ATP6). Two of the genotypic groups, namely amplified fragment length polymorphism (AFLP)5/VGIII and AFLP6/VGII, formed monophyletic lineages. The AFLP4/VGI genotypic group, however, possessed five different mitochondrial genotypes that did not form a monophyletic lineage. The majority of these isolates contained mitochondrial genomes that are partially identical to those found in isolates belonging to AFLP6/VGII, which is causing the ongoing and expanding Vancouver Island outbreak. Two out of four AFLP7/VGIV isolates contained an AFLP4/VGI allele of MtLrRNA. These observations are best explained by assuming a process of mitochondrial recombination. If this is true, mitochondrial recombination seems possible between cells belonging to different genotypic groups of C. gattii, especially between AFLP6/VGII or AFLP7/VGIV and AFLP4/VGI. We also have to assume that mitochondria, most likely, were transferred from cells belonging to AFLP6/VGII to AFLP4/VGI. As such a process of mitochondrial recombination is only possible after cell-cell conjugation, this may also allow the further exchange of genetic material, for example nuclear or plasmid in nature, between different genotypes of C. gattii. This may be relevant as it may provide a possible mechanism contributing to the modulation of virulence attributes of isolates, such as has been observed in the ongoing Vancouver Island outbreak of C. gattii.},
}
@article {pmid19306844,
year = {2009},
author = {Mahlknecht, U and Voelter-Mahlknecht, S},
title = {Fluorescence in situ hybridization and chromosomal organization of the sirtuin 4 gene (Sirt4) in the mouse.},
journal = {Biochemical and biophysical research communications},
volume = {382},
number = {4},
pages = {685-690},
doi = {10.1016/j.bbrc.2009.03.092},
pmid = {19306844},
issn = {1090-2104},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cells, Cultured ; Chromosome Mapping ; Chromosomes/genetics ; *Gene Dosage ; Gene Expression ; In Situ Hybridization, Fluorescence ; Mice ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Sirtuins/classification/*genetics ; },
abstract = {The sirtuins (SIRT1-7), also being referred to as class III HDACs, exert NAD-dependent deacetylase and/or ADP-ribosyltransferase activities in various cellular compartments including the cell nucleus, the cytoplasm and the mitochondria. The sirtuins play a central role in epigenetic gene silencing, DNA repair and recombination, cell-cycle, microtubule organization, and in the regulation of aging. SIRT4 is a mitochondrial protein that lacks deacetylase activities but efficiently works as an ADP-ribosyltransferase. We have isolated and characterized the murine Sirt4 genomic sequence, which spans a region of 12kb and which has one single genomic locus. Determination of the exon-intron splice junctions established that SIRT4 is encoded by 6 exons. The 1648bp murine Sirt4 transcript encodes a 418 aa protein with a predictive molecular weight of 47.3kDa. Fluorescence in situ hybridization analysis identified a single genomic locus for murine Sirt4 gene on chromosome 5F and is neighbored by the PLA2G1B and PXN genes.},
}
@article {pmid19326079,
year = {2009},
author = {Lee, SM and Hoang, MH and Han, HJ and Kim, HS and Lee, K and Kim, KE and Kim, DH and Lee, SY and Chung, WS},
title = {Pathogen inducible voltage-dependent anion channel (AtVDAC) isoforms are localized to mitochondria membrane in Arabidopsis.},
journal = {Molecules and cells},
volume = {27},
number = {3},
pages = {321-327},
doi = {10.1007/s10059-009-0041-z},
pmid = {19326079},
issn = {0219-1032},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Microscopy, Confocal ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Isoforms ; Voltage-Dependent Anion Channels/biosynthesis/genetics/metabolism ; Yeasts/genetics/metabolism ; },
abstract = {Voltage-dependent anion channels (VDACs) are reported to be porin-type, beta-barrel diffusion pores. They are prominently localized in the outer mitochondrial membrane and are involved in metabolite exchange between the organelle and the cytosol. In this study, we have investigated a family of VDAC isoforms in Arabidopsis thaliana (AtVDAC). We have shown that the heterologous expression of AtVDAC proteins can functionally complement a yeast mutant lacking the endogenous mitochondrial VDAC gene. AtVDACs tagged with GFP were localized to mitochondria in both yeast and plant cells. We also looked at the response of AtVDACs to biotic and abiotic stresses and found that four AtVDAC transcripts were rapidly up-regulated in response to a bacterial pathogen.},
}
@article {pmid19335829,
year = {2009},
author = {Ready, PD and Testa, JM and Wardhana, AH and Al-Izzi, M and Khalaj, M and Hall, MJ},
title = {Phylogeography and recent emergence of the Old World screwworm fly, Chrysomya bezziana, based on mitochondrial and nuclear gene sequences.},
journal = {Medical and veterinary entomology},
volume = {23 Suppl 1},
number = {},
pages = {43-50},
doi = {10.1111/j.1365-2915.2008.00771.x},
pmid = {19335829},
issn = {1365-2915},
mesh = {Animals ; Base Pairing ; Cell Nucleus/*genetics ; Cytochromes b/*genetics ; DNA/genetics/isolation &amp; purification ; DNA Primers ; Diptera/classification/*genetics ; Gene Amplification ; Geography ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {A previous study had identified an African and an Asian race of the Old World screwworm fly, Chrysomya bezziana Villeneuve (Diptera: Calliphoridae), based on the 3' terminal 279 basepairs (bp) of the mitochondrial cytochrome b gene. The current study improved the phylogeographic resolution of cytochrome b for this species by characterizing more of the gene (the 3' terminal 715 bp) and by sampling more geographical populations, including Oman, Iran, Hong Kong and the Indonesian islands of Sulawesi and East Sumba. Strong support was found for recognizing an African race, but not for a monophyletic Asian race. The cladistic and genealogical relationships among the Asian populations were complex. There was sufficient genetic homogeneity throughout separate regions (mainland Asia and each Indonesian island) to suggest that there are no reproductive barriers within each region that might necessitate the production of more than one strain for control by the sterile insect technique (SIT). Primers were designed for the amplification by polymerase chain reaction of two nuclear loci, the highly conserved elongation factor-1alphagene and the less conserved white gene, and the preliminary results indicated that these genes showed the same pattern of small-scale regional variation as cytochrome b. The cytochrome b haplotypes are useful markers for identifying the geographical origins of any emerging infestations of the species: the absence of Indonesian and African haplotypes in the Middle East demonstrates that the large-scale transport of livestock is not spreading Old World screwworm.},
}
@article {pmid19363601,
year = {2009},
author = {Kim, S and Lee, YP and Lim, H and Ahn, Y and Sung, SK},
title = {Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.).},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {119},
number = {1},
pages = {189-198},
pmid = {19363601},
issn = {1432-2242},
mesh = {Animals ; *Base Sequence ; Chloroplasts/*genetics ; *DNA, Plant/analysis/genetics ; *Genetic Markers ; Genetic Variation ; Genome ; Genome, Mitochondrial/genetics ; Molecular Sequence Data ; Phylogeny ; Raphanus/classification/*cytology/*genetics ; Sequence Alignment ; },
abstract = {Four types of cytoplasms (Ogura, DCGMS, DBRMF1, and DBRMF2) were identified in the previous studies using molecular markers based on mitochondrial genome variations in radish (Raphanus sativus L.). However, mtDNA markers have limitations in obtaining clear results due to complexity of radish mitochondrial genomes. To improve fidelity, molecular markers based on variation of chloroplast genome sequences were developed in this study. We searched for the sequence variations of chloroplast genome among the four cytoplasm types in 11 noncoding intergenic regions of ~8.7 kb. Highly variable intergenic regions between trnK and rps16 were identified, and a couple of 4-34 bp indels were used to develop a simple PCR-based marker that distinguished the four cytoplasm types based on the PCR product length polymorphism. Two additional cpDNA markers were developed by using a single nucleotide polymorphism and 17-bp insertion. Analysis of 90 accessions using both mtDNA and cpDNA markers showed the perfect match of results of both the markers, suggesting strict co-transmission of mitochondria and chloroplast in radish. Phylogenetic trees showed that two male-sterility inducing cytoplasms, Ogura and DCGMS, were closely related to DBRMF1 and DBRMF2, respectively. Analysis of 120 radish germplasms introduced from diverse countries showed that the frequency of male-sterility inducing mitotypes of Ogura and DCGMS was very low, and DCGMS was predominately detected in eastern European countries. Majority of accessions from Europe and Asia were shown to contain DBRMF2 and DBRMF1 mitotypes, respectively.},
}
@article {pmid19366667,
year = {2009},
author = {Funes, S and Hasona, A and Bauerschmitt, H and Grubbauer, C and Kauff, F and Collins, R and Crowley, PJ and Palmer, SR and Brady, LJ and Herrmann, JM},
title = {Independent gene duplications of the YidC/Oxa/Alb3 family enabled a specialized cotranslational function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {16},
pages = {6656-6661},
pmid = {19366667},
issn = {1091-6490},
support = {R01 DE008007/DE/NIDCR NIH HHS/United States ; DE08007/DE/NIDCR NIH HHS/United States ; },
mesh = {Bacterial Proteins/*genetics ; Electron Transport Complex IV/*genetics ; *Gene Duplication ; Genetic Complementation Test ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics ; Models, Genetic ; Mutation/genetics ; Nuclear Proteins/*genetics ; Phylogeny ; Protein Binding ; *Protein Biosynthesis ; Ribosomes/metabolism ; Saccharomyces cerevisiae/cytology/*genetics ; Streptococcus mutans/*genetics ; Time Factors ; },
abstract = {YidC/Oxa/Alb3 family proteins catalyze the insertion of integral membrane proteins in bacteria, mitochondria, and chloroplasts, respectively. Unlike gram-negative organisms, gram-positive bacteria express 2 paralogs of this family, YidC1/SpoIIIJ and YidC2/YgjG. In Streptococcus mutans, deletion of yidC2 results in a stress-sensitive phenotype similar to that of mutants lacking the signal recognition particle (SRP) protein translocation pathway, while deletion of yidC1 has a less severe phenotype. In contrast to eukaryotes and gram-negative bacteria, SRP-deficient mutants are viable in S. mutans; however, double SRP-yidC2 mutants are severely compromised. Thus, YidC2 may enable loss of the SRP by playing an independent but overlapping role in cotranslational protein insertion into the membrane. This is reminiscent of the situation in mitochondria that lack an SRP pathway and where Oxa1 facilitates cotranslational membrane protein insertion by binding directly to translation-active ribosomes. Here, we show that OXA1 complements a lack of yidC2 in S. mutans. YidC2 also functions reciprocally in oxa1-deficient Saccharomyces cerevisiae mutants and mediates the cotranslational insertion of mitochondrial translation products into the inner membrane. YidC2, like Oxa1, contains a positively charged C-terminal extension and associates with translating ribosomes. Our results are consistent with a gene-duplication event in gram-positive bacteria that enabled the specialization of a YidC isoform that mediates cotranslational activity independent of an SRP pathway.},
}
@article {pmid19376118,
year = {2009},
author = {Reis, K and Fransson, A and Aspenström, P},
title = {The Miro GTPases: at the heart of the mitochondrial transport machinery.},
journal = {FEBS letters},
volume = {583},
number = {9},
pages = {1391-1398},
doi = {10.1016/j.febslet.2009.04.015},
pmid = {19376118},
issn = {1873-3468},
mesh = {Animals ; Biological Transport ; Calcium/metabolism ; GTP Phosphohydrolases/*metabolism ; Homeostasis ; Humans ; Mitochondria/*enzymology/metabolism ; Phylogeny ; },
abstract = {Mitochondria are organelles of elaborate structure that in addition to supplying cellular energy, have significant roles in calcium homeostasis and apoptosis. Failure to maintain mitochondrial dynamics results in neurodegenerative diseases and neuromuscular pathologies. The Miro GTPases, which constitute a unique subgroup of the Ras superfamily, have emerged as essential regulators of mitochondrial morphogenesis and trafficking along microtubules. Miro GTPases function as calcium-dependent sensors in the control of mitochondrial motility. Increased awareness of the biological function of Miro GTPases can contribute to elucidate the molecular mechanisms underlying diseases caused by deregulated mitochondrial dynamics.},
}
@article {pmid19383096,
year = {2009},
author = {Reich, M and Göbel, C and Kohler, A and Buée, M and Martin, F and Feussner, I and Polle, A},
title = {Fatty acid metabolism in the ectomycorrhizal fungus Laccaria bicolor.},
journal = {The New phytologist},
volume = {182},
number = {4},
pages = {950-964},
doi = {10.1111/j.1469-8137.2009.02819.x},
pmid = {19383096},
issn = {1469-8137},
mesh = {Biosynthetic Pathways/genetics ; Chromatography, Thin Layer ; Fatty Acid Synthases/chemistry/genetics ; Fatty Acids/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Laccaria/enzymology/genetics/*metabolism ; Mycorrhizae/enzymology/genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Pseudotsuga/microbiology ; },
abstract = {Here, the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolorwas explored with the aim of constructing a genome-wide inventory of genes involved in fatty acid metabolism. Sixty-three genes of the major pathways were annotated and validated by the detection of the corresponding transcripts. Seventy-one per cent belonged to multigene families of up to five members. In the mycelium of L. bicolor, 19 different fatty acids were detected, including at low concentrations palmitvaccenic acid (16:1(11Z)), which is known to be a marker for arbuscular mycorrhizal fungi. The pathways of fatty acid biosynthesis and degradation in L. bicolor were reconstructed using lipid composition, gene annotation and transcriptional analysis. Annotation results indicated that saturated fatty acids were degraded in mitochondria, whereas degradation of modified fatty acids was confined to peroxisomes. Fatty acid synthase (FAS) was the second largest protein annotated in L. bicolor. Phylogenetic analysis indicated that L. bicolor, Ustilago maydis and Coprinopsis cinerea have a vertebrate-like type I FAS encoded as a single protein, whereas in other basidiomycetes, including the human pathogenic basidiomycete Cryptococcus neoformans, and in most ascomycetes FAS is composed of the two structurally distinct subunits α and β.},
}
@article {pmid19386803,
year = {2009},
author = {Grant, N and Onda, Y and Kakizaki, Y and Ito, K and Watling, J and Robinson, S},
title = {Two cys or not two cys? That is the question; alternative oxidase in the thermogenic plant sacred Lotus.},
journal = {Plant physiology},
volume = {150},
number = {2},
pages = {987-995},
pmid = {19386803},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Cysteine/*metabolism ; Diamide/pharmacology ; Disulfides/metabolism ; Glyoxylates/metabolism ; Immunoblotting ; Isoenzymes/metabolism ; Mitochondria/drug effects/enzymology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Nelumbo/drug effects/*enzymology ; Oxidoreductases/chemistry/*metabolism ; Oxygen/metabolism ; Phylogeny ; Plant Proteins ; Protein Multimerization/drug effects ; Pyruvic Acid/metabolism ; Succinates/metabolism ; *Temperature ; Alternative Oxidase ; },
abstract = {Sacred lotus (Nelumbo nucifera) regulates temperature in its floral chamber to 32 degrees C to 35 degrees C across ambient temperatures of 8 degrees C to 40 degrees C with heating achieved through high alternative pathway fluxes. In most alternative oxidase (AOX) isoforms, two cysteine residues, Cys(1) and Cys(2), are highly conserved and play a role in posttranslational regulation of AOX. Further control occurs via interaction of reduced Cys(1) with alpha-keto acids, such as pyruvate. Here, we report on the in vitro regulation of AOX isolated from thermogenic receptacle tissues of sacred lotus. AOX protein was mostly present in the reduced form, and only a small fraction could be oxidized with diamide. Cyanide-resistant respiration in isolated mitochondria was stimulated 4-fold by succinate but not pyruvate or glyoxylate. Insensitivity of the alternative pathway of respiration to pyruvate and the inability of AOX protein to be oxidized by diamide suggested that AOX in these tissues may lack Cys(1). Subsequently, we isolated two novel cDNAs for AOX from thermogenic tissues of sacred lotus, designated as NnAOX1a and NnAOX1b. Deduced amino acid sequences of both confirmed that Cys(1) had been replaced by serine; however, Cys(2) was present. This contrasts with AOXs from thermogenic Aroids, which contain both Cys(1) and Cys(2). An additional cysteine was present at position 193 in NnAOX1b. The significance of the sequence data for regulation of the AOX protein in thermogenic sacred lotus is discussed and compared with AOXs from other thermogenic and nonthermogenic species.},
}
@article {pmid19439189,
year = {2009},
author = {Hoyos-Carvajal, L and Orduz, S and Bissett, J},
title = {Genetic and metabolic biodiversity of Trichoderma from Colombia and adjacent neotropic regions.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {46},
number = {9},
pages = {615-631},
doi = {10.1016/j.fgb.2009.04.006},
pmid = {19439189},
issn = {1096-0937},
mesh = {*Biodiversity ; Carbon/metabolism ; Central America ; DNA, Fungal/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Genes, Fungal/genetics ; Genetic Variation ; Metabolome ; Mexico ; Mitochondria/metabolism ; Phylogeny ; Sequence Analysis, DNA ; South America ; Species Specificity ; Trichoderma/*genetics/isolation &amp; purification/*metabolism ; },
abstract = {The genus Trichoderma has been studied for production of enzymes and other metabolites, as well as for exploitation as effective biological control agents. The biodiversity of Trichoderma has seen relatively limited study over much of the neotropical region. In the current study we assess the biodiversity of 183 isolates from Mexico, Guatemala, Panama, Ecuador, Peru, Brazil and Colombia, using morphological, metabolic and genetic approaches. A comparatively high diversity of species was found, comprising 29 taxa: Trichoderma asperellum (60 isolates), Trichoderma atroviride (3), Trichoderma brevicompactum (5), Trichoderma crassum (3), Trichoderma erinaceum (3), Trichoderma gamsii (2), Trichoderma hamatum (2), Trichoderma harzianum (49), Trichoderma koningiopsis (6), Trichoderma longibrachiatum (3), Trichoderma ovalisporum (1), Trichoderma pubescens (2), Trichoderma rossicum (4), Trichoderma spirale (1), Trichoderma tomentosum (3), Trichoderma virens (8), Trichoderma viridescens (7) and Hypocrea jecorina (3) (anamorph: Trichoderma reesei), along with 11 currently undescribed species. T. asperellum was the prevalent species and was represented by two distinct genotypes with different metabolic profiles and habitat preferences. The second predominant species, T. harzianum, was represented by three distinct genotypes. The addition of 11 currently undescribed species is evidence of the considerable unresolved biodiversity of Trichoderma in neotropical regions. Sequencing of the internal transcribed spacer regions (ITS) of the ribosomal repeat could not differentiate some species, and taken alone gave several misidentifications in part due to the presence of nonorthologous copies of the ITS in some isolates.},
}
@article {pmid19450731,
year = {2009},
author = {Vickers, TJ and Murta, SM and Mandell, MA and Beverley, SM},
title = {The enzymes of the 10-formyl-tetrahydrofolate synthetic pathway are found exclusively in the cytosol of the trypanosomatid parasite Leishmania major.},
journal = {Molecular and biochemical parasitology},
volume = {166},
number = {2},
pages = {142-152},
pmid = {19450731},
issn = {1872-9428},
support = {R01 AI021903/AI/NIAID NIH HHS/United States ; R01 AI029646/AI/NIAID NIH HHS/United States ; R01 AI031078/AI/NIAID NIH HHS/United States ; R37 AI021903/AI/NIAID NIH HHS/United States ; AI21903/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Biological Transport ; Biosynthetic Pathways ; Cytosol/*enzymology/metabolism ; Kinetics ; Leishmania major/classification/*enzymology/genetics/metabolism ; Leishmaniasis, Cutaneous/*parasitology ; Leucovorin/*analogs &amp; derivatives/biosynthesis ; Mice ; Mice, Inbred BALB C ; Mitochondria/genetics/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/genetics/*metabolism ; },
abstract = {In most organisms 10-formyl-tetrahydrofolate (10-CHO-THF) participates in the synthesis of purines in the cytosol and formylation of mitochondrial initiator methionyl-tRNA(Met). Here we studied 10-CHO-THF biosynthesis in the protozoan parasite Leishmania major, a purine auxotroph. Two distinct synthetic enzymes are known, a bifunctional methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (DHCH) or formyl-tetrahydrofolate ligase (FTL), and phylogenomic profiling revealed considerable diversity for these in trypanosomatids. All species surveyed contain a DHCH1, which was shown recently to be essential in L. major. A second DHCH2 occurred only in L. infantum, L. mexicana and T. cruzi, and as a pseudogene in L. major. DHCH2s bear N-terminal extensions and we showed a LiDHCH2-GFP fusion was targeted to the mitochondrion. FTLs were found in all species except Trypanosoma brucei. L. major ftl(-) null mutants were phenotypically normal in growth, differentiation, animal infectivity and sensitivity to a panel of pteridine analogs, but grew more slowly when starved for serine or glycine, as expected for amino acids that are substrates in C1-folate metabolism. Cell fractionation and western blotting showed that both L. major DHCH1 and FTL were localized to the cytosol and not the mitochondrion. These localization data predict that in L. major cytosolic 10-formyl-tetrahydrofolate must be transported into the mitochondrion to support methionyl-tRNA(Met) formylation. The retention in all the trypanosomatids of at least one enzyme involved in 10-formyl-tetrahydrofolate biosynthesis, and the essentiality of this metabolite in L. major, suggests that this pathway represents a promising new area for chemotherapeutic attack in these parasites.},
}
@article {pmid19457430,
year = {2009},
author = {Calo-Mata, P and Pascoal, A and Fernández-No, I and Böhme, K and Gallardo, JM and Barros-Velázquez, J},
title = {Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea.},
journal = {Analytical biochemistry},
volume = {391},
number = {2},
pages = {127-134},
doi = {10.1016/j.ab.2009.05.020},
pmid = {19457430},
issn = {1096-0309},
mesh = {Animals ; Mitochondria/*genetics ; Penaeidae/*classification/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*analysis/genetics ; RNA, Transfer, Val/*analysis/genetics ; Species Specificity ; },
abstract = {In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)(Val) genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNA(Val) genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNA(Val) marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNA(Val) gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNA(Val) region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNA(Val) marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation.},
}
@article {pmid19462511,
year = {2008},
author = {Deng, W and Luo, K and Li, Z and Yang, Y},
title = {Molecular cloning and characterization of a mitochondrial dicarboxylate/tricarboxylate transporter gene in Citrus junos response to aluminum stress.},
journal = {Mitochondrial DNA},
volume = {19},
number = {4},
pages = {376-384},
pmid = {19462511},
issn = {1940-1736},
mesh = {Aluminum/toxicity ; Amino Acid Sequence ; Base Sequence ; Carrier Proteins/*genetics ; Citrus/drug effects/*genetics/*metabolism ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Dicarboxylic Acid Transporters/*genetics ; Gene Expression/drug effects ; *Genes, Mitochondrial/drug effects ; *Genes, Plant/drug effects ; Mitochondria/drug effects/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {A mitochondrial dicarboxylate/tricarboxylate carrier gene, CjDTC, was isolated from Citrus junos by the rapid amplification of cDNA ends and the Y-shaped adaptor-dependent extension methods. It consisted of a 472-base pair (bp) upstream regulatory region and an 897-bp open reading frame encoding a protein of 299 amino acids. Homologous analysis revealed that CjDTC protein might be a plant dicarboxylate/tricarboxylate carrier protein involved in the mitochondria dicarboxylate/tricarboxylate transport. The putative light responsiveness and salicylic acid responsiveness regulatory elements were identified in the upstream regulatory region of CjDTC. Southern blot analysis demonstrated the presence of a single CjDTC gene located on the genome of citrus. As shown by northern hybridization, CjDTC was expressed in all plant tissues examined and the highest transcript level was observed in roots with significantly lower transcript amounts in leaves and stems. Moreover, real-time polymerase chain reaction analysis demonstrated that CjDTC expression was induced by aluminum treatment, suggesting that CjDTC protein might be involved in the excretion of organic acids and rhizotoxic aluminum tolerance.},
}
@article {pmid19477263,
year = {2009},
author = {Bodzioch, M and Lapicka-Bodzioch, K and Zapala, B and Kamysz, W and Kiec-Wilk, B and Dembinska-Kiec, A},
title = {Evidence for potential functionality of nuclearly-encoded humanin isoforms.},
journal = {Genomics},
volume = {94},
number = {4},
pages = {247-256},
doi = {10.1016/j.ygeno.2009.05.006},
pmid = {19477263},
issn = {1089-8646},
mesh = {Adult ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Apoptosis/*genetics ; Cell Nucleus/genetics ; Cells, Cultured ; Chromosomes, Human ; Chromosomes, Mammalian ; Computational Biology/methods ; Consensus Sequence ; DNA, Complementary ; Dose-Response Relationship, Drug ; Genome, Human ; Heterozygote ; Homozygote ; Humans ; Intracellular Signaling Peptides and Proteins/genetics/*metabolism ; Isoleucine/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Neuroprotective Agents/*pharmacology ; Open Reading Frames/genetics ; Pan troglodytes ; Peptide Fragments/chemistry/*genetics/*metabolism ; Peptide Mapping ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Rhodamines/metabolism ; Sequence Homology, Amino Acid ; Staurosporine/pharmacology ; Time Factors ; Umbilical Veins/cytology ; beta Carotene/pharmacology ; },
abstract = {Humanin (HN) is a recently identified neuroprotective and antiapoptotic peptide derived from a portion of the mitochondrial MT-RNR2 gene. We provide bioinformatic and expression data suggesting the existence of 13 MT-RNR2-like nuclear loci predicted to maintain the open reading frames of 15 distinct full-length HN-like peptides. At least ten of these nuclear genes are expressed in human tissues, and respond to staurosporine (STS) and beta-carotene. Sequence comparisons of the nuclear HN isoforms and their homologues in other species reveal two consensus motifs, encompassing residues 5-11 (GFS/NCLLL), and 14-19 (SEIDLP/S). Proline vs serine in position 19 may determine whether the peptide is secreted or not, while threonine in position 13 may be important for cell surface receptor binding. Cytoprotection against the STS-induced apoptosis conferred by the polymorphic HN5 variant, in which threonine in position 13 is replaced with isoleucine, is reduced compared to the wild type HN5 peptide.},
}
@article {pmid19483474,
year = {2009},
author = {Rigden, DJ and Michels, PA and Ginger, ML},
title = {Autophagy in protists: Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion.},
journal = {Autophagy},
volume = {5},
number = {6},
pages = {784-794},
doi = {10.4161/auto.8838},
pmid = {19483474},
issn = {1554-8635},
mesh = {Animals ; *Autophagy ; Eukaryotic Cells/*cytology ; Humans ; Mitochondria/*metabolism ; *Phylogeny ; Reproducibility of Results ; Saccharomyces cerevisiae/cytology ; },
abstract = {Autophagy describes the process by which eukaryotes selectively and nonselectively target cytoplasm and entire organelles for lysosomal or (in yeast) vacuolar degradation. More than 30 different proteins contribute to this complex process, and it is widely recognized that the term autophagy does not describe merely a single linear pathway by which intracellular components are routed for lysosomal degradation. Yet, while autophagy has been unequivocally demonstrated in evolutionarily diverse organisms and the importance of autophagy in many aspects of human health and development is becoming ever more apparent, the extent to which autophagy in different taxa draws on a conserved cohort of readily recognizable proteins is not particularly clear. Here, we address this issue by comprehensive mapping of known autophagy components across a taxonomically diverse range of unicellular eukaryotes. Unexpectedly, our analysis points to independent examples of secondary loss of macroautophagy, the best understood of the autophagy pathways, in two parasites and one extremophile. Additionally, while our data point towards autophagy being an ancient innovation, utilizing conserved core machinery, it is also clear that lineage-specific moderation (e.g., probable loss of Atg17 in some unikonts) and elaboration (paralogue expansion) of the core macroautophagy pathway occurs readily. Finally, we also consider the interplay between autophagy and organelle turnover in protists. Here, there are likely to be intriguing issues, as exemplified by mitochondrial turnover. In contrast to the dynamic mitochondrial fusion and fission observed in many eukaryotes (including yeast), cell cycle regulated division of a single mitochondrion occurs in some protists. Yet, in these organisms mitochondrial function can often be rapidly remodeled; we contend that in these species turnover of mitochondrial proteins is the product of intraorganellar protease activity.},
}
@article {pmid19494790,
year = {2009},
author = {Sapag, A and González-Martínez, G and Lobos-González, L and Encina, G and Tampier, L and Israel, Y and Quintanilla, ME},
title = {Polymorphisms in mitochondrial genes encoding complex I subunits are maternal factors of voluntary alcohol consumption in the rat.},
journal = {Pharmacogenetics and genomics},
volume = {19},
number = {7},
pages = {528-537},
doi = {10.1097/FPC.0b013e32832dc12a},
pmid = {19494790},
issn = {1744-6872},
mesh = {Alcohol Drinking/*genetics ; Amino Acids/genetics ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Computational Biology ; Electron Transport Complex I/chemistry/*genetics ; Exons/genetics ; Female ; Genes, Mitochondrial/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Protein Subunits/chemistry/*genetics ; Rats ; },
abstract = {OBJECTIVE: Alcohol is detoxified in the liver by oxidizing enzymes that require nicotinamide adenine dinucleotide (NAD+) such that, in the rat, the availability of NAD+ contributes to control voluntary ethanol intake. The UChA and UChB lines of Wistar rats drink low and high amounts of ethanol respectively and differ in the capacity of their mitochondria to oxidize NADH into NAD+. This function resides in complex I of the respiratory chain and its variation is linked to genes transmitted through the maternal line. The aim of this study was to identify the genetic basis for the difference in the reoxidation of NADH in these nondrinker (UChA) and drinker (UChB) rats.<br><br>METHODS: Seven mitochondrial genes and two chromosome X genes encoding complex I subunits from rats of both lineages were amplified from liver DNA and sequenced.<br><br>RESULTS: The UChA and UChB rat lines differ in their Nd2, Nd4, Nd5 and Nd6 mitochondrial genes and in the encoded proteins. Most noteworthy are ND2 and ND4 whose amino acid variations lead to changes in three-dimensional structure models. The ND2 proteins also differ in the number of predicted transmembrane domains. The Nd1 and Nd3 genes have silent substitutions, whereas Nd4L and the exonic sequences of the nuclear genes Ndufa1 and Ndufb11 show no differences between the UChA and UChB lines.<br><br>CONCLUSION: Amino acid variations in four complex I subunits encoded in the mitochondrial genome may contribute to explain the differences between UChA and UChB rats in their capacity to reoxidize NADH and in their alcohol intake, suggesting that mitochondrial genes may constitute maternal factors of alcoholism.},
}
@article {pmid19497865,
year = {2009},
author = {Liberles, SD and Horowitz, LF and Kuang, D and Contos, JJ and Wilson, KL and Siltberg-Liberles, J and Liberles, DA and Buck, LB},
title = {Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {24},
pages = {9842-9847},
pmid = {19497865},
issn = {1091-6490},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; In Situ Hybridization, Fluorescence ; Mice ; Neurons/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Receptors, Formyl Peptide/classification/genetics/*metabolism ; Vomeronasal Organ/cytology/*metabolism ; },
abstract = {The identification of receptors that detect environmental stimuli lays a foundation for exploring the mechanisms and neural circuits underlying sensation. The mouse vomeronasal organ (VNO), which detects pheromones and other semiochemicals, has 2 known families of chemoreceptors, V1Rs and V2Rs. Here, we report a third family of mouse VNO receptors comprising 5 of 7 members of the formyl peptide receptor (FPR) family. Unlike other FPRs, which function in the immune system, these FPRs are selectively expressed in VNO neurons in patterns strikingly similar to those of V1Rs and V2Rs. Each FPR is expressed in a different small subset of neurons that are highly dispersed in the neuroepithelium, consistently coexpress either G alpha(i2) or G alpha(o), and lack other chemoreceptors examined. Given the presence of formylated peptides in bacteria and mitochondria, possible roles for VNO FPRs include the assessment of conspecifics or other species based on variations in normal bacterial flora or mitochondrial proteins.},
}
@article {pmid19523874,
year = {2009},
author = {Cavalier-Smith, T and Lewis, R and Chao, EE and Oates, B and Bass, D},
title = {Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour.},
journal = {Protist},
volume = {160},
number = {3},
pages = {452-479},
doi = {10.1016/j.protis.2009.03.003},
pmid = {19523874},
issn = {1618-0941},
mesh = {Animals ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*physiology/*ultrastructure ; Genes, rRNA ; Microscopy ; Microscopy, Electron ; Molecular Sequence Data ; Organelles/*ultrastructure ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Unlike Helkesimastix faecicola and H. major, Helkesimastix marina is marine, ingests bacteria, is probably also a cannibal, and differs in cell cycle ciliary behaviour. Daughter kinetids have mirror symmetry; pre-division cilia beat asymmetrically. We sequenced its 18S rDNA and studied its ultrastructure to clarify its taxonomy. Helkesimastix (Helkesimastigidae fam. n.) differs unexpectedly radically from cercomonads, lacking their complex microtubular ciliary roots, grouping not with them but with Sainouridae within Pansomonadida. Longitudinal cortical microtubules emanate from a dense apical centrosomal plate, where a striated rhizoplast attaches the nucleus, and two very short subparallel centrioles attach by dense fibres. The marginally more posterior centriole, attached to the centrosomal plate by a dense forked fibre, bears the long 9+2 gliding posterior cilium and a microtubular root; the left-side, nucleus-attached, left centriole bears an immotile ciliary stump with abnormal axoneme of nine disorganized mainly singlet microtubules, unlike the sainourid anterior papilla. Both transitional regions have a proximal lattice, the posterior centriole with slender hub. Sainouroidea superfam. n. (Sainouridae; Helkesimastigidae) have homologous cytoskeletal geometry. Dorsal Golgi dictyosome and posterior microbody are attached to the nuclear envelope, which has slender micro-invaginations and probably a cortical lattice. Bacteria are digested posteriorly in association with numerous mitochondria with flat cristae.},
}
@article {pmid19535739,
year = {2009},
author = {Ramírez, O and Ojeda, A and Tomàs, A and Gallardo, D and Huang, LS and Folch, JM and Clop, A and Sánchez, A and Badaoui, B and Hanotte, O and Galman-Omitogun, O and Makuza, SM and Soto, H and Cadillo, J and Kelly, L and Cho, IC and Yeghoyan, S and Pérez-Enciso, M and Amills, M},
title = {Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds.},
journal = {Molecular biology and evolution},
volume = {26},
number = {9},
pages = {2061-2072},
doi = {10.1093/molbev/msp118},
pmid = {19535739},
issn = {1537-1719},
mesh = {Africa ; Animals ; *Breeding ; Chromosomes, Mammalian/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Europe ; Asia, Eastern ; Genetic Markers ; Geography ; Haplotypes ; Heterozygote ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; Sus scrofa/classification/*genetics ; Y Chromosome/*genetics ; },
abstract = {We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent.},
}
@article {pmid19535740,
year = {2009},
author = {Tofanelli, S and Bertoncini, S and Castrì, L and Luiselli, D and Calafell, F and Donati, G and Paoli, G},
title = {On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages.},
journal = {Molecular biology and evolution},
volume = {26},
number = {9},
pages = {2109-2124},
doi = {10.1093/molbev/msp120},
pmid = {19535740},
issn = {1537-1719},
mesh = {Asian People ; Black People/*genetics ; Chromosomes, Human, Y/genetics ; Computer Simulation ; DNA, Mitochondrial/genetics ; *Fathers ; Female ; *Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Humans ; Madagascar ; Male ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Mothers ; *Phylogeny ; Time Factors ; },
abstract = {The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelated individuals from inland (Merina) and coastal (Antandroy, Antanosy, and Antaisaka) ethnic groups. This allowed performance of a multilevel analysis in which the diversity among main ethnic divisions, lineage ancestries, and modes of inheritance could be concurrently evaluated. Admixture was confirmed to result from the encounter of African and Southeast Asian people with minor recent male contributions from Europe. However, new scenarios are depicted about Malagasy admixture history. The distribution of ancestral components was ethnic and sex biased, with the Asian ancestry appearing more conserved in the female than in the male gene pool and in inland than in coastal groups. A statistic based on haplotype sharing (D(HS)), showing low sampling error and time linearity over the last 200 generations, was introduced here for the first time and helped to integrate our results with linguistic and archeological data. The focus about the origin of Malagasy lineages was enlarged in space and pushed back in time. Homelands could not be pinpointed but appeared to comprise two vast areas containing different populations from sub-Saharan Africa and South East Asia. The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).},
}
@article {pmid19555461,
year = {2009},
author = {Gibellini, F and Hunter, WN and Smith, TK},
title = {The ethanolamine branch of the Kennedy pathway is essential in the bloodstream form of Trypanosoma brucei.},
journal = {Molecular microbiology},
volume = {73},
number = {5},
pages = {826-843},
pmid = {19555461},
issn = {1365-2958},
support = {/WT_/Wellcome Trust/United Kingdom ; 067441/WT_/Wellcome Trust/United Kingdom ; 083481/WT_/Wellcome Trust/United Kingdom ; 082596/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Blood/*parasitology ; DNA, Protozoan/chemistry/genetics ; Gene Knockout Techniques ; Genes, Essential ; Genes, Protozoan ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Phosphatidylethanolamines/*analysis ; Phylogeny ; RNA Nucleotidyltransferases/*genetics/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Spectrometry, Mass, Electrospray Ionization ; Trypanosoma brucei brucei/*chemistry/cytology/isolation &amp; purification/ultrastructure ; },
abstract = {Phosphatidylethanolamine (GPEtn), a major phospholipid component of trypanosome membranes, is synthesized de novo from ethanolamine through the Kennedy pathway. Here the composition of the GPEtn molecular species in the bloodstream form of Trypanosoma brucei is determined, along with new insights into phospholipid metabolism, by in vitro and in vivo characterization of a key enzyme of the Kennedy pathway, the cytosolic ethanolamine-phosphate cytidylyltransferase (TbECT). Gene knockout indicates that TbECT is essential for growth and survival, thus highlighting the importance of the Kennedy pathway for the pathogenic stage of the African trypanosome. Phosphatiylserine decarboxylation, a potential salvage pathway, does not appear to be active in cultured bloodstream form T. brucei, and it is not upregulated even when the Kennedy pathway is disrupted. In vivo metabolic labelling and phospholipid composition analysis by ESI-MS/MS of the knockout cells confirmed a significant decrease in GPEtn species, as well as changes in the relative abundance of other phospholipid species. Reduction in GPEtn levels had a profound influence on the morphology of the mutants and it compromised mitochondrial structure and function, as well as glycosylphosphatidylinositol anchor biosynthesis. TbECT is therefore genetically validated as a potential drug target against the African trypanosome.},
}
@article {pmid19578062,
year = {2009},
author = {Oberto, J and Breuil, N and Hecker, A and Farina, F and Brochier-Armanet, C and Culetto, E and Forterre, P},
title = {Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance.},
journal = {Nucleic acids research},
volume = {37},
number = {16},
pages = {5343-5352},
pmid = {19578062},
issn = {1362-4962},
mesh = {Animals ; Bacterial Proteins/classification/genetics ; Caenorhabditis elegans/genetics/ultrastructure ; Caenorhabditis elegans Proteins/genetics/*physiology ; DNA, Mitochondrial/analysis ; Escherichia coli Proteins/genetics ; Ethidium/pharmacology ; Genes, Lethal ; *Genome, Mitochondrial ; Longevity ; Mitochondria/ultrastructure ; Mitochondrial Proteins/classification/genetics/*physiology ; Mutation ; Oxidative Stress ; Phylogeny ; Saccharomyces cerevisiae/genetics/ultrastructure ; Saccharomyces cerevisiae Proteins/genetics/*physiology ; },
abstract = {Yeast Qri7 and human OSGEPL are members of the orthologous Kae1(OSGEP)/YgjD protein family, the last class of universally conserved proteins without assigned function. Phylogenetic analyses indicate that the eukaryotic Qri7(OSGEPL) proteins originated from bacterial YgjD proteins. We have recently shown that the archaeal Kae1 protein is a DNA-binding protein that exhibits apurinic endonuclease activity in vitro. We show here that the Qri7/OSGEPL proteins localize in mitochondria and are involved in mitochondrial genome maintenance in two model eukaryotic organisms, Saccharomyces cerevisiae and Caenorhabditis elegans. Furthermore, S. cerevisiae Qri7 complements the loss of the bacterial YgjD protein in Escherichia coli, suggesting that Qri7/OSGEPL and YgjD proteins have retained similar functions in modern organisms. We suggest to name members of the Kae1(OSGEP)/YgjD family UGMP, for Universal Genome Maintenance Proteins.},
}
@article {pmid19589724,
year = {2009},
author = {Bass, D and Howe, AT and Mylnikov, AP and Vickerman, K and Chao, EE and Edwards Smallbone, J and Snell, J and Cabral, C and Cavalier-Smith, T},
title = {Phylogeny and classification of Cercomonadida (Protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov.},
journal = {Protist},
volume = {160},
number = {4},
pages = {483-521},
doi = {10.1016/j.protis.2009.01.004},
pmid = {19589724},
issn = {1618-0941},
mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Eukaryota/*classification/cytology/genetics ; Genes, rRNA ; Microscopy, Electron, Scanning ; Microscopy, Interference ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; },
abstract = {Cercomonads (=Cercomonadida) are biflagellate gliding bacterivorous protozoa, abundant and diverse in soil and freshwater. We establish 56 new species based on 165 cultures, differential interference contrast microscopy, and 18S and ITS2 rDNA sequencing, and a new genus Cavernomonas studied by scanning electron microscopy. We fundamentally revise the phylogeny and classification of cercomonad Cercozoa. We describe 40 Cercomonas species (35 novel), six Eocercomonas (five novel), two Cavernomonas, and 18 Paracercomonas species (14 novel). We obtained additional cercomonad clade A (Cercomonas, Eocercomonas, Cavernomonas) sequences from multiple environmental DNA libraries. The most commonly cultivated genotypes are not the commonest in environmental DNA, suggesting that cercomonad ecology is far more complex than implied by laboratory cultures. Cercomonads have never been isolated from saline environments, although some species can grow in semi-saline media in the laboratory, and environmental DNA libraries regularly detect them in coastal marine sediments. The first ultrastructural study of an anaerobic cercozoan, Paracercomonas anaerobica sp. nov., a highly divergent cercomonad, shows much simpler ciliary roots than in clade A cercomonads, a ciliary hub-lattice and axosome, and mitochondria with tubular cristae, consistent with it being only facultatively anaerobic. We also describe Agitata tremulans gen. et sp. nov., previously misidentified as Cercobodo (=Dimastigamoeba) agilis Moroff.},
}
@article {pmid19602081,
year = {2009},
author = {Visvesvara, GS and Sriram, R and Qvarnstrom, Y and Bandyopadhyay, K and Da Silva, AJ and Pieniazek, NJ and Cabral, GA},
title = {Paravahlkampfia francinae n. sp. masquerading as an agent of primary amoebic meningoencephalitis.},
journal = {The Journal of eukaryotic microbiology},
volume = {56},
number = {4},
pages = {357-366},
doi = {10.1111/j.1550-7408.2009.00410.x},
pmid = {19602081},
issn = {1550-7408},
support = {5P30 NS047463/NS/NINDS NIH HHS/United States ; },
mesh = {Adolescent ; Amphotericin B/administration &amp; dosage ; Animals ; Antiprotozoal Agents/administration &amp; dosage ; Central Nervous System Protozoal Infections/*parasitology ; DNA, Protozoan/analysis/genetics ; Genes, rRNA ; Humans ; Male ; Mice ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Protozoan Infections/*parasitology ; Schizopyrenida/drug effects/*pathogenicity/*physiology/*ultrastructure ; Species Specificity ; Virulence ; },
abstract = {Paravahlkampfia francinae n. sp., a new species of the free-living amoeba genus Paravahlkampfia, designated as CDC:V595, was isolated from the cerebrospinal fluid of a patient with headache, sore throat, and vomiting, typical symptoms of primary amoebic meningoencephalitis (PAM) caused by Naegleria fowleri. The isolate grew at 33 degrees C, 37 degrees C, 40 degrees C, and 42 degrees C and destroyed mammalian cell cultures. However, it did not kill young mice upon intranasal inoculation. P. francinae does not produce flagellates and does not grow on agar plates coated with Gram-negative bacteria such as Escherichia coli, the usual food source of Paravahlkampfia ustiana, the type species of the genus. The trophozoite at light microscopy exhibited eruptive locomotion and possessed a single vesicular nucleus. Ultrastructurally, the trophozoites had numerous mitochondria with discoidal cristae but did not have a Golgi apparatus. The trophozoites differentiated into cysts after consuming most of the monolayer. The cyst had an inner well-differentiated endocyst and an outer thin, wrinkled, and wavy ectocyst with no pores. During excystation trophozoites ruptured the cyst wall and emerged from the cysts. A unique feature seen in the cysts was the presence of bacterial endosymbionts, both in the endoplasm and within the cyst wall. Full-length sequencing analysis of the 18S and 5.8S RNA genes of P. francinae showed that they were distinct from those of other Paravahlkampfia species. The patient recovered within a few days indicating that some of the previously reported cases of PAM that survived may have been due to P. francinae.},
}
@article {pmid19602083,
year = {2009},
author = {Park, JS and Kolisko, M and Heiss, AA and Simpson, AG},
title = {Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. g., n. sp., a deep-branching relative of diplomonads.},
journal = {The Journal of eukaryotic microbiology},
volume = {56},
number = {4},
pages = {373-384},
doi = {10.1111/j.1550-7408.2009.00412.x},
pmid = {19602083},
issn = {1550-7408},
mesh = {Animals ; DNA, Protozoan/analysis/genetics ; *Diplomonadida/classification/genetics/ultrastructure ; Flagella/ultrastructure ; Genes, rRNA ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We describe Hicanonectes teleskopos n. g., n. sp., a heterotrophic flagellate isolated from low-oxygen marine sediment. Hicanonectes teleskopos has a ventral groove and two unequal flagella, and rapidly rotates during swimming. At the ultrastructural level H. teleskopos is a "typical excavate": it displays flagellar vanes, a split right microtubular root, "I,""B," and "C" fibres, a singlet microtubular root, and a possible composite fibre. Small subunit rRNA (SSU rRNA) gene phylogenies and an "arched" B fibre demonstrate that H. teleskopos belongs to Fornicata (i.e. diplomonads, retortamonads, and relatives). It forms a clade with the deep-branching fornicate Carpediemonas, with moderate-to-strong bootstrap support, although their SSU rRNA gene sequences are quite dissimilar. Hicanonectes differs from Carpediemonas in cell shape, swimming behaviour, number of basal bodies (i.e. 4 vs. 3), number of flagellar vanes (i.e. 2 vs. 3), anterior root organization, and by having a cytopharynx. Like Carpediemonas and Dysnectes, Hicanonectes has conspicuous mitochondrion-like organelles that lack cristae and superficially resemble the hydrogenosomes of parabasalids, rather than the mitosomes of their closer relatives the diplomonads (e.g. Giardia).},
}
@article {pmid19607930,
year = {2009},
author = {Monteiro-Vitorello, CB and Hausner, G and Searles, DB and Gibb, EA and Fulbright, DW and Bertrand, H},
title = {The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {46},
number = {11},
pages = {837-848},
doi = {10.1016/j.fgb.2009.07.005},
pmid = {19607930},
issn = {1096-0937},
mesh = {Ascomycota/*genetics ; DNA, Mitochondrial/*genetics ; Endonucleases/metabolism ; *Genes, Fungal ; Introns ; Mitochondria/*genetics ; Phylogeny ; Plasmids ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; },
abstract = {The mt-rns gene of Cryphonectria parasitica is 9872bp long and includes two group I and two group II introns. An analysis of intronic protein-encoding sequences revealed that LAGLIDADG ORFs, which usually are associated with group I introns, were transferred at least twice into group II introns. A plasmid-like mitochondrial element (plME) that appears in high amounts in previously mutagen-induced mit1 and mit2 hypovirulent mutants of the Ep155 standard virulent strain of C. parasitica was found to be derived from a short region of the mt-rns gene, including the exon 1 and most of the first intron. The plME is a 4.2-kb circular, multimeric DNA and an autonomously-replicating mtDNA fragment. Although sexual transmission experiments indicate that the plME does not directly cause hypovirulence, its emergence is one manifestation of the many complex molecular and genetic events that appear to underlie this phenotype.},
}
@article {pmid19632785,
year = {2009},
author = {Wu, SG and Wang, GT and Xi, BW and Xiong, F and Liu, T and Nie, P},
title = {Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene.},
journal = {Veterinary parasitology},
volume = {164},
number = {2-4},
pages = {248-256},
doi = {10.1016/j.vetpar.2009.04.030},
pmid = {19632785},
issn = {1873-2550},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics/metabolism ; Fish Diseases/epidemiology ; Fishes ; Gene Expression Regulation/physiology ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Spirurida/*enzymology/*genetics ; Spirurida Infections/veterinary ; },
abstract = {The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the approximately 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst=0.70, P<0.00001; Nm=0.21) and Minjiang River (Fst=0.73, P<0.00001; Nm=0.18) groups, while low Fst value (Fst=0.018, P>0.05) and high rate of migration (Nm=28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (<or=0.12) and high Nm values (>3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst>or=0.59; Nm<1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage.},
}
@article {pmid19656201,
year = {2009},
author = {Wriessnegger, T and Sunga, AJ and Cregg, JM and Daum, G},
title = {Identification of phosphatidylserine decarboxylases 1 and 2 from Pichia pastoris.},
journal = {FEMS yeast research},
volume = {9},
number = {6},
pages = {911-922},
doi = {10.1111/j.1567-1364.2009.00544.x},
pmid = {19656201},
issn = {1567-1364},
support = {P 21429/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Amino Acid Sequence ; Carboxy-Lyases/*genetics/*metabolism ; Cell Membrane/chemistry ; Fatty Acids/analysis ; Gene Deletion ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Molecular Sequence Data ; Phosphatidylethanolamines/*metabolism ; Phylogeny ; Pichia/chemistry/*enzymology/genetics/growth &amp; development ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; },
abstract = {Genetic manipulation of lipid biosynthetic enzymes allows modification of cellular membranes. We made use of this strategy and constructed mutants in phospholipid metabolism of Pichia pastoris, which is widely used in biotechnology for expression of heterologous proteins. Here we describe identification of two P. pastoris phosphatidylserine decarboxylases (PSDs) encoded by genes homologous to PSD1 and PSD2 from Saccharomyces cerevisiae. Using P. pastoris psd1Delta and psd2Delta mutants we investigated the contribution of the respective gene products to phosphatidylethanolamine synthesis, membrane composition and cell growth. Deletion of PSD1 caused loss of PSD activity in mitochondria, a severe growth defect on minimal media and depletion of cellular and mitochondrial phosphatidylethanolamine levels. This defect could not be compensated by Psd2p, but by supplementation with ethanolamine, which is the substrate for the cytidine diphosphate (CDP)-ethanolamine pathway, the third route of phosphatidylethanolamine synthesis in yeast. Fatty acid analysis showed selectivity of both Psd1p and Psd2p in vivo for the synthesis of unsaturated phosphatidylethanolamine species. Phosphatidylethanolamine species containing palmitic acid (16:0), however, were preferentially assembled into mitochondria. In summary, this study provides first insight into membrane manipulation of P. pastoris, which may serve as a useful method to modify cell biological properties of this microorganism for biotechnological purposes.},
}
@article {pmid19679512,
year = {2009},
author = {Holmes, RS and Goldberg, E},
title = {Computational analyses of mammalian lactate dehydrogenases: human, mouse, opossum and platypus LDHs.},
journal = {Computational biology and chemistry},
volume = {33},
number = {5},
pages = {379-385},
pmid = {19679512},
issn = {1476-928X},
support = {R01 HD005863/HD/NICHD NIH HHS/United States ; HD05863/HD/NICHD NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; *Computer Simulation ; Databases, Genetic ; Humans ; Lactate Dehydrogenases/*genetics ; Mice ; *Models, Genetic ; Molecular Sequence Data ; *Opossums/genetics ; Phylogeny ; *Platypus/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; },
abstract = {Computational methods were used to predict the amino acid sequences and gene locations for mammalian lactate dehydrogenase (LDH) genes and proteins using genome sequence databanks. Human LDHA, LDHC and LDH6A genes were located in tandem on chromosome 11, while LDH6B and LDH6C genes were on chromosomes 15 and 12, respectively. Opossum LDHC and LDH6B genes were located in tandem with the opossum LDHA gene on chromosome 5 and contained 7 (LDHA and LDHC) or 8 (LDH6B) exons. An amino acid sequence prediction for the opossum LDH6B subunit gave an extended N-terminal sequence, similar to the human and mouse LDH6B sequences, which may support the export of this enzyme into mitochondria. The platypus genome contained at least 3 LDH genes encoding LDHA, LDHB and LDH6B subunits. Phylogenetic studies and sequence analyses indicated that LDHA, LDHB and LDH6B genes are present in all mammalian genomes examined, including a monotreme species (platypus), whereas the LDHC gene may have arisen more recently in marsupial mammals.},
}
@article {pmid19683530,
year = {2010},
author = {Týc, J and Faktorová, D and Kriegová, E and Jirků, M and Vávrová, Z and Maslov, DA and Lukes, J},
title = {Probing for primary functions of prohibitin in Trypanosoma brucei.},
journal = {International journal for parasitology},
volume = {40},
number = {1},
pages = {73-83},
doi = {10.1016/j.ijpara.2009.07.008},
pmid = {19683530},
issn = {1879-0135},
mesh = {Animals ; DNA, Mitochondrial/genetics/metabolism ; Membrane Potentials ; *Mitochondria/metabolism/ultrastructure ; Phylogeny ; Prohibitins ; *Protein Biosynthesis ; Protozoan Proteins/genetics/metabolism ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; *Trypanosoma brucei brucei/genetics/growth &amp; development/metabolism/ultrastructure ; },
abstract = {Prohibitins (PHBs) 1 and 2 are small conserved proteins implicated in a number of functions in the mitochondrion, as well as in the nucleus of eukaryotic cells. The current understanding of PHB functions comes from studies of model organisms such as yeast, worm and mouse, but considerable debate remains with regard to the primary functions of these ubiquitous proteins. We exploit the tractable reverse genetics of Trypanosoma brucei, the causative agent of African sleeping sickness, in order to specifically analyse the function of PHB in this highly divergent eukaryote. Using inducible RNA interference (RNAi) we show that PHB1 is essential in T. brucei, where it is confined to the cell's single mitochondrion forming a high molecular weight complex. PHB1 and PHB2 appear to be indispensible for mitochondrial translation. Their ablation leads to a decrease in mitochondrial membrane potential, however no effect on the level of reactive oxygen species was observed. Flagellates lacking either PHB1 or both PHB1 and PHB2 exhibit significant morphological changes of their organelle, most notably its inflation. Even long after the loss of the PHB proteins, mtDNA was unaltered and mitochondrial cristae remained present, albeit displaced to the periphery of the mitochondrion, which is in contrast to other eukaryotes.},
}
@article {pmid19691417,
year = {2010},
author = {Iezhova, TA and Valkiūnas, G and Loiseau, C and Smith, TB and Sehgal, RN},
title = {Haemoproteus cyanomitrae sp. nov. (Haemosporida: Haemoproteidae) from a widespread African songbird, the olive sunbird, Cyanomitra olivacea.},
journal = {The Journal of parasitology},
volume = {96},
number = {1},
pages = {137-143},
doi = {10.1645/GE-2198.1},
pmid = {19691417},
issn = {1937-2345},
mesh = {Animals ; Bayes Theorem ; Bird Diseases/epidemiology/*parasitology ; Cameroon/epidemiology ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/isolation &amp; purification ; Erythrocytes/parasitology ; Ghana/epidemiology ; Haemosporida/*classification/genetics/growth &amp; development ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Alignment/veterinary ; Songbirds/*parasitology ; Trees ; Tropical Climate ; },
abstract = {Haemoproteus (Parahaemoproteus) cyanomitrae n. sp. (Haemosporida: Haemoproteidae) was found in the olive sunbird, Cyanomitra olivacea (Nectariniidae), in rain forests of tropical Africa. It is described based on the morphology of its blood stages and a segment of the mitochondrial cytochrome b gene (GenBank accession FJ404696), which can be used for molecular identification and diagnosis of this species. Fully grown gametocytes of new parasite are similar to many other species of haemoproteids of passeriform birds, so are not easily distinguishable from many of them at this stage of their development. Haemoproteus cyanomitrae can be readily distinguished from the majority of described species of avian haemoproteids, primarily due to its growing dumbbell-shaped gametocytes and advanced halteridial gametocytes, both of which do not touch the envelope of infected erythrocytes along their entire margin. Pigment granules are most frequently clamped in 1, or several, groups in gametocytes, with larger group of pigment granules usually located close to one end of the gametocyte; asymmetric position of pigment granules in gametocytes a characteristic feature of this parasite. Illustrations of blood stages of the new species are given, and phylogenetic analysis identifies DNA lineages closely related to this parasite, which is widespread in African rain forests, but has been recorded only in the olive sunbird so far. It is probable that H. cyanomitrae is transmitted throughout the range of the olive sunbird in Africa.},
}
@article {pmid19699241,
year = {2009},
author = {de Miguel, N and Braun, N and Bepperling, A and Kriehuber, T and Kastenmüller, A and Buchner, J and Angel, SO and Haslbeck, M},
title = {Structural and functional diversity in the family of small heat shock proteins from the parasite Toxoplasma gondii.},
journal = {Biochimica et biophysica acta},
volume = {1793},
number = {11},
pages = {1738-1748},
doi = {10.1016/j.bbamcr.2009.08.005},
pmid = {19699241},
issn = {0006-3002},
mesh = {Amino Acid Motifs/physiology ; Animals ; Heat-Shock Proteins, Small/*genetics/metabolism ; *Phylogeny ; Protein Structure, Quaternary/physiology ; Protozoan Proteins/*genetics/metabolism ; Structure-Activity Relationship ; Toxoplasma/*genetics/metabolism ; },
abstract = {Small heat shock proteins (sHsps) are ubiquitous molecular chaperones which prevent the nonspecific aggregation of non-native proteins. Five potential sHsps exist in the parasite Toxoplasma gondii. They are located in different intracellular compartments including mitochondria and are differentially expressed during the parasite's life cycle. Here, we analyzed the structural and functional properties of all five proteins. Interestingly, this first in vitro characterization of sHsps from protists showed that all T. gondii sHsps exhibit the characteristic properties of sHsps such as oligomeric structure and chaperone activity. However, differences in their quaternary structure and in their specific chaperone properties exist. On the structural level, the T. gondii sHsps can be divided in small (12-18 subunits) and large (24-32 subunits) oligomers. Furthermore, they differ in their interaction with non-native proteins. While some bind substrates tightly, others interact more transiently. The chaperone activity of the three more mono-disperse T. gondii sHsps is regulated by temperature with a decrease in temperature leading to the activation of chaperone activity, suggesting an adaption to specific steps of the parasite's life cycle.},
}
@article {pmid19717741,
year = {2009},
author = {Rada, P and Smíd, O and Sutak, R and Dolezal, P and Pyrih, J and Zársky, V and Montagne, JJ and Hrdy, I and Camadro, JM and Tachezy, J},
title = {The monothiol single-domain glutaredoxin is conserved in the highly reduced mitochondria of Giardia intestinalis.},
journal = {Eukaryotic cell},
volume = {8},
number = {10},
pages = {1584-1591},
pmid = {19717741},
issn = {1535-9786},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Giardia lamblia/*metabolism ; Glutaredoxins/*chemistry ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Phylogeny ; Sequence Alignment ; },
abstract = {The highly reduced mitochondria (mitosomes) of Giardia intestinalis are recently discovered organelles for which, it was suggested, iron-sulfur cluster assembly was their only conserved function. However, only an incomplete set of the components required for FeS cluster biogenesis was localized to the mitosomes. Via proteomic analysis of a mitosome-rich cellular fraction together with immunofluorescence microscopy, we identified a novel mitosomal protein homologous to monothiol glutaredoxins containing a CGFS motif at the active site. Sequence analysis revealed the presence of long nonconserved N-terminal extension of 77 amino acids, which was absent in the mature protein. Expression of the complete and N-terminally truncated forms of the glutaredoxin indicated that the extension is involved in glutaredoxin import into mitosomes. However, the mechanism of preprotein processing is unclear, as the mitosomal processing peptidase is unable to cleave this type of extension. The recombinant mature protein was shown to form a homodimeric structure, which binds a labile FeS cluster. The cluster is stabilized by glutathione and dithiothreitol. Phylogenetic analysis showed that giardial glutaredoxin is related to the mitochondrial monothiol glutaredoxins involved in FeS cluster assembly. The identification of a mitochondrial-type monothiol glutaredoxin in the mitosomes of G. intestinalis thus completes the mitosomal FeS cluster biosynthetic pathway and provides further evidence for the mitochondrial origin of these organelles.},
}
@article {pmid19732154,
year = {2009},
author = {Beninati, T and Riegler, M and Vilcins, IM and Sacchi, L and McFadyen, R and Krockenberger, M and Bandi, C and O'Neill, SL and Lo, N},
title = {Absence of the symbiont Candidatus Midichloria mitochondrii in the mitochondria of the tick Ixodes holocyclus.},
journal = {FEMS microbiology letters},
volume = {299},
number = {2},
pages = {241-247},
doi = {10.1111/j.1574-6968.2009.01757.x},
pmid = {19732154},
issn = {1574-6968},
mesh = {Alphaproteobacteria/*isolation &amp; purification/*physiology ; Animals ; Australia ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Ixodes/*microbiology/*physiology ; Male ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; },
abstract = {Candidatus Midichloria mitochondrii (M. mitochondrii) belongs to a novel clade of bacteria within the order Rickettsiales. Recent PCR-based screening studies indicate that it is present in a number of blood-sucking arthropods, as well as the blood of some vertebrates. Its medical and veterinary significance remains to be determined. Electron microscopic examinations of M. mitochondrii have thus far been conducted on two infected tick species. Remarkably, the bacterium was found in abundance within the mitochondria of the ovarian cells of each tick species. This makes it the only characterized bacterium able to invade the mitochondria of any multicellular organism. To examine whether mitochondrial invasion is a consistent characteristic of M. mitochondrii, we examined two tick species found in Eastern Australia. One of these species, Ixodes holocyclus, was infected with two M. mitochondrii strains; however, no bacteria were seen in the mitochondria. Comparative studies involving these strains may shed light on the unique phenomenon of mitochondrial invasion.},
}
@article {pmid19744143,
year = {2009},
author = {Lei, CZ and Su, R and Bower, MA and Edwards, CJ and Wang, XB and Weining, S and Liu, L and Xie, WM and Li, F and Liu, RY and Zhang, YS and Zhang, CM and Chen, H},
title = {Multiple maternal origins of native modern and ancient horse populations in China.},
journal = {Animal genetics},
volume = {40},
number = {6},
pages = {933-944},
doi = {10.1111/j.1365-2052.2009.01950.x},
pmid = {19744143},
issn = {1365-2052},
mesh = {Animals ; China ; DNA, Mitochondrial/analysis ; Horses/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.},
}
@article {pmid19750009,
year = {2009},
author = {Hou, Y and Lin, S},
title = {Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.},
journal = {PloS one},
volume = {4},
number = {9},
pages = {e6978},
pmid = {19750009},
issn = {1932-6203},
mesh = {Chloroplasts/metabolism ; Dinoflagellida ; Eukaryota/genetics ; Expressed Sequence Tags ; Gene Dosage ; *Genome ; Mitochondria/metabolism ; Models, Genetic ; Phylogeny ; Proteins/genetics ; Regression Analysis ; Sequence Analysis, DNA/methods ; },
abstract = {The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10)-transformed protein-coding gene number (Y') versus log(10)-transformed genome size (X', genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p<0.001, R(2)>0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6) kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245x10(6) kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.},
}
@article {pmid19766093,
year = {2010},
author = {Luévano-Martínez, LA and Moyano, E and de Lacoba, MG and Rial, E and Uribe-Carvajal, S},
title = {Identification of the mitochondrial carrier that provides Yarrowia lipolytica with a fatty acid-induced and nucleotide-sensitive uncoupling protein-like activity.},
journal = {Biochimica et biophysica acta},
volume = {1797},
number = {1},
pages = {81-88},
doi = {10.1016/j.bbabio.2009.09.003},
pmid = {19766093},
issn = {0006-3002},
mesh = {Biological Transport ; Fatty Acids/pharmacology ; Guanosine Diphosphate/metabolism ; Ion Channels/metabolism ; Membrane Potentials/physiology ; Mitochondria/*metabolism/physiology ; Mitochondrial Proteins/metabolism ; *Oxygen Consumption ; Phylogeny ; Succinates/metabolism ; Sulfates/metabolism ; Uncoupling Protein 1 ; Vancomycin/pharmacology ; Yarrowia/*metabolism ; },
abstract = {Uncoupling proteins (UCPs) are mitochondrial carriers distributed throughout the eukaryotic kingdoms. While genes coding for UCPs have been identified in plants and animals, evidences for the presence of UCPs in fungi and protozoa are only functional. Here, it is reported that in the yeast Yarrowia lipolytica there is a fatty acid-promoted and GDP-sensitive uncoupling activity indicating the presence of a UCP. The uncoupling activity is higher in the stationary phase than in the mid-log growth phase. The in silico search on the Y. lipolytica genome led to the selection of two genes with the highest homology to the UCP family, XM_503525 and XM_500457. By phylogenetic analysis, XP_503525 was predicted to be an oxaloacetate carrier while XP_500457 would be a dicarboxylate carrier. Each of these two genes was cloned and heterologously expressed in Saccharomyces cerevisiae and the resulting phenotype was analyzed. The transport activity of the two gene products confirmed the phylogenetic predictions. In addition, only mitochondria isolated from yeasts expressing XP_503525 showed bioenergetic properties characteristic of a UCP: the proton conductance was increased by linoleic acid and inhibited by GDP. It is concluded that the XM_503525 gene from Y. lipolytica encodes for an oxaloacetate carrier although, remarkably, it also displays an uncoupling activity stimulated by fatty acids and inhibited by nucleotides.},
}
@article {pmid19767615,
year = {2009},
author = {Messmer, M and Pütz, J and Suzuki, T and Suzuki, T and Sauter, C and Sissler, M and Catherine, F},
title = {Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.},
journal = {Nucleic acids research},
volume = {37},
number = {20},
pages = {6881-6895},
pmid = {19767615},
issn = {1362-4962},
mesh = {Base Sequence ; Databases, Nucleic Acid ; Humans ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry/*metabolism ; RNA, Mitochondrial ; RNA, Transfer, Asp/*chemistry/*metabolism ; Transcription, Genetic ; },
abstract = {Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNA(Asp) in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNA(Asp) including predominantly the cloverleaf. On the contrary, the native tRNA(Asp) folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis-Westhof interactions, the tertiary network core building rules apply to all tRNA(Asp) from mammalian mitochondria.},
}
@article {pmid19805190,
year = {2009},
author = {Stonebloom, S and Burch-Smith, T and Kim, I and Meinke, D and Mindrinos, M and Zambryski, P},
title = {Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {40},
pages = {17229-17234},
pmid = {19805190},
issn = {1091-6490},
support = {R56 GM045244/GM/NIGMS NIH HHS/United States ; GM45244/GM/NIGMS NIH HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM045244/GM/NIGMS NIH HHS/United States ; HG-000205/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Biological Transport ; DEAD-box RNA Helicases/classification/genetics/*metabolism ; Flowers/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified ; Plasmodesmata/*metabolism ; Protons ; Reactive Oxygen Species/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/metabolism ; Sequence Homology, Amino Acid ; Nicotiana/genetics/metabolism ; },
abstract = {Plants have intercellular channels, plasmodesmata (PD), that span the cell wall to enable cell-to-cell transport of micro- and macromolecules. We identified an Arabidopsis thaliana embryo lethal mutant increased size exclusion limit 1 (ise1) that results in increased PD-mediated transport of fluorescent tracers. The ise1 mutants have a higher frequency of branched and twinned PD than wild-type embryos. Silencing of ISE1 in mature Nicotiana benthamiana leaves also leads to increased PD transport, as monitored by intercellular movement of a GFP fusion to the tobacco mosaic virus movement protein. ISE1 encodes a putative plant-specific DEAD-box RNA helicase that localizes specifically to mitochondria. The N-terminal 100 aa of ISE1 specify mitochondrial targeting. Mitochondrial metabolism is compromised severely in ise1 mutant embryos, because their mitochondrial proton gradient is disrupted and reactive oxygen species production is increased. Although mitochondria are essential for numerous cell-autonomous functions, the present studies demonstrate that mitochondrial function also regulates the critical cell non-cell-autonomous function of PD.},
}
@article {pmid19806442,
year = {2009},
author = {Atamna, H},
title = {Amino acids variations in amyloid-beta peptides, mitochondrial dysfunction, and new therapies for Alzheimer's disease.},
journal = {Journal of bioenergetics and biomembranes},
volume = {41},
number = {5},
pages = {457-464},
pmid = {19806442},
issn = {1573-6881},
mesh = {Alzheimer Disease/etiology/*metabolism/therapy ; Amino Acid Sequence ; Amyloid beta-Peptides/*chemistry/genetics/*metabolism ; Animals ; Brain/metabolism ; Electron Transport Complex IV/metabolism ; Genetic Variation ; Heme/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {Soluble oligomers and/or aggregates of Amyloid-beta (Abeta) are viewed by many as the principal cause for neurodegeneration in Alzheimer's disease (AD). However, the mechanism by which Abeta and its aggregates cause neurodegeneration is not clear. The toxicity of Abeta has been attributed to its hydrophobicity. However, many specific mitochondrial cytopathologies e.g., loss of complex IV, loss of iron homeostasis, or oxidative damage cannot be explained by Abeta's hydrophobicity. In order to understand the role of Abeta in these cytopathologies we hypothesized that Abeta impairs specific metabolic pathways. We focused on heme metabolism because it links iron, mitochondria, and Abeta. We generated experimental evidence showing that Abeta alters heme metabolism in neuronal cells. Furthermore, we demonstrated that Abeta binds to and depletes intracellular regulatory heme (forming an Abeta-heme complex), which provides a strong molecular connection between Abeta and heme metabolism. We showed that heme depletion leads to key cytopathologies identical to those seen in AD including loss of iron homeostasis and loss of mitochondrial complex IV. Abeta-heme exhibits a peroxidase-like catalytic activity, which catalytically accelerates oxidative damage. Interestingly, the amino acids sequence of rodent Abeta (roAbeta) and human Abeta (huAbeta) is identical except for three amino acids within the hydrophilic region, which is also the heme-binding motif that we identified. We found that huAbeta, unlike roAbeta, binds heme tightly and forms a peroxidase. Although, roAbeta and huAbeta equally form fibrils and aggregates, rodents do not develop AD-like neuropathology. These findings led us to propose a new mechanism for mitochondrial dysfunction and huAbeta's neurotoxicity. This mechanism prompted the development of methylene blue (MB), which increased heme synthesis, complex IV, and mitochondrial function. Thus, MB may delay the onset and progression of AD and serve as a lead to develop novel drugs to treat AD.},
}
@article {pmid19818876,
year = {2010},
author = {Lu, J and Qian, Y and Li, Z and Yang, A and Zhu, Y and Li, R and Yang, L and Tang, X and Chen, B and Ding, Y and Li, Y and You, J and Zheng, J and Tao, Z and Zhao, F and Wang, J and Sun, D and Zhao, J and Meng, Y and Guan, MX},
title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the deafness-associated 12S rRNA 1555A&gt;G mutation.},
journal = {Mitochondrion},
volume = {10},
number = {1},
pages = {69-81},
pmid = {19818876},
issn = {1872-8278},
support = {R01 DC007696/DC/NIDCD NIH HHS/United States ; R01 DC005230/DC/NIDCD NIH HHS/United States ; R01DC07696/DC/NIDCD NIH HHS/United States ; R01DC05230/DC/NIDCD NIH HHS/United States ; R03 DC004958/DC/NIDCD NIH HHS/United States ; },
mesh = {Adolescent ; Aminoglycosides/adverse effects ; Base Sequence ; Child ; Child, Preschool ; China ; DNA, Mitochondrial/*genetics ; Deafness/chemically induced/*genetics/*physiopathology ; Haplotypes/*genetics ; Hearing Loss/chemically induced/genetics/physiopathology ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; *Mutation ; Phenotype ; Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {Mitochondrial 12S rRNA 1555A>G mutation is one of the important causes of aminoglycoside-induced and nonsyndromic deafness. Our previous investigations showed that the A1555G mutation was a primary factor underlying the development of deafness but was insufficient to produce deafness phenotype. However, it has been proposed that mitochondrial haplotypes modulate the phenotypic manifestation of the 1555A>G mutation. Here, we performed systematic and extended mutational screening of 12S rRNA gene in a cohort of 1742 hearing-impaired Han Chinese pediatric subjects from Zhejiang Province, China. Among these, 69 subjects with aminoglycoside-induced and nonsyndromic deafness harbored the homoplasmic 1555A>G mutation. These translated to a frequency of approximately 3.96% for the 1555A>G mutation in this hearing-impaired population. Clinical and genetic characterizations of 69 Chinese families carrying the 1555A>G mutation exhibited a wide range of penetrance and expressivity of hearing impairment. The average penetrances of deafness were 29.5% and 17.6%, respectively, when aminoglycoside-induced hearing loss was included or excluded. Furthermore, the average age-of-onset for deafness without aminoglycoside exposure ranged from 5 and 30years old, with the average of 14.5years. Their mitochondrial genomes exhibited distinct sets of polymorphisms belonging to ten Eastern Asian haplogroups A, B, C, D, F, G, M, N, R and Y, respectively. These indicated that the 1555A>G mutation occurred through recurrent origins and founder events. The haplogroup D accounted for 40.6% of the patient's mtDNA samples but only 25.8% of the Chinese control mtDNA samples. Strikingly, these Chinese families carrying mitochondrial haplogroup B exhibited higher penetrance and expressivity of hearing loss. In addition, the mitochondrial haplogroup specific variants: 15927G>A of haplogroup B5b, 12338T>C of haplogroup F2, 7444G>A of haplogroup B4, 5802T>C, 10454T>C, 12224C>T and 11696G>A of D4 haplogroup, 5821G>A of haplogroup C, 14693A>G of haplogroups Y2 and F, and 15908T>C of Y2 may enhance the penetrace of hearing loss in these Chinese families. Moreover, the absence of mutation in nuclear modifier gene TRMU suggested that TRMU may not be a modifier for the phenotypic expression of the 1555A>G mutation in these Chinese families. These observations suggested that mitochondrial haplotypes modulate the variable penetrance and expressivity of deafness among these Chinese families.},
}
@article {pmid19835962,
year = {2010},
author = {Lin, YC and Lee, FF and Wu, CL and Chen, JC},
title = {Molecular cloning and characterization of a cytosolic manganese superoxide dismutase (cytMnSOD) and mitochondrial manganese superoxide dismutase (mtMnSOD) from the kuruma shrimp Marsupenaeus japonicus.},
journal = {Fish &amp; shellfish immunology},
volume = {28},
number = {1},
pages = {143-150},
doi = {10.1016/j.fsi.2009.10.012},
pmid = {19835962},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cytosol/enzymology ; Gene Expression/genetics/immunology ; Hemocytes/immunology ; Mitochondria/enzymology ; Molecular Sequence Data ; Penaeidae/*genetics/immunology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Superoxide Dismutase/*genetics ; Vibrio Infections/immunology ; Vibrio alginolyticus/immunology ; },
abstract = {A cytosolic manganese superoxide dismutase (cytMnSOD) gene and a mitochondrial manganese superoxide dismutase (mtMnSOD) gene were cloned from the kuruma shrimp Marsupenaeus japonicus using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) method. The open reading frame (ORF) of cytMnSOD is 861 bp and encodes a 287 amino acids (aa) protein with a 61 aa leader sequence, whereas the ORF of mtMnSOD is 663 bp and encodes a 221 aa protein with a 21 aa mitochondrial-targeting sequence in the N-terminus. The calculated molecular mass of translated protein of cytMnSOD and mtMnSOD is 31.4 kDa and 24.3 kDa with an estimated pI of 5.62 and 7.27, respectively. The deduced amino acid sequence of cytMnSOD has similarity of 50.2% to that of mtMnSOD. Both cytMnSOD and mtMnSOD contain a manganese superoxide dismutase domain (DVWEHAYY), and four conserved amino acids responsible for binding manganese. Both cytMnSOD and mtMnSOD of M. japonicus were expressed in haemocytes, eyestalk, muscle, intestine, gill, and hepatopancreas. Both cytMnSOD and mtMnSOD transcripts in haemocytes of M. japonicus significantly increased 6 h after injection of Vibrio alginolyticus, and 12 h after injection of beta-glucan, indicating induction of SOD system response in a short time.},
}
@article {pmid19859730,
year = {2009},
author = {Ito-Inaba, Y and Hida, Y and Inaba, T},
title = {What is critical for plant thermogenesis? Differences in mitochondrial activity and protein expression between thermogenic and non-thermogenic skunk cabbages.},
journal = {Planta},
volume = {231},
number = {1},
pages = {121-130},
pmid = {19859730},
issn = {1432-2048},
mesh = {Amino Acid Sequence ; Araceae/cytology/enzymology/genetics/*physiology ; Cell Respiration ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Ion Channels/chemistry/genetics/metabolism ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Organ Specificity/genetics ; Oxidoreductases/chemistry/genetics/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Temperature ; Uncoupling Protein 1 ; Alternative Oxidase ; },
abstract = {Thermogenesis during the blooming of inflorescence is found in several but not all aroids. To understand what is critical for thermogenesis, we investigated the difference between thermogenic and non-thermogenic skunk cabbages (Symplocarpus renifolius and Lysichiton camtschatcensis), which are closely related in morphology and phylogeny. Critical parameters of mitochondrial biogenesis, including density, respiratory activity, and protein expression were compared between these two species. Mitochondrial density, respiratory activity, and the amount of alternative oxidase (AOX) in L. camtschatcensis spadix mitochondria were lower than in S. renifolius spadix mitochondria, while the level of uncoupling protein (UCP) was higher. AOX and UCP mRNAs in L. camtschatcensis were constitutively expressed in various tissues, such as the spadix, the spathe, the stalk, and the leaves. cDNA encoding two putative thermogenic proteins, AOX and UCP were isolated from L. camtschatcensis, and their primary structure was analyzed by multiple alignment and phylogenetic tree reconstruction. AOX and UCP protein of two the skunk cabbage species are closely related in structure, compared with other isoforms in thermogenic plants. Our results suggest that mitochondrial density, respiratory activity, and protein expression, rather than the primary structure of AOX or UCP proteins, may play critical roles in thermogenesis in plants.},
}
@article {pmid19895685,
year = {2009},
author = {de Graaf, RM and van Alen, TA and Dutilh, BE and Kuiper, JW and van Zoggel, HJ and Huynh, MB and Görtz, HD and Huynen, MA and Hackstein, JH},
title = {The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.},
journal = {BMC genomics},
volume = {10},
number = {},
pages = {514},
pmid = {19895685},
issn = {1471-2164},
mesh = {Electron Transport ; Electron Transport Complex IV/genetics ; Euplotes/*genetics/metabolism ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Ribosomal Proteins/genetics ; },
abstract = {BACKGROUND: There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome.<br><br>RESULTS: The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region) piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals.<br><br>CONCLUSION: The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial genes from other sources.},
}
@article {pmid19902250,
year = {2010},
author = {Nilles-Bije, ML and Rivera, WL},
title = {Ultrastructural and molecular characterization of Balantidium coli isolated in the Philippines.},
journal = {Parasitology research},
volume = {106},
number = {2},
pages = {387-394},
pmid = {19902250},
issn = {1432-1955},
mesh = {Animals ; Balantidiasis/parasitology/*veterinary ; Balantidium/classification/*genetics/isolation &amp; purification/*ultrastructure ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Organelles/ultrastructure ; Philippines ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*parasitology ; },
abstract = {Balantidium coli is a ciliated protozoon inhabiting the colon of swine, rodents, horses, nonhuman primates and humans. In association with disease triggered by other infectious agents, B. coli may become a pathogenic opportunist. This study describes the isolation, cultivation, morphological as well as molecular characterization of B. coli isolated from the large intestine of a pig in the Philippines. Based on scanning and transmission electron microscopy, this protozoon presents a dense ciliation in the oral structure and somatic cilia that are arranged in a more transverse field. Oral and somatic monokinetids were identified in the cortex of the organism. The presence of heterokaryotic nuclear condition is evident, and the cell body of the ciliate shows numerous mucocysts, several food vacuoles, mitochondria, endoplasmic reticulum, and contractile vacuoles. Polymerase chain reaction and phylogenetic analysis based on the small subunit ribosomal RNA gene were performed in order to compare our isolate with other previously reported B. coli isolates. The full-length sequence of the SSU rRNA gene of the isolate showed 99% similarity to other B. coli isolates reported in the GenBank. Phylogenetic analysis revealed that the isolate clustered with previously reported B. coli isolates from gorillas, pig, and ostrich. To date, no studies on the ultrastructure and phylogeny of B. coli isolated in the Philippines have been reported. Results from this study may serve as a baseline data for further ultrastructural and phylogenetic studies on this organism. This study also suggests that morphological characteristics along with molecular identification are essential for validating and identifying species of Balantidium.},
}
@article {pmid19929881,
year = {2010},
author = {Richter, U and Kühn, K and Okada, S and Brennicke, A and Weihe, A and Börner, T},
title = {A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis.},
journal = {The Plant journal : for cell and molecular biology},
volume = {61},
number = {4},
pages = {558-569},
pmid = {19929881},
issn = {1365-313X},
mesh = {Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Genetic Complementation Test ; Methyltransferases/genetics/*metabolism ; Mitochondria/*enzymology/genetics ; Mutagenesis, Insertional ; Mutation ; Phylogeny ; RNA, Plant/genetics ; RNA, Ribosomal, 18S/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; },
abstract = {S-adenosyl-L-methionine-dependent rRNA dimethylases mediate the methylation of two conserved adenosines near the 3' end of the rRNA in the small ribosomal subunits of bacteria, archaea and eukaryotes. Proteins related to this family of dimethylases play an essential role as transcription factors (mtTFBs) in fungal and animal mitochondria. Human mitochondrial rRNA is methylated and human mitochondria contain two related mtTFBs, one proposed to act as rRNA dimethylase, the other as transcription factor. The nuclear genome of Arabidopsis thaliana encodes three dimethylase/mtTFB-like proteins, one of which, Dim1B, is shown here to be imported into mitochondria. Transcription initiation by mitochondrial RNA polymerases appears not to be stimulated by Dim1B in vitro. In line with this finding, phylogenetic analyses revealed Dim1B to be more closely related to a group of eukaryotic non-mitochondrial rRNA dimethylases (Dim1s) than to fungal and animal mtTFBs. We found that Dim1B was capable of substituting the E. coli rRNA dimethylase activity of KsgA. Moreover, we observed methylation of the conserved adenines in the 18S rRNA of Arabidopsis mitochondria; this modification was not detectable in a mutant lacking Dim1B. These data provide evidence: (i) for rRNA methylation in Arabidopsis mitochondria; and (ii) that Dim1B is the enzyme catalyzing this process.},
}
@article {pmid19943893,
year = {2010},
author = {Smith, S and Turbill, C and Suchentrunk, F},
title = {Introducing mother's curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares.},
journal = {Molecular ecology},
volume = {19},
number = {1},
pages = {36-43},
doi = {10.1111/j.1365-294X.2009.04444.x},
pmid = {19943893},
issn = {1365-294X},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Fertility/genetics ; *Genetic Fitness ; Genetics, Population ; Haplotypes ; Hares/*genetics ; Infertility, Male/*genetics ; Male ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Mitochondrial DNA mutations create variation in the efficiency of the oxidative phosphorylation pathway and therefore cellular energy production. Mildly deleterious mutations may reduce the performance of sperm cells in particular, due to their high energy requirements and low number of mitochondria, yet have little or no effect on the viability of somatic cells or ova. Mutations will be maintained in the population, despite the fitness cost for males, because mtDNA is passed down the female line. We looked for this so-called mother's curse effect in our captive colony of European brown hares. Significantly reduced male reproductive success was detected for a divergent haplotype that could be traced back to hares imported from a remote population. Median reproductive success for these hares was 0.17 compared to 0.49 for the indigenous haplotypes (Wilcoxon rank-sum, P = 0.002). No difference was detected for female reproductive success, nor were we able to find a nuclear DNA component to variation in male fertility. Our data are strong evidence for a mother's curse effect persisting despite multiple crossings over seven generations. These data raise important issues relating to the reproductive fitness of small or intermixing populations and have particular implications for the management of populations for conservation.},
}
@article {pmid19966073,
year = {2009},
author = {Gebert, M and Meschenmoser, K and Svidová, S and Weghuber, J and Schweyen, R and Eifler, K and Lenz, H and Weyand, K and Knoop, V},
title = {A root-expressed magnesium transporter of the MRS2/MGT gene family in Arabidopsis thaliana allows for growth in low-Mg2+ environments.},
journal = {The Plant cell},
volume = {21},
number = {12},
pages = {4018-4030},
pmid = {19966073},
issn = {1532-298X},
mesh = {Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cation Transport Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Expression Regulation, Plant ; Gene Knockout Techniques ; Genetic Complementation Test ; Magnesium/*metabolism ; Multigene Family ; Mutagenesis, Insertional ; Mutation ; Phylogeny ; Plant Roots/genetics/*growth &amp; development/metabolism ; Plants, Genetically Modified/genetics ; RNA, Plant/genetics ; Saccharomyces cerevisiae/metabolism ; Nicotiana/genetics ; },
abstract = {The MRS2/MGT gene family in Arabidopsis thaliana belongs to the superfamily of CorA-MRS2-ALR-type membrane proteins. Proteins of this type are characterized by a GMN tripeptide motif (Gly-Met-Asn) at the end of the first of two C-terminal transmembrane domains and have been characterized as magnesium transporters. Using the recently established mag-fura-2 system allowing direct measurement of Mg(2+) uptake into mitochondria of Saccharomyces cerevisiae, we find that all members of the Arabidopsis family complement the corresponding yeast mrs2 mutant. Highly different patterns of tissue-specific expression were observed for the MRS2/MGT family members in planta. Six of them are expressed in root tissues, indicating a possible involvement in plant magnesium supply and distribution after uptake from the soil substrate. Homozygous T-DNA insertion knockout lines were obtained for four members of the MRS2/MGT gene family. A strong, magnesium-dependent phenotype of growth retardation was found for mrs2-7 when Mg(2+) concentrations were lowered to 50 microM in hydroponic cultures. Ectopic overexpression of MRS2-7 from the cauliflower mosaic virus 35S promoter results in complementation and increased biomass accumulation. Green fluorescent protein reporter gene fusions indicate a location of MRS2-7 in the endomembrane system. Hence, contrary to what is frequently found in analyses of plant gene families, a single gene family member knockout results in a strong, environmentally dependent phenotype.},
}
@article {pmid19968861,
year = {2010},
author = {Poliak, P and Van Hoewyk, D and Oborník, M and Zíková, A and Stuart, KD and Tachezy, J and Pilon, M and Lukes, J},
title = {Functions and cellular localization of cysteine desulfurase and selenocysteine lyase in Trypanosoma brucei.},
journal = {The FEBS journal},
volume = {277},
number = {2},
pages = {383-393},
pmid = {19968861},
issn = {1742-4658},
support = {R01 AI065935/AI/NIAID NIH HHS/United States ; AI065935/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Carbon-Sulfur Lyases/genetics/*metabolism ; Cell Compartmentation ; Cytosol/enzymology ; Genes, Protozoan ; Lyases/antagonists &amp; inhibitors/genetics/*metabolism ; Mitochondria/enzymology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; Trypanosoma brucei brucei/*enzymology/genetics ; },
abstract = {Nfs-like proteins have cysteine desulfurase (CysD) activity, which removes sulfur (S) from cysteine, and provides S for iron-sulfur cluster assembly and the thiolation of tRNAs. These proteins also have selenocysteine lyase activity in vitro, and cleave selenocysteine into alanine and elemental selenium (Se). It was shown previously that the Nfs-like protein called Nfs from the parasitic protist Trypanosoma brucei is a genuine CysD. A second Nfs-like protein is encoded in the nuclear genome of T. brucei. We called this protein selenocysteine lyase (SCL) because phylogenetic analysis reveals that it is monophyletic with known eukaryotic selenocysteine lyases. The Nfs protein is located in the mitochondrion, whereas the SCL protein seems to be present in the nucleus and cytoplasm. Unexpectedly, downregulation of either Nfs or SCL protein leads to a dramatic decrease in both CysD and selenocysteine lyase activities concurrently in the mitochondrion and the cytosolic fractions. Because loss of Nfs causes a growth phenotype but loss of SCL does not, we propose that Nfs can fully complement SCL, whereas SCL can only partially replace Nfs under our growth conditions.},
}
@article {pmid20019817,
year = {2009},
author = {Salas, A and Fachal, L and Marcos-Alonso, S and Vega, A and Martinón-Torres, F and , },
title = {Investigating the role of mitochondrial haplogroups in genetic predisposition to meningococcal disease.},
journal = {PloS one},
volume = {4},
number = {12},
pages = {e8347},
pmid = {20019817},
issn = {1932-6203},
mesh = {Chi-Square Distribution ; Child, Preschool ; DNA, Mitochondrial/genetics ; Demography ; Female ; *Genetic Predisposition to Disease ; Genetics, Population ; Haplotypes/*genetics ; Humans ; Male ; Meningococcal Infections/*genetics/pathology ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {BACKGROUND AND AIMS: Meningococcal disease remains one of the most important infectious causes of death in industrialized countries. The highly diverse clinical presentation and prognosis of Neisseria meningitidis infections are the result of complex host genetics and environmental interactions. We investigated whether mitochondrial genetic background contributes to meningococcal disease (MD) susceptibility.<br><br>Prospective controlled study was performed through a national research network on MD that includes 41 Spanish hospitals. Cases were 307 paediatric patients with confirmed MD, representing the largest series of MD patients analysed to date. Two independent sets of ethnicity-matched control samples (CG1 [N = 917]), and CG2 [N = 616]) were used for comparison. Cases and controls underwent mtDNA haplotyping of a selected set of 25 mtDNA SNPs (mtSNPs), some of them defining major European branches of the mtDNA phylogeny. In addition, 34 ancestry informative markers (AIMs) were genotyped in cases and CG2 in order to monitor potential hidden population stratification. Samples of known African, Native American and European ancestry (N = 711) were used as classification sets for the determination of ancestral membership of our MD patients. A total of 39 individuals were eliminated from the main statistical analyses (including fourteen gypsies) on the basis of either non-Spanish self-reported ancestry or the results of AIMs indicating a European membership lower than 95%. Association analysis of the remaining 268 cases against CG1 suggested an overrepresentation of the synonym mtSNP G11719A variant (Pearson's chi-square test; adjusted P-value = 0.0188; OR [95% CI] = 1.63 [1.22-2.18]). When cases were compared with CG2, the positive association could not be replicated. No positive association has been observed between haplogroup (hg) status of cases and CG1/CG2 and hg status of cases and several clinical variants.<br><br>CONCLUSIONS: We did not find evidence of association between mtSNPs and mtDNA hgs with MD after carefully monitoring the confounding effect of population sub-structure. MtDNA variability is particularly stratified in human populations owing to its low effective population size in comparison with autosomal markers and therefore, special care should be taken in the interpretation of seeming signals of positive associations in mtDNA case-control association studies.},
}
@article {pmid20035036,
year = {2010},
author = {Sienkiewicz-Porzucek, A and Sulpice, R and Osorio, S and Krahnert, I and Leisse, A and Urbanczyk-Wochniak, E and Hodges, M and Fernie, AR and Nunes-Nesi, A},
title = {Mild reductions in mitochondrial NAD-dependent isocitrate dehydrogenase activity result in altered nitrate assimilation and pigmentation but do not impact growth.},
journal = {Molecular plant},
volume = {3},
number = {1},
pages = {156-173},
pmid = {20035036},
issn = {1674-2052},
mesh = {Citric Acid Cycle/genetics/physiology ; Isocitrate Dehydrogenase/classification/genetics/*metabolism ; Solanum lycopersicum/*enzymology/genetics/growth &amp; development/*metabolism ; Mitochondria/*enzymology ; Nitrates/*metabolism ; Oligonucleotide Array Sequence Analysis ; Photosynthesis/genetics/physiology ; Phylogeny ; Pigmentation/genetics/physiology ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified/enzymology/genetics/growth &amp; development/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {Transgenic tomato (Solanum lycopersicum) plants were generated expressing a fragment of the mitochondrial NAD-dependent isocitrate dehydrogenase gene (SlIDH1) in the antisense orientation. The transgenic plants displayed a mild reduction in the activity of the target enzyme in the leaves but essentially no visible alteration in growth from the wild-type. Fruit size and yield were, however, reduced. These plants were characterized by relatively few changes in photosynthetic parameters, but they displayed a minor decrease in maximum photosynthetic efficiency (Fv/Fm). Furthermore, a clear reduction in flux through the tricarboxylic acid (TCA) cycle was observed in the transformants. Additionally, biochemical analyses revealed that the transgenic lines exhibited considerably altered metabolism, being characterized by slight decreases in the levels of amino acids, intermediates of the TCA cycle, photosynthetic pigments, starch, and NAD(P)H levels, but increased levels of nitrate and protein. Results from these studies show that even small changes in mitochondrial NAD-dependent isocitrate dehydrogenase activity lead to noticeable alterations in nitrate assimilation and suggest the presence of different strategies by which metabolism is reprogrammed to compensate for this deficiency.},
}
@article {pmid20042393,
year = {2009},
author = {Cao, GL and Xue, RY and Zhu, YX and Wei, YH and Gong, CL},
title = {[Analysis of the aminoacyl-tRNA synthetase genes of silkworm (Bombyx mori)].},
journal = {Yi chuan = Hereditas},
volume = {31},
number = {12},
pages = {1248-1258},
doi = {10.3724/sp.j.1005.2009.01248},
pmid = {20042393},
issn = {0253-9772},
mesh = {Amino Acyl-tRNA Synthetases/chemistry/*genetics/metabolism ; Animals ; Bombyx/chemistry/classification/*enzymology/genetics ; Cytoplasm/chemistry/enzymology/genetics ; Insect Proteins/chemistry/*genetics/metabolism ; Mitochondria/chemistry/enzymology/genetics ; Molecular Conformation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; },
abstract = {For further research on number, type, composition and origin of Bombyx mori aminoacyl-tRNA synthetase (BmaaRS) genes, in silico cloning was performed with Bombyx mori genomic and EST databases. There might be two different sets of aaRS nuclear gene in Bombxy nori genome, which encode mitochondrial BmaaRS and cytoplasmic BmaaRS, respectively. Among BmaaRS genes, there were 2 genes encoding mitochondrial BmSerRS, but no genes encoding cytoplasmic BmHisRS and mitochondrial BmGlnRS, BmLysRS, BmGlyRS, and BmThrRS. The functions of these absent genes could be directly replaced by other proteins with similar functions, or might undergo their distinct BmaaRS functions based on the alternative splice of one certain BmaaRS mRNA. Evidence of EST indicated that BmaaRS performed different alternative splicing patterns. The homology comparison and advanced structural analysis of BmaaRS demonstrated the existence of extended domains of BmaaRS. This is because some different BmaaRSs contained similar domain. Moreover, BmaaRSs with similar functions possessed the similar tertiary structure. Phylogenetic analysis revealed that BmaaRS encoded by two various sources of BmaaRS genes. Mitochondrial and cytoplasmic BmaaRS had different origin.},
}
@article {pmid20042613,
year = {2010},
author = {Horibata, Y and Sugimoto, H},
title = {StarD7 mediates the intracellular trafficking of phosphatidylcholine to mitochondria.},
journal = {The Journal of biological chemistry},
volume = {285},
number = {10},
pages = {7358-7365},
pmid = {20042613},
issn = {1083-351X},
mesh = {Amino Acid Sequence ; Animals ; Biological Transport/physiology ; Carrier Proteins/classification/genetics/*metabolism ; Cell Line ; Cytoplasmic Vesicles/metabolism ; Liver/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphatidylcholines/*metabolism ; Phylogeny ; Protein Isoforms/genetics/*metabolism ; Rats ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Subcellular Fractions/metabolism ; },
abstract = {Steroidogenic acute regulatory protein-related lipid transfer (START) domains, found in 15 mammalian proteins termed StarD1-StarD15, are lipid-binding domains implicated in the intracellular lipid transport systems. In the present study, we analyzed the lipid ligand and function of StarD7. We found two variable forms of mammalian StarD7, termed StarD7-I and StarD7-II. Unlike StarD7-II, StarD7-I contained a mitochondrial-targeting sequence in its N terminus. Overexpressed StarD7-I tagged with V5/His in HEPA-1 cells was mainly observed in the mitochondria of cells prepared at low cellular density, but it was distributed in the cytoplasm of high density cells. StarD7-II was constantly distributed in the cytoplasm at any cellular density. Endogenous StarD7 in HEPA-1 cells and rat liver was also distributed in both the cytoplasm and the mitochondria. A protease K protection assay indicated that the mitochondrial StarD7 was associated with the outer mitochondrial membrane. The purified recombinant StarD7 specifically catalyzed the transfer of PC between lipid vesicles in vitro. Furthermore, the intracellular transport of fluorescent PC that was exogenously incorporated into the mitochondria was increased in cells that overexpressed StarD7-I. These results suggest that StarD7 facilitates the delivery of PC to mitochondria in non-vesicular system.},
}
@article {pmid20061302,
year = {2010},
author = {Tominaga, M and Harada, A and Kinoshita, T and Shimazaki, K},
title = {Biochemical characterization of calcineurin B-like-interacting protein kinase in Vicia guard cells.},
journal = {Plant &amp; cell physiology},
volume = {51},
number = {3},
pages = {408-421},
doi = {10.1093/pcp/pcq006},
pmid = {20061302},
issn = {1471-9053},
mesh = {Amino Acid Sequence ; Calcineurin/metabolism ; Calcium/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Mitochondrial Membranes/metabolism ; Molecular Sequence Data ; Phosphorylation ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Binding ; Protein Serine-Threonine Kinases/genetics/*metabolism ; Sequence Alignment ; Vicia faba/*genetics/metabolism ; },
abstract = {Protein phosphorylation is crucial in the signaling of guard cells in response to various factors, including light, ABA and CO2, and calcium plays a central role in these signaling processes. Despite extensive studies on the functional role of Ca(2+)-regulated protein kinases in plants, relatively little is known about the biochemical properties of the kinases in guard cells. To investigate this, we isolated the VfCIPK1 [Vicia faba calcineurin B-like calcium-binding protein (CBL)-interacting protein kinase 1] cDNA from guard cells of Vicia faba L., which encodes a Ca(2+)-regulated protein kinase that belongs to the SnRK3 subgroup, and characterized VfCIPK1 at the biochemical level. VfCIPK1 genes were expressed in guard cells and roots, but not in mesophyll cells. The VfCIPK1 protein was localized on the outer membrane of mitochondria in guard cells and interacted with VfCBL1. The immunoprecipitation experiments indicated that VfCIPK1 interacted with VfCBL1 in vivo. The recombinant VfCIPK1 phosphorylated myelin basic protein as a substrate and the activity was increased by VfCBL1, and this activity showed a maximum in the absence of Ca2+ and decreased by an elevation of the Ca2+ concentration. A pull-down assay and the measurement of surface plasmon resonance indicated that the interaction between VfCIPK1 and VfCBL1 was decreased by Ca2+. These results suggest that VfCIPK1 may be negatively regulated by cytosolic Ca2+ through VfCBL1 and may be related to mitochondrial functions in guard cells. This is the first report that shows the inhibitory effect of Ca2+ on CIPK activity in the presence of CBL.},
}
@article {pmid20086128,
year = {2010},
author = {Ivanina, AV and Eilers, S and Kurochkin, IO and Chung, JS and Techa, S and Piontkivska, H and Sokolov, EP and Sokolova, IM},
title = {Effects of cadmium exposure and intermittent anoxia on nitric oxide metabolism in eastern oysters, Crassostrea virginica.},
journal = {The Journal of experimental biology},
volume = {213},
number = {3},
pages = {433-444},
doi = {10.1242/jeb.038059},
pmid = {20086128},
issn = {1477-9145},
mesh = {Amino Acid Sequence ; Anaerobiosis/drug effects ; Animals ; Cadmium/*toxicity ; Cell Respiration/drug effects ; Crassostrea/*drug effects/enzymology/genetics/*metabolism ; *Environmental Exposure ; Gene Expression Regulation, Enzymologic/drug effects ; Gills/drug effects/enzymology ; Mitochondria/drug effects/metabolism ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Nitric Oxide Synthase/chemistry/genetics/metabolism ; Oxidation-Reduction/drug effects ; Phylogeny ; Polyamines/pharmacology ; RNA, Messenger/genetics/metabolism ; S-Nitroso-N-Acetylpenicillamine/pharmacology ; Sequence Alignment ; },
abstract = {Nitric oxide (NO) is an intracellular signaling molecule synthesized by a group of enzymes called nitric oxide synthases (NOS) and involved in regulation of many cellular functions including mitochondrial metabolism and bioenergetics. In invertebrates, the involvement of NO in bioenergetics and metabolic responses to environmental stress is poorly understood. We determined sensitivity of mitochondrial and cellular respiration to NO and the effects of cadmium (Cd) and intermittent anoxia on NO metabolism in eastern oysters, Crassostrea virginica. NOS activity was strongly suppressed by exposure to 50 microg l(-1) Cd for 30 days (4.76 vs 1.19 pmol NO min(-1) mg(-1) protein in control and Cd-exposed oysters, respectively) and further decreased during anoxic exposure in Cd-exposed oysters but not in their control counterparts. Nitrate/nitrite content (indicative of NO levels) decreased during anoxic exposure to less than 10% of the normoxic values and recovered within 1 h of re-oxygenation in control oysters. In Cd-exposed oysters, the recovery of the normoxic NO levels lagged behind, reflecting their lower NOS activity. Oyster mitochondrial respiration was inhibited by exogenous NO, with sensitivity on a par with that of mammalian mitochondria, and ADP-stimulated mitochondrial respiration was significantly more sensitive to NO than resting respiration. In isolated gill cells, manipulations of endogenous NOS activity either with a specific NOS inhibitor (aminoguanidine) or a NOS substrate (L-arginine) had no effect on respiration, likely due to the fact that mitochondria in the resting state are relatively NO insensitive. Likewise, Cd-induced stimulation of cellular respiration did not correlate with decreased NOS activity in isolated gill cells. High sensitivity of phosphorylating (ADP-stimulated) oyster mitochondria to NO suggests that regulation of bioenergetics is an evolutionarily conserved function of NO and that NO-dependent regulation of metabolism may be most prominent under the conditions of high metabolic flux when the ADP-to-ATP ratio is high.},
}
@article {pmid20106903,
year = {2010},
author = {Chiu, WC and Chang, CP and Wen, WL and Wang, SW and Wang, CC},
title = {Schizosaccharomyces pombe possesses two paralogous valyl-tRNA synthetase genes of mitochondrial origin.},
journal = {Molecular biology and evolution},
volume = {27},
number = {6},
pages = {1415-1424},
doi = {10.1093/molbev/msq025},
pmid = {20106903},
issn = {1537-1719},
mesh = {Amino Acid Sequence ; Aminoacylation ; Cytoplasm/metabolism ; Gene Knockout Techniques ; *Genes, Essential ; *Genes, Fungal ; Genetic Complementation Test ; Histocytochemistry ; Microscopy, Fluorescence ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Schizosaccharomyces/cytology/*enzymology/genetics/metabolism ; Sequence Alignment ; Valine-tRNA Ligase/*genetics/metabolism ; },
abstract = {Previous studies showed that VAS1 of Saccharomyces cerevisiae encodes both cytosolic and mitochondrial forms of valyl-tRNA synthetase (ValRS) through alternative initiation of translation. We show herein that except for Schizosaccharomyces pombe, all yeast species studied contained a single ValRS gene encoding both forms, and all of the mature protein forms deduced from those genes possessed an N-terminal appended domain (Ad) that was absent from their bacterial relatives. In contrast, S. pombe contained two distinct nuclear ValRS genes, one encoding the mitochondrial form and the other its cytosolic counterpart. Although the cytosolic form closely resembles other yeast ValRS sequences (approximately 60% identity), the mitochondrial form exhibits significant divergence from others (approximately 35% identity). Both genes are active and essential for the survival of the yeast. Most conspicuously, the mitochondrial form lacks the characteristic Ad. A phylogenetic analysis further suggested that both forms of S. pombe ValRS are of mitochondrial origin, and the mitochondrial form is ancestral to the cytoplasmic form.},
}
@article {pmid20124190,
year = {2010},
author = {Séveno, M and Séveno-Carpentier, E and Voxeur, A and Menu-Bouaouiche, L and Rihouey, C and Delmas, F and Chevalier, C and Driouich, A and Lerouge, P},
title = {Characterization of a putative 3-deoxy-D-manno-2-octulosonic acid (Kdo) transferase gene from Arabidopsis thaliana.},
journal = {Glycobiology},
volume = {20},
number = {5},
pages = {617-628},
doi = {10.1093/glycob/cwq011},
pmid = {20124190},
issn = {1460-2423},
mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/*genetics ; Gene Expression Regulation, Plant/*genetics ; Molecular Sequence Data ; Mutation ; Pectins/biosynthesis/chemistry ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Transferases/chemistry/*genetics/isolation &amp; purification ; },
abstract = {The structures of the pectic polysaccharide rhamnogalacturonan II (RG-II) pectin constituent are remarkably evolutionary conserved in all plant species. At least 12 different glycosyl residues are present in RG-II. Among them is the seldom eight-carbon sugar 3-deoxy-d-manno-octulosonic acid (Kdo) whose biosynthetic pathway has been shown to be conserved between plants and Gram-negative bacteria. Kdo is formed in the cytosol by the condensation of phosphoenol pyruvate with d-arabinose-5-P and then activated by coupling to cytidine monophosphate (CMP) prior to its incorporation in the Golgi apparatus by a Kdo transferase (KDTA) into the nascent polysaccharide RG-II. To gain new insight into RG-II biosynthesis and function, we isolated and characterized null mutants for the unique putative KDTA (AtKDTA) encoded in the Arabidopsis genome. We provide evidence that, in contrast to mutants affecting the RG-II biosynthesis, the extinction of the AtKDTA gene expression does not result in any developmental phenotype in the AtkdtA plants. Furthermore, the structure of RG-II from the null mutants was not altered and contained wild-type amount of Rha-alpha(1-5)Kdo side chain. The cellular localization of AtKDTA was investigated by using laser scanning confocal imaging of the protein fused to green fluorescent protein. In agreement with its cellular prediction, the fusion protein was demonstrated to be targeted to the mitochondria. These data, together with data deduced from sequence analyses of higher plant genomes, suggest that AtKDTA encodes a putative KDTA involved in the synthesis of a mitochondrial not yet identified lipid A-like molecule rather than in the synthesis of the cell wall RG-II.},
}
@article {pmid20132446,
year = {2010},
author = {Suematsu, T and Yokobori, S and Morita, H and Yoshinari, S and Ueda, T and Kita, K and Takeuchi, N and Watanabe, Y},
title = {A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi.},
journal = {Molecular microbiology},
volume = {75},
number = {6},
pages = {1445-1454},
doi = {10.1111/j.1365-2958.2010.07067.x},
pmid = {20132446},
issn = {1365-2958},
mesh = {Borrelia burgdorferi/*enzymology/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Guanosine Triphosphate/metabolism ; Humans ; Molecular Sequence Data ; Peptide Elongation Factor G/*metabolism ; Phylogeny ; Prokaryotic Initiation Factor-3/metabolism ; *Protein Biosynthesis ; Ribosomal Proteins/metabolism ; Ribosomes/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Translation elongation factor G (EF-G) in bacteria plays two distinct roles in different phases of the translation system. EF-G catalyses the translocation of tRNAs on the ribosome in the elongation step, as well as the dissociation of the post-termination state ribosome into two subunits in the recycling step. In contrast to this conventional view, it has very recently been demonstrated that the dual functions of bacterial EF-G are distributed over two different EF-G paralogues in human mitochondria. In the present study, we show that the same division of roles of EF-G is also found in bacteria. Two EF-G paralogues are found in the spirochaete Borrelia burgdorferi, EF-G1 and EF-G2. We demonstrate that EF-G1 is a translocase, while EF-G2 is an exclusive recycling factor. We further demonstrate that B. burgdorferi EF-G2 does not require GTP hydrolysis for ribosome disassembly, provided that translation initiation factor 3 (IF-3) is present in the reaction. These results indicate that two B. burgdorferi EF-G paralogues are close relatives to mitochondrial EF-G paralogues rather than the conventional bacterial EF-G, in both their phylogenetic and biochemical features.},
}
@article {pmid20141629,
year = {2010},
author = {Singh, A and Singh, U and Mittal, D and Grover, A},
title = {Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes.},
journal = {BMC genomics},
volume = {11},
number = {},
pages = {95},
pmid = {20141629},
issn = {1471-2164},
mesh = {Adenosine Triphosphatases/*genetics ; Chloroplasts/genetics ; Cloning, Molecular ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; *Genome, Plant ; Heat-Shock Proteins/*genetics ; Hot Temperature ; Molecular Chaperones/*genetics ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Oryza/*genetics ; Phylogeny ; Plant Proteins/genetics ; Plants, Genetically Modified/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; Stress, Physiological ; },
abstract = {BACKGROUND: ClpB-cyt/HSP100 protein acts as chaperone, mediating disaggregation of denatured proteins. Previous studies have shown that ClpB-cyt/HSP100 gene belongs to the group class I Clp ATPase proteins and ClpB-cyt/HSP100 transcript is regulated by heat stress and developmental cues.<br><br>RESULTS: Nine ORFs were noted to constitute rice class I Clp ATPases in the following manner: 3 ClpB proteins (ClpB-cyt, Os05g44340; ClpB-m, Os02g08490; ClpB-c, Os03g31300), 4 ClpC proteins (ClpC1, Os04g32560; ClpC2, Os12g12580; ClpC3, Os11g16590; ClpC4, Os11g16770) and 2 ClpD proteins (ClpD1, Os02g32520; ClpD2, Os04g33210). Using the respective signal sequences cloned upstream to GFP/CFP reporter proteins and transient expression studies with onion epidermal cells, evidence is provided that rice ClpB-m and Clp-c proteins are indeed localized to their respective cell locations mitochondria and chloroplasts, respectively. Associated with their diverse cell locations, domain structures of OsClpB-c, OsClpB-m and OsClpB-cyt proteins are noted to possess a high-level conservation. OsClpB-cyt transcript is shown to be enriched at milk and dough stages of seed development. While expression of OsClpB-m was significantly less as compared to its cytoplasmic and chloroplastic counterparts in different tissues, this transcript showed highest heat-induced expression amongst the 3 ClpB proteins. OsClpC1 and OsClpC2 are predicted to be chloroplast-localized as is the case with all known plant ClpC proteins. However, the fact that OsClpC3 protein appears mitochondrial/chloroplastic with equal probability and OsClpC4 a plasma membrane protein reflects functional diversity of this class. Different class I Clp ATPase transcripts were noted to be cross-induced by a host of different abiotic stress conditions. Complementation assays of Deltahsp104 mutant yeast cells showed that OsClpB-cyt, OsClpB-m, OsClpC1 and OsClpD1 have significantly positive effects. Remarkably, OsClpD1 gene imparted appreciably high level tolerance to the mutant yeast cells.<br><br>CONCLUSIONS: Rice class I Clp ATPase gene family is constituted of 9 members. Of these 9, only 3 belonging to ClpB group are heat stress regulated. Distribution of ClpB proteins to different cell organelles indicates that their functioning might be critical in different cell locations. From the complementation assays, OsClpD1 appears to be more effective than OsClpB-cyt protein in rescuing the thermosensitive defect of the yeast ScDeltahsp104 mutant cells.},
}
@article {pmid20143628,
year = {2009},
author = {Myl'nikov, AP},
title = {[Ultrastructure and phylogeny of colpodellids (Colpodellida, Alveolata)].},
journal = {Izvestiia Akademii nauk. Seriia biologicheskaia},
volume = {},
number = {6},
pages = {685-694},
pmid = {20143628},
issn = {1026-3470},
mesh = {Apicomplexa/*physiology/*ultrastructure ; Flagella/physiology/ultrastructure ; *Phylogeny ; },
abstract = {The structure of cells of the predatory flagellates Colpodella pseudoedax and C. unguis was studied. The cell was found to contain two heterodynamic flagellae, three-membrane pellicle, micropores, subpellicular microtubulae, microtubular open conoid, roptries, micronemes, extrusive organelles (trichocysts), and mitochondria with tubular cristae. Upon discharging, trichocysts form cross-striated bands. The thin-walled cylinder lies in the transitional zone of the flagellae. Cells reproduce by means of longitudinal binary fission. The similarities between given species and other colpodelids and such between perkinsea, sporozoans, and dinoflagellates are discussed.},
}
@article {pmid20144467,
year = {2010},
author = {Dallai, R and Mercati, D and Bu, Y and Yin, YW},
title = {Spermatogenesis and sperm structure of Acerella muscorum, (Ionescu, 1930) (Hexapoda, Protura).},
journal = {Tissue &amp; cell},
volume = {42},
number = {2},
pages = {97-104},
doi = {10.1016/j.tice.2010.01.001},
pmid = {20144467},
issn = {1532-3072},
mesh = {Animals ; Centrioles/physiology/ultrastructure ; Cytoplasm/physiology/ultrastructure ; Fertilization/physiology ; Invertebrates/physiology/*ultrastructure ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Species Specificity ; Spermatids/physiology/ultrastructure ; Spermatocytes/physiology/ultrastructure ; Spermatogenesis/*physiology ; Spermatozoa/physiology/*ultrastructure ; Testis/physiology/*ultrastructure ; },
abstract = {The general organization of the male genital system, the spermatogenesis and the sperm structure of the proturan Acerella muscorum have been described. At the apex of testis apical huge cells are present; their cytoplasm contains a conventional centriole, a large amount of dense material and several less electron-dense masses surrounded by mitochondria. Spermatocytes have normal centrioles and are interconnected by cytoplasmic bridges. Such bridges seem to be absent between spermatid cells and justify the lack of synchronization of cell maturation. Spermatids are almost globular cells with a spheroidal nucleus and a large mass of dense material corresponding to the centriole adjunct. Within this mass a centriole is preserved. Mitochondria of normal structure are located between the nucleus and the plasma membrane. The spermatids are surrounded by a thick membrane. No flagellar structure is formed. Sperm have a compact spheroidal nucleus, a large cap of centriole adjunct material within which a centriole is still visible. A layer of mitochondria is located over the nucleus. The cytoplasm is reduced in comparison to spermatids; many dense bodies are interspersed with sperm in the testicular lumen. The sperm are small, immotile cells of about 2.5-3microm in diameter.},
}
@article {pmid20153693,
year = {2010},
author = {Wylezich, C and Nies, G and Mylnikov, AP and Tautz, D and Arndt, H},
title = {An evaluation of the use of the LSU rRNA D1-D5 domain for DNA-based taxonomy of eukaryotic protists.},
journal = {Protist},
volume = {161},
number = {3},
pages = {342-352},
doi = {10.1016/j.protis.2010.01.003},
pmid = {20153693},
issn = {1618-0941},
mesh = {Classification/*methods ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/*genetics ; Genes, rRNA ; Molecular Biology/*methods ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; },
abstract = {Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater.},
}
@article {pmid20154424,
year = {2009},
author = {Hosaka, K and Sanetomo, R},
title = {Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species.},
journal = {Genes &amp; genetic systems},
volume = {84},
number = {5},
pages = {371-378},
doi = {10.1266/ggs.84.371},
pmid = {20154424},
issn = {1341-7568},
mesh = {Chloroplasts/genetics ; DNA Primers/chemistry/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Genetic Markers/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Solanum tuberosum/*classification/*genetics/growth &amp; development ; },
abstract = {A total of 476 accessions of seven cultivated and 32 wild potato species previously characterized by nuclear DNA (nDNA) and chloroplast DNA (ctDNA) marker analyses were employed to the mitochondrial DNA (mtDNA) marker analysis. Fourteen simple sequence repeat (SSR) markers with mononucleotide repeat regions were developed from the potato mtDNA, although their variability was extremely low. Six mtDNA markers including three developed SSR markers disclosed 40 banding patterns that discriminated 63 different mtDNAs. For the same set of samples, 72 ctDNA banding patterns discriminated 129 different ctDNAs. Consequently, 164 haplotypes were distinguished. The correlation between ctDNA and mtDNA differentiation was positive (r = 0.226), but poor when compared with that between ctDNA and nDNA (r = 0.415), which likely lowered the utility of mtDNA polymorphisms in evaluating relationships among these species. Nevertheless, a finding of a unique mtDNA type in all T-type ctDNA holders (S. tuberosum and S. tarijense) strongly supports S. tarijense functioned as a maternal ancestor of potato.},
}
@article {pmid20156838,
year = {2010},
author = {Lapaille, M and Escobar-Ramírez, A and Degand, H and Baurain, D and Rodríguez-Salinas, E and Coosemans, N and Boutry, M and Gonzalez-Halphen, D and Remacle, C and Cardol, P},
title = {Atypical subunit composition of the chlorophycean mitochondrial F1FO-ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme.},
journal = {Molecular biology and evolution},
volume = {27},
number = {7},
pages = {1630-1644},
doi = {10.1093/molbev/msq049},
pmid = {20156838},
issn = {1537-1719},
mesh = {Adenosine Triphosphate/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; Chlorophyta/*enzymology/genetics/growth &amp; development ; Dimerization ; *Drug Resistance ; Mitochondria/*enzymology ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics/*metabolism ; Oligomycins/*pharmacology ; Phylogeny ; Protein Subunits/antagonists &amp; inhibitors/genetics/*metabolism ; Protons ; RNA, Small Interfering/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {In yeast, mammals, and land plants, mitochondrial F(1)F(O)-ATP synthase (complex V) is a remarkable enzymatic machinery that comprises about 15 conserved subunits. Peculiar among eukaryotes, complex V from Chlamydomonadales algae (order of chlorophycean class) has an atypical subunit composition of its peripheral stator and dimerization module, with nine subunits of unknown evolutionary origin (Asa subunits). In vitro, this enzyme exhibits an increased stability of its dimeric form, and in vivo, Chlamydomonas reinhardtii cells are insensitive to oligomycins, which are potent inhibitors of proton translocation through the F(O) moiety. In this work, we showed that the atypical features of the Chlamydomonadales complex V enzyme are shared by the other chlorophycean orders. By biochemical and in silico analyses, we detected several atypical Asa subunits in Scenedesmus obliquus (Sphaeropleales) and Chlorococcum ellipsoideum (Chlorococcales). In contrast, complex V has a canonical subunit composition in other classes of Chlorophytes (Trebouxiophyceae, Prasinophyceae, and Ulvophyceae) as well as in Streptophytes (land plants), and in Rhodophytes (red algae). Growth, respiration, and ATP levels in Chlorophyceae were also barely affected by oligomycin concentrations that affect representatives of the other classes of Chlorophytes. We finally studied the function of the Asa7 atypical subunit by using RNA interference in C. reinhardtii. Although the loss of Asa7 subunit has no impact on cell bioenergetics or mitochondrial structures, it destabilizes in vitro the enzyme dimeric form and renders growth, respiration, and ATP level sensitive to oligomycins. Altogether, our results suggest that the loss of canonical components of the complex V stator happened at the root of chlorophycean lineage and was accompanied by the recruitment of novel polypeptides. Such a massive modification of complex V stator features might have conferred novel properties, including the stabilization of the enzyme dimeric form and the shielding of the proton channel. In these respects, we discuss an evolutionary scenario for F(1)F(O)-ATP synthase in the whole green lineage (i.e., Chlorophyta and Streptophyta).},
}
@article {pmid20163596,
year = {2009},
author = {Wu, YP and Guan, WJ and Zhao, QJ and He, XH and Pu, YB and Huo, JH and Xie, JF and Han, JL and Rao, SQ and Ma, YH},
title = {A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds.},
journal = {Animal science journal = Nihon chikusan Gakkaiho},
volume = {80},
number = {4},
pages = {372-380},
doi = {10.1111/j.1740-0929.2009.00659.x},
pmid = {20163596},
issn = {1740-0929},
mesh = {Animals ; China ; Complementarity Determining Regions/*genetics ; DNA, Mitochondrial/genetics ; Female ; Goats/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {As the fast pace of genomic research continues to identify mitochondrial lineages in animals, it has become apparent that many independent studies are needed to support a robust phylogenetic inference. The aim of this study was thus to further characterize the maternal lineage, proposed to originate in southwestern region of China, using a wider survey of diverse goat breeds in China. To this end, we sequenced the mitochondrial hypervariable region 1 (HVR1) of the mtDNA control region in 145 goats of 12 Chinese breeds. Phylogenetic analysis revealed that Chinese goats were classified into four distinct lineages (A, B, C and D) as previously reported. A Mantel test and the analysis of Analysis of Molecular Variance (ANOVA) indicated that there was not an obvious geographic structure among Chinese goat breeds. Population expansion analysis based on mismatch distribution and Fu's Fs statistic indicate that two expansion events in Chinese goats occurred respectively at about 11 and 29 mutational time units ago, revealing two star-like subclades in lineage B corresponding to two population expansion events. Moreover, lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China. Multiple lines of evidence from this study and previous studies indicate that for Chinese goats mtDNA lineage B originated from the southwestern region of China.},
}
@article {pmid20167078,
year = {2010},
author = {Doucet-Beaupré, H and Breton, S and Chapman, EG and Blier, PU and Bogan, AE and Stewart, DT and Hoeh, WR},
title = {Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {50},
pmid = {20167078},
issn = {1471-2148},
mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata).<br><br>RESULTS: Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida).<br><br>CONCLUSION: The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.},
}
@article {pmid20192695,
year = {2010},
author = {Nakagawa, E and Kobayashi, M and Suzuki, M and Tsubota, T},
title = {Genetic variation in the harbor seal (Phoca vitulina) and spotted seal (Phoca largha) around Hokkaido, Japan, based on mitochondrial cytochrome b sequences.},
journal = {Zoological science},
volume = {27},
number = {3},
pages = {263-268},
doi = {10.2108/zsj.27.263},
pmid = {20192695},
issn = {0289-0003},
mesh = {Animals ; Cytochromes b/*genetics/metabolism ; DNA/genetics ; *Genetic Variation ; Japan ; Mitochondria/*enzymology ; Phoca/*genetics ; Phylogeny ; },
abstract = {The harbor seal (Phoca vitulina) and spotted seal (Phoca largha) are the main seal species around Hokkaido, Japan. While some investigations have been conducted on the ecology and morphology of these two species, there is a lack of genetic information. We studied variation in mitochondrial cytochrome b sequences in the two species. Fifteen haplotypes were observed in 39 harbor seals from Erimo, Akkeshi, and Nosappu, and 23 were observed in 31 spotted seals from Erimo, Akkeshi, Nosappu, Rausu, Yagishiri Island, and Hamamasu. Phylogenetic trees showed two harbor seal lineages: Group I contained primarily haplotypes from Erimo, and Group II contained haplotypes from Akkeshi and Nosappu. Because the Erimo population had fewer haplotypes and less nucleotide diversity than the Akkeshi and Nosappu populations, we considered it to be Isolated from the others. In contrast, genetic variance within populations of spotted seals (97.3%) was far higher than that among populations (2.7%), determined by analysis of molecular variance. There were no significant difference among the spotted seal populations, indicating the absence of distinct lineages around Hokkaido. The differences in the genetic population structure between the two species could have been generated by their ecological differences. This study provides basic genetic information on these seal species and will contribute to the conservation and management of fisheries and seals throughout Hokkaido.},
}
@article {pmid20192696,
year = {2010},
author = {Ito, M and Jiang, W and Sato, JJ and Zhen, Q and Jiao, W and Goto, K and Sato, H and Ishiwata, K and Oku, Y and Chai, JJ and Kamiya, H},
title = {Molecular phylogeny of the subfamily Gerbillinae (Muridae, Rodentia) with emphasis on species living in the Xinjiang-Uygur Autonomous Region of China and based on the mitochondrial cytochrome b and cytochrome c oxidase subunit II genes.},
journal = {Zoological science},
volume = {27},
number = {3},
pages = {269-278},
doi = {10.2108/zsj.27.269},
pmid = {20192696},
issn = {0289-0003},
mesh = {Animals ; China ; Cytochromes b/*genetics ; Electron Transport Complex IV/*genetics ; Gene Expression Regulation ; Gerbillinae/*genetics ; Mitochondria/genetics/*metabolism ; *Phylogeny ; },
abstract = {Rodents belonging to the subfamily Gerbillinae and living in the Xinjiang-Uygur autonomous region of China were collected in field surveys between 2001 and 2003. We found four Meriones species, including M. chengi M. liycus, M. meridianus, and M. tamariscinus, as well as related species from different genera, Rhombomys opimus and Brachiones przewaliskii For phylogenetic analyses of these gerbilline species, DNA sequences of parts of the mitochondrial cytochrome b (Cytb) and cytochrome c oxidase subunit II (COII) genes were examined with the neighbor Joining, maximum parsimony, maximum likelihood, and Bayesian inference methods. Our phylogenetic analyses suggest that the genus Meriones is not monophyletic and place M. tamaricinus as the sister taxon to a clade comprising Brachiones, Psammomys, Rhombomys, and the other Meriones species. The remaining Meriones species separate into three lineages: M. meridianus (including M. chengi), Meriones unguiculatus, and a clade that includes multiple Meriones species originating from Asia, the Middle East, and Africa. The phylogenetic relationships among the genera Brachines, Meriones, Psammomys, and Rhombomys remain ambiguous, probably due to the saturation of mutations that occurs in fast-evolving mitochondrial DNA. In addition, intraspecific variation was observed for M. meridianus, and this mostly correlated with collection localities, i.e., the northern and southern parts of the Xinjiang region. This variation corresponded to interspecific levels of divergence among other lineages of Meriones. Interestingly, no differences were observed in either the Cytb or COII gene sequences isolated from M. chengi collected from the Turfan Basin in the north and those from M. meridianus in the south, suggesting that M. chengi may be a synonym of M. meridianus.},
}
@article {pmid20202479,
year = {2010},
author = {Wang, KC and Kondo, H and Hirono, I and Aoki, T},
title = {The Marsupenaeus japonicus voltage-dependent anion channel (MjVDAC) protein is involved in white spot syndrome virus (WSSV) pathogenesis.},
journal = {Fish &amp; shellfish immunology},
volume = {29},
number = {1},
pages = {94-103},
doi = {10.1016/j.fsi.2010.02.020},
pmid = {20202479},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Membrane Potential, Mitochondrial/immunology ; Molecular Sequence Data ; Penaeidae/genetics/immunology/*virology ; *Phylogeny ; RNA/chemistry/genetics ; RNA Interference/immunology ; Random Amplified Polymorphic DNA Technique ; Sequence Alignment ; Sequence Analysis, DNA ; Voltage-Dependent Anion Channels/genetics/*immunology ; White spot syndrome virus 1/*immunology ; },
abstract = {Voltage-dependent anion channel (VDAC) proteins abound in the outer membrane of mitochondria. They play an important role in mitochondrial membrane permeabilization (MMP), which can lead to stress-induced cellular apoptosis and necrosis. Several pathogens regulate this MMP in their host cells to benefit their replication cycle, while in other cases, the host can use the same mechanism to combat pathogenesis. In this study, the first shrimp VDAC gene was identified and characterized from Marsupenaeus japonicus (MjVDAC). Its open reading frame (ORF) contained 849 bp encoding 282 amino acids. The deduced MjVDAC protein includes the 4-element eukaryotic porin signature motif, the conserved ATP binding motif (the GLK motif) and a VKAKV-like sequence known in other organisms to be involved in the protein's incorporation in the mitochondrial outer membrane. Tissue tropism analysis indicated that MjVDAC is abundant in the heart, muscle, stomach and pleopod. MjVDAC proteins colocalized with mitochondria in transiently transfected Sf9 cells and in shrimp hemocytes. dsRNA silencing of shrimp VDAC delayed white spot syndrome virus (WSSV) infection by 1 day in different shrimp organs. Taken together, these findings suggest that MjVDAC is likely to be involved in WSSV pathogenesis.},
}
@article {pmid20226718,
year = {2010},
author = {Van Aken, O and Whelan, J and Van Breusegem, F},
title = {Prohibitins: mitochondrial partners in development and stress response.},
journal = {Trends in plant science},
volume = {15},
number = {5},
pages = {275-282},
doi = {10.1016/j.tplants.2010.02.002},
pmid = {20226718},
issn = {1878-4372},
mesh = {Animals ; Humans ; Mitochondria/*metabolism ; Phylogeny ; Plant Development ; Plants/genetics/*metabolism ; Prohibitins ; Repressor Proteins/*metabolism ; Signal Transduction ; *Stress, Physiological ; },
abstract = {Twelve years after their discovery in plants, prohibitins (PHBs) have retained their status as some of the most enigmatic mitochondrial proteins. Although the original hypothesis that PHBs act as negative cell cycle regulators has lost its impetus in plants, the essential molecular function(s) PHB complexes perform in the inner mitochondrial membrane are now beginning to be understood. We review the current state of knowledge to propose a unifying model that positions the PHB complex as a universal protein scaffold for key mitochondrial processes, including protein processing, respiratory chain function and mitochondrial DNA organization. Furthermore, recent findings indicate that PHBs play an active role in stress tolerance and are involved in triggering retrograde signals in response to stress and mitochondrial dysfunction.},
}
@article {pmid20233703,
year = {2010},
author = {Liu, SP and Wang, K and Yuan, XP and Wang, DQ and Yue, XJ and Chen, DQ},
title = {[Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River].},
journal = {Yi chuan = Hereditas},
volume = {32},
number = {3},
pages = {254-263},
doi = {10.3724/sp.j.1005.2010.00254},
pmid = {20233703},
issn = {0253-9772},
mesh = {Animals ; China ; Cytochromes b/genetics ; Fishes/classification/*genetics ; Genetic Variation/*genetics ; Genetics, Population ; Geography ; Haplotypes/genetics ; Phylogeny ; },
abstract = {The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among populations.},
}
@article {pmid20304999,
year = {2010},
author = {Bullerwell, CE and Burger, G and Gott, JM and Kourennaia, O and Schnare, MN and Gray, MW},
title = {Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa.},
journal = {Eukaryotic cell},
volume = {9},
number = {5},
pages = {762-773},
pmid = {20304999},
issn = {1535-9786},
support = {R01 GM054663/GM/NIGMS NIH HHS/United States ; MOP-4124/CAPMC/CIHR/Canada ; GM54663/GM/NIGMS NIH HHS/United States ; },
mesh = {Amoebozoa/cytology/*genetics ; Animals ; Base Sequence ; Cell Fractionation ; Computational Biology ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Dictyostelium/genetics ; Genome, Mitochondrial/*genetics ; Hartmannella/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Physarum polycephalum/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 5S/chemistry/*genetics ; Ribosome Subunits, Large, Eukaryotic/genetics ; Sequence Homology, Amino Acid ; },
abstract = {5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.},
}
@article {pmid20333239,
year = {2010},
author = {Dolezal, P and Dagley, MJ and Kono, M and Wolynec, P and Likić, VA and Foo, JH and Sedinová, M and Tachezy, J and Bachmann, A and Bruchhaus, I and Lithgow, T},
title = {The essentials of protein import in the degenerate mitochondrion of Entamoeba histolytica.},
journal = {PLoS pathogens},
volume = {6},
number = {3},
pages = {e1000812},
pmid = {20333239},
issn = {1553-7374},
mesh = {Animals ; Cytoplasmic Vesicles/metabolism ; Entamoeba histolytica/genetics/*metabolism ; Genome, Protozoan ; Markov Chains ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phosphate Transport Proteins/genetics/metabolism ; Phosphates/metabolism ; Phylogeny ; Protein Transport/*physiology ; Protozoan Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics ; },
abstract = {Several essential biochemical processes are situated in mitochondria. The metabolic transformation of mitochondria in distinct lineages of eukaryotes created proteomes ranging from thousands of proteins to what appear to be a much simpler scenario. In the case of Entamoeba histolytica, tiny mitochondria known as mitosomes have undergone extreme reduction. Only recently a single complete metabolic pathway of sulfate activation has been identified in these organelles. The E. histolytica mitosomes do not produce ATP needed for the sulfate activation pathway and for three molecular chaperones, Cpn60, Cpn10 and mtHsp70. The already characterized ADP/ATP carrier would thus be essential to provide cytosolic ATP for these processes, but how the equilibrium of inorganic phosphate could be maintained was unknown. Finally, how the mitosomal proteins are translocated to the mitosomes had remained unclear. We used a hidden Markov model (HMM) based search of the E. histolytica genome sequence to discover candidate (i) mitosomal phosphate carrier complementing the activity of the ADP/ATP carrier and (ii) membrane-located components of the protein import machinery that includes the outer membrane translocation channel Tom40 and membrane assembly protein Sam50. Using in vitro and in vivo systems we show that E. histolytica contains a minimalist set up of the core import components in order to accommodate a handful of mitosomal proteins. The anaerobic and parasitic lifestyle of E. histolytica has produced one of the simplest known mitochondrial compartments of all eukaryotes. Comparisons with mitochondria of another amoeba, Dictystelium discoideum, emphasize just how dramatic the reduction of the protein import apparatus was after the loss of archetypal mitochondrial functions in the mitosomes of E. histolytica.},
}
@article {pmid20336381,
year = {2011},
author = {Feng, Y and Li, Q and Kong, L and Zheng, X},
title = {DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) based on mitochondrial COI and 16S rRNA genes.},
journal = {Molecular biology reports},
volume = {38},
number = {1},
pages = {291-299},
pmid = {20336381},
issn = {1573-4978},
mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Pectinidae/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under the terms DNA barcoding or DNA taxonomy. In this study, we have sequenced partial sequences of mitochondrial COI and 16S rRNA genes from 63 specimens of 8 species of Pectinidae to assess whether DNA barcodes can efficiently distinguish these species. Sequences from homologous regions of four other species of this family were gathered from GenBank. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species. When using neighbour-joining clustering based on COI and 16S genes, all species fell into reciprocally monophyletic clades with high bootstrap values. These evidenced that these scallop species can be efficiently identified by DNA barcoding. Evolutionary relationships of Pectinidae were also examined using the two mitochondrial genes. The results are almost consistent with Waller's classification, which was proposed on the basis of shell microstructure and the morphological characteristics of juveniles.},
}
@article {pmid20381646,
year = {2010},
author = {Augot, D and Sauvage, F and Jouet, D and Simphal, E and Veuille, M and Couloux, A and Kaltenbach, ML and Depaquit, J},
title = {Discrimination of Culicoides obsoletus and Culicoides scoticus, potential bluetongue vectors, by morphometrical and mitochondrial cytochrome oxidase subunit I analysis.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {10},
number = {5},
pages = {629-637},
doi = {10.1016/j.meegid.2010.03.016},
pmid = {20381646},
issn = {1567-7257},
mesh = {Animals ; Bluetongue/epidemiology/*transmission ; Bluetongue virus ; Ceratopogonidae/*anatomy &amp; histology/*classification/enzymology/genetics ; DNA, Mitochondrial/analysis ; Electron Transport Complex IV/*genetics ; Female ; Insect Vectors/*anatomy &amp; histology/*classification/enzymology/genetics ; Male ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Protein Subunits/*genetics ; },
abstract = {Biting midges of the Culicoides obsoletus Meigen species complex (Diptera: Ceratopogonidae) are increasingly suspected as vectors of the recent emergence of bluetongue virus in Europe. Within this complex, identification of the C. obsoletus and Culicoides scoticus females is considered as difficult or sometimes not possible while the identification of males is easy, based on genitalia observation. Nolan et al. (2007) concluded that the distinction of C. obsoletus and C. scoticus females is not possible according to morphology but require molecular analyses. In 2010, the identification of biting midges is done under a stereomicroscope without specific identification within the C. obsoletus species complex. However, such a specific identification distinguishing C. obsoletus s. str. and C. scoticus s. str. is crucial to identify the European competent vectors of the virus, their relative abundances and then accurately assess the risk. We performed morphometric analyses of head, genitalia and thorax of females combined with sequencing of the cytochrome oxidase I barcode fragment of mitochondrial DNA on 88 specimens in order to have a molecular identification of our sampled species. As we knew the actual species of individuals thanks to molecular results, we explored the discriminant power of 15 morphometric variables to distinguish the females according to their species. Multivariate analyses were performed on the morphometric measurements to identify and validate a combination of variables leading to an accurate species identification. It appears that females of C. obsoletus and C. scoticus can be accurately distinguished based on only four variables: width between chitinous plates, length and width of spermathecae1 and length of spermatheca2. This approach should improve the accuracy of morphologically-based species identification.},
}
@article {pmid20388489,
year = {2010},
author = {Rial, E and Rodríguez-Sánchez, L and Gallardo-Vara, E and Zaragoza, P and Moyano, E and González-Barroso, MM},
title = {Lipotoxicity, fatty acid uncoupling and mitochondrial carrier function.},
journal = {Biochimica et biophysica acta},
volume = {1797},
number = {6-7},
pages = {800-806},
doi = {10.1016/j.bbabio.2010.04.001},
pmid = {20388489},
issn = {0006-3002},
mesh = {Animals ; Carrier Proteins/genetics/metabolism ; Fatty Acids/*metabolism/*toxicity ; Humans ; Ion Channels/genetics/metabolism ; Mitochondria/*drug effects/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; Oxidative Phosphorylation ; Oxidative Stress/drug effects ; Phylogeny ; Uncoupling Agents/metabolism/toxicity ; Uncoupling Protein 1 ; },
abstract = {Diseases like obesity, diabetes or generalized lipodystrophy cause a chronic elevation of circulating fatty acids that can become cytotoxic, a condition known as lipotoxicity. Fatty acids cause oxidative stress and alterations in mitochondrial structure and function. The uncoupling of the oxidative phosphorylation is one of the most recognized deleterious fatty acid effects and several metabolite transporters are known to mediate in their action. The fatty acid interaction with the carriers leads to membrane depolarization and/or the conversion of the carrier into a pore. The result is the opening of the permeability transition pore and the initiation of apoptosis. Unlike the other members of the mitochondrial carrier superfamily, the eutherian uncoupling protein UCP1 has evolved to achieve its heat-generating capacity in the physiological context provided by the brown adipocyte and therefore it is activated by the low fatty acid concentrations generated by the noradrenaline-stimulated lipolysis.},
}
@article {pmid20421194,
year = {2010},
author = {Ohara, K and Sasaki, K and Yazaki, K},
title = {Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.},
journal = {Journal of experimental botany},
volume = {61},
number = {10},
pages = {2683-2692},
pmid = {20421194},
issn = {1460-2431},
mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Enzyme Assays ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Intracellular Space/metabolism ; Organ Specificity/genetics ; Oryza/*enzymology/genetics ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plastoquinone/chemistry/metabolism ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Subcellular Fractions/enzymology ; Substrate Specificity ; Ubiquinone/biosynthesis/chemistry ; },
abstract = {Long chain prenyl diphosphates are crucial biosynthetic precursors of ubiquinone (UQ) in many organisms, ranging from bacteria to humans, as well as precursors of plastoquinone in photosynthetic organisms. The cloning and characterization of two solanesyl diphosphate synthase genes, OsSPS1 and OsSPS2, in Oryza sativa is reported here. OsSPS1 was highly expressed in root tissue whereas OsSPS2 was found to be high in both leaves and roots. Enzymatic characterization using recombinant proteins showed that both OsSPS1 and OsSPS2 could produce solanesyl diphosphates as their final product, while OsSPS1 showed stronger activity than OsSPS2. However, an important biological difference was observed between the two genes: OsSPS1 complemented the yeast coq1 disruptant, which does not form UQ, whereas OsSPS2 only very weakly complemented the growth defect of the coq1 mutant. HPLC analyses showed that both OsSPS1 and OsSPS2 yeast transformants produced UQ9 instead of UQ6, which is the native yeast UQ. According to the complementation study, the UQ9 levels in OsSPS2 transformants were much lower than that of OsSPS1. Green fluorescent protein fusion analyses showed that OsSPS1 localized to mitochondria, while OsSPS2 localized to plastids. This suggests that OsSPS1 is involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria, whereas OsSPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation. These findings indicate that O. sativa has a different mechanism for the supply of isoprenoid precursors in UQ biosynthesis from Arabidopsis thaliana, in which SPS1 provides a prenyl moiety for UQ9 at the endoplasmic reticulum.},
}
@article {pmid20461407,
year = {2010},
author = {Li, J and Zhao, GH and Zou, FC and Mo, XH and Yuan, ZG and Ai, L and Li, HL and Weng, YB and Lin, RQ and Zhu, XQ},
title = {Combined mitochondrial 16S and 12S rDNA sequences: an effective genetic marker for inter-species phylogenetic analysis of zoonotic trematodes.},
journal = {Parasitology research},
volume = {107},
number = {3},
pages = {561-569},
pmid = {20461407},
issn = {1432-1955},
mesh = {Animals ; China/epidemiology ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Female ; Genetic Markers/*genetics ; Genetic Variation ; Humans ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Schistosoma japonicum/classification/*genetics ; Schistosomiasis japonica/epidemiology/parasitology ; Sequence Analysis, DNA ; Species Specificity ; Zoonoses/epidemiology/*parasitology ; },
abstract = {The present study studied the genetic variation among Schistosoma japonicum isolates from different endemic regions in mainland China and examined the phylogenetic relationships of zoonotic trematodes using the combined mitochondrial 16S and 12S ribosomal DNA sequences. The fragments of 16S and 12S rDNA were amplified from 22 S. japonicum isolates, and sequenced, and the relevant sequences of other nine trematode species belonging to six genera in four families were downloaded from GenBank, and their phylogenetic relationships were re-constructed by unweighted pair-group method with arithmetic averages analyses using the combined 16S and 12S rDNA sequences, with Trichinella spiralis as outgroup. The results showed that the partial sequences of mitochondrial 16S and 12S rDNA of S. japonicum were 757 and 797 bp, respectively, and they were quite conserved among the S. japonicum isolates. Phylogenetic analysis revealed that the combined 16S and 12S rDNA sequences were not able to distinguish S. japonicum isolates in mountainous areas from those in lake/marshland areas in mainland China. However, the combined sequences could distinguish different species of zoonotic trematodes. Therefore, the combined mitochondrial 16S and 12S rDNA sequences provide an effective molecular marker for the inter-species phylogenetic analysis and differential identification of zoonotic trematodes.},
}
@article {pmid20470834,
year = {2010},
author = {Týc, J and Long, S and Jirků, M and Lukes, J},
title = {YCF45 protein, usually associated with plastids, is targeted into the mitochondrion of Trypanosoma brucei.},
journal = {Molecular and biochemical parasitology},
volume = {173},
number = {1},
pages = {43-47},
doi = {10.1016/j.molbiopara.2010.05.002},
pmid = {20470834},
issn = {1872-9428},
mesh = {Cell Line ; Gene Transfer, Horizontal ; Humans ; Mitochondria/genetics/*metabolism ; Phylogeny ; Plastids/genetics/*metabolism ; Protein Transport ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma brucei brucei/classification/genetics/*metabolism ; },
abstract = {YCF45 belongs to a family of proteins of unknown function usually located in the chloroplast of plants. Its highly conserved homologues were found in the genomes of several Trypanosoma and Leishmania species. HA(3)-tagging of the YCF45 protein with the start codon as annotated in the Gene(DB) revealed its cytosolic localization in the cultured procyclic stage of Trypanosoma brucei. However, when a more upstream located start codon was used in another HA(3)-tagged construct, the resulting protein was targeted to the mitochondrion. We propose that YCF45 was acquired by an ancestral trypanosomatid by horizontal gene transfer and in the absence of a plastid was re-targeted to the mitochondrion.},
}
@article {pmid20494640,
year = {2011},
author = {Liu, C and Wang, SY and Zhao, M and Xu, ZY and Hu, YH and Chen, F and Zhang, RZ and Gao, GF and Yu, YS and Kong, QP},
title = {Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China.},
journal = {Forensic science international. Genetics},
volume = {5},
number = {1},
pages = {e4-10},
doi = {10.1016/j.fsigen.2010.04.007},
pmid = {20494640},
issn = {1878-0326},
mesh = {Asian People/*genetics ; China ; Complementarity Determining Regions/genetics ; DNA Fingerprinting ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Ethnicity/*genetics ; Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Humans ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; *Polymorphism, Genetic ; Reference Standards ; },
abstract = {Gelao ethnic group, an aboriginal population residing in southwest China, has undergone a long and complex evolutionary process. To investigate the genetic structure of this ancient ethnic group, mitochondrial DNA (mtDNA) polymorphisms of 102 Gelao individuals were collected and analyzed in this study. With the aid of the information extracted from control-region hypervariable segments (HVSs) I and II as well as some necessary coding-region segments, phylogenetic status of all mtDNAs under study were determined by means of classifying into various defined haplogroups. The southern-prevalent haplogroups B, R9, and M7 account for 45.1% of the gene pool, whereas northern-prevalent haplogroups A, D, G, N9, and M8 consist of 39.2%. Haplogroup distribution indicates that the Gelao bears signatures of southern populations and possesses some regional characters. In the PC map, Gelao clusters together with populations with Bai-Yue tribe origin as well as the local Han and the Miao. The results demonstrate the complexity of Gelao population and the data can well supplement the China mtDNA database.},
}
@article {pmid20528687,
year = {2010},
author = {Shiflett, AM and Johnson, PJ},
title = {Mitochondrion-related organelles in eukaryotic protists.},
journal = {Annual review of microbiology},
volume = {64},
number = {},
pages = {409-429},
pmid = {20528687},
issn = {1545-3251},
support = {T32 A1007323//PHS HHS/United States ; F32 A108004//PHS HHS/United States ; R37 A127857//PHS HHS/United States ; R01 A1069058//PHS HHS/United States ; F32 AI080084/AI/NIAID NIH HHS/United States ; R37 AI027857/AI/NIAID NIH HHS/United States ; },
mesh = {Eukaryota/*genetics/*metabolism/ultrastructure ; *Genes, Mitochondrial ; Iron-Sulfur Proteins/metabolism ; Metabolic Networks and Pathways ; Mitochondria/*genetics/*metabolism/ultrastructure ; Phylogeny ; Sequence Homology ; },
abstract = {The discovery of mitochondrion-type genes in organisms thought to lack mitochondria led to the demonstration that hydrogenosomes share a common ancestry with mitochondria, as well as the discovery of mitosomes in multiple eukaryotic lineages. No examples of examined eukaryotes lacking a mitochondrion-related organelle exist, implying that the endosymbiont that gave rise to the mitochondrion was present in the first eukaryote. These organelles, known as hydrogenosomes, mitosomes, or mitochondrion-like organelles, are typically reduced, both structurally and biochemically, relative to classical mitochondria. However, despite their diversification and adaptation to different niches, all appear to play a role in Fe-S cluster assembly, as observed for mitochondria. Although evidence supports the use of common protein targeting mechanisms in the biogenesis of these diverse organelles, divergent features are also apparent. This review examines the metabolism and biogenesis of these organelles in divergent unicellular microbes, with a focus on parasitic protists.},
}
@article {pmid20538375,
year = {2010},
author = {Lakatos, A and Derbeneva, O and Younes, D and Keator, D and Bakken, T and Lvova, M and Brandon, M and Guffanti, G and Reglodi, D and Saykin, A and Weiner, M and Macciardi, F and Schork, N and Wallace, DC and Potkin, SG and , },
title = {Association between mitochondrial DNA variations and Alzheimer's disease in the ADNI cohort.},
journal = {Neurobiology of aging},
volume = {31},
number = {8},
pages = {1355-1363},
pmid = {20538375},
issn = {1558-1497},
support = {R01 NS041850/NS/NINDS NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; U24-RR021992/RR/NCRR NIH HHS/United States ; P20 RR020837/RR/NCRR NIH HHS/United States ; U24 RR021992/RR/NCRR NIH HHS/United States ; U01 AG024904-01/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; U19 AG010483/AG/NIA NIH HHS/United States ; UL1 RR025774/RR/NCRR NIH HHS/United States ; 3U01AG024904-03S5/AG/NIA NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; U19 AG023122-01/AG/NIA NIH HHS/United States ; NS41850/NS/NINDS NIH HHS/United States ; NS211328/NS/NINDS NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; P01 HL058120/HL/NHLBI NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; },
mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/diagnosis/*genetics ; Case-Control Studies ; Cohort Studies ; DNA, Mitochondrial/*genetics ; Female ; Follow-Up Studies ; Genes, Mitochondrial/genetics ; Genetic Association Studies/methods ; Genetic Variation/*genetics ; Humans ; Longitudinal Studies ; Male ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Prospective Studies ; Random Allocation ; },
abstract = {Despite the central role of amyloid deposition in the development of Alzheimer's disease (AD), the pathogenesis of AD still remains elusive at the molecular level. Increasing evidence suggests that compromised mitochondrial function contributes to the aging process and thus may increase the risk of AD. Dysfunctional mitochondria contribute to reactive oxygen species (ROS) which can lead to extensive macromolecule oxidative damage and the progression of amyloid pathology. Oxidative stress and amyloid toxicity leave neurons chemically vulnerable. Because the brain relies on aerobic metabolism, it is apparent that mitochondria are critical for the cerebral function. Mitochondrial DNA sequence changes could shift cell dynamics and facilitate neuronal vulnerability. Therefore we postulated that mitochondrial DNA sequence polymorphisms may increase the risk of AD. We evaluated the role of mitochondrial haplogroups derived from 138 mitochondrial polymorphisms in 358 Caucasian Alzheimer's Disease Neuroimaging Initiative (ADNI) subjects. Our results indicate that the mitochondrial haplogroup UK may confer genetic susceptibility to AD independently of the apolipoprotein E4 (APOE4) allele.},
}
@article {pmid20568109,
year = {2010},
author = {Monticone, M and Panfoli, I and Ravera, S and Puglisi, R and Jiang, MM and Morello, R and Candiani, S and Tonachini, L and Biticchi, R and Fabiano, A and Cancedda, R and Boitani, C and Castagnola, P},
title = {The nuclear genes Mtfr1 and Dufd1 regulate mitochondrial dynamic and cellular respiration.},
journal = {Journal of cellular physiology},
volume = {225},
number = {3},
pages = {767-776},
doi = {10.1002/jcp.22279},
pmid = {20568109},
issn = {1097-4652},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; *Cell Respiration/genetics ; *Energy Metabolism/genetics ; Gene Expression Regulation, Developmental ; HeLa Cells ; Humans ; In Situ Hybridization ; Leydig Cells/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/*metabolism ; Mitochondrial Proteins/deficiency/genetics/*metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Phylogeny ; Polymerase Chain Reaction ; RNA Interference ; RNA, Messenger/metabolism ; Sertoli Cells/metabolism ; Spermatids/metabolism ; Spermatocytes/metabolism ; Testis/cytology/*metabolism ; Transfection ; },
abstract = {Dufd1 (DUF729 domain containing 1) is related to Mtfr1 (mitochondrial fission regulator 1), a gene involved in the regulation of antioxidant activity in the mouse testis. The present study was undertaken to better understand their role in regulating mitochondrial architecture and function in the mouse. We show that Dufd1 is expressed as a 2 kb mRNA and has a more specific tissue pattern compared to Mtfr1, with highest level of expression in testes, lower level in spleen, and negligible levels in other organs and/or tissues. In the male gonad, Dufd1 mRNA expression increases during postnatal development, similarly to Mtfr1. In situ hybridization and real-time PCR analyses show that Dufd1 is expressed in the seminiferous tubules by middle-late pachytene spermatocytes and spermatids. In transfected cells, the Dufd1-tagged protein is located in mitochondria, associated with the tips of mitochondrial tubules and to tubules constrictions, and induces mitochondrial fission although with a lesser efficiency than Mtfr1. We also found that both endogenous Dufd1 and Mtfr1 proteins are associated with membrane-enriched subcellular fractions, including mitochondria. Inhibition of Mtfr1 and/or Dufd1 expression, in a testicular germ cells line, severely impairs O(2) consumption and indicates that both genes are required for mitochondrial respiration. Accordingly, analysis of testes mitochondria from Mtfr1-deficient mice reveals severely reduced O(2) consumption and ATP synthesis compared to wt animals. These data show that, in murine testis, Dufd1 and Mtfr1 have redundant functions related to mitochondrial physiology and represent genes with a potential role in testicular function.},
}
@article {pmid20633537,
year = {2010},
author = {Sterky, FH and Ruzzenente, B and Gustafsson, CM and Samuelsson, T and Larsson, NG},
title = {LRPPRC is a mitochondrial matrix protein that is conserved in metazoans.},
journal = {Biochemical and biophysical research communications},
volume = {398},
number = {4},
pages = {759-764},
doi = {10.1016/j.bbrc.2010.07.019},
pmid = {20633537},
issn = {1090-2104},
mesh = {Animals ; Conserved Sequence ; HeLa Cells ; Humans ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Neoplasm Proteins/classification/genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; Repetitive Sequences, Amino Acid ; },
abstract = {LRPPRC (also called LRP130) is an RNA-binding pentatricopeptide repeat protein. LRPPRC has been recognized as a mitochondrial protein, but has also been shown to regulate nuclear gene transcription and to bind specific RNA molecules in both the nucleus and the cytoplasm. We here present a bioinformatic analysis of the LRPPRC primary sequence, which reveals that orthologs to the LRPPRC gene are restricted to metazoan cells and that all of the corresponding proteins contain mitochondrial targeting signals. To address the subcellular localization further, we have carefully analyzed LRPPRC in mammalian cells and identified a single isoform that is exclusively localized to mitochondria. The LRPPRC protein is imported to the mitochondrial matrix and its mitochondrial targeting sequence is cleaved upon entry.},
}
@article {pmid20640581,
year = {2010},
author = {Li, A and Chen, Y and Zhao, X and Niu, Y and Cong, P and Zhang, Z and Chen, W and Jiang, W and Mo, D},
title = {Characterization and transcriptional regulation analysis of the porcine TNFAIP8L2 gene.},
journal = {Molecular genetics and genomics : MGG},
volume = {284},
number = {3},
pages = {185-195},
pmid = {20640581},
issn = {1617-4623},
mesh = {Animals ; Base Sequence ; Binding Sites/genetics ; Cell Line ; Cell Nucleus/metabolism ; Chromosomes, Mammalian/genetics ; Cloning, Molecular ; Endoplasmic Reticulum/metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation ; Green Fluorescent Proteins/genetics/metabolism ; Intracellular Signaling Peptides and Proteins/classification/*genetics ; Luciferases/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Radiation Hybrid Mapping ; Regulatory Sequences, Nucleic Acid/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Swine/*genetics ; Tetradecanoylphorbol Acetate/pharmacology ; Transcription Factor AP-1/metabolism ; Transcription Initiation Site ; Transcription, Genetic/drug effects ; },
abstract = {Tumor necrosis factor alpha-induced protein 8-like 2 (TNFAIP8L2) is a new member of the tumor necrosis factor-alpha-induced protein 8 (TNFAIP8) family that functions as an important factor in the maintenance of immune homeostasis. In this study, we cloned the cDNA sequences and analyzed the genomic structure of porcine TNFAIP8L2. RH mapping using the IMpRH panel showed that this gene was closely linked to microsatellite marker SW512 in pig chromosome 4. Subcellular localization analysis showed GFP-TNFAIP8L2 fusion protein distributed in nucleus as well as cytoplasm including mitochondria and endoplasmic reticulum. Real-time PCR analysis revealed that porcine TNFAIP8L2 was more highly expressed in spleen than other tissues. To understand its characterization of transcriptional regulation, we cloned approximately 2 kb of 5'-regulatory region upstream to the porcine TNFAIP8L2 translational start site and generated sequential deletion constructs evaluated in dual-luciferase reporter assay. The results demonstrated that its core promoter is 435 base pairs (bp) upstream to the transcription initiation site. Then, site-directed mutation experiment combined with electrophoretic mobility shift assay (EMSA) indicated that M-CAT binding factor (MCBF) and activator protein 1 (AP-1) were important transcription factors for porcine TNFAIP8L2. These findings provide an important basis for further understanding of porcine TNFAIP8L2 regulation and function in swine.},
}
@article {pmid20641018,
year = {2010},
author = {Feng, J and Zhao, J and Li, J and Zhang, L and Jiang, L},
title = {Functional characterization of the PP2C phosphatase CaPtc2p in the human fungal pathogen Candida albicans.},
journal = {Yeast (Chichester, England)},
volume = {27},
number = {9},
pages = {753-764},
doi = {10.1002/yea.1778},
pmid = {20641018},
issn = {1097-0061},
mesh = {Antifungal Agents/toxicity ; Azoles/toxicity ; Candida albicans/drug effects/*enzymology/genetics ; Cytoplasm/enzymology ; Fungal Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Profiling ; Humans ; Hydroxyurea/toxicity ; Methyl Methanesulfonate/toxicity ; Mitochondria/enzymology ; Phosphoprotein Phosphatases/deficiency/*metabolism ; Phylogeny ; Protein Phosphatase 2C ; Sequence Homology, Amino Acid ; Sodium Dodecyl Sulfate/toxicity ; },
abstract = {Type 2C protein phosphatases (PP2C) are monomeric enzymes and their activities require the presence of magnesium or manganese ion. There are seven PP2C-like genes in Candida albicans. In this study, we demonstrate that CaPtc2p is a PP2C phosphatase. Surprisingly, in addition to the cytoplasmic localization, CaPtc2p is partially associated with mitochondria in yeast-form and filamentous cells of C. albicans. Expression of CaPTC2 is developmentally regulated during the serum-induced filamentation. Deletion of CaPTC2 renders C. albicans cells sensitive to SDS and azole antifungals, as well as the DNA methylation agent methylmethane sulphonate and the DNA synthesis inhibitor hydroxyurea. Therefore, CaPtc2p might fulfil multiple functions, including the regulation of mitochondrial physiology and checkpoint recovery from DNA damage in C. albicans cells.},
}
@article {pmid20659325,
year = {2010},
author = {Syrjänen, L and Tolvanen, M and Hilvo, M and Olatubosun, A and Innocenti, A and Scozzafava, A and Leppiniemi, J and Niederhauser, B and Hytönen, VP and Gorr, TA and Parkkila, S and Supuran, CT},
title = {Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates.},
journal = {BMC biochemistry},
volume = {11},
number = {},
pages = {28},
pmid = {20659325},
issn = {1471-2091},
mesh = {Amino Acid Sequence ; Animals ; Carbonic Anhydrases/*chemistry/*classification/genetics ; Databases, Protein ; Dimerization ; Drosophila Proteins/*chemistry/*classification/genetics ; Drosophila melanogaster/*enzymology ; Enzyme Inhibitors/chemistry/pharmacology ; Kinesics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sulfonamides/chemistry/pharmacology ; },
abstract = {BACKGROUND: The beta-carbonic anhydrase (CA, EC 4.2.1.1) enzymes have been reported in a variety of organisms, but their existence in animals has been unclear. The purpose of the present study was to perform extensive sequence analysis to show that the beta-CAs are present in invertebrates and to clone and characterize a member of this enzyme family from a representative model organism of the animal kingdom, e.g., Drosophila melanogaster.<br><br>RESULTS: The novel beta-CA gene, here named DmBCA, was identified from FlyBase, and its orthologs were searched and reconstructed from sequence databases, confirming the presence of beta-CA sequences in 55 metazoan species. The corresponding recombinant enzyme was produced in Sf9 insect cells, purified, kinetically characterized, and its inhibition was investigated with a series of simple, inorganic anions. Holoenzyme molecular mass was defined by dynamic light scattering analysis and gel filtration, and the results suggested that the holoenzyme is a dimer. Double immunostaining confirmed predictions based on sequence analysis and localized DmBCA protein to mitochondria. The enzyme showed high CO2 hydratase activity, with a kcat of 9.5 x 105 s-1 and a kcat/KM of 1.1 x 108 M-1s-1. DmBCA was appreciably inhibited by the clinically-used sulfonamide acetazolamide, with an inhibition constant of 49 nM. It was moderately inhibited by halides, pseudohalides, hydrogen sulfide, bisulfite and sulfate (KI values of 0.67 - 1.36 mM) and more potently by sulfamide (KI of 0.15 mM). Bicarbonate, nitrate, nitrite and phenylarsonic/boronic acids were much weaker inhibitors (KIs of 26.9 - 43.7 mM).<br><br>CONCLUSIONS: The Drosophila beta-CA represents a highly active mitochondrial enzyme that is a potential model enzyme for anti-parasitic drug development.},
}
@article {pmid20663713,
year = {2011},
author = {Moriyama, T and Terasawa, K and Sato, N},
title = {Conservation of POPs, the plant organellar DNA polymerases, in eukaryotes.},
journal = {Protist},
volume = {162},
number = {1},
pages = {177-187},
doi = {10.1016/j.protis.2010.06.001},
pmid = {20663713},
issn = {1618-0941},
mesh = {Animals ; DNA-Directed DNA Polymerase/isolation &amp; purification/*metabolism ; Mitochondria/enzymology ; Nucleic Acid Synthesis Inhibitors ; Organelles/*enzymology ; Phylogeny ; Rats ; Species Specificity ; Tetrahymena thermophila/*enzymology ; },
abstract = {POPs, plant organellar DNA polymerases, have been isolated from various photosynthetic eukaryotes. Previously, we purified the native POP of Cyanidioschyzon merolae(CmPOP) from whole cellular extracts and showed that CmPOP has DNA polymerase activity with a high processivity and a 3'-5' exonuclease activity, and its expression is related to cell proliferation. In rice, the recombinant protein of POP has activities found in CmPOP, and high fidelity of POP has also been demonstrated. These facts suggest that POPs are involved in the replication of organellar genomes. POPs are also conserved in most non-opisthokont eukaryotes, which lack DNA polymerase γ (Polγ), a mitochondrial replication enzyme in opisthokonts (fungi and animals). The ciliateTetrahymena thermophilacontains a single gene for a putative POP (TetPOP). Immunoblot analysis demonstrated that TetPOP is localized in mitochondria, and TetPOP has been purified from mitochondria through a column chromatography series. Sensitivity to phosphonoacetate and dideoxyTTP was examined in POPs (TetPOP and CmPOP) or POP-containing organelles (chloroplasts of Arabidopsis) and other polymerases (DNA polymerase I and mitochondria of rat liver, which contain Polγ), and the results suggest that high sensitivity to phosphonoacetate is unique to POPs in Family-A DNA polymerases. Finally, we propose a model for the succession of organellar DNA polymerases.},
}
@article {pmid20676380,
year = {2010},
author = {Capra, JA and Paeschke, K and Singh, M and Zakian, VA},
title = {G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.},
journal = {PLoS computational biology},
volume = {6},
number = {7},
pages = {e1000861},
pmid = {20676380},
issn = {1553-7358},
support = {T32 GN003284//PHS HHS/United States ; R37 GM026938/GM/NIGMS NIH HHS/United States ; P50 GM071508/GM/NIGMS NIH HHS/United States ; R01 GM026938/GM/NIGMS NIH HHS/United States ; R01 GM076275/GM/NIGMS NIH HHS/United States ; GM076275/GM/NIGMS NIH HHS/United States ; T32 HG003284/HG/NHGRI NIH HHS/United States ; },
mesh = {Base Sequence ; *Conserved Sequence ; DNA Breaks, Double-Stranded ; DNA, Fungal/*chemistry ; *G-Quadruplexes ; *Genome, Fungal ; Markov Chains ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA ; Yeasts/genetics ; },
abstract = {G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.},
}
@article {pmid20680393,
year = {2010},
author = {Bao, J and Sack, MN},
title = {Protein deacetylation by sirtuins: delineating a post-translational regulatory program responsive to nutrient and redox stressors.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {67},
number = {18},
pages = {3073-3087},
pmid = {20680393},
issn = {1420-9071},
support = {ZIA HL006047/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Acetylation ; Humans ; Mitochondria/enzymology ; Neoplasms/enzymology ; Neurons/enzymology ; Oxidation-Reduction ; Phylogeny ; *Protein Processing, Post-Translational ; Proteins/*metabolism ; Sirtuins/classification/*metabolism ; },
abstract = {Lysine acetylation/deacetylation is increasingly being recognized as common post-translational modification that appears to be broadly operational throughout the cell. The functional roles of these modifications, outside of the nucleus, have not been extensively studied. Moreover, as acetyl-CoA donates the acetyl group for acetylation, nutrient availability and energetic status may be pivotal in this modification. Similarly, nutrient limitation is associated with the deacetylation reaction. This modification is orchestrated by a novel family of sirtuin deacetylases that function in a nutrient and redox dependent manner and targets non-histone protein deacetylation. In compartment-specific locations, candidate target proteins undergoing lysine-residue deacetylation are being identified. Through these investigations, the functional role of this post-translational modification is being delineated. We review the sirtuin family proteins, discuss their functional effects on target proteins, and postulate on potential biological programs and disease processes that may be modified by sirtuin-mediated deacetylation of target proteins.},
}
@article {pmid20686707,
year = {2010},
author = {Kao, KC and Schwartz, K and Sherlock, G},
title = {A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities.},
journal = {PLoS genetics},
volume = {6},
number = {7},
pages = {e1001038},
pmid = {20686707},
issn = {1553-7404},
support = {F32 GM079113/GM/NIGMS NIH HHS/United States ; R01 HG003328/HG/NHGRI NIH HHS/United States ; },
mesh = {*Genetic Speciation ; Genome, Fungal ; *Genome-Wide Association Study ; Mitochondria ; Models, Genetic ; Polymorphism, Genetic ; Saccharomyces/*genetics ; Saccharomyces cerevisiae ; },
abstract = {The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts, which have small genomes and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair, comprising a mitochondrially targeted product of a nuclear gene and a mitochondrially encoded locus, has been found. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. We report here the first detailed genome-wide analysis of rare meiotic products from an otherwise sterile hybrid and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions, likely involving multiple loci having weak effects, may be responsible for their post-zygotic separation. The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that the accumulation of polymorphisms leads to gamete inviability due to the activities of anti-recombination mechanisms and/or incompatibilities between the species' transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation.},
}
@article {pmid20714705,
year = {2011},
author = {Tan, Y and Li, S and Xie, H and Duan, S and Wang, T and Zhu, Y},
title = {Genetical and molecular analysis reveals a cooperating relationship between cytoplasmic male sterility- and fertility restoration-related genes in Oryza species.},
journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik},
volume = {122},
number = {1},
pages = {9-19},
pmid = {20714705},
issn = {1432-2242},
mesh = {Blotting, Southern ; Cell Nucleus/genetics ; Cluster Analysis ; Crosses, Genetic ; Cytoplasm/*genetics ; DNA, Plant/genetics ; Fertility/genetics ; Genes, Mitochondrial/genetics ; Genes, Plant/*genetics ; Hybridization, Genetic ; Oryza/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Plant Infertility/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Seeds/genetics ; Species Specificity ; Subcellular Fractions/metabolism ; },
abstract = {Although the characterization of genes associated with cytoplasmic male sterility (CMS) and fertility restoration (Rf) has been well documented, the evolutionary relationship between nuclear Rf and CMS factors in mitochondria in Oryza species is still less understood. Here, 41 accessions from 7 Oryza species with AA genome were employed for analyzing the evolutionary relationships between the CMS factors and Rf candidates on chromosome 10. The phylogenetic tree based on restriction fragment length polymorphism patterns of CMS-associated mitochondrial genes showed that these 41 Oryza accessions fell into 3 distinct groups. Another phylogenetic tree based on PCR profiles of the nuclear Rf candidates on chromosome 10 was also established, and three groups were distinctively grouped. The accessions in each subgroup/group of the two phylogenetic trees are well parallel to each other. Furthermore, the 41 investigated accessions were test-crossed with Honglian (gametophytic type) and Wild-abortive (sporophytic type) CMS, and 5 groups were classified according to their restoring ability. The accessions in the same subgroup of the two phylogenetic trees shared similar fertility restoring pattern. Therefore, we conclude that the CMS-associated mitotypes are compatible to the Rf candidate-related nucleotypes, CMS and Rf have a parallel evolutionary relation in the Oryza species.},
}
@article {pmid20728567,
year = {2011},
author = {Dallai, R and Mercati, D and Carapelli, A and Nardi, F and Machida, R and Sekiya, K and Frati, F},
title = {Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s.},
journal = {Arthropod structure &amp; development},
volume = {40},
number = {1},
pages = {77-92},
doi = {10.1016/j.asd.2010.08.001},
pmid = {20728567},
issn = {1873-5495},
mesh = {Animals ; Genitalia, Male/anatomy &amp; histology ; Insect Proteins ; Insecta/*anatomy &amp; histology/physiology ; Male ; Microtubules/ultrastructure ; Phylogeny ; Spermatogenesis ; Spermatozoa/ultrastructure ; },
abstract = {Sperm ultrastructure and spermiogenesis of the dipluran Japygidae (Japyx solifugus, Metajapyx braueri and Occasjapyx japonicus) and Campodeidae (Campodea sp.) were studied with the aim of looking for potential characters for the reconstruction of the phylogenetic relationships of basal hexapods. Both Japygidae and Campodeidae share a common sperm axonemal model 9+9+2, provided with nine accessory microtubules. These microtubules, however, after their formation lose the usual position around the 9+2 and migrate between the two mitochondria. In Japygidae, four of these microtubules are very short and were observed beneath the nucleus after negative staining and serial sections. Accessory microtubules have 13 protofilaments in their tubular wall. Diplura have a sperm morphology which is very different from that of the remaining Entognatha (Protura+Collembola). On the basis of the present results, the presence of accessory microtubules suggests that Diplura are the sister-group of the Insecta s.s.. Moreover, Japygidae and Campodeidae differ with regards to the relative position of the sperm components, the former having the axoneme starting from beneath the nucleus (above which sits the short acrosome), while the latter having a long apical acrosome and a nucleus running parallel with the proximal part of the axoneme. The present study also allowed to redescribe the male genital system of Japyx.},
}
@article {pmid20738684,
year = {2009},
author = {França, GF and Oliveira, C and Quagio-Grassiotto, I},
title = {Spermatic cell characteristics in Gymnotiformes (Teleostei: Ostariophysi) and their phylogenetic meaning.},
journal = {Journal of fish biology},
volume = {75},
number = {9},
pages = {2226-2243},
doi = {10.1111/j.1095-8649.2009.02439.x},
pmid = {20738684},
issn = {1095-8649},
mesh = {Animals ; Gymnotiformes/genetics/*physiology ; Male ; Microscopy, Electron, Transmission ; *Phylogeny ; Spermatogenesis/*physiology ; Spermatozoa/*ultrastructure ; },
abstract = {Spermatic characteristics were studied in representatives of the families Rhamphichthyidae, Sternopygidae and Apteronotidae, and compared with pre-existent data from Gymnotidae and Hypopomidae. The spermatic characteristics found in Gymnotiformes were also compared with data from other Ostariophysi spermatic cells. The spermatic characteristics as the type of spermiogenesis and the structural pattern of the sperm, considering nuclear form, pattern of chromatin condensation, nuclear fossa and its relation with the centriolar complex, form and localization of mitochondria, form of midpiece, presence or absence of cytoplasmic canal and cytoplasmic sleeve, and flagellar fins were utilized. The comparative analysis of the spermatic cell of Gymnotiformes better support the previous proposals for the order considering Gymnotidae as a derived group, than the more recent ones that located Gymnotidae in a basal position as the sister group of the remaining Gymnotiformes. Regarding the Ostariophysi, the comparative analyses based on the spermatic cell characteristics is consistent with a recent systematic proposal that consider Gymnotiformes as a sister group of Characiformes.},
}
@article {pmid20811767,
year = {2010},
author = {Singh, A and Grover, A},
title = {Plant Hsp100/ClpB-like proteins: poorly-analyzed cousins of yeast ClpB machine.},
journal = {Plant molecular biology},
volume = {74},
number = {4-5},
pages = {395-404},
pmid = {20811767},
issn = {1573-5028},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Heat-Shock Proteins/genetics/*physiology ; Heat-Shock Response ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/*physiology ; Sequence Alignment ; Yeasts/genetics/metabolism ; },
abstract = {ClpB/Hsp100 proteins act as chaperones, mediating disaggregation of denatured proteins. Recent work shows that apart from cytoplasm, these proteins are localized to nuclei, chloroplasts, mitochondria and plasma membrane. While ClpB/Hsp100 genes are essentially stress-induced (mainly heat stress) in vegetative organs of the plant body, expression of ClpB/Hsp100 proteins is noted to be constitutive in plant reproductive structures like pollen grains, developing embryos, seeds etc. With global warming looming large on the horizon, ways to genetically engineer plants against high temperature stress are urgently needed. Yeast mutants unable to synthesize active ClpB/Hsp100 protein show a clear thermosensitive phenotype. ClpB/Hsp100 proteins are implicated in high temperature stress tolerance in plants. We herein highlight the selected important facets of this protein family in plants.},
}
@article {pmid20816094,
year = {2010},
author = {Nouws, J and Nijtmans, L and Houten, SM and van den Brand, M and Huynen, M and Venselaar, H and Hoefs, S and Gloerich, J and Kronick, J and Hutchin, T and Willems, P and Rodenburg, R and Wanders, R and van den Heuvel, L and Smeitink, J and Vogel, RO},
title = {Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I.},
journal = {Cell metabolism},
volume = {12},
number = {3},
pages = {283-294},
doi = {10.1016/j.cmet.2010.08.002},
pmid = {20816094},
issn = {1932-7420},
mesh = {Acyl-CoA Dehydrogenase, Long-Chain/chemistry/classification/genetics/metabolism ; Acyl-CoA Dehydrogenases/chemistry/classification/genetics/*metabolism ; Adaptor Proteins, Signal Transducing/genetics/metabolism ; Amino Acid Sequence ; Animals ; Cells, Cultured ; Electron Transport Complex I/*biosynthesis ; Fatty Acids/metabolism ; Female ; Fibroblasts/cytology/physiology ; Humans ; Infant ; Male ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; NADH Dehydrogenase/genetics/metabolism ; Oxidation-Reduction ; *Oxidative Phosphorylation ; Phylogeny ; Pregnancy ; Protein Structure, Tertiary ; RNA Interference ; Sequence Analysis ; Sequence Analysis, DNA ; },
abstract = {Acyl-CoA dehydrogenase 9 (ACAD9) is a recently identified member of the acyl-CoA dehydrogenase family. It closely resembles very long-chain acyl-CoA dehydrogenase (VLCAD), involved in mitochondrial beta oxidation of long-chain fatty acids. Contrary to its previously proposed involvement in fatty acid oxidation, we describe a role for ACAD9 in oxidative phosphorylation. ACAD9 binds complex I assembly factors NDUFAF1 and Ecsit and is specifically required for the assembly of complex I. Furthermore, ACAD9 mutations result in complex I deficiency and not in disturbed long-chain fatty acid oxidation. This strongly contrasts with its evolutionary ancestor VLCAD, which we show is not required for complex I assembly and clearly plays a role in fatty acid oxidation. Our results demonstrate that two closely related metabolic enzymes have diverged at the root of the vertebrate lineage to function in two separate mitochondrial metabolic pathways and have clinical implications for the diagnosis of complex I deficiency.},
}
@article {pmid20819227,
year = {2010},
author = {Zhao, W and Yu, H and Li, S and Huang, Y},
title = {Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {272},
pmid = {20819227},
issn = {1471-2148},
mesh = {Amino Acid Sequence ; Endoribonucleases/*chemistry/*genetics ; Fungal Proteins/*chemistry/*genetics ; Humans ; Male ; Molecular Sequence Data ; Neoplasm Proteins/*chemistry/genetics ; Phylogeny ; Prostatic Neoplasms/*genetics ; Sequence Homology, Amino Acid ; },
abstract = {BACKGROUND: tRNase Z is the endonuclease that is responsible for the 3'-end processing of tRNA precursors, a process essential for tRNA 3'-CCA addition and subsequent tRNA aminoacylation. Based on their sizes, tRNase Zs can be divided into the long (tRNase ZL) and short (tRNase ZS) forms. tRNase ZL is thought to have arisen from a tandem gene duplication of tRNase ZS with further sequence divergence. The species distribution of tRNase Z is complex. Fungi represent an evolutionarily diverse group of eukaryotes. The recent proliferation of fungal genome sequences provides an opportunity to explore the structural and functional diversity of eukaryotic tRNase Zs.<br><br>RESULTS: We report a survey and analysis of candidate tRNase Zs in 84 completed fungal genomes, spanning a broad diversity of fungi. We find that tRNase ZL is present in all fungi we have examined, whereas tRNase ZS exists only in the fungal phyla Basidiomycota, Chytridiomycota and Zygomycota. Furthermore, we find that unlike the Pezizomycotina and Saccharomycotina, which contain a single tRNase ZL, Schizosaccharomyces fission yeasts (Taphrinomycotina) contain two tRNase ZLs encoded by two different tRNase ZL genes. These two tRNase ZLs are most likely localized to the nucleus and mitochondria, respectively, suggesting partitioning of tRNase Z function between two different tRNase ZLs in fission yeasts. The fungal tRNase Z phylogeny suggests that tRNase ZSs are ancestral to tRNase ZLs. Additionally, the evolutionary relationship of fungal tRNase ZLs is generally consistent with known phylogenetic relationships among the fungal species and supports tRNase ZL gene duplication in certain fungal taxa, including Schizosaccharomyces fission yeasts. Analysis of tRNase Z protein sequences reveals putative atypical substrate binding domains in most fungal tRNase ZSs and in a subset of fungal tRNase ZLs. Finally, we demonstrate the presence of pseudo-substrate recognition and catalytic motifs at the N-terminal halves of tRNase ZLs.<br><br>CONCLUSIONS: This study describes the first comprehensive identification and sequence analysis of candidate fungal tRNase Zs. Our results support the proposal that tRNase ZL has evolved as a result of duplication and diversification of the tRNase ZS gene.},
}
@article {pmid20820906,
year = {2010},
author = {Wang, CM and Way, TD and Chang, YC and Yen, NT and Hu, CL and Nien, PC and Jea, YS and Chen, LR and Kao, JY},
title = {The origin of the white Roman goose.},
journal = {Biochemical genetics},
volume = {48},
number = {11-12},
pages = {938-943},
doi = {10.1007/s10528-010-9374-8},
pmid = {20820906},
issn = {1573-4927},
mesh = {Animals ; Base Sequence ; China ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Geese/*genetics ; Models, Statistical ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; Sequence Analysis ; },
abstract = {In order to avoid interference from nuclear copies of mitochondrial DNA (numts), mtDNA of the white Roman goose (domestic goose) was extracted from liver mitochondria. The mtDNA control region was amplified using a long PCR strategy and then sequenced. Neighbor-joining, maximum parsimony, and maximum-likelihood approaches were implemented using the 1,177 bp mtDNA control region sequences to compute the phylogenetic relationships of the domestic goose with other geese. The resulting identity values for the white Roman geese were 99.1% (1,166/1,177) with western graylag geese and 98.8% (1,163/1,177) with eastern graylag geese. In molecular phylogenetic trees, the white Roman goose was grouped in the graylag lineage, indicating that the white Roman goose came from the graylag goose (Anser anser). Thus, the scientific name of the white Roman goose should be Anser anser 'White Roman.'},
}
@article {pmid20829360,
year = {2010},
author = {Carrie, C and Giraud, E and Duncan, O and Xu, L and Wang, Y and Huang, S and Clifton, R and Murcha, M and Filipovska, A and Rackham, O and Vrielink, A and Whelan, J},
title = {Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes.},
journal = {The Journal of biological chemistry},
volume = {285},
number = {46},
pages = {36138-36148},
pmid = {20829360},
issn = {1083-351X},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/classification/genetics/metabolism/*physiology ; Blotting, Western ; Conserved Sequence ; DNA, Bacterial/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Essential/genetics ; Green Fluorescent Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Molecular Sequence Data ; Multienzyme Complexes/genetics/metabolism ; Mutagenesis, Insertional ; Mutation ; Oligonucleotide Array Sequence Analysis ; Peroxisomes/*metabolism ; Phylogeny ; Protein Transport ; Sequence Homology, Amino Acid ; Superoxide Dismutase/genetics/metabolism ; },
abstract = {The disulfide relay system of the mitochondrial intermembrane space has been extensively characterized in Saccharomyces cerevisiae. It contains two essential components, Mia40 and Erv1. The genome of Arabidopsis thaliana contains a single gene for each of these components. Although insertional inactivation of Erv1 leads to a lethal phenotype, inactivation of Mia40 results in no detectable deleterious phenotype. A. thaliana Mia40 is targeted to and accumulates in mitochondria and peroxisomes. Inactivation of Mia40 results in an alteration of several proteins in mitochondria, an absence of copper/zinc superoxide dismutase (CSD1), the chaperone for superoxide dismutase (Ccs1) that inserts copper into CSD1, and a decrease in capacity and amount of complex I. In peroxisomes the absence of Mia40 leads to an absence of CSD3 and a decrease in abnormal inflorescence meristem 1 (Aim1), a β-oxidation pathway enzyme. Inactivation of Mia40 leads to an alteration of the transcriptome of A. thaliana, with genes encoding peroxisomal proteins, redox functions, and biotic stress significantly changing in abundance. Thus, the mechanistic operation of the mitochondrial disulfide relay system is different in A. thaliana compared with other systems, and Mia40 has taken on new roles in peroxisomes and mitochondria.},
}
@article {pmid20838623,
year = {2010},
author = {Castro, H and Romao, S and Carvalho, S and Teixeira, F and Sousa, C and Tomás, AM},
title = {Mitochondrial redox metabolism in trypanosomatids is independent of tryparedoxin activity.},
journal = {PloS one},
volume = {5},
number = {9},
pages = {e12607},
pmid = {20838623},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Cell Survival ; Humans ; Leishmania infantum/chemistry/classification/genetics/*metabolism ; Leishmaniasis, Visceral/parasitology ; Male ; Mice ; Mice, Inbred BALB C ; Mitochondria/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Protein Transport ; Protozoan Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Thioredoxins/chemistry/genetics/*metabolism ; Trypanosomatina/chemistry/classification/genetics/metabolism ; },
abstract = {Tryparedoxins (TXNs) are oxidoreductases unique to trypanosomatids (including Leishmania and Trypanosoma parasites) that transfer reducing equivalents from trypanothione, the major thiol in these organisms, to sulfur-dependent peroxidases and other dithiol proteins. The existence of a TXN within the mitochondrion of trypanosomatids, capable of driving crucial redox pathways, is considered a requisite for normal parasite metabolism. Here this concept is shown not to apply to Leishmania. First, removal of the Leishmania infantum mitochondrial TXN (LiTXN2) by gene-targeting, had no significant effect on parasite survival, even in the context of an animal infection. Second, evidence is presented that no other TXN is capable of replacing LiTXN2. In fact, although a candidate substitute for LiTXN2 (LiTXN3) was found in the genome of L. infantum, this was shown in biochemical assays to be poorly reduced by trypanothione and to be unable to reduce sulfur-containing peroxidases. Definitive conclusion that LiTXN3 cannot directly reduce proteins located within inner mitochondrial compartments was provided by analysis of its subcellular localization and membrane topology, which revealed that LiTXN3 is a tail-anchored (TA) mitochondrial outer membrane protein presenting, as characteristic of TA proteins, its N-terminal end (containing the redox-active domain) exposed to the cytosol. This manuscript further proposes the separation of trypanosomatid TXN sequences into two classes and this is supported by phylogenetic analysis: i) class I, encoding active TXNs, and ii) class II, coding for TA proteins unlikely to function as TXNs. Trypanosoma possess only two TXNs, one belonging to class I (which is cytosolic) and the other to class II. Thus, as demonstrated for Leishmania, the mitochondrial redox metabolism in Trypanosoma may also be independent of TXN activity. The major implication of these findings is that mitochondrial functions previously thought to depend on the provision of electrons by a TXN enzyme must proceed differently.},
}
@article {pmid20853063,
year = {2010},
author = {Kim, MI and Wan, X and Kim, MJ and Jeong, HC and Ahn, NH and Kim, KG and Han, YS and Kim, I},
title = {Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences.},
journal = {Molecules and cells},
volume = {30},
number = {5},
pages = {409-425},
doi = {10.1007/s10059-010-0141-9},
pmid = {20853063},
issn = {0219-1032},
mesh = {Animals ; Base Sequence ; Butterflies/classification/enzymology/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The molecular phylogenetic relationships among true butterfly families (superfamily Papilionoidea) have been a matter of substantial controversy; this debate has led to several competing hypotheses. Two of the most compelling of those hypotheses involve the relationships of (Nymphalidae + Lycaenidae) + (Pieridae + Papilionidae) and (((Nymphalidae + Lycaenidae) + Pieridae) + Papilionidae). In this study, approximately 3,500 nucleotide sequences from cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-1 alpha (EF-1α) were sequenced from 83 species belonging to four true butterfly families, along with those of three outgroup species belonging to three lepidopteran superfamilies. These sequences were subjected to phylogenetic reconstruction via Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP) algorithms. The monophyletic Pieridae and monophyletic Papilionidae evidenced good recovery in all analyses, but in some analyses, the monophylies of the Lycaenidae and Nymphalidae were hampered by the inclusion of single species of the lycaenid subfamily Miletinae and the nymphalid subfamily Danainae. Excluding those singletons, all phylogenetic analyses among the four true butterfly families clearly identified the Nymphalidae as the sister to the Lycaenidae and identified this group as a sister to the Pieridae, with the Papilionidae identified as the most basal linage to the true butterfly, thus supporting the hypothesis: (Papilionidae + (Pieridae + (Nymphalidae + Lycaenidae))).},
}
@article {pmid20868295,
year = {2011},
author = {Sevrioukova, IF},
title = {Apoptosis-inducing factor: structure, function, and redox regulation.},
journal = {Antioxidants &amp; redox signaling},
volume = {14},
number = {12},
pages = {2545-2579},
pmid = {20868295},
issn = {1557-7716},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis/physiology ; Apoptosis Inducing Factor/*chemistry/classification/genetics/*metabolism ; Catalytic Domain ; Electron Transport/physiology ; Gene Expression Regulation ; Humans ; Mitochondria/metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; *Protein Conformation ; Protein Folding ; Protein Isoforms/*chemistry/genetics/*metabolism ; Sequence Alignment ; Signal Transduction/physiology ; },
abstract = {Apoptosis-inducing factor (AIF) is a flavin adenine dinucleotide-containing, NADH-dependent oxidoreductase residing in the mitochondrial intermembrane space whose specific enzymatic activity remains unknown. Upon an apoptotic insult, AIF undergoes proteolysis and translocates to the nucleus, where it triggers chromatin condensation and large-scale DNA degradation in a caspase-independent manner. Besides playing a key role in execution of caspase-independent cell death, AIF has emerged as a protein critical for cell survival. Analysis of in vivo phenotypes associated with AIF deficiency and defects, and identification of its mitochondrial, cytoplasmic, and nuclear partners revealed the complexity and multilevel regulation of AIF-mediated signal transduction and suggested an important role of AIF in the maintenance of mitochondrial morphology and energy metabolism. The redox activity of AIF is essential for optimal oxidative phosphorylation. Additionally, the protein is proposed to regulate the respiratory chain indirectly, through assembly and/or stabilization of complexes I and III. This review discusses accumulated data with respect to the AIF structure and outlines evidence that supports the prevalent mechanistic view on the apoptogenic actions of the flavoprotein, as well as the emerging concept of AIF as a redox sensor capable of linking NAD(H)-dependent metabolic pathways to apoptosis.},
}
@article {pmid20870040,
year = {2011},
author = {Douglas, KC and Halbert, ND and Kolenda, C and Childers, C and Hunter, DL and Derr, JN},
title = {Complete mitochondrial DNA sequence analysis of Bison bison and bison-cattle hybrids: function and phylogeny.},
journal = {Mitochondrion},
volume = {11},
number = {1},
pages = {166-175},
doi = {10.1016/j.mito.2010.09.005},
pmid = {20870040},
issn = {1872-8278},
mesh = {Animals ; Base Sequence ; Bison/classification/*genetics ; Cattle/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; *Hybridization, Genetic ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; *Sequence Analysis, DNA ; },
abstract = {Complete mitochondrial DNA (mtDNA) genomes from 43 bison and bison-cattle hybrids were sequenced and compared with other bovids. Selected animals reflect the historical range and current taxonomic structure of bison. This study identified regions of potential nuclear-mitochondrial incompatibilities in hybrids, provided a complete mtDNA phylogenetic tree for this species, and uncovered evidence of bison population substructure. Seventeen bison haplotypes defined by 66 polymorphic sites were discovered, whereas 728 fixed differences and 86 non-synonymous mutations were identified between bison and bison-cattle hybrid sequences. The potential roles of the mtDNA genome in the function of hybrid animals and bison taxonomy are discussed.},
}
@article {pmid20880032,
year = {2010},
author = {Park, JS and Kolisko, M and Simpson, AG},
title = {Cell morphology and formal description of Ergobibamus cyprinoides n. g., n. sp., another Carpediemonas-like relative of diplomonads.},
journal = {The Journal of eukaryotic microbiology},
volume = {57},
number = {6},
pages = {520-528},
doi = {10.1111/j.1550-7408.2010.00506.x},
pmid = {20880032},
issn = {1550-7408},
mesh = {Canada ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diplomonadida/*classification/genetics/isolation &amp; purification/ultrastructure ; Genes, rRNA ; Geologic Sediments/*parasitology ; Microscopy ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; },
abstract = {About 20 new isolates of Carpediemonas-like organisms (CLOs) have been reported since 2006. Small subunit rRNA gene phylogenies divide CLOs into six major clades: four contain described exemplars (i.e. Carpediemonas, Dysnectes, Hicanonectes, and Kipferlia), but two include only undescribed organisms. Here we describe a representative of one of these latter clades as Ergobibamus cyprinoides n. g., n. sp., and catalogue its ultrastructure. Ergobibamus cyprinoides is a bean-shaped biflagellated cell, 7-11.5 μm long, with a conspicuous groove. Instead of classical mitochondria there are cristae-lacking rounded organelles 300-400 nm in diameter. The posterior flagellum has a broad ventral vane and small dorsal vane. There are normally four basal bodies, two non-flagellated. There is one anterior root (AR), containing six microtubules. The posterior flagellar apparatus follows the "typical excavate" pattern of a splitting right root supported by fibres "I,""B," and "A," a "composite" fibre, a singlet root, and a left root (LR) with a "C" fibre. The B fibre originates against the LR--a synapomorphy of the taxon Fornicata--supporting the assignation of Ergobibamus to Fornicata, along with diplomonads, retortamonads, and other CLOs. Distinctive features of E. cyprinoides include the complexity of the AR, which is intermediate between Hicanonectes, and Carpediemonas and Dysnectes, and a dorsal extension of the C fibre.},
}
@article {pmid20888427,
year = {2011},
author = {Amer, S and Dar, Y and Ichikawa, M and Fukuda, Y and Tada, C and Itagaki, T and Nakai, Y},
title = {Identification of Fasciola species isolated from Egypt based on sequence analysis of genomic (ITS1 and ITS2) and mitochondrial (NDI and COI) gene markers.},
journal = {Parasitology international},
volume = {60},
number = {1},
pages = {5-12},
doi = {10.1016/j.parint.2010.09.003},
pmid = {20888427},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Buffaloes/parasitology ; Cattle/parasitology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Egypt/epidemiology ; Fasciola/*classification/*genetics/*isolation &amp; purification ; Fascioliasis/*epidemiology/parasitology/*veterinary ; Genes, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sheep/parasitology ; },
abstract = {Fascioliasis has a negative impact on the farming industry in both developed and developing countries, rather than a public health challenge. This study was performed to identify Fasciola sp. from different definitive hosts (buffalo, cattle, and sheep) based on the molecular parameters and spermatogenesis. Ninety-one adult flukes were collected from livers of slaughtered animals at abattoirs in different prefectures in Egypt. Microscopic examination of the analyzed flukes showed many normal spermatozoa in the seminal vesicles (spermic), suggesting that they have the ability of spermatogenesis. This study showed that no parthenogenic Fasciola species occurred in Egypt. Molecular analysis was performed utilizing genomic (ITS1 and ITS2) and mitochondrial (NDI and COI) gene markers. Whereas 16 animals proved to have infection with a single Fasciola species, 2 were infected with both F. hepatica and F. gigantica. The results indicated that sheep were prone to F. hepatica (8 out of 10 animals) more than F. gigantica infection. Sequences of ITS1 and ITS2 ribosomal region indicated that the flukes were categorized into 3 groups F. hepatica-type (47), F. gigantica-type (42) and 2 flukes possessed sequences of both types indicating an existence of different alleles at the same loci. Unique overlapping of T/C bases were detected in both ITS1 (Position 96) and ITS2 (Position 416). Based on results of mitochondrial gene markers (NDI and COI), flukes were classified into F. hepatica-type and F. gigantica-type. Extensive intra-sequence polymorphism was detected at both markers. NDI and COI sequences of Egyptian strain of F. gigantica showed pronounced diversity compared with relevant sequences at database.},
}
@article {pmid20922212,
year = {2010},
author = {Cavallaro, G},
title = {Genome-wide analysis of eukaryotic twin CX9C proteins.},
journal = {Molecular bioSystems},
volume = {6},
number = {12},
pages = {2459-2470},
doi = {10.1039/c0mb00058b},
pmid = {20922212},
issn = {1742-2051},
mesh = {Amino Acid Motifs ; Amino Acids ; Animals ; Cluster Analysis ; Eukaryotic Cells/*metabolism ; Genome/*genetics ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Multiprotein Complexes/chemistry/metabolism ; Phylogeny ; Protein Structure, Secondary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; },
abstract = {Twin CX(9)C proteins are eukaryotic proteins that derive their name from their characteristic motif, consisting of two pairs of cysteines that form two disulfide bonds stabilizing a coiled coil-helix-coiled coil-helix (CHCH) fold. The best characterized of these proteins are Cox17, a copper chaperone acting in cytochrome c oxidase biogenesis, and Mia40, the central component of a system for protein import into the mitochondrial inter-membrane space (IMS). However, the range of possible functions for these proteins is unclear. Here, we performed a systematic search of twin CX(9)C proteins in eukaryotic organisms, and classified them into groups of putative homologues, by combining bioinformatics methods with literature analysis. Our results suggest that the functions of most twin CX(9)C proteins vary around the common theme of playing a scaffolding role, which can tie their observed roles in mitochondrial structure and function. This study will enhance the present annotation of eukaryotic proteomes, and will provide a rational basis for future experimental work aimed at a deeper understanding of this remarkable class of proteins.},
}
@article {pmid20927717,
year = {2010},
author = {Md-Zain, BM and Mohamad, M and Ernie-Muneerah, MA and Ampeng, A and Jasmi, A and Lakim, M and Mahani, MC},
title = {Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences.},
journal = {Genetics and molecular research : GMR},
volume = {9},
number = {4},
pages = {1987-1996},
doi = {10.4238/vol9-4gmr942},
pmid = {20927717},
issn = {1676-5680},
mesh = {Algorithms ; Animals ; Base Sequence ; Cercopithecidae/*classification/genetics ; Cytochromes c/*genetics ; DNA Primers ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter- and intra-subfamily levels.},
}
@article {pmid20943133,
year = {2010},
author = {Giachini, AJ and Hosaka, K and Nouhra, E and Spatafora, J and Trappe, JM},
title = {Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences.},
journal = {Fungal biology},
volume = {114},
number = {2-3},
pages = {224-234},
doi = {10.1016/j.funbio.2010.01.002},
pmid = {20943133},
issn = {1878-6146},
mesh = {Basidiomycota/*classification/*genetics ; DNA, Fungal/analysis/genetics/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/classification/*genetics ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Phylogenetic relationships among Geastrales, Gomphales, Hysterangiales, and Phallales were estimated via combined sequences: nuclear large subunit ribosomal DNA (nuc-25S-rDNA), mitochondrial small subunit ribosomal DNA (mit-12S-rDNA), and mitochondrial atp6 DNA (mit-atp6-DNA). Eighty-one taxa comprising 19 genera and 58 species were investigated, including members of the Clathraceae, Gautieriaceae, Geastraceae, Gomphaceae, Hysterangiaceae, Phallaceae, Protophallaceae, and Sphaerobolaceae. Although some nodes deep in the tree could not be fully resolved, some well-supported lineages were recovered, and the interrelationships among Gloeocantharellus, Gomphus, Phaeoclavulina, and Turbinellus, and the placement of Ramaria are better understood. Both Gomphus sensu lato and Ramaria sensu lato comprise paraphyletic lineages within the Gomphaceae. Relationships of the subgenera of Ramaria sensu lato to each other and to other members of the Gomphales were clarified. Within Gomphus sensu lato, Gomphus sensu stricto, Turbinellus, Gloeocantharellus and Phaeoclavulina are separated by the presence/absence of clamp connections, spore ornamentation (echinulate, verrucose, subreticulate or reticulate), and basidiomal morphology (fan-shaped, funnel-shaped or ramarioid). Gautieria, a sequestrate genus in the Gautieriaceae, was recovered as monophyletic and nested with members of Ramaria subgenus Ramaria. This agrees with previous observations of traits shared by these two ectomycorrhizal taxa, such as the presence of fungal mats in the soil. Clavariadelphus was recovered as a sister group to Beenakia, Kavinia, and Lentaria. The results reaffirm relationships between the Geastrales, Gomphales, Hysterangiales, and the Phallales, suggesting extensive convergence in basidiomal morphology among members of these groups. A more extensive sampling that focuses on other loci (protein-coding genes have been shown to be phylogenetically informative) may be useful to answer questions about evolutionary relationships among these fungal groups.},
}
@article {pmid20958223,
year = {2010},
author = {Oh, DJ and Oh, BS and Jung, MM and Jung, YH},
title = {Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations.},
journal = {Mitochondrial DNA},
volume = {21},
number = {5},
pages = {151-159},
doi = {10.3109/19401736.2010.503241},
pmid = {20958223},
issn = {1940-1744},
mesh = {Animals ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Perciformes/*classification/*genetics ; *Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.},
}
@article {pmid20977744,
year = {2010},
author = {Hardouin, EA and Chapuis, JL and Stevens, MI and van Vuuren, JB and Quillfeldt, P and Scavetta, RJ and Teschke, M and Tautz, D},
title = {House mouse colonization patterns on the sub-Antarctic Kerguelen Archipelago suggest singular primary invasions and resilience against re-invasion.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {325},
pmid = {20977744},
issn = {1471-2148},
mesh = {Animals ; DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; *Geography ; Haplotypes/genetics ; Mice ; Microsatellite Repeats/genetics ; Phylogeny ; Y Chromosome/genetics ; },
abstract = {BACKGROUND: Starting from Western Europe, the house mouse (Mus musculus domesticus) has spread across the globe in historic times. However, most oceanic islands were colonized by mice only within the past 300 years. This makes them an excellent model for studying the evolutionary processes during early stages of new colonization. We have focused here on the Kerguelen Archipelago, located within the sub-Antarctic area and compare the patterns with samples from other Southern Ocean islands.<br><br>RESULTS: We have typed 18 autosomal and six Y-chromosomal microsatellite loci and obtained mitochondrial D-loop sequences for a total of 534 samples, mainly from the Kerguelen Archipelago, but also from the Falkland Islands, Marion Island, Amsterdam Island, Antipodes Island, Macquarie Island, Auckland Islands and one sample from South Georgia. We find that most of the mice on the Kerguelen Archipelago have the same mitochondrial haplotype and all share the same major Y-chromosomal haplotype. Two small islands (Cochons Island and Cimeti&#xe8;re Island) within the archipelago show a different mitochondrial haplotype, are genetically distinct for autosomal loci, but share the major Y-chromosomal haplotype. In the mitochondrial D-loop sequences, we find several single step mutational derivatives of one of the major mitochondrial haplotypes, suggesting an unusually high mutation rate, or the occurrence of selective sweeps in mitochondria.<br><br>CONCLUSIONS: Although there was heavy ship traffic for over a hundred years to the Kerguelen Archipelago, it appears that the mice that have arrived first have colonized the main island (Grande Terre) and most of the associated small islands. The second invasion that we see in our data has occurred on islands that are detached from Grande Terre and were likely to have had no resident mice prior to their arrival. The genetic data suggest that the mice of both primary invasions originated from related source populations. Our data suggest that an area colonized by mice is refractory to further introgression, possibly due to fast adaptations of the resident mice to local conditions.},
}
@article {pmid20978534,
year = {2011},
author = {Zaragoza, MV and Brandon, MC and Diegoli, M and Arbustini, E and Wallace, DC},
title = {Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny.},
journal = {European journal of human genetics : EJHG},
volume = {19},
number = {2},
pages = {200-207},
pmid = {20978534},
issn = {1476-5438},
support = {NS21328/NS/NINDS NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; K08 HL081222/HL/NHLBI NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Cardiomyopathies/*genetics/pathology ; Child ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Echocardiography ; Female ; Genes, Mitochondrial ; *Genetic Variation ; Humans ; Infant ; Italy ; Male ; Middle Aged ; Mitochondria/genetics ; Mitochondrial Diseases/*genetics/pathology ; Mutation ; Pedigree ; *Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause cardiomyopathy and heart failure. Owing to a high mutation rate, mtDNA defects may occur at any nucleotide in its 16 569 bp sequence. Complete mtDNA sequencing may detect pathogenic mutations, which can be difficult to interpret because of normal ethnic/geographic-associated haplogroup variation. Our goal is to show how to identify candidate mtDNA mutations by sorting out polymorphisms using readily available online tools. The purpose of this approach is to help investigators in prioritizing mtDNA variants for functional analysis to establish pathogenicity. We analyzed complete mtDNA sequences from 29 Italian patients with mitochondrial cardiomyopathy or suspected disease. Using MITOMASTER and PhyloTree, we characterized 593 substitution variants by haplogroup and allele frequencies to identify all novel, non-haplogroup-associated variants. MITOMASTER permitted determination of each variant's location, amino acid change and evolutionary conservation. We found that 98% of variants were common or rare, haplogroup-associated variants, and thus unlikely to be primary cause in 80% of cases. Six variants were novel, non-haplogroup variants and thus possible contributors to disease etiology. Two with the greatest pathogenic potential were heteroplasmic, nonsynonymous variants: m.15132T>C in MT-CYB for a patient with hypertrophic dilated cardiomyopathy and m.6570G>T in MT-CO1 for a patient with myopathy. In summary, we have used our automated information system, MITOMASTER, to make a preliminary distinction between normal mtDNA variation and pathogenic mutations in patient samples; this fast and easy approach allowed us to select the variants for traditional analysis to establish pathogenicity.},
}
@article {pmid21035093,
year = {2010},
author = {Han, L and Qin, G and Kang, D and Chen, Z and Gu, H and Qu, LJ},
title = {A nuclear-encoded mitochondrial gene AtCIB22 is essential for plant development in Arabidopsis.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {37},
number = {10},
pages = {667-683},
doi = {10.1016/S1673-8527(09)60085-0},
pmid = {21035093},
issn = {1673-8527},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/*growth &amp; development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cell Nucleus/genetics ; Ethanol/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Germination/drug effects ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Mutation ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Proteins ; Plants, Genetically Modified ; RNA Interference ; Recombinant Fusion Proteins/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Homology, Amino Acid ; Sucrose/pharmacology ; Alternative Oxidase ; },
abstract = {Complex I (the NADH:ubiquinone oxidoreductase) of the mitochondrial respiratory chain is a complicated, multi-subunit, membrane-bound assembly and contains more than 40 different proteins in higher plants. In this paper, we characterize the Arabidopsis homologue (designated as AtCIB22) of the B22 subunit of eukaryotic mitochondrial Complex I. AtCIB22 is a single-copy gene and is highly conserved throughout eukaryotes. AtCIB22 protein is located in mitochondria and the AtCIB22 gene is widely expressed in different tissues. Mutant Arabidopsis plants with a disrupted AtCIB22 gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. Stress analysis indicates that the AtCIB22 mutants' seed germination and early seedling growth are severely inhibited by sucrose deprivation stress but more tolerant to ethanol stress. Molecular analysis reveals that in moderate knockdown AtCIB22 mutants, genes including cell redox proteins and stress related proteins are significantly up-regulated, and that in severe knockdown AtCIB22 mutants, the alternative respiratory pathways including NDA1, NDB2, AOX1a and AtPUMP1 are remarkably elevated. These data demonstrate that AtCIB22 is essential for plant development and mitochondrial electron transport chains in Arabidopsis. Our findings also enhance our understanding about the physiological role of Complex I in plants.},
}
@article {pmid21037180,
year = {2010},
author = {Barberà, MJ and Ruiz-Trillo, I and Tufts, JY and Bery, A and Silberman, JD and Roger, AJ},
title = {Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties.},
journal = {Eukaryotic cell},
volume = {9},
number = {12},
pages = {1913-1924},
pmid = {21037180},
issn = {1535-9786},
mesh = {Amino Acid Sequence ; Eukaryota/classification/*enzymology/metabolism/ultrastructure ; Hydrogenase/chemistry/genetics/*metabolism ; Mitochondria/chemistry/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Pyruvate Synthase/chemistry/genetics/*metabolism ; Sequence Alignment ; },
abstract = {Protists that live under low-oxygen conditions often lack conventional mitochondria and instead possess mitochondrion-related organelles (MROs) with distinct biochemical functions. Studies of mostly parasitic organisms have suggested that these organelles could be classified into two general types: hydrogenosomes and mitosomes. Hydrogenosomes, found in parabasalids, anaerobic chytrid fungi, and ciliates, metabolize pyruvate anaerobically to generate ATP, acetate, CO(2), and hydrogen gas, employing enzymes not typically associated with mitochondria. Mitosomes that have been studied have no apparent role in energy metabolism. Recent investigations of free-living anaerobic protists have revealed a diversity of MROs with a wider array of metabolic properties that defy a simple functional classification. Here we describe an expressed sequence tag (EST) survey and ultrastructural investigation of the anaerobic heteroloboseid amoeba Sawyeria marylandensis aimed at understanding the properties of its MROs. This organism expresses typical anaerobic energy metabolic enzymes, such as pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenase, and associated hydrogenase maturases with apparent organelle-targeting peptides, indicating that its MRO likely functions as a hydrogenosome. We also identified 38 genes encoding canonical mitochondrial proteins in S. marylandensis, many of which possess putative targeting peptides and are phylogenetically related to putative mitochondrial proteins of its heteroloboseid relative Naegleria gruberi. Several of these proteins, such as a branched-chain alpha keto acid dehydrogenase, likely function in pathways that have not been previously associated with the well-studied hydrogenosomes of parabasalids. Finally, morphological reconstructions based on transmission electron microscopy indicate that the S. marylandensis MROs form novel cup-like structures within the cells. Overall, these data suggest that Sawyeria marylandensis possesses a hydrogenosome of mitochondrial origin with a novel combination of biochemical and structural properties.},
}
@article {pmid21070620,
year = {2010},
author = {Cuenca, A and Petersen, G and Seberg, O and Davis, JI and Stevenson, DW},
title = {Are substitution rates and RNA editing correlated?.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {349},
pmid = {21070620},
issn = {1471-2148},
mesh = {Alismatales/*genetics ; Mitochondrial Proteins/classification/genetics ; Phylogeny ; RNA Editing/*genetics ; RNA, Plant/*genetics ; },
abstract = {BACKGROUND: RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.<br><br>RESULTS: We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).<br><br>CONCLUSIONS: The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.},
}
@article {pmid21072538,
year = {2011},
author = {Yang, B and Cai, J and Cheng, X},
title = {Identification of astigmatid mites using ITS2 and COI regions.},
journal = {Parasitology research},
volume = {108},
number = {2},
pages = {497-503},
pmid = {21072538},
issn = {1432-1955},
mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Mites/classification/*genetics ; Mitochondria/enzymology ; Phylogeny ; Species Specificity ; },
abstract = {Identification of astigmatid mites based on their morphological characteristics is difficult because of the similarity of their organs, especially in immature mites. The ribosomal second internal transcribed spacer (ITS2) and the mitochondrial cytochrome oxidase subunit I (COI) regions are highly conserved in the eukaryotes and are usually used as barcodes. The ITS2 and COI regions of six species of astigmatid mites (Aleuroglyphus ovatus, Blomia tropicalis, Dermatophagoides farinae, Dermatophagoides pteronyssinus, Euroglyphus maynei, Tyrophagus putrescentiae) were obtained by polymerase chain reaction and sequenced. The lengths of the ITS2 sequences varied from 316 to 488 bp, while the COI regions were 377 or 378 bp long. Considering the ITS2 genes, the intraspecific genetic distance was in the range of 0.00-0.077844, whereas the interspecific genetic distance was 0.202426-0.912959. The values were 0.000-0.029748 and 0.138403-0.279304 for intra- and interspecific genetic distances when COI genes were used. The phylogenetic trees inferred from the ITS2 and the COI regions, by using maximum parsimony and neighbor-joining methods, were identical to those based on their morphological classification. Thus, the ITS2 and COI regions can be applied as barcodes to identify different species of astigmatid mites.},
}
@article {pmid21074581,
year = {2011},
author = {Morada, M and Smid, O and Hampl, V and Sutak, R and Lam, B and Rappelli, P and Dessì, D and Fiori, PL and Tachezy, J and Yarlett, N},
title = {Hydrogenosome-localization of arginine deiminase in Trichomonas vaginalis.},
journal = {Molecular and biochemical parasitology},
volume = {176},
number = {1},
pages = {51-54},
pmid = {21074581},
issn = {1872-9428},
support = {R01 AI049785/AI/NIAID NIH HHS/United States ; },
mesh = {Gene Expression Regulation, Enzymologic ; Hydrolases/genetics/*metabolism ; Organelles/enzymology ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Trichomonas vaginalis/*enzymology/*genetics ; },
abstract = {The arginine dihydrolase (ADH) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating ATP. Subcellular localization of the ADH pathway enzymes in Trichomonas vaginalis revealed that arginine deiminase (ADI) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. However the other enzymes of the ADH pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. Three gene sequences of T. vaginalis ADI (ADI 1-3) were identified in the T. vaginalis genome, all having putative mitochondrial targeting sequences. The ADI sequences were cloned and used to probe T. vaginalis using a carboxyterminal di-hemogglutinin epitope tag which demonstrated co-localization with malic enzyme confirming the hydrogenosome localization of this enzyme.},
}
@article {pmid21075209,
year = {2012},
author = {Glor, RE and Laport, RG},
title = {Are subspecies of Anolis lizards that differ in dewlap color and pattern also genetically distinct? A mitochondrial analysis.},
journal = {Molecular phylogenetics and evolution},
volume = {64},
number = {2},
pages = {255-260},
doi = {10.1016/j.ympev.2010.11.004},
pmid = {21075209},
issn = {1095-9513},
mesh = {Animals ; Bahamas ; DNA, Mitochondrial/*genetics ; Dominican Republic ; Female ; Genetic Drift ; Genetic Variation ; Haplotypes ; Lizards/*classification/*genetics ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Pigmentation ; RNA, Transfer/genetics/metabolism ; Skin ; Species Specificity ; },
abstract = {Subspecies of Anolis lizards are often defined on the basis of geographic variation in the color and pattern of the dewlap, an extensible throat fan considered central to species recognition and sexual selection. Among the most impressive examples of this phenomenon are two species of trunk anoles found across Hispaniola and the Bahamas: Anolis distichus is divided into 16 subspecies with dewlap colors ranging from deep wine red to pale yellow while Anolis brevirostris is divided into three subspecies with dewlaps ranging from pale yellow to orange. Limited sampling of allozyme data indicates some genetic divergence among subspecies and suggests that they may deserve recognition at the species-level. Our goal here is to use more comprehensive geographic sampling of mtDNA haplotypes to test whether the five subspecies of A. distichus and three subspecies of A. brevirostris that occur in the Dominican Republic correspond with genetically distinct populations that may warrant recognition under the general lineage concept. We obtain an aligned dataset of 1462bp comprised of the genes encoding ND2 and adjacent tRNAs from 76 individuals of A. distichus from 28 localities and 12 individuals of A. brevirostris from five localities. We find that haplotypes sampled from each Dominican subspecies of A. distichus form well-supported and deeply divergent clades (>10% uncorrected sequence divergence). Strong concordance between mtDNA haplotype structure and previously diagnosed phenotypic variation in traits central to interspecific communication (i.e., the dewlap) leads us to hypothesize that each of the presently recognized Dominican subspecies of A. distichus and A. brevirostris deserves elevation to full species status under the general lineage concept.},
}
@article {pmid21078193,
year = {2010},
author = {Carrie, C and Murcha, MW and Whelan, J},
title = {An in silico analysis of the mitochondrial protein import apparatus of plants.},
journal = {BMC plant biology},
volume = {10},
number = {},
pages = {249},
pmid = {21078193},
issn = {1471-2229},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; Chlorella/genetics/metabolism ; Genetic Variation ; Membrane Transport Proteins/classification/*genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phaeophyceae/genetics/metabolism ; Phylogeny ; Picea/genetics/metabolism ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Rhodophyta/genetics/metabolism ; Sequence Alignment/methods ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {BACKGROUND: An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.<br><br>RESULTS: The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, (C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes (S. moellendorffii) and gymnosperms (P. glauca). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria.<br><br>CONCLUSIONS: It is proposed that the observed functional divergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, diversity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or diverged in a lineage specific manner.},
}
@article {pmid21087461,
year = {2010},
author = {Martínez-Fernández, M and Bernatchez, L and Rolán-Alvarez, E and Quesada, H},
title = {Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis.},
journal = {BMC evolutionary biology},
volume = {10},
number = {},
pages = {356},
pmid = {21087461},
issn = {1471-2148},
mesh = {Adaptation, Physiological/*genetics ; Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; Ecology ; Electron Transport Complex IV/genetics ; Female ; *Gene Expression Profiling ; Gene Flow ; *Genetic Speciation ; Male ; Sequence Analysis, DNA ; Snails/*genetics ; },
abstract = {BACKGROUND: In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation.<br><br>RESULTS: Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. &#x3b1;-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals.<br><br>CONCLUSIONS: At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.},
}
@article {pmid21103375,
year = {2010},
author = {Fourrage, C and Chevalier, S and Houliston, E},
title = {A highly conserved Poc1 protein characterized in embryos of the hydrozoan Clytia hemisphaerica: localization and functional studies.},
journal = {PloS one},
volume = {5},
number = {11},
pages = {e13994},
pmid = {21103375},
issn = {1932-6203},
mesh = {Animals ; Blotting, Western ; Cell Cycle Proteins/classification/genetics/*metabolism ; Centrioles/*metabolism ; DNA, Complementary/chemistry/genetics ; Embryo, Nonmammalian/embryology/*metabolism ; Female ; Fluorescent Antibody Technique ; Gene Expression Regulation, Developmental ; Gene Library ; Hydrozoa/embryology/genetics/*metabolism ; In Situ Hybridization ; Microscopy, Confocal ; Molecular Sequence Data ; Oocytes/metabolism ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Poc1 (Protein of Centriole 1) proteins are highly conserved WD40 domain-containing centriole components, well characterized in the alga Chlamydomonas, the ciliated protazoan Tetrahymena, the insect Drosophila and in vertebrate cells including Xenopus and zebrafish embryos. Functions and localizations related to the centriole and ciliary axoneme have been demonstrated for Poc1 in a range of species. The vertebrate Poc1 protein has also been reported to show an additional association with mitochondria, including enrichment in the specialized "germ plasm" region of Xenopus oocytes. We have identified and characterized a highly conserved Poc1 protein in the cnidarian Clytia hemisphaerica. Clytia Poc1 mRNA was found to be strongly expressed in eggs and early embryos, showing a punctate perinuclear localization in young oocytes. Fluorescence-tagged Poc1 proteins expressed in developing embryos showed strong localization to centrioles, including basal bodies. Anti-human Poc1 antibodies decorated mitochondria in Clytia, as reported in human cells, but failed to recognise endogenous or fluorescent-tagged Clytia Poc1. Injection of specific morpholino oligonucleotides into Clytia eggs prior to fertilization to repress Poc1 mRNA translation interfered with cell division from the blastula stage, likely corresponding to when neosynthesis normally takes over from maternally supplied protein. Cell cycle lengthening and arrest were observed, phenotypes consistent with an impaired centriolar biogenesis or function. The specificity of the defects could be demonstrated by injection of synthetic Poc1 mRNA, which restored normal development. We conclude that in Clytia embryos, Poc1 has an essentially centriolar localization and function.},
}
@article {pmid21130768,
year = {2011},
author = {Qi, Y and Wang, H and Zou, Y and Liu, C and Liu, Y and Wang, Y and Zhang, W},
title = {Over-expression of mitochondrial heat shock protein 70 suppresses programmed cell death in rice.},
journal = {FEBS letters},
volume = {585},
number = {1},
pages = {231-239},
doi = {10.1016/j.febslet.2010.11.051},
pmid = {21130768},
issn = {1873-3468},
mesh = {*Apoptosis ; Blotting, Western ; Cell Survival ; Chromatin/metabolism ; DNA Fragmentation ; Gene Expression Regulation, Plant ; HSP70 Heat-Shock Proteins/classification/genetics/*metabolism ; Hot Temperature ; Hydrogen Peroxide/pharmacology ; In Situ Nick-End Labeling ; Membrane Potential, Mitochondrial ; Microscopy, Fluorescence ; Oryza/cytology/genetics/*metabolism ; Oxidants/pharmacology ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants, Genetically Modified ; Protoplasts/cytology/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; },
abstract = {In this study, we identified and functionally characterized the mitochondrial heat shock protein 70 (mtHsp70). Over-expression of mtHsp70 suppressed heat- and H(2)O(2)-induced programmed cell death (PCD) in rice protoplasts, as reflected by higher cell viability, decreased DNA laddering and chromatin condensation. Mitochondrial membrane potential (Δψ(m)) after heat shock was destroyed gradually in protoplasts, but mtHsp70 over-expression showed higher Δψ(m) relative to the vector control cells, and partially inhibited cytochrome c release from mitochondria to cytosol. Heat treatment also significantly increased reactive oxygen species (ROS) generation, a phenomenon not observed in protoplasts over-expressing mtHsp70. Together, these results suggest that mtHsp70 may suppress PCD in rice protoplasts by maintaining mitochondrial Δψ(m) and inhibiting the amplification of ROS.},
}
@article {pmid21143489,
year = {2011},
author = {Dana, N and Megens, HJ and Crooijmans, RP and Hanotte, O and Mwacharo, J and Groenen, MA and van Arendonk, JA},
title = {East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis.},
journal = {Animal genetics},
volume = {42},
number = {2},
pages = {125-133},
doi = {10.1111/j.1365-2052.2010.02134.x},
pmid = {21143489},
issn = {1365-2052},
mesh = {Animals ; Asia, Southeastern ; Base Sequence ; Breeding ; Chickens/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Europe ; Female ; *Genetic Variation ; Haplotypes ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Netherlands ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; },
abstract = {Understanding the complex origin of domesticated populations is of vital importance for understanding, preserving and exploiting breed genetic diversity. Here, we aim to assess Asian contributions to European traditional breeds and western commercial chickens for mitochondrial genetic diversity. To this end, a 365-bp fragment of the chicken mtDNA D-loop region of 16 Dutch fancy breeds (113 individuals) was surveyed, comprising almost the entire breed diversity of The Netherlands. We also sequenced the same fragment for 160 commercial birds representing all important commercial types from multiple commercial companies that together represent more than 50% of the worldwide commercial value. We identified 20 different haplotypes. The haplotypes clustered into five clades. The commonest clade (E-clade) supposedly originates from the Indian subcontinent. In addition, both in commercial chicken and Dutch fancy breeds, many haplotypes were found with a clear East Asian origin. However, the erratic occurrence of many different East Asian mitochondrial clades indicates that there were many independent instances where breeders used imported exotic chickens for enhancing local breeds. Nucleotide diversity and haplotype diversity analyses showed the influence of the introgression of East Asian chicken on genetic diversity. All populations that had haplotypes of multiple origin displayed high inferred diversity, as opposed to most populations that had only a single mitochondrial haplotype signature. Most fancy breeds were found to have a much lower within-population diversity compared to broilers and layers, although this is not the case for mitochondrial estimates in fancy breeds that have multiple origin haplotypes.},
}
@article {pmid21143683,
year = {2010},
author = {Soto, G and Fox, R and Ayub, N and Alleva, K and Guaimas, F and Erijman, EJ and Mazzella, A and Amodeo, G and Muschietti, J},
title = {TIP5;1 is an aquaporin specifically targeted to pollen mitochondria and is probably involved in nitrogen remobilization in Arabidopsis thaliana.},
journal = {The Plant journal : for cell and molecular biology},
volume = {64},
number = {6},
pages = {1038-1047},
doi = {10.1111/j.1365-313X.2010.04395.x},
pmid = {21143683},
issn = {1365-313X},
mesh = {Aquaporins/genetics/*metabolism ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Hydrogen-Ion Concentration ; Mitochondria/*genetics ; Mutagenesis, Insertional ; Nitrogen/*metabolism ; Phylogeny ; Pollen Tube/*genetics ; RNA, Plant/genetics ; Water/metabolism ; },
abstract = {In plant sexual reproduction, water and solute movement are tightly regulated, suggesting the involvement of aquaporins. We previously identified TIP5;1 and TIP1;3 as the only Arabidopsis aquaporin genes that are selectively and highly expressed in mature pollen, and showed that they can transport both water and urea when expressed in Xenopus oocytes. Here, we show that TIP5;1 has unusual characteristics, as its water transport activity is regulated by pH. Analysis of the water transport activity of a mutant version of TIP5;1 (TIP5;1-H131A) and amino acid alignment with other plant aquaporins regulated by pH suggested that a conserved motif is involved in pH sensing. GFP-TIP5;1 is located in the mitochondria of pollen tubes. The single mutants tip1;3 and tip5;1, as well as the tip1;3 tip5;1 double mutant, are fertile, but all mutants had shorter than normal pollen tubes when germinated in vitro in the absence of exogenous nitrogen. Thus, we propose that TIP5;1 and TIP1;3 are involved in nitrogen recycling in pollen tubes of Arabidopsis thaliana.},
}
@article {pmid21148414,
year = {2011},
author = {Voss, B and Meinecke, L and Kurz, T and Al-Babili, S and Beck, CF and Hess, WR},
title = {Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii.},
journal = {Plant physiology},
volume = {155},
number = {2},
pages = {892-905},
pmid = {21148414},
issn = {1532-2548},
mesh = {Chlamydomonas reinhardtii/drug effects/*genetics ; Cluster Analysis ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; Heat-Shock Proteins/genetics/metabolism ; Hemin/*pharmacology ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/genetics/metabolism ; Protoporphyrins/*pharmacology ; RNA, Plant/genetics ; },
abstract = {Retrograde signaling is a pathway of communication from mitochondria and plastids to the nucleus in the context of cell differentiation, development, and stress response. In Chlamydomonas reinhardtii, the tetrapyrroles magnesium-protoporphyrin IX and heme are only synthesized within the chloroplast, and they have been implicated in the retrograde control of nuclear gene expression in this unicellular green alga. Feeding the two tetrapyrroles to Chlamydomonas cultures was previously shown to transiently induce five nuclear genes, three of which encode the heat shock proteins HSP70A, HSP70B, and HSP70E. In contrast, controversial results exist on the possible role of magnesium-protoporphyrin IX in the repression of genes for light-harvesting proteins in higher plants, raising the question of how important this mode of regulation is. Here, we used genome-wide transcriptional profiling to measure the global impact of these tetrapyrroles on gene regulation and the scope of the response. We identified almost 1,000 genes whose expression level changed transiently but significantly. Among them were only a few genes for photosynthetic proteins but several encoding enzymes of the tricarboxylic acid cycle, heme-binding proteins, stress-response proteins, as well as proteins involved in protein folding and degradation. More than 50% of the latter class of genes was also regulated by heat shock. The observed drastic fold changes at the RNA level did not correlate with similar changes in protein concentrations under the tested experimental conditions. Phylogenetic profiling revealed that genes of putative endosymbiontic origin are not overrepresented among the responding genes. This and the transient nature of changes in gene expression suggest a signaling role of both tetrapyrroles as secondary messengers for adaptive responses affecting the entire cell and not only organellar proteins.},
}
@article {pmid21172831,
year = {2011},
author = {Breton, S and Stewart, DT and Shepardson, S and Trdan, RJ and Bogan, AE and Chapman, EG and Ruminas, AJ and Piontkivska, H and Hoeh, WR},
title = {Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?.},
journal = {Molecular biology and evolution},
volume = {28},
number = {5},
pages = {1645-1659},
pmid = {21172831},
issn = {1537-1719},
support = {R15 GM086782/GM/NIGMS NIH HHS/United States ; GM86782-01A1/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics/metabolism ; Female ; Fresh Water ; Likelihood Functions ; Male ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Ovum/metabolism ; Phylogeny ; Protein Structure, Secondary ; Sequence Analysis, DNA ; Sex Characteristics ; Sex Determination Analysis/*methods ; Transcription, Genetic ; Unionidae/classification/*genetics/metabolism ; },
abstract = {Mitochondrial (mt) function depends critically on optimal interactions between components encoded by mt and nuclear DNAs. mitochondrial DNA (mtDNA) inheritance (SMI) is thought to have evolved in animal species to maintain mito-nuclear complementarity by preventing the spread of selfish mt elements thus typically rendering mtDNA heteroplasmy evolutionarily ephemeral. Here, we show that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years. We demonstrate that the only exception to SMI in the animal kingdom, that is, the doubly uniparental mtDNA inheritance system in bivalves, with its three-way interactions among egg mt-, sperm mt- and nucleus-encoded gene products, is tightly associated with the maintenance of separate male and female sexes (dioecy) in freshwater mussels. Specifically, this mother-through-daughter and father-through-son mtDNA inheritance system, containing highly differentiated mt genomes, is found in all dioecious freshwater mussel species. Conversely, all hermaphroditic species lack the paternally transmitted mtDNA (=possess SMI) and have heterogeneous macromutations in the recently discovered, novel protein-coding gene (F-orf) in their maternally transmitted mt genomes. Using immunoelectron microscopy, we have localized the F-open reading frame (ORF) protein, likely involved in specifying separate sexes, in mitochondria and in the nucleus. Our results support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels. Concomitantly, our study demonstrates novel features for animal mt genomes: the existence of additional, lineage-specific, mtDNA-encoded proteins with functional significance and the involvement of mtDNA-encoded proteins in extra-mt functions. Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as "noncoding," found in a large proportion of animal mt genomes.},
}
@article {pmid21177940,
year = {2011},
author = {Richards, JG},
title = {Physiological, behavioral and biochemical adaptations of intertidal fishes to hypoxia.},
journal = {The Journal of experimental biology},
volume = {214},
number = {Pt 2},
pages = {191-199},
doi = {10.1242/jeb.047951},
pmid = {21177940},
issn = {1477-9145},
mesh = {*Acclimatization ; Animals ; Behavior, Animal ; Fishes/metabolism/*physiology ; Oxygen/*metabolism ; Phylogeny ; },
abstract = {Hypoxia survival in fish requires a well-coordinated response to either secure more O(2) from the hypoxic environment or to limit the metabolic consequences of an O(2) restriction at the mitochondria. Although there is a considerable amount of information available on the physiological, behavioral, biochemical and molecular responses of fish to hypoxia, very little research has attempted to determine the adaptive value of these responses. This article will review current attempts to use the phylogenetically corrected comparative method to define physiological and behavioral adaptations to hypoxia in intertidal fish and further identify putatively adaptive biochemical traits that should be investigated in the future. In a group of marine fishes known as sculpins, from the family Cottidae, variation in hypoxia tolerance, measured as a critical O(2) tension (P(crit)), is primarily explained by variation in mass-specific gill surface area, red blood cell hemoglobin-O(2) binding affinity, and to a lesser extent variation in routine O(2) consumption rate (M(O(2))). The most hypoxia-tolerant sculpins consistently show aquatic surface respiration (ASR) and aerial emergence behavior during hypoxia exposure, but no phylogenetically independent relationship has been found between the thresholds for initiating these behaviors and P(crit). At O(2) levels below P(crit), hypoxia survival requires a rapid reorganization of cellular metabolism to suppress ATP consumption to match the limited capacity for O(2)-independent ATP production. Thus, it is reasonable to speculate that the degree of metabolic rate suppression and the quantity of stored fermentable fuel is strongly selected for in hypoxia-tolerant fishes; however, these assertions have not been tested in a phylogenetic comparative model.},
}
@article {pmid21182560,
year = {2011},
author = {Anderson, OR and Wang, W and Faucher, SP and Bi, K and Shuman, HA},
title = {A new heterolobosean amoeba Solumitrus palustris n. g., n. sp. isolated from freshwater marsh soil.},
journal = {The Journal of eukaryotic microbiology},
volume = {58},
number = {1},
pages = {60-67},
doi = {10.1111/j.1550-7408.2010.00520.x},
pmid = {21182560},
issn = {1550-7408},
support = {R01 AI023549/AI/NIAID NIH HHS/United States ; 5R01AI23549/AI/NIAID NIH HHS/United States ; 5R01AI064481/AI/NIAID NIH HHS/United States ; },
mesh = {Amoeba/*classification/genetics/growth &amp; development/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Fresh Water/*parasitology ; Molecular Sequence Data ; Phylogeny ; Soil/*parasitology ; Wetlands ; },
abstract = {During the course of research on the bacterial feeding behavior and resistance of amoebae to virulent pathogens, we isolated a new strain of amoeba from organic rich soil at the margin of freshwater swamp in the northeastern United States. Light microscopic morphology is characteristically heterolobosean, resembling vahlkampfiids, including a broadened, limax shape, and eruptive locomotion, but occasionally becoming more contracted and less elongated with lateral or anterior bulges and somewhat branching sparse, uroidal filaments. Electron microscopic evidence, including mitochondria with flattened cristae surrounded by rough endoplasmic reticulum, further indicates a heterolobosean affinity. The solitary nucleus contains a centrally located nucleolus. Cysts are rounded with occasionally an eccentrically located nucleus. The cyst walls are relatively thin, becoming crenated, and loosely enclosing the cyst when mature. Molecular genetic evidence places this isolate among the Heterolobosea, branching most closely in a clade including Allovahlkampfia spelaea and previously isolated, un-named strains of soil amoebae. Based on differentiated features, including morphology of the uroid, cyst wall structure, and molecular genetic evidence that distinguish it from A. spelaea, a new genus and species, Solumitrus palustris, is proposed for this new heterolobosean.},
}
@article {pmid21190582,
year = {2010},
author = {Jimenez-Lopez, JC and Gachomo, EW and Seufferheld, MJ and Kotchoni, SO},
title = {The maize ALDH protein superfamily: linking structural features to functional specificities.},
journal = {BMC structural biology},
volume = {10},
number = {},
pages = {43},
pmid = {21190582},
issn = {1472-6807},
mesh = {Aldehyde Dehydrogenase/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chemical Phenomena ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/isolation &amp; purification/*metabolism ; Models, Molecular ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Protein Binding ; Protein Structure, Quaternary ; Sequence Alignment ; Static Electricity ; Zea mays/*enzymology/*genetics/metabolism ; },
abstract = {BACKGROUND: The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Gene annotation and functional characterization of gene products are important to uncover novel protein functionality.<br><br>RESULTS: In this paper, we identify, and annotate members of all the maize aldehyde dehydrogenase (ALDH) gene superfamily according to the revised nomenclature criteria developed by ALDH Gene Nomenclature Committee (AGNC). The maize genome contains 24 unique ALDH sequences encoding members of ten ALDH protein families including the previously identified male fertility restoration RF2A gene, which encodes a member of mitochondrial class 2 ALDHs. Using computational modeling analysis we report here the identification, the physico-chemical properties, and the amino acid residue analysis of a novel tunnel like cavity exclusively found in the maize sterility restorer protein, RF2A/ALDH2B2 by which this protein is suggested to bind variably long chain molecular ligands and/or potentially harmful molecules.<br><br>CONCLUSIONS: Our finding indicates that maize ALDH superfamily is the most expanded of plant ALDHs ever characterized, and the mitochondrial maize RF2A/ALDH2B2 is the only plant ALDH that harbors a newly defined pocket/cavity with suggested functional specificity.},
}
@article {pmid21203427,
year = {2010},
author = {Hendrich, L and Pons, J and Ribera, I and Balke, M},
title = {Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.},
journal = {PloS one},
volume = {5},
number = {12},
pages = {e14448},
pmid = {21203427},
issn = {1932-6203},
mesh = {Animals ; Australia ; Classification ; Coleoptera ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing ; Genetic Variation ; Insecta ; Likelihood Functions ; Mitochondria/*metabolism ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.<br><br>We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). S&#xf8;rensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.<br><br>CONCLUSION/SIGNIFICANCE: Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and &#x3b2;-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.},
}
@article {pmid21207102,
year = {2011},
author = {Traba, J and Satrústegui, J and del Arco, A},
title = {Adenine nucleotide transporters in organelles: novel genes and functions.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {68},
number = {7},
pages = {1183-1206},
pmid = {21207102},
issn = {1420-9071},
mesh = {Adenine Nucleotides/*metabolism ; Animals ; Eukaryota/cytology/metabolism ; Humans ; Mitochondrial ADP, ATP Translocases/chemistry/classification/*genetics/*metabolism ; Organelles/*metabolism ; Phylogeny ; Protein Conformation ; Protein Isoforms/chemistry/genetics/metabolism ; },
abstract = {In eukaryotes, cellular energy in the form of ATP is produced in the cytosol via glycolysis or in the mitochondria via oxidative phosphorylation and, in photosynthetic organisms, in the chloroplast via photophosphorylation. Transport of adenine nucleotides among cell compartments is essential and is performed mainly by members of the mitochondrial carrier family, among which the ADP/ATP carriers are the best known. This work reviews the carriers that transport adenine nucleotides into the organelles of eukaryotic cells together with their possible functions. We focus on novel mechanisms of adenine nucleotide transport, including mitochondrial carriers found in organelles such as peroxisomes, plastids, or endoplasmic reticulum and also mitochondrial carriers found in the mitochondrial remnants of many eukaryotic parasites of interest. The extensive repertoire of adenine nucleotide carriers highlights an amazing variety of new possible functions of adenine nucleotide transport across eukaryotic organelles.},
}
@article {pmid21252340,
year = {2011},
author = {Rebbeck, CA and Leroi, AM and Burt, A},
title = {Mitochondrial capture by a transmissible cancer.},
journal = {Science (New York, N.Y.)},
volume = {331},
number = {6015},
pages = {303},
doi = {10.1126/science.1197696},
pmid = {21252340},
issn = {1095-9203},
mesh = {Animals ; Coyotes/genetics ; Dog Diseases/*genetics/metabolism/pathology ; Dogs/genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Mitochondria/genetics/metabolism ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Venereal Tumors, Veterinary/*genetics/*metabolism/pathology ; Wolves/genetics ; },
abstract = {Canine transmissible venereal tumor (CTVT) is an infectious cell line circulating in many feral dog populations. It originated once, about 10,000 years ago. Phylogenetic analyses of mitochondrial sequences from dogs, wolves, and a geographically diverse collection of CTVT samples indicate that the cancer has periodically acquired mitochondria from its host. We suggest that this may be because the cancer's own mitochondria have a tendency to degenerate, due to high mutation rates and relaxed selection, resulting in host mitochondria being more fit.},
}
@article {pmid21273215,
year = {2011},
author = {Grobler, JP and Jones, JW and Johnson, NA and Neves, RJ and Hallerman, EM},
title = {Homogeneity at nuclear microsatellite loci masks mitochondrial haplotype diversity in the endangered fanshell pearlymussel (Cyprogenia stegaria).},
journal = {The Journal of heredity},
volume = {102},
number = {2},
pages = {196-206},
doi = {10.1093/jhered/esq120},
pmid = {21273215},
issn = {1465-7333},
mesh = {Alleles ; Animals ; Bivalvia/*genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Frequency ; *Genetic Variation ; Genetics, Population ; Geography ; *Haplotypes ; *Microsatellite Repeats ; Mitochondria/*genetics ; Molecular Sequence Data ; Ohio ; Phylogeny ; Tennessee ; },
abstract = {We report on multiple patterns of differentiation and connectivity in the fanshell pearlymussel (Cyprogenia stegaria), based on different markers. Knowledge of genetic variation and genetic connectivity among remaining populations of this federally endangered species is needed to initiate implementation of the species recovery plan. We collected tissue samples from 96 specimens from the Green, Rolling Fork, and Licking Rivers, tributaries to the Ohio River, and the Clinch River, a tributary to the Tennessee River, providing broad coverage of the current distributional range of the species. Results from 7 nuclear DNA microsatellite markers suggested minimal population-level differentiation, whereas a mitochondrial DNA (mtDNA) marker (ND1) exhibited significant differentiation between C. stegaria in the Clinch River and the Ohio River populations. The ND1 data also confirm the existence of 2 distinct mtDNA lineages in the genus that transcends species boundaries. Further analyses suggest that the disproportionally strong signal from 2 very divergent ND1 lineages possibly masks finer-grained structure in the Ohio River population, based on one of the mtDNA lineages only. We recommend further sampling to confirm the absence of one lineage from the upper Clinch River drainage and suggest that provisional management guidelines should limit reciprocal exchanges among C. stegaria populations from the Clinch River and those in the Ohio River system.},
}
@article {pmid21307286,
year = {2011},
author = {Araújo, WL and Nunes-Nesi, A and Osorio, S and Usadel, B and Fuentes, D and Nagy, R and Balbo, I and Lehmann, M and Studart-Witkowski, C and Tohge, T and Martinoia, E and Jordana, X and Damatta, FM and Fernie, AR},
title = {Antisense inhibition of the iron-sulphur subunit of succinate dehydrogenase enhances photosynthesis and growth in tomato via an organic acid-mediated effect on stomatal aperture.},
journal = {The Plant cell},
volume = {23},
number = {2},
pages = {600-627},
pmid = {21307286},
issn = {1532-298X},
mesh = {Biomass ; Carbon Dioxide/metabolism ; *Citric Acid Cycle ; Cloning, Molecular ; Iron-Sulfur Proteins/metabolism ; Solanum lycopersicum/genetics/*growth &amp; development ; Mitochondria/metabolism ; Oxygen Consumption ; *Photosynthesis ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plant Stomata/*drug effects ; Plant Transpiration ; Plants, Genetically Modified/genetics/growth &amp; development ; RNA, Antisense/genetics ; RNA, Plant/genetics ; Succinate Dehydrogenase/genetics/*metabolism ; },
abstract = {Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the Sl SDH2-2 gene encoding the iron sulfur subunit of the succinate dehydrogenase protein complex in the antisense orientation under the control of the 35S promoter exhibit an enhanced rate of photosynthesis. The rate of the tricarboxylic acid (TCA) cycle was reduced in these transformants, and there were changes in the levels of metabolites associated with the TCA cycle. Furthermore, in comparison to wild-type plants, carbon dioxide assimilation was enhanced by up to 25% in the transgenic plants under ambient conditions, and mature plants were characterized by an increased biomass. Analysis of additional photosynthetic parameters revealed that the rate of transpiration and stomatal conductance were markedly elevated in the transgenic plants. The transformants displayed a strongly enhanced assimilation rate under both ambient and suboptimal environmental conditions, as well as an elevated maximal stomatal aperture. By contrast, when the Sl SDH2-2 gene was repressed by antisense RNA in a guard cell-specific manner, changes in neither stomatal aperture nor photosynthesis were observed. The data obtained are discussed in the context of the role of TCA cycle intermediates both generally with respect to photosynthetic metabolism and specifically with respect to their role in the regulation of stomatal aperture.},
}
@article {pmid21315164,
year = {2011},
author = {Carvalho-Costa, LF and Piorski, NM and Willis, SC and Galetti, PM and Ortí, G},
title = {Molecular systematics of the neotropical shovelnose catfish genus Pseudoplatystoma Bleeker 1862 based on nuclear and mtDNA markers.},
journal = {Molecular phylogenetics and evolution},
volume = {59},
number = {1},
pages = {177-194},
doi = {10.1016/j.ympev.2011.02.005},
pmid = {21315164},
issn = {1095-9513},
mesh = {Animals ; Bayes Theorem ; Catfishes/classification/*genetics ; Cytochromes b/genetics ; Genes, RAG-1 ; Genetic Markers ; Haplotypes ; Introns ; Likelihood Functions ; Mitochondria/*genetics ; Multilocus Sequence Typing ; *Phylogeny ; Rivers ; South America ; Tropical Climate ; },
abstract = {Pseudoplatystoma is a commercially important genus of Neotropical migratory catfishes widely distributed in all major river basins of South America. Historically, only three species were recognized, but a recent revision proposed eight putative morphospecies for the genus. A molecular study based on mitochondria DNA (mtDNA) provided support for recognition of only some of the species and raised questions about species boundaries in this group. We present a more encompassing analysis based on mtDNA (cytochrome b, 818bp) and nuclear DNA-based phylogenies (Rag1 intron 1, 664bp and S7 intron 1, 635bp) for a more extensive sampling (279 individuals from 42 localities) of all putative species in all major river basins. Patterns generated by individual gene genealogies and a multispecies coalescent analysis provided evidence to suggest recognition of only four distinct species in this genus: Pseudoplatystoma magdaleniatum, Pseudoplatystoma corruscans, Pseudoplatystoma tigrimun (sensu lato) and Pseudoplatystoma fasciatum (sensu lato). The species phylogeny places P. magdaleniatum as the sister group to all the other species in the genus, but the relationships among P. fasciatum s.l, P. tigrimum s.l., and P. corruscans could not be resolved with confidence.},
}
@article {pmid21325020,
year = {2011},
author = {Kim, YK and Hong, YJ and Min, MS and Kim, KS and Kim, YJ and Voloshina, I and Myslenkov, A and Smith, GJ and Cuong, ND and Tho, HH and Han, SH and Yang, DH and Kim, CB and Lee, H},
title = {Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis.},
journal = {The Journal of heredity},
volume = {102},
number = {2},
pages = {165-174},
doi = {10.1093/jhered/esq121},
pmid = {21325020},
issn = {1465-7333},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Republic of Korea ; Ursidae/*genetics ; },
abstract = {The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed.},
}
@article {pmid21333758,
year = {2011},
author = {de la Rua, N and Stevens, L and Dorn, PL},
title = {High genetic diversity in a single population of Triatoma sanguisuga (LeConte, 1855) inferred from two mitochondrial markers: Cytochrome b and 16S ribosomal DNA.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {11},
number = {3},
pages = {671-677},
doi = {10.1016/j.meegid.2011.02.009},
pmid = {21333758},
issn = {1567-7257},
mesh = {Animals ; Base Sequence ; Cytochromes b/*genetics ; Disease Vectors ; Female ; Genetic Markers ; Genetic Variation ; Haplotypes ; Host-Parasite Interactions ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/*genetics ; Triatoma/classification/*genetics/parasitology ; Trypanosoma cruzi/physiology ; },
abstract = {Chagas disease remains endemic across much of Latin America, but is largely enzootic--restricted to wild mammals and triatomine vectors in the United States. Within the United States, there are ten recognized species of triatomines and 18 mammals reported naturally infected with Trypanosoma cruzi, the causative agent of Chagas disease. However, only six cases of autochthonous vector-borne transmission of T. cruzi to humans have been reported in the United States. As a follow-up to the sixth reported case, triatomine insects were collected from the index case site, in a rural area of New Orleans, LA, USA. During the summer months of 2006 and 2007, 344 Triatoma sanguisuga were collected and showed a T. cruzi infection prevalence of 56%. A subset of these insects was analyzed to infer intraspecific genetic variation from a 606 bp fragment of cytochrome b (n=54) and a 340 bp fragment of 16S ribosomal DNA (n=17). From the 54 samples, 37 cytb haplotypes (H(d)=0.978) were observed and 14.7% of positions were polymorphic. Phylogenetic analysis divides the population into two distinct groups with an average pairwise genetic distance of ~5%. The 16S rDNA sequences revealed 6 haplotypes among 17 specimens (H(d)=0.713) with 1.2% of the positions exhibiting polymorphisms. 16S polymorphism data support the concept of two groups within this single population. The genetic distance of Group 1 from Group 2 suggests that Group 1 could represent a sub-species as this level of divergence is similar to that observed among other triatomine subspecies.},
}
@article {pmid21352954,
year = {2011},
author = {Piccinali, RV and Marcet, PL and Ceballos, LA and Kitron, U and Gürtler, RE and Dotson, EM},
title = {Genetic variability, phylogenetic relationships and gene flow in Triatoma infestans dark morphs from the Argentinean Chaco.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {11},
number = {5},
pages = {895-903},
pmid = {21352954},
issn = {1567-7257},
support = {R01 TW005836/TW/FIC NIH HHS/United States ; #R01TW05836/TW/FIC NIH HHS/United States ; },
mesh = {Animals ; Argentina ; Base Sequence ; DNA, Intergenic ; Electron Transport Complex IV ; Gene Expression Regulation ; *Gene Flow ; *Genetic Variation ; Haplotypes ; Mitochondria/enzymology ; Phylogeny ; Pigments, Biological ; Triatoma/*genetics ; },
abstract = {The recent discovery of sylvatic populations of Triatoma infestans outside the Andean Valleys of Bolivia prompted an evolutionary question about the putative ancestral area of origin and dispersal of the species, and an epidemiological question regarding the possible role of these sylvatic populations in the recolonization process of insecticide-treated houses. The finding of a population of sylvatic melanic T. infestans (dark morphs) in the Argentinean dry Chaco at 7 km from a peridomestic bug population of typical coloration gave us the opportunity to test both questions simultaneously by employing phylogenetic and population genetic approaches. For this purpose we analyzed sylvatic and peridomestic bugs using sequence-based mitochondrial and nuclear markers (mtCOI and ITS-1) and microsatellites. Sylvatic bugs were confirmed to be T. infestans and not hybrids, and showed high levels of genetic variability and departures from neutral expectations for mtCOI variation. New ITS-1 and mtCOI haplotypes were recorded, as well as haplotypes shared with peridomestic and/or domestic bugs from previous records. The peridomestic population was invariant for ITS-1 and mtCOI, but showed variability for microsatellites and signatures of a population bottleneck, probably due to a limited number of founders. Phylogenetic analyses were consistent with the presence of ancestral haplotypes in sylvatic bugs. According to F-statistics and assignment methods there was a significant differentiation between sylvatic and peridomestic bugs and gene flow was low and asymmetric, with more bugs moving from the peridomicile to the sylvatic environment. These results support the hypothesis of the Chaco region as the area of origin of T. infestans, and a limited role of sylvatic melanic T. infestans in peridomestic infestation in the Argentinean Chaco.},
}
@article {pmid21365259,
year = {2011},
author = {Tachibana, M and Allen, AE and Kikutani, S and Endo, Y and Bowler, C and Matsuda, Y},
title = {Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.},
journal = {Photosynthesis research},
volume = {109},
number = {1-3},
pages = {205-221},
pmid = {21365259},
issn = {1573-5079},
mesh = {Amino Acid Sequence ; Carbon Dioxide/*metabolism ; Carbonic Anhydrases/genetics/*metabolism ; Cell Membrane/enzymology/metabolism/ultrastructure ; Chloroplasts/enzymology/metabolism/ultrastructure ; Cloning, Molecular ; Diatoms/*enzymology/genetics/metabolism/ultrastructure ; Gene Expression Regulation, Enzymologic ; Green Fluorescent Proteins ; Mitochondria/enzymology/metabolism/ultrastructure ; Phylogeny ; RNA, Messenger/genetics ; Recombinant Fusion Proteins ; Seawater ; Sequence Alignment ; Transformation, Genetic ; },
abstract = {It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO(2) conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO(2) and 5% CO(2). However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO(2). Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm. These results suggest that CAs are constitutively present in the four chloroplastic membrane systems in P. tricornutum and that CO(2) responsive CAs occur in the pyrenoid of P. tricornutum, and in the stroma and periplasm of T. pseudonana.},
}
@article {pmid21376606,
year = {2011},
author = {Araújo, VA and Lino-Neto, J and de Sousa Ramalho, F and Zanuncio, JC and Serrão, JE},
title = {Ultrastructure and heteromorphism of spermatozoa in five species of bugs (Pentatomidae: Heteroptera).},
journal = {Micron (Oxford, England : 1993)},
volume = {42},
number = {6},
pages = {560-567},
doi = {10.1016/j.micron.2011.02.001},
pmid = {21376606},
issn = {1878-4291},
mesh = {Acrosome/ultrastructure ; Animals ; Axoneme ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Heteroptera/genetics/*ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Phylogeny ; Spermatozoa/metabolism/*ultrastructure ; },
abstract = {Pentatomidae is one of the largest Heteroptera families, comprising about 10% of the species estimated for the suborder. In spite of existing studies, doubts remain regarding the systematics of Pentatomomorpha. In this study, five species of Pentatomidae spermatozoa were examined to achieve characteristics that enable inferences in the phylogeny of the group and in behavioral issues associated with the presence of polymorphisms. Spermatozoa polymorphisms, characterized by two classes of sizes, are found in Podisus nigrispinus, Podisus distinctus, and Brontocoris tabidus, whereas Thynacanta marginata (Dallas) and Supputius cincticeps have single-size spermatozoa. The head region consists of an acrosome, a nucleus, and part of the centriolar adjunct. In the more anterior region, the nucleus is parallel to the centriolar adjunct. In the nucleus-flagellum transition region, the nucleus overlaps the anterior region of the mitochondrial derivatives, just above the axoneme. The mitochondrial derivatives and the axoneme run the entire extent of the flagellum. In species in which the spermatozoa are polymorphic, the larger spermatozoa have derivatives mitochondrial approximately 3-fold larger than the smaller spermatozoa. Characteristics derived from the morphology of spermatozoa indicate synapomorphies and are promising for systematic studies.},
}
@article {pmid21388704,
year = {2011},
author = {Fernández-Ocaña, A and Chaki, M and Luque, F and Gómez-Rodríguez, MV and Carreras, A and Valderrama, R and Begara-Morales, JC and Hernández, LE and Corpas, FJ and Barroso, JB},
title = {Functional analysis of superoxide dismutases (SODs) in sunflower under biotic and abiotic stress conditions. Identification of two new genes of mitochondrial Mn-SOD.},
journal = {Journal of plant physiology},
volume = {168},
number = {11},
pages = {1303-1308},
doi = {10.1016/j.jplph.2011.01.020},
pmid = {21388704},
issn = {1618-1328},
mesh = {Chloroplasts/genetics/metabolism ; Cloning, Molecular ; Computational Biology ; Gene Expression Regulation, Plant ; *Genes, Mitochondrial ; Genes, Plant ; Helianthus/enzymology/*genetics/microbiology ; Mitochondria/genetics/metabolism ; Oomycetes/pathogenicity ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plant Roots/genetics/metabolism ; Seedlings/enzymology/microbiology ; Sequence Analysis, Protein ; *Stress, Physiological ; Superoxide Dismutase/genetics/*metabolism ; Superoxides/analysis ; Temperature ; },
abstract = {Superoxide dismutases (SODs) are a family of metalloenzymes that catalyse the disproportionation of superoxide radicals into hydrogen peroxide and oxygen. In sunflower (Helianthus annuus L.) seedlings, two new Mn-SOD isozymes, designated as I and II, were identified. However, no evidence for a Fe-SOD was found. Both Mn-SOD I and Mn-SOD II have a cleaved sequence of 14 residues that target the mitochondrion with a probability of 81% and 95%, respectively. The gene expression of these new mitochondrial Mn-SODs as well as the previously reported cytosolic and chloroplastic CuZnSODs was analyzed by real-time quantitative reverse transcription-PCR. This was done in the main organs (roots, hypocotyls, and cotyledons) of sunflower seedlings and also under biotic (infection by the pathogen Plasmopara halstedii) and abiotic stress conditions, including high and low temperature and mechanical wounding. Both CuZn-SODs had a gene expression of 1000-fold higher than that of mitochondrial Mn-SODs. And the expression of the Mn-SOD I was approximately 12-fold higher than that of Mn-SOD II. The Mn-SOD I showed a significant modulation in response to the assayed biotic and abiotic stresses even when it had no apparent oxidative stress, such as low temperature. Thus, it is proposed that the mitochondrial Mn-SOD I gene could act as an early sensor of adverse conditions to prevent potential oxidative damage.},
}
@article {pmid21421812,
year = {2011},
author = {Watkins, KP and Rojas, M and Friso, G and van Wijk, KJ and Meurer, J and Barkan, A},
title = {APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain.},
journal = {The Plant cell},
volume = {23},
number = {3},
pages = {1082-1092},
pmid = {21421812},
issn = {1532-298X},
mesh = {Arabidopsis/genetics ; Arabidopsis Proteins/chemistry/*genetics ; Carrier Proteins/*genetics ; Chloroplasts/*genetics/metabolism ; Introns/*genetics ; Phylogeny ; *RNA Splicing ; RNA, Messenger/analysis ; RNA-Binding Proteins/*genetics/metabolism ; Zea mays/genetics ; },
abstract = {Arabidopsis thaliana APO1 is required for the accumulation of the chloroplast photosystem I and NADH dehydrogenase complexes and had been proposed to facilitate the incorporation of [4Fe-4S] clusters into these complexes. The identification of maize (Zea mays) APO1 in coimmunoprecipitates with a protein involved in chloroplast RNA splicing prompted us to investigate a role for APO1 in splicing. We show here that APO1 promotes the splicing of several chloroplast group II introns: in Arabidopsis apo1 mutants, ycf3-intron 2 remains completely unspliced, petD intron splicing is strongly reduced, and the splicing of several other introns is compromised. These splicing defects can account for the loss of photosynthetic complexes in apo1 mutants. Recombinant APO1 from both maize and Arabidopsis binds RNA with high affinity in vitro, demonstrating that DUF794, the domain of unknown function that makes up almost the entirety of APO1, is an RNA binding domain. We provide evidence that DUF794 harbors two motifs that resemble zinc fingers, that these bind zinc, and that they are essential for APO1 function. DUF794 is found in a plant-specific protein family whose members are all predicted to localize to mitochondria or chloroplasts. Thus, DUF794 adds a new example to the repertoire of plant-specific RNA binding domains that emerged as a product of nuclear-organellar coevolution.},
}
@article {pmid21423759,
year = {2011},
author = {Darling, JA},
title = {Interspecific hybridization and mitochondrial introgression in invasive carcinus shore crabs.},
journal = {PloS one},
volume = {6},
number = {3},
pages = {e17828},
pmid = {21423759},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Brachyura/*genetics ; Cluster Analysis ; Factor Analysis, Statistical ; Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; *Hybridization, Genetic ; *Introduced Species ; Japan ; Linkage Disequilibrium/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {Interspecific hybridization plays an important role in facilitating adaptive evolutionary change. More specifically, recent studies have demonstrated that hybridization may dramatically influence the establishment, spread, and impact of invasive populations. In Japan, previous genetic evidence for the presence of two non-native congeners, the European green crab Carcinus maenas and the Mediterranean green crab C. aestuarii, has raised questions regarding the possibility of hybridization between these sister species. Here I present analysis based on both nuclear microsatellites and the mitochondrial cytochrome C oxidase subunit I (COI) gene which unambiguously argues for a hybrid origin of Japanese Carcinus. Despite the presence of mitochondrial lineages derived from both C. maenas and C. aestuarii, the Japanese population is panmictic at nuclear loci and has achieved cytonuclear equilibrium throughout the sampled range in Japan. Furthermore, analysis of admixture at nuclear loci indicates dramatic introgression of the C. maenas mitochondrial genome into a predominantly C. aestuarii nuclear background. These patterns, along with inferences drawn from the observational record, argue for a hybridization event pre-dating the arrival of Carcinus in Japan. The clarification of both invasion history and evolutionary history afforded by genetic analysis provides information that may be critically important to future studies aimed at assessing risks posed by invasive Carcinus populations to Japan and the surrounding region.},
}
@article {pmid21428694,
year = {2011},
author = {Morel, F and Aninat, C},
title = {The glutathione transferase kappa family.},
journal = {Drug metabolism reviews},
volume = {43},
number = {2},
pages = {281-291},
doi = {10.3109/03602532.2011.556122},
pmid = {21428694},
issn = {1097-9883},
mesh = {Amino Acid Sequence ; Animals ; Glutathione Transferase/chemistry/genetics/*physiology ; Humans ; Isoenzymes ; Mitochondria/enzymology ; Molecular Sequence Data ; Organ Specificity ; Peroxisomes/enzymology ; Phylogeny ; Sequence Alignment ; Species Specificity ; Substrate Specificity ; },
abstract = {Glutathione transferase (GST) kappa, also named mitochondrial GST, is a very ancient protein family with orthologs in bacteria and eukaryotes. Both the structure and the subcellular localization of GSTK1-1, in mitochondria and peroxisomes, make this enzyme distinct from cytosolic GSTs. Rodent and human GSTK1 exhibit activity towards a number of model GST substrates and, in Caenorhabditis elegans, this enzyme may be involved in energy and lipid metabolism, two functions related to mitochondria and peroxisomes. Interestingly, GST kappa is also a key regulator of adiponectin biosynthesis and multimerization suggesting that it might function as a chaperone to facilitate correct folding and assembly of proteins. Since adiponectin expression has been correlated with insulin resistance, obesity and diabetes, GSTK1 expression level which is negatively correlated with obesity in mice and human adipose tissues may be an important factor in these metabolic disorders. Furthermore, a polymorphism in the hGSTK1 promoter has been associated with insulin secretion and fat deposition.},
}
@article {pmid21434420,
year = {2010},
author = {Maĭkova, OO and Itskovich, VB and Semiturkina, NA and Kaliuzhnaia, OV and Belikov, SI},
title = {[Phylogenetic position of sponges from Chagytaĭ and Tore-Khol' lakes].},
journal = {Genetika},
volume = {46},
number = {12},
pages = {1670-1677},
pmid = {21434420},
issn = {0016-6758},
mesh = {Animals ; Base Sequence ; Fresh Water ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Porifera/*genetics ; RNA, Transfer, Met/genetics ; RNA, Transfer, Tyr/genetics ; Siberia ; Untranslated Regions ; },
abstract = {Morphological and molecular genetic data for freshwater sponges from the lakes of Tuva Depression, Baikalospongia dzhegatajensis (Rezvo, 1936), forms Dzh05 and Dzh06, from Chagatai Lake, as well as forms TKhl and TKh2, from the Lake Tore-Khol, were obtained and examined. In the sponges examined, which on phylogenetic tree clustered together with the Ephydatia fluviatilis (Linneaus, 1758) sponge from the family Spongillidae, the ITS rDNA regions were sequenced. Comparison of highly variable interal spacer regions of the mitochondrial genome was performed using corresponding sequences of three sponges from the family Spongillidae (E. fluviatilis, E. muelleri and Spongilla lacustris), sponges from the Chagatai and Tore-Khol lakes (Dzh06 and TKh2) with an unknown status, and sponges from the Baikalian family Lubomirskiidae. Minimum genetic differences were observed between E. fluviatilis, Dzh06, and TKh2 (from 0.003 to 0.01% of nucleotide substitutions), while maximum differences were found between the species of Lubomirskiidae and Spongillidae (from 0.928 to 2.06%). The data obtained indicated that sponges from Chagatai and Tore-Khol lakes were most close to E. fluviatilis.},
}
@article {pmid21453719,
year = {2011},
author = {Schindeldecker, M and Stark, M and Behl, C and Moosmann, B},
title = {Differential cysteine depletion in respiratory chain complexes enables the distinction of longevity from aerobicity.},
journal = {Mechanisms of ageing and development},
volume = {132},
number = {4},
pages = {171-179},
doi = {10.1016/j.mad.2011.03.002},
pmid = {21453719},
issn = {1872-6216},
mesh = {Aerobiosis ; Aging ; Animals ; Cell Nucleus/metabolism ; Cysteine/*metabolism ; *Electron Transport ; Humans ; Membrane Proteins/chemistry ; Mitochondria/metabolism ; Oxidative Stress ; Oxygen Consumption ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sulfhydryl Compounds/chemistry ; Time Factors ; },
abstract = {Mitochondrially encoded proteins in long-lived animals exhibit a characteristic anomaly on the amino acid usage level: they abstain from the use of cysteine in a lifespan-dependent fashion. Here, we have further investigated this phenomenon by analyzing respiratory chain complex subunits individually. We find that complex I cysteine depletion is the almost exclusive carrier of the cysteine-lifespan correlation, whereas complex IV cysteine depletion is uniform in all aerobic animals, unrelated to longevity, but even more pronounced than complex I cysteine depletion in the longest-lived species. In nuclear encoded subunits of the respiratory chain, we find lifespan-independent cysteine depletion ranging from moderate in complex I to severe in complex V. However, a separate analysis of the transmembrane domains of these proteins unmasks an intramembrane pattern of cysteine usage that significantly correlates with longevity. Hence, cysteine usage in the respiratory chain seems to be governed by two independent molecular mechanisms acting on the protein level: a global trend of cysteine avoidance in all proteins, and a specific effect on transmembrane domain cysteines that reflects longevity. To account for these characteristic patterns, a thiyl radical-based molecular mechanism of intramembrane hydrophobic cross-linking is discussed.},
}
@article {pmid21474435,
year = {2011},
author = {Pouvreau, B and Baud, S and Vernoud, V and Morin, V and Py, C and Gendrot, G and Pichon, JP and Rouster, J and Paul, W and Rogowsky, PM},
title = {Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis.},
journal = {Plant physiology},
volume = {156},
number = {2},
pages = {674-686},
pmid = {21474435},
issn = {1532-2548},
mesh = {Arabidopsis/genetics ; Base Sequence ; Fatty Acids/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Duplicate/*genetics ; Genes, Plant/*genetics ; Genetic Complementation Test ; Glycolysis/genetics ; Models, Biological ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Plant Oils/*metabolism ; Plant Proteins/*genetics/metabolism ; Seeds/*genetics ; Transcription Factors/metabolism ; Triglycerides/biosynthesis ; Zea mays/*genetics ; },
abstract = {WRINKLED1 (WRI1), a key regulator of seed oil biosynthesis in Arabidopsis (Arabidopsis thaliana), was duplicated during the genome amplification of the cereal ancestor genome 90 million years ago. Both maize (Zea mays) coorthologs ZmWri1a and ZmWri1b show a strong transcriptional induction during the early filling stage of the embryo and complement the reduced fatty acid content of Arabidopsis wri1-4 seeds, suggesting conservation of molecular function. Overexpression of ZmWri1a not only increases the fatty acid content of the mature maize grain but also the content of certain amino acids, of several compounds involved in amino acid biosynthesis, and of two intermediates of the tricarboxylic acid cycle. Transcriptomic experiments identified 18 putative target genes of this transcription factor, 12 of which contain in their upstream regions an AW box, the cis-element bound by AtWRI1. In addition to functions related to late glycolysis and fatty acid biosynthesis in plastids, the target genes also have functions related to coenzyme A biosynthesis in mitochondria and the production of glycerol backbones for triacylglycerol biosynthesis in the cytoplasm. Interestingly, the higher seed oil content in ZmWri1a overexpression lines is not accompanied by a reduction in starch, thus opening possibilities for the use of the transgenic maize lines in breeding programs.},
}
@article {pmid21485362,
year = {2011},
author = {Demari-Silva, B and Vesgueiro, FT and Sallum, MA and Marrelli, MT},
title = {Taxonomic and phylogenetic relationships between species of the genus Culex (Diptera: culicidae) from Brazil inferred from the cytochrome c oxidase I mitochondrial gene.},
journal = {Journal of medical entomology},
volume = {48},
number = {2},
pages = {272-279},
doi = {10.1603/me09293},
pmid = {21485362},
issn = {0022-2585},
mesh = {Animals ; Brazil ; Culex/*enzymology/*genetics ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic/physiology ; Insect Proteins/genetics/*metabolism ; Larva/enzymology/genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; Protein Subunits ; Pupa/enzymology/genetics ; },
abstract = {Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.},
}
@article {pmid21491374,
year = {2011},
author = {Ang, KC and Leow, JW and Yeap, WK and Hood, S and Mahani, MC and Md-Zain, BM},
title = {Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers.},
journal = {Genetics and molecular research : GMR},
volume = {10},
number = {2},
pages = {640-649},
doi = {10.4238/vol10-2gmr1011},
pmid = {21491374},
issn = {1676-5680},
mesh = {Base Sequence ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Female ; Genetic Markers ; Humans ; Malaysia/ethnology ; Male ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.},
}
@article {pmid21497132,
year = {2012},
author = {Ota, S and Vaulot, D},
title = {Lotharella reticulosa sp. nov.: a highly reticulated network forming chlorarachniophyte from the Mediterranean Sea.},
journal = {Protist},
volume = {163},
number = {1},
pages = {91-104},
doi = {10.1016/j.protis.2011.02.004},
pmid = {21497132},
issn = {1618-0941},
mesh = {Cercozoa/classification/genetics/*growth &amp; development/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; Seawater/*parasitology ; },
abstract = {A new chlorarachniophyte Lotharella reticulosa sp. nov. is described from a culture isolated from the Mediterranean Sea. This strain is maintained as strain RCC375 at the Roscoff Culture Collection, France. This species presents a multiphasic life cycle: vegetative cells of this species were observed to be coccoid, but amoeboid cells with filopodia and globular suspended cells were also present in the life cycle, both of which were not dominant phases. Flagellate cells were also observed but remained very rare in culture. The vegetative cells were 9-16 μm in diameter and highly vacuolated, containing several green chloroplasts with a projecting pyrenoid, mitochondria, and a nucleus. The chloroplast was surrounded by four membranes possessing a nucleomorph in the periplastidial compartment near the pyrenoid base. According to ultrastructural observations of the pyrenoid and nucleomorph, the present species belongs to the genus Lotharella in the phylum Chlorarachniophyta. This taxonomic placement is consistent with the molecular phylogenetic trees of the 18S rRNA gene and ITS sequences. This species showed a unique colonization pattern. Clusters of cells extended cytoplasmic strands radially. Then, amoeboid cells being born proximately moved distally along the cytoplasmic strand like on a "railway track". Subsequently the amoeboid cell became coccoid near the strand. In this way, daughter cells were dispersed evenly on the substratum. We also observed that the present species regularly formed a structure of filopodial nodes in mid-stage and later-stage cultures, which is a novel phenotype in chlorarachniophytes. The unique colonization pattern and other unique features demonstrate that RCC375 is a new chlorarachniophyte belonging to genus Lotharella, which we describe as Lotharella reticulosa sp. nov.},
}
@article {pmid21497133,
year = {2011},
author = {Yamaguchi, H and Nakayama, T and Kai, A and Inouye, I},
title = {Taxonomy and phylogeny of a new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov. (Gymnodiniales, Dinophyceae), and its cryptophyte symbiont.},
journal = {Protist},
volume = {162},
number = {4},
pages = {650-667},
doi = {10.1016/j.protis.2011.01.002},
pmid = {21497133},
issn = {1618-0941},
mesh = {Cluster Analysis ; Cryptophyta/*classification/genetics/isolation &amp; purification/physiology ; DNA, Ribosomal/chemistry/genetics ; Dinoflagellida/*classification/cytology/genetics/*parasitology ; Microscopy ; Organelles ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; },
abstract = {A new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov., was described using light microscopy, electron microscopy and phylogengetic analysis based on partial LSU rDNA sequences. Cells were dorsiventrally flattened, elongate-elliptical in ventral view. There was no displacement of the cingulum encircling the anterior part of the cell. The cingulum was curved posteriorly at the terminal junction with the sulcus. The sulcus was generally narrow but expanded in the posterior end. The epicone possessed an apical groove made of one and one-half counterclockwise revolutions. Phylogenetic analysis based on LSU rDNA showed that the sequence of G. myriopyrenoides was included in the Gymnodiniales sensu stricto clade and had special affinities with the species Amphidinium poecilochroum and Gymnodinium acidotum, which also harbor kleptochloroplasts. Phylogenetic analysis based on plastid-encoded SSU rDNA and ultrastructural observations suggested that the symbionts of G. myriopyrenoides were cryptophytes of the genus Chroomonas or Hemiselmis. Organelles including the nucleus, the nucleomorph, mitochondria, Golgi bodies and large chloroplasts remained in the cytoplasm of the symbionts, but not the periplast, ejectosomes or flagellar apparatus. The symbiotic level of G. myriopyrenoides was estimated to be a relatively early stage in the unarmored kleptoplastidal dinoflagellates.},
}
@article {pmid21505865,
year = {2011},
author = {Barrero-Sicilia, C and Hernando-Amado, S and González-Melendi, P and Carbonero, P},
title = {Structure, expression profile and subcellular localisation of four different sucrose synthase genes from barley.},
journal = {Planta},
volume = {234},
number = {2},
pages = {391-403},
pmid = {21505865},
issn = {1432-2048},
mesh = {Anaerobiosis ; Cell Membrane/metabolism ; Cold Temperature ; Cytoplasm/metabolism ; DNA, Complementary/chemistry/genetics ; Droughts ; Gene Expression Regulation, Plant/genetics ; Germination ; Glucosyltransferases/chemistry/genetics/*metabolism ; Hordeum/*genetics/*metabolism/ultrastructure ; Isoenzymes/chemistry/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; RNA, Plant/genetics/isolation &amp; purification ; Recombinant Fusion Proteins ; Seeds/genetics/metabolism ; Sodium Chloride/pharmacology ; Stress, Physiological ; Sucrose/metabolism ; Water/metabolism ; },
abstract = {Genes encoding two new isoforms of sucrose synthase from barley, HvSs3 and HvSs4, have been characterised and their expression patterns compared with those previously described for HvSs1 and HvSs2, in different organs and during seed maturation and germination. Their response to several abiotic stimuli has also been investigated in leaves: HvSs1 is up-regulated by anoxia and HvSs3 by water deprivation while no response is observed to 150 mM NaCl treatment; HvSs1 and HvSs3 are also induced by cold temperatures. Using translational fusions and transient expression analyses, the four isozymes have been localised not only to the cytoplasm but also along several cytoplasmic tracks and at the inner side of the cell membrane; besides, HvSS1 is also associated with mitochondria, a localisation that has been predicted in silico with the TargetP and Predotar programmes. These data suggest distinct although partially overlapping roles, for the four barley sucrose synthase isoforms, in the channelling of carbon towards different metabolic pathways within the cell.},
}
@article {pmid21513896,
year = {2011},
author = {Heras, S and Roldán, MI},
title = {Phylogenetic inference in Odontesthes and Atherina (Teleostei: Atheriniformes) with insights into ecological adaptation.},
journal = {Comptes rendus biologies},
volume = {334},
number = {4},
pages = {273-281},
doi = {10.1016/j.crvi.2011.03.004},
pmid = {21513896},
issn = {1768-3238},
mesh = {Adaptation, Biological/*physiology ; Animals ; Classification ; Cytochromes b/genetics ; DNA/genetics ; *Environment ; Fishes/classification/*physiology ; Fresh Water ; Genetic Variation ; Haplotypes ; Mitochondria/metabolism ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Seawater ; Smegmamorpha ; Species Specificity ; },
abstract = {This contribution provides an insight into Atheriniformes systematics based on four mitochondrial regions: 12S rRNA, cytb, COI and control region (2794bp in total). In the Atherinopsoidei (New World silversides), comparisons among five species of Odontesthes, O. argentinensis, O. bonariensis, O. smitti, O. hatcheri and O. incisa revealed a putative marine-freshwater pairing pattern of Odontesthes species, possibly driven by sea level fluctuations of South American waters. This study represents the first data on molecular phylogeny of Odontesthes species that can be of usefulness to biodiversity conservation policies. In the Atherinoidei (Old World silversides), Atherina boyeri was corroborated as a species complex constituted by a marine form, a marine with dark spots form and a brackish form. Concretely, Odontesthes and Atherina may represent geographically replicated models to study genetic adaptation and speciation of marine species to brackish and freshwater habitats. In addition, phylogenetic analyses supported Odontesthes and Atherina as monophyletic taxa and their separation into two differentiated suborders Atherinopsoidei and Atherinoidei, respectively.},
}
@article {pmid21526402,
year = {2012},
author = {Sýkorová, Z and Börstler, B and Zvolenská, S and Fehrer, J and Gryndler, M and Vosátka, M and Redecker, D},
title = {Long-term tracing of Rhizophagus irregularis isolate BEG140 inoculated on Phalaris arundinacea in a coal mine spoil bank, using mitochondrial large subunit rDNA markers.},
journal = {Mycorrhiza},
volume = {22},
number = {1},
pages = {69-80},
pmid = {21526402},
issn = {1432-1890},
mesh = {Base Sequence ; Coal Mining ; Czech Republic ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Genetic Markers ; Glomeromycota/*genetics/isolation &amp; purification/physiology ; Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Mycorrhizae/genetics/*isolation &amp; purification/physiology ; Phalaris/*microbiology/physiology ; Phylogeny ; Plant Roots/microbiology ; Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; },
abstract = {During the last decade, the application of arbuscular mycorrhizal fungi (AMF) as bioenhancers has increased significantly. However, until now, it has been difficult to verify the inoculation success in terms of fungal symbiont establishment in roots of inoculated plants because specific fungal strains could not be detected within colonized roots. Using mitochondrial large subunit ribosomal DNA, we show that Rhizophagus irregularis (formerly known as Glomus intraradices) isolate BEG140 consists of two different haplotypes. We developed nested PCR assays to specifically trace each of the two haplotypes in the roots of Phalaris arundinacea from a field experiment in a spoil bank of a former coal mine, where BEG140 was used as inoculant. We revealed that despite the relatively high diversity of native R. irregularis strains, R. irregularis BEG140 survived and proliferated successfully in the field experiment and was found significantly more often in the inoculated than control plots. This work is the first one to show tracing of an inoculated AMF isolate in the roots of target plants and to verify its survival and propagation in the field. These results will have implications for basic research on the ecology of AMF at the intraspecific level as well as for commercial users of mycorrhizal inoculation.},
}
@article {pmid21558255,
year = {2010},
author = {O'Brien, KM and Mueller, IA},
title = {The unique mitochondrial form and function of Antarctic channichthyid icefishes.},
journal = {Integrative and comparative biology},
volume = {50},
number = {6},
pages = {993-1008},
doi = {10.1093/icb/icq038},
pmid = {21558255},
issn = {1557-7023},
mesh = {*Adaptation, Physiological ; Animals ; Antarctic Regions ; Cold Temperature ; Hemoglobins/genetics/metabolism ; Mitochondria/enzymology/genetics/*metabolism/ultrastructure ; Muscle Fibers, Skeletal/cytology/metabolism ; Myocytes, Cardiac/cytology/metabolism ; Myoglobin/genetics/metabolism ; Nitric Oxide/metabolism ; Perciformes/classification/*genetics/*metabolism ; Phylogeny ; },
abstract = {Antarctic icefishes of the family Channichthyidae are the only vertebrate animals that as adults do not express the circulating oxygen-binding protein hemoglobin (Hb). Six of the 16 family members also lack the intracellular oxygen-binding protein myoglobin (Mb) in the ventricle of their hearts and all lack Mb in oxidative skeletal muscle. The loss of Hb has led to substantial remodeling in the cardiovascular system of icefishes to facilitate adequate oxygenation of tissues. One of the more curious adaptations to the loss of Hb and Mb is an increase in mitochondrial density in cardiac myocytes and oxidative skeletal muscle fibers. The proliferation of mitochondria in the aerobic musculature of icefishes does not arise through a canonical pathway of mitochondrial biogenesis. Rather, the biosynthesis of mitochondrial phospholipids is up-regulated independently of the synthesis of proteins and mitochondrial DNA, and newly-synthesized phospholipids are targeted primarily to the outer-mitochondrial membrane. Consequently, icefish mitochondria have a higher lipid-to-protein ratio compared to those from red-blooded species. Elevated levels of nitric oxide in the blood plasma of icefishes, compared to red-blooded notothenioids, may mediate alterations in mitochondrial density and architecture. Modifications in mitochondrial structure minimally impact state III respiration rates but may significantly enhance intracellular diffusion of oxygen. The rate of oxygen diffusion is greater within the hydrocarbon core of membrane lipids compared to the aqueous cytosol and impeded only by proteins within the lipid bilayer. Thus, the proliferation of icefish's mitochondrial membranes provides an optimal conduit for the intracellular diffusion of oxygen and compensates for the loss of Hb and Mb. Currently little is known about how mitochondrial phospholipid synthesis is regulated and integrated into mitochondrial biogenesis. The unique architecture of the oxidative muscle cells of icefishes highlights the need for further studies in this area.},
}
@article {pmid21595926,
year = {2011},
author = {Blanco, R and Mayordomo, E and Montoya, J and Ruiz-Pesini, E},
title = {Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge.},
journal = {BMC bioinformatics},
volume = {12},
number = {},
pages = {174},
pmid = {21595926},
issn = {1471-2105},
mesh = {*Algorithms ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Humans ; Mitochondria/*genetics ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis.<br><br>RESULTS: We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies.<br><br>CONCLUSIONS: The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.},
}
@article {pmid21607544,
year = {2012},
author = {Salgado, MC and Metón, I and Anemaet, IG and González, JD and Fernández, F and Baanante, IV},
title = {Hepatocyte nuclear factor 4α transactivates the mitochondrial alanine aminotransferase gene in the kidney of Sparus aurata.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {14},
number = {1},
pages = {46-62},
pmid = {21607544},
issn = {1436-2236},
mesh = {Alanine Transaminase/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cloning, Molecular ; DNA, Complementary/genetics ; Gene Expression Regulation, Enzymologic ; Hepatocyte Nuclear Factor 4/genetics/*metabolism ; Intracellular Signaling Peptides and Proteins ; Kidney/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Real-Time Polymerase Chain Reaction ; Response Elements ; Sea Bream/*metabolism ; },
abstract = {Alanine aminotransferase (ALT) plays an important role in amino acid metabolism and gluconeogenesis. The preference of carnivorous fish for protein amino acids instead of carbohydrates as a source of energy lead us to study the transcriptional regulation of the mitochondrial ALT (mALT) gene and to characterize the enzyme kinetics and modulation of mALT expression in the kidney of gilthead sea bream (Sparus aurata) under different nutritional and hormonal conditions. 5'-Deletion analysis of mALT promoter in transiently transfected HEK293 cells, site-directed mutagenesis and electrophoretic mobility shift assays allowed us to identify HNF4α as a new factor involved in the transcriptional regulation of mALT expression. Quantitative RT-PCR assays showed that starvation and the administration of streptozotocin (STZ) decreased HNF4α levels in the kidney of S. aurata, leading to the downregulation of mALT transcription. Analysis of the tissue distribution showed that kidney, liver, and intestine were the tissues with higher mALT and HNF4α expression. Kinetic analysis indicates that mALT enzyme is more efficient in catalyzing the conversion of L: -alanine to pyruvate than the reverse reaction. From these results, we conclude that HNF4α transactivates the mALT promoter and that the low levels of mALT expression found in the kidney of starved and STZ-treated fish result from a decreased expression of HNF4α. Our findings suggest that the mALT isoenzyme plays a major role in oxidazing dietary amino acids, and points to ALT as a target for a biotechnological action to spare protein and optimize the use of dietary nutrients for fish culture.},
}
@article {pmid21618648,
year = {2011},
author = {Goizet, C and Depienne, C and Benard, G and Boukhris, A and Mundwiller, E and Solé, G and Coupry, I and Pilliod, J and Martin-Négrier, ML and Fedirko, E and Forlani, S and Cazeneuve, C and Hannequin, D and Charles, P and Feki, I and Pinel, JF and Ouvrard-Hernandez, AM and Lyonnet, S and Ollagnon-Roman, E and Yaouanq, J and Toutain, A and Dussert, C and Fontaine, B and Leguern, E and Lacombe, D and Durr, A and Rossignol, R and Brice, A and Stevanin, G},
title = {REEP1 mutations in SPG31: frequency, mutational spectrum, and potential association with mitochondrial morpho-functional dysfunction.},
journal = {Human mutation},
volume = {32},
number = {10},
pages = {1118-1127},
doi = {10.1002/humu.21542},
pmid = {21618648},
issn = {1098-1004},
mesh = {Adolescent ; Adult ; Aged ; Base Sequence ; Child ; Child, Preschool ; Energy Metabolism ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Membrane Transport Proteins/*genetics ; Middle Aged ; Mitochondria/*metabolism ; Muscle, Skeletal/metabolism/pathology ; *Mutation ; Mutation Rate ; Pedigree ; Phenotype ; Sequence Deletion ; Spastic Paraplegia, Hereditary/*genetics/metabolism ; Young Adult ; },
abstract = {Hereditary spastic paraplegias (HSP) constitute a heterogeneous group of neurodegenerative disorders characterized at least by slowly progressive spasticity of the lower limbs. Mutations in REEP1 were recently associated with a pure dominant HSP, SPG31. We sequenced all exons of REEP1 and searched for rearrangements by multiplex ligation-dependent probe amplification (MLPA) in a large panel of 175 unrelated HSP index patients from kindreds with dominant inheritance (AD-HSP), with either pure (n = 102) or complicated (n = 73) forms of the disease, after exclusion of other known HSP genes. We identified 12 different heterozygous mutations, including two exon deletions, associated with either a pure or a complex phenotype. The overall mutation rate in our clinically heterogeneous sample was 4.5% in French families with AD-HSP. The phenotype was restricted to pyramidal signs in the lower limbs in most patients but nine had a complex phenotype associating axonal peripheral neuropathy (= 5/11 patients) including a Silver-like syndrome in one patient, and less frequently cerebellar ataxia, tremor, dementia. Interestingly, we evidenced abnormal mitochondrial network organization in fibroblasts of one patient in addition to defective mitochondrial energy production in both fibroblasts and muscle, but whether these anomalies are directly or indirectly related to the mutations remains uncertain.},
}
@article {pmid21619630,
year = {2011},
author = {Pigneur, LM and Marescaux, J and Roland, K and Etoundi, E and Descy, JP and Van Doninck, K},
title = {Phylogeny and androgenesis in the invasive Corbicula clams (Bivalvia, Corbiculidae) in Western Europe.},
journal = {BMC evolutionary biology},
volume = {11},
number = {},
pages = {147},
pmid = {21619630},
issn = {1471-2148},
mesh = {Americas ; Animals ; Asia ; Corbicula/anatomy &amp; histology/enzymology/*genetics ; Cytochrome b Group/genetics ; Europe ; Haplotypes ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Spermatozoa/cytology ; },
abstract = {BACKGROUND: The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with American and Asian Corbicula clams. We studied several populations from West European river basins (Meuse, Seine, Rhine and Rhône) through an "integrative taxonomy" approach. We combined morphology, partial mitochondrial COI and cyt b sequences and eleven microsatellite loci. Furthermore, we looked for discrepancies between mtDNA and nrDNA/morphology, indicative of androgenesis between lineages.<br><br>RESULTS: There are three Corbicula morphotypes in Western Europe associated to three mitochondrial lineages and three genotypes. Form R shares the same COI haplotype as the American form A and the Japanese C. leana. Form S and the American form C have the same haplotype, although their morphologies seem divergent. The European form Rlc belongs to the same mitochondrial lineage as both the American form B and the Asian C. fluminea.Interestingly, within each haplotype/genotype or lineage, no genetic diversity was found although their invasive success is high. Moreover, we detected rare mismatches between mtDNA and nrDNA/morphology, indicative of androgenesis and mitochondrial capture between form R and form S and therefore challenging the phylogenetic relatedness and the species status within this genus. The global phylogenetic analysis revealed that the sexual Corbicula lineages seem restricted to the native areas while their androgenetic relatives are widespread and highly invasive.<br><br>CONCLUSIONS: We clarified the discrepancies and incongruent results found in the literature about the European morphotypes of Corbicula and associated mitochondrial lineages. The three West European morphotypes belong to three distinct nuclear and mitochondrial lineages. However mitochondrial capture occurs in sympatric populations of forms R and S. The species status of the morphotypes therefore remains doubtful. Moreover the androgenetic lineages seem widely distributed compared to their sexual relatives, suggesting that androgenesis and invasive success may be linked in the genus Corbicula.},
}
@article {pmid21670310,
year = {2011},
author = {Bochman, ML and Judge, CP and Zakian, VA},
title = {The Pif1 family in prokaryotes: what are our helicases doing in your bacteria?.},
journal = {Molecular biology of the cell},
volume = {22},
number = {12},
pages = {1955-1959},
pmid = {21670310},
issn = {1939-4586},
support = {R01 GM026938/GM/NIGMS NIH HHS/United States ; R37 GM026938/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*enzymology/genetics ; Base Sequence ; DNA Helicases/genetics/*metabolism ; DNA Repair ; DNA Replication ; Mitochondria/genetics/metabolism ; Phylogeny ; Recombination, Genetic ; },
abstract = {Pif1 family helicases, which are found in nearly all eukaryotes, have important roles in both nuclear and mitochondrial genome maintenance. Recently, the increasing availability of genome sequences has revealed that Pif1 helicases are also widely found in diverse prokaryotes, but it is currently unknown what physiological function(s) prokaryotic Pif1 helicases might perform. This Perspective aims to briefly introduce the reader to the well-studied eukaryotic Pif1 family helicases and speculate on what roles such enzymes may play in bacteria. On the basis of our hypotheses, we predict that Pif1 family helicases are important for resolving common issues that arise during DNA replication, recombination, and repair rather than functioning in a eukaryotic-specific manner.},
}
@article {pmid21673740,
year = {2011},
author = {McDevitt, AD and Vega, R and Rambau, RV and Yannic, G and Herman, JS and Hayden, TJ and Searle, JB},
title = {Colonization of Ireland: revisiting 'the pygmy shrew syndrome' using mitochondrial, Y chromosomal and microsatellite markers.},
journal = {Heredity},
volume = {107},
number = {6},
pages = {548-557},
pmid = {21673740},
issn = {1365-2540},
mesh = {Animals ; Cytochromes b/genetics ; Genetic Variation ; Human Activities ; Humans ; Ireland ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Shrews/classification/*genetics/*growth &amp; development ; Y Chromosome/*genetics ; },
abstract = {There is great uncertainty about how Ireland attained its current fauna and flora. Long-distance human-mediated colonization from southwestern Europe has been seen as a possible way that Ireland obtained many of its species; however, Britain has (surprisingly) been neglected as a source area for Ireland. The pygmy shrew has long been considered an illustrative model species, such that the uncertainty of the Irish colonization process has been dubbed 'the pygmy shrew syndrome'. Here, we used new genetic data consisting of 218 cytochrome (cyt) b sequences, 153 control region sequences, 17 Y-intron sequences and 335 microsatellite multilocus genotypes to distinguish between four possible hypotheses for the colonization of the British Isles, formulated in the context of previously published data. Cyt b sequences from western Europe were basal to those found in Ireland, but also to those found in the periphery of Britain and several offshore islands. Although the central cyt b haplotype in Ireland was found in northern Spain, we argue that it most likely occurred in Britain also, from where the pygmy shrew colonized Ireland as a human introduction during the Holocene. Y-intron and microsatellite data are consistent with this hypothesis, and the biological traits and distributional data of pygmy shrews argue against long-distance colonization from Spain. The compact starburst of the Irish cyt b expansion and the low genetic diversity across all markers strongly suggests a recent colonization. This detailed molecular study of the pygmy shrew provides a new perspective on an old colonization question.},
}
@article {pmid21674231,
year = {2011},
author = {Bengtsson, J and Eriksson, KM and Hartmann, M and Wang, Z and Shenoy, BD and Grelet, GA and Abarenkov, K and Petri, A and Rosenblad, MA and Nilsson, RH},
title = {Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.},
journal = {Antonie van Leeuwenhoek},
volume = {100},
number = {3},
pages = {471-475},
doi = {10.1007/s10482-011-9598-6},
pmid = {21674231},
issn = {1572-9699},
mesh = {Archaea/*genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Eukaryota/*genetics/isolation &amp; purification ; Metagenome ; Metagenomics/instrumentation/*methods ; Mitochondria/*genetics ; Phylogeny ; Ribosome Subunits, Small/*genetics ; Sequence Alignment ; *Software ; },
abstract = {The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.},
}
@article {pmid21685886,
year = {2011},
author = {Baughman, JM and Perocchi, F and Girgis, HS and Plovanich, M and Belcher-Timme, CA and Sancak, Y and Bao, XR and Strittmatter, L and Goldberger, O and Bogorad, RL and Koteliansky, V and Mootha, VK},
title = {Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter.},
journal = {Nature},
volume = {476},
number = {7360},
pages = {341-345},
pmid = {21685886},
issn = {1476-4687},
support = {R01 GM077465/GM/NIGMS NIH HHS/United States ; R24 DK080261/DK/NIDDK NIH HHS/United States ; DK080261/DK/NIDDK NIH HHS/United States ; GM0077465/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Calcium/metabolism ; Calcium Channels/*chemistry/genetics/*metabolism ; *Genomics ; HEK293 Cells ; HeLa Cells ; Humans ; Ion Transport ; Mice ; Mitochondria, Liver/metabolism ; Mitochondrial Membranes/chemistry/metabolism ; Molecular Sequence Data ; Mutant Proteins/genetics/metabolism ; Phylogeny ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; },
abstract = {Mitochondria from diverse organisms are capable of transporting large amounts of Ca(2+) via a ruthenium-red-sensitive, membrane-potential-dependent mechanism called the uniporter. Although the uniporter's biophysical properties have been studied extensively, its molecular composition remains elusive. We recently used comparative proteomics to identify MICU1 (also known as CBARA1), an EF-hand-containing protein that serves as a putative regulator of the uniporter. Here, we use whole-genome phylogenetic profiling, genome-wide RNA co-expression analysis and organelle-wide protein coexpression analysis to predict proteins functionally related to MICU1. All three methods converge on a novel predicted transmembrane protein, CCDC109A, that we now call 'mitochondrial calcium uniporter' (MCU). MCU forms oligomers in the mitochondrial inner membrane, physically interacts with MICU1, and resides within a large molecular weight complex. Silencing MCU in cultured cells or in vivo in mouse liver severely abrogates mitochondrial Ca(2+) uptake, whereas mitochondrial respiration and membrane potential remain fully intact. MCU has two predicted transmembrane helices, which are separated by a highly conserved linker facing the intermembrane space. Acidic residues in this linker are required for its full activity. However, an S259A point mutation retains function but confers resistance to Ru360, the most potent inhibitor of the uniporter. Our genomic, physiological, biochemical and pharmacological data firmly establish MCU as an essential component of the mitochondrial Ca(2+) uniporter.},
}
@article {pmid21695207,
year = {2011},
author = {Johnson, RA and McFadden, GI and Goodman, CD},
title = {Characterization of two malaria parasite organelle translation elongation factor G proteins: the likely targets of the anti-malarial fusidic acid.},
journal = {PloS one},
volume = {6},
number = {6},
pages = {e20633},
pmid = {21695207},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/drug effects/metabolism ; Computational Biology ; Fusidic Acid/*pharmacology ; Life Cycle Stages/drug effects ; Malaria/*parasitology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Organelles/drug effects/*metabolism ; Parasites/drug effects/growth &amp; development/*metabolism ; Peptide Elongation Factor G/chemistry/*metabolism ; Phylogeny ; Plasmodium falciparum/drug effects/growth &amp; development ; Protein Biosynthesis/*drug effects ; Protozoan Proteins/chemistry/*metabolism ; Sequence Alignment ; },
abstract = {Malaria parasites harbour two organelles with bacteria-like metabolic processes that are the targets of many anti-bacterial drugs. One such drug is fusidic acid, which inhibits the translation component elongation factor G. The response of P. falciparum to fusidic acid was characterised using extended SYBR-Green based drug trials. This revealed that fusidic acid kills in vitro cultured P. falciparum parasites by immediately blocking parasite development. Two bacterial-type protein translation elongation factor G genes are identified as likely targets of fusidic acid. Sequence analysis suggests that these proteins function in the mitochondria and apicoplast and both should be sensitive to fusidic acid. Microscopic examination of protein-reporter fusions confirm the prediction that one elongation factor G is a component of parasite mitochondria whereas the second is a component of the relict plastid or apicoplast. The presence of two putative targets for a single inhibitory compound emphasizes the potential of elongation factor G as a drug target in malaria.},
}
@article {pmid21743250,
year = {2011},
author = {Robinson, JL and Hall, JR and Charman, M and Ewart, KV and Driedzic, WR},
title = {Molecular analysis, tissue profiles, and seasonal patterns of cytosolic and mitochondrial GPDH in freeze-resistant rainbow smelt (Osmerus mordax).},
journal = {Physiological and biochemical zoology : PBZ},
volume = {84},
number = {4},
pages = {363-376},
doi = {10.1086/660162},
pmid = {21743250},
issn = {1537-5293},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Acclimatization ; Amino Acid Sequence ; Animals ; Cytosol/metabolism ; DNA, Complementary/genetics ; Electrophoresis ; Freezing ; Gene Dosage ; Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Glycerol/blood/metabolism ; Glycerolphosphate Dehydrogenase/*genetics/*metabolism ; Liver/enzymology/metabolism ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Newfoundland and Labrador ; Osmeriformes/*genetics/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Protein Isoforms/genetics/metabolism ; RNA, Messenger/metabolism ; Salmon/metabolism ; Seasons ; Species Specificity ; },
abstract = {Rainbow smelt (Osmerus mordax) is an anadromous teleost that, beginning in late fall, accumulates plasma glycerol in excess of 200 mM, which subsequently decreases in the spring. The activity of cytosolic glycerol-3-phosphate dehydrogenase (cGPDH) is higher (i) in liver of smelt than in that of Atlantic salmon and capelin (nonglycerol accumulators), (ii) in liver of smelt maintained at 1°C than in that of smelt held at 8°-10°C, and (iii) in smelt liver than in smelt muscle, heart, brain, or kidney. In addition, transcript levels of cGPDH in liver peak in December during the onset of glycerol production and then decline over the remainder of the season. There are four cGPDH protein isoforms in smelt liver that are present regardless of glycerol production status. A minimum of four cGPDH gene copies identified by Southern blotting provide adequate genetic potential to yield multiple protein isoforms. A full-length cDNA for smelt mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH) was cloned and characterized. The 2,790-bp cDNA contains a 109-bp 5'UTR, a 2,193-bp open reading frame, and a 488-bp 3'UTR; transcripts are ubiquitously expressed in both warm- and cold-acclimated smelt tissues. Smelt mGPDH encodes a 730-aa protein that clusters with that of zebrafish and frog and contains several common structural motifs. mGPDH transcript levels generally increase late in the seasonal glycerol cycle, and mGPDH enzyme activity increases significantly during the glycerol decrease phase. Taken together, these findings suggest that liver cGPDH and mGPDH play a key role in the glycerol accumulation and decrease phases, respectively.},
}
@article {pmid21748354,
year = {2012},
author = {Najm, NA and Silaghi, C and Bell-Sakyi, L and Pfister, K and Passos, LM},
title = {Detection of bacteria related to Candidatus Midichloria mitochondrii in tick cell lines.},
journal = {Parasitology research},
volume = {110},
number = {1},
pages = {437-442},
pmid = {21748354},
issn = {1432-1955},
mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; Animals ; Cell Line ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Female ; Ixodes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Many ticks have been shown to be infected with intracellular bacteria. One of these bacteria is Candidatus Midichloria mitochondrii which is the only characterized bacterium that has the ability to invade the mitochondria within ovarian cells and consume them without any effect on the female tick's reproduction. In the present study, eight cell lines derived from the ticks Ixodes ricinus, Ixodes scapularis, Rhipicephalus (Boophilus) microplus, and Rhipicephalus (Boophilus) decoloratus were examined for the presence of the bacterium Ca. Midichloria mitochondrii. PCR assays for this bacterium were carried out using two sets of primers targeting the eubacterial 16SrRNA gene and a set of primers specific for the gyrB gene of Ca. Midichloria mitochondrii. With the 16S rRNA primers, DNA was amplified from two cell lines (R. (B.) decoloratus line BDE/CTVM14 and I. ricinus line IRE/CTVM19) on one out of three occasions each. Sequencing of the PCR products showed that the two cell lines gave sequences with 100% similarity to Ca. Midichloria mitochondrii. However, all cell lines, including the two positive cell lines, were negative with the specific primers. Phylogenetic analysis shows that our sequences belong to the subclass α-proteobacteria. They were identical to the sequences amplified from the tick I. ricinus. The results suggest that two cell lines, IRE/CTVM19 and BDE/CTVM14, may contain bacteria closely related to Ca. Midichloria mitochondrii and identical with it in a 350-bp part of the 16S rRNA gene sequence. To our knowledge, this constitutes the first report of the presence of DNA similar to the DNA of Ca. Midichloria mitochondrii in tick cell lines.},
}
@article {pmid21760940,
year = {2011},
author = {Schlüter, A and Ruiz-Trillo, I and Pujol, A},
title = {Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation.},
journal = {PloS one},
volume = {6},
number = {7},
pages = {e21989},
pmid = {21760940},
issn = {1932-6203},
mesh = {Acyl Coenzyme A/metabolism ; Eukaryota/metabolism ; Fatty Acids/*metabolism ; *Genomics ; Metabolic Networks and Pathways ; Mitochondria/*genetics ; Models, Biological ; Myxococcales/*genetics ; Oxidation-Reduction ; *Phylogeny ; Proteins/genetics ; },
abstract = {BACKGROUND: The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.<br><br>Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid &#x3b2;-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results support a prokaryotic origin, different from &#x3b1;-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.},
}
@article {pmid21776000,
year = {2011},
author = {Schlebusch, CM and de Jongh, M and Soodyall, H},
title = {Different contributions of ancient mitochondrial and Y-chromosomal lineages in 'Karretjie people' of the Great Karoo in South Africa.},
journal = {Journal of human genetics},
volume = {56},
number = {9},
pages = {623-630},
doi = {10.1038/jhg.2011.71},
pmid = {21776000},
issn = {1435-232X},
mesh = {Black People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; South Africa/ethnology ; },
abstract = {The Karretjie people of the South African Great Karoo are itinerants who subsist by sheep shearing. Although officially classified 'Coloured', they are aware of their Khoe and San roots. To investigate the maternal and paternal ancestries of the Karretjie people we analyzed their mitochondrial and Y-chromosome DNA variation. Their genetic ancestry was compared with a neighboring group of 'Coloured' individuals. We found that the mitochondrial DNA (mtDNA) haplogroup L0d was present in all the Karretjie people examined, suggesting a maternal contribution, exclusively from the Khoe and San, whereas the paternal ancestry in males was more heterogeneous. The Coloured sample, on the other hand, were found to have a lower frequency of L0d (64.5%), but did harbor other African (27.6%) and non-African (7.9%) mtDNA haplogroups. Similar to the Karretjie people, the Y-chromosome lineages identified in the Coloured group had heterogeneous origins. This study also enabled an assessment of mtDNA variation within L0d sub-haplogroups. All seven of the L0d sub-clades were identified in the combined sample and were used to construct an L0d network.},
}
@article {pmid21783224,
year = {2011},
author = {Rizwan-ul-Haq, M and Gong, L and Hu, M and Luo, J},
title = {Apolipophorin III and transmission electron microscopy as toxicity indicators for harmaline and tea saponin in Spodoptera exigua (Noctuidae: Lepidoptera).},
journal = {Chemosphere},
volume = {85},
number = {6},
pages = {995-1001},
doi = {10.1016/j.chemosphere.2011.06.089},
pmid = {21783224},
issn = {1879-1298},
mesh = {Amino Acid Sequence ; Animals ; Apolipoproteins/chemistry/*genetics ; Base Sequence ; Gene Expression Regulation/drug effects ; Harmaline/*toxicity ; Intestinal Mucosa/drug effects/ultrastructure ; *Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Saponins/*toxicity ; Sequence Analysis, DNA ; Spodoptera/*drug effects/genetics/ultrastructure ; Tea/*chemistry ; Toxicity Tests/*methods ; },
abstract = {Apolipophorin III, traditionally known for lipid transport in insects is fairly established as toxicity indicator against harmaline and tea saponin during this study. Apolipophorin III expressed in the hemolymph and midgut tissues of 3rd, 4th, 5th larval instars and pupae of Spodoptera exigua. Apolipophorin III presence was further confirmed by achieving its partial cDNA (Genbank accession no. FJ606822) of 448bp. qRT PCR revealed that tea saponin resulted in significant reduction of gene expression in 3rd and 4th larval instars but increased in 5th instar as compared to control. Harmaline caused gradual increase of gene expression in 3rd, 4th and 5th instars after feeding on the treated diet. Fifth instar larvae synonymously resulted in the highest gene expressions against both the biochemicals. After the injection of harmaline and tea saponin abrupt increase in gene expression of 4th, 5th larval instar and pupae was observed as compared to control treatment. Transmission electron microscopy of midgut epithelium after being fed with harmaline and tea saponin depicted certain cytological changes. Harmaline treatment lead to cytoplasm vacuolization, mitochondrial disruption, spherocrystals with concentric layers, irregular nucleus and floating nuclei in cytoplasm. Tea saponin treatment resulted in denser cytoplasm, higher intracellular osmotic concentration and reduced complement of apical microvilli. Cells were found to have only a few mitochondria and glycogen deposits in comparison to control treatment.},
}
@article {pmid21790065,
year = {2011},
author = {Tang, KF and Pantoja, CR and Redman, RM and Navarro, SA and Lightner, DV},
title = {Ultrastructural and sequence characterization of Penaeus vannamei nodavirus (PvNV) from Belize.},
journal = {Diseases of aquatic organisms},
volume = {94},
number = {3},
pages = {179-187},
doi = {10.3354/dao02335},
pmid = {21790065},
issn = {0177-5103},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Belize ; Genome, Viral ; Molecular Sequence Data ; Nodaviridae/*genetics/*ultrastructure ; Penaeidae/*virology ; Phylogeny ; RNA, Viral/*genetics ; Viral Proteins/genetics/metabolism ; },
abstract = {The Penaeus vannamei nodavirus (PvNV), which causes muscle necrosis in Penaeus vannamei from Belize, was identified in 2005. Infected shrimp show clinical signs of white, opaque lesions in the tail muscle. Under transmission electron microscopy, the infected cells exhibit increases in various organelles, including mitochondria, Golgi stacks, and rough endoplasmic reticulum. Cytoplasmic inclusions containing para-crystalline arrays of virions were visualized. The viral particle is spherical in shape and 19 to 27 nm in diameter. A cDNA library was constructed from total RNA extracted from infected shrimp. Through nucleotide sequencing from the cDNA clones and northern blot hybridization, the PvNV genome was shown to consist of 2 segments: RNA1 (3111 bp) and RNA2 (1183 bp). RNA1 contains 2 overlapped open reading frames (ORF A and B), which may encode a RNA-dependent RNA polymerase (RdRp) and a B2 protein, respectively. RNA2 contains a single ORF that may encode the viral capsid protein. Sequence analyses showed the presence of 4 RdRp characteristic motifs and 2 conserved domains (RNA-binding B2 protein and viral coat protein) in the PvNV genome. Phylogenetic analysis based on the translated amino acid sequence of the RdRp reveals that PvNV is a member of the genus Alphanodavirus and closely related to Macrobrachium rosenbergii nodavirus (MrNV). In a study investigating potential PvNV vectors, we monitored the presence of PvNV by RT-PCR in seabird feces and various aquatic organisms collected around a shrimp farm in Belize. PvNV was detected in mosquitofish, seabird feces, barnacles, and zooplankton, suggesting that PvNV can be spread via these carriers.},
}
@article {pmid21803970,
year = {2011},
author = {Deen, PM and Robben, JH},
title = {Succinate receptors in the kidney.},
journal = {Journal of the American Society of Nephrology : JASN},
volume = {22},
number = {8},
pages = {1416-1422},
doi = {10.1681/ASN.2010050481},
pmid = {21803970},
issn = {1533-3450},
mesh = {Adipose Tissue/metabolism ; Animals ; Apoptosis ; Citric Acid Cycle ; Humans ; Kidney/metabolism ; Kidney Diseases/metabolism ; Lipolysis ; Mice ; Mitochondria/metabolism ; Models, Biological ; Phylogeny ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Purinergic P2Y/metabolism ; Retinal Diseases/pathology ; Succinates/chemistry/*metabolism ; Tissue Distribution ; },
abstract = {The G protein-coupled succinate and α-ketoglutarate receptors are closely related to the family of P2Y purinoreceptors. Although the α-ketoglutarate receptor is almost exclusively expressed in the kidney, its function is unknown. In contrast, the succinate receptor, SUCRN1, is expressed in a variety of tissues, including blood cells, adipose tissue, liver, retina, and the kidney. Recent evidence suggests SUCRN1 and its succinate ligand are novel detectors of local stress, including ischemia, hypoxia, toxicity, and hyperglycemia. Local levels of succinate in the kidney also activate the renin-angiotensin system and together with SUCRN1 may play a key role in the development of hypertension and the complications of diabetes mellitus, metabolic disease, and liver damage. This makes the succinate receptor a promising drug target to counteract an expanding number of interrelated disorders.},
}
@article {pmid21864691,
year = {2011},
author = {Derkarabetian, S and Ledford, J and Hedin, M},
title = {Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America.},
journal = {Molecular phylogenetics and evolution},
volume = {61},
number = {3},
pages = {844-853},
doi = {10.1016/j.ympev.2011.08.004},
pmid = {21864691},
issn = {1095-9513},
mesh = {Animals ; Arachnida/*anatomy &amp; histology/*genetics ; Bayes Theorem ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Geography ; Introns/genetics ; Male ; Mitochondria/genetics ; North America ; Penis/*anatomy &amp; histology/ultrastructure ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Population Dynamics ; Software ; },
abstract = {The southern Rocky Mountains and adjacent Intermontane Plateau Highlands region of western North America is a geographically diverse area with an active geologic history. Given the topological complexity and extensive geologic activity, organisms inhabiting this region are expected to show some degree of morphological and genetic divergence, especially populations found on the southern montane 'sky islands' of this region. Here we examine the phylogeographic history and diversification of a montane forest inhabiting harvestmen, Sclerobunus robustus, using a combination of genetic and morphological data. Divergence time estimates indicate that much of the diversification within and between major groups S. robustus predate the Pleistocene glacial cycles. The most widespread subspecies, Sclerobunus robustus robustus, is recovered as six genetically distinct, geographically cohesive mitochondrial phylogroups. Gene tree data for a single nuclear gene reveals congruent, albeit slightly more conservative, patterns of genetic divergence. Despite high levels of genetic divergence throughout their distribution, phylogroups show extreme conservation in somatic and reproductive morphology. This uncoupling of morphological and genetic differentiation may be due to morphological conservatism associated with a conserved microhabitat preference. Based on these data, it is obvious that S. robustus has undergone some level of cryptic diversification.},
}
@article {pmid21867770,
year = {2011},
author = {Ichikawa, M and Bawn, S and Maw, NN and Htun, LL and Thein, M and Gyi, A and Sunn, K and Katakura, K and Itagaki, T},
title = {Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers.},
journal = {Parasitology international},
volume = {60},
number = {4},
pages = {474-479},
doi = {10.1016/j.parint.2011.08.007},
pmid = {21867770},
issn = {1873-0329},
mesh = {Animals ; Biomarkers/analysis ; Cattle ; Cattle Diseases/epidemiology/*parasitology/transmission ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Fasciola/classification/*genetics/isolation &amp; purification ; Fascioliasis/epidemiology/*parasitology/transmission/*veterinary ; Haplotypes ; Male ; Mitochondria/chemistry/genetics ; Myanmar ; NADH Dehydrogenase/analysis/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Restriction Fragment Length ; Protein Subunits/analysis/genetics ; Sequence Analysis, DNA ; Spermatogenesis/*genetics ; },
abstract = {Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants.},
}
@article {pmid21872668,
year = {2011},
author = {Salicini, I and Ibáñez, C and Juste, J},
title = {Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic.},
journal = {Molecular phylogenetics and evolution},
volume = {61},
number = {3},
pages = {888-898},
doi = {10.1016/j.ympev.2011.08.010},
pmid = {21872668},
issn = {1095-9513},
mesh = {Alleles ; Animals ; Arctic Regions ; Bayes Theorem ; Cell Nucleus/genetics ; Chiroptera/*genetics ; Cluster Analysis ; Genetic Loci/*genetics ; Genetic Markers ; Geography ; Introns/genetics ; Mediterranean Region ; Mitochondria/genetics ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Software ; Species Specificity ; },
abstract = {Delimiting species is a crucial issue for many biological disciplines and is of primary importance for designing effective conservation plans. Traditional taxonomy based on morphological characters can be misled by the presence of phenotypic plesiomorphism or adaptative convergence. The use of multiple locus genetic data appears thus as a powerful tool for recognizing species boundaries. In this study, we used six nuclear introns and two mitochondrial markers to conduct a phylogenetic study of the Myotis nattereri species complex in the Western Palearctic. We combined tree-based and non-tree-based analyses, and also used concatenated phylogenetic methods of the separated nuclear and mitochondrial dataset as well as a recent coalescence-based multilocus approach. The strong concordance between the results of the analyses conducted confirms that M. nattereri is a paraphyletic group that is composed of four well-differentiated lineages in the study area. In the framework of the unified species concept, these four clades can be confidently considered as four valid species. This recognition of new cryptic species in the Western Mediterranean region shows that the biodiversity of this well-studied area is still not fully understood.},
}
@article {pmid21888892,
year = {2011},
author = {Gessmann, D and Flinner, N and Pfannstiel, J and Schlösinger, A and Schleiff, E and Nussberger, S and Mirus, O},
title = {Structural elements of the mitochondrial preprotein-conducting channel Tom40 dissolved by bioinformatics and mass spectrometry.},
journal = {Biochimica et biophysica acta},
volume = {1807},
number = {12},
pages = {1647-1657},
doi = {10.1016/j.bbabio.2011.08.006},
pmid = {21888892},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Animals ; Computational Biology/*methods ; Fungal Proteins/*chemistry/classification/genetics/metabolism ; Mass Spectrometry/*methods ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/*chemistry/classification/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurospora crassa/chemistry/cytology ; Phylogeny ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; Voltage-Dependent Anion Channel 1/chemistry/genetics ; },
abstract = {Most mitochondrial proteins are imported into mitochondria from the cytosolic compartment. Proteins destined for the outer or inner membrane, the inter-membrane space, or the matrix are recognized and translocated by the TOM machinery containing the specialized protein import channel Tom40. The latter is a protein with β-barrel shape, which is suggested to have evolved from a porin-type protein. To obtain structural insights in the absence of a crystal structure the membrane topology of Tom40 from Neurospora crassa was determined by limited proteolysis combined with mass spectrometry. The results were interpreted on the basis of a structural model that has been generated for NcTom40 by using the structure of mouse VDAC-1 as a template and amino acid sequence information of approximately 270 different Tom40 and approximately 480 VDAC amino acid sequences for refinement. The model largely explains the observed accessible cleavage sites and serves as a structural basis for the investigation of physicochemical properties of the ensemble of our Tom40 sequence data set. By this means we discovered two conserved polar slides in the pore interior. One is possibly involved in the positioning of a pore-inserted helix; the other one might be important for mitochondrial pre-sequence peptide binding as it is only present in Tom40 but not in VDAC proteins. The outer surface of the Tom40 barrel reveals two conserved amino acid clusters. They may be involved in binding other components of the TOM complex or bridging components of the TIM machinery of the mitochondrial inner membrane.},
}
@article {pmid21890067,
year = {2011},
author = {Krakowetz, CN and Lindsay, LR and Chilton, NB},
title = {Genetic diversity in Ixodes scapularis (Acari: Ixodidae) from six established populations in Canada.},
journal = {Ticks and tick-borne diseases},
volume = {2},
number = {3},
pages = {143-150},
doi = {10.1016/j.ttbdis.2011.05.003},
pmid = {21890067},
issn = {1877-9603},
mesh = {Animals ; *Arachnid Vectors/classification/genetics ; Borrelia burgdorferi/pathogenicity ; Canada ; Endemic Diseases/*prevention &amp; control ; Genetics, Population/*methods ; Haplotypes ; Humans ; *Ixodes/classification/genetics ; Lyme Disease/epidemiology/microbiology/transmission ; Mitochondria/*chemistry/genetics ; Molecular Typing ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Public Health ; RNA, Ribosomal, 16S/analysis ; Rodentia ; Sequence Analysis, DNA ; },
abstract = {Although Ixodes scapularis is the most important vector of Borrelia burgdorferi sensu stricto, the causative agent of Lyme disease in North America, little is known of the genetic diversity in this tick species within the recently established populations in Canada. In the present study, 153 I. scapularis adults collected from southern Canada were compared genetically using single-strand conformation polymorphism (SSCP) analyses in combination with DNA sequencing of the mitochondrial 16S rRNA gene. Nineteen haplotypes were detected, 8 of which have not been reported in the U.S.A. One 'new' haplotype was only detected at Lunenburg, Nova Scotia, and comprised 38% of the ticks examined for that population. The population in the southeast corner of Manitoba contained 3 'new' haplotypes. Although the most common haplotype (Is-1) was present in all 6 populations of I. scapularis in Canada, there were significant differences in the genetic structure among population. This suggests different geographical origins for the tick populations in Canada, which may be related to the transportation of larval and nymphal ticks by migratory passerines using different flyways. Determination of the origins of the endemic populations of I. scapularis in Canada, as well as those predicted to establish in the near future, has important implications with respect to understanding the risk of exposure to pathogenic bacteria infecting these ticks.},
}
@article {pmid21907205,
year = {2011},
author = {Mazet, M and Harijan, RK and Kiema, TR and Haapalainen, AM and Morand, P and Morales, J and Bringaud, F and Wierenga, RK and Michels, PA},
title = {The characterization and evolutionary relationships of a trypanosomal thiolase.},
journal = {International journal for parasitology},
volume = {41},
number = {12},
pages = {1273-1283},
doi = {10.1016/j.ijpara.2011.07.009},
pmid = {21907205},
issn = {1879-0135},
mesh = {Acetyl-CoA C-Acyltransferase/*genetics/*metabolism ; Cloning, Molecular ; Cluster Analysis ; Computational Biology/methods ; Escherichia coli/genetics ; Gene Expression ; Gene Expression Profiling ; Humans ; Isoenzymes/genetics ; Leishmania/enzymology ; Mitochondria/enzymology ; Phylogeny ; Protein Sorting Signals ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma/*enzymology ; },
abstract = {Thiolases are enzymes that remove an acetyl-coenzyme A group from acyl-CoA in the catabolic β-oxidation of fatty acids, or catalyse the reverse condensation reaction for anabolic processes such as the biosynthesis of sterols and ketone bodies. In humans, six homologous isoforms of thiolase have been described, differing from each other in sequence, oligomeric state, substrate specificity and subcellular localization. A bioinformatics analysis of parasite genomes, being (i) different species of African trypanosomes, (ii) Trypanosoma cruzi and (iii) Leishmania spp., using the six human sequences as queries, showed that the distribution of thiolases in human and each of the studied Trypanosomatidae is completely different. Only one of these isoforms, called SCP2-thiolase, was found in each of the Trypanosomatidae, whereas the TFE-thiolase was also found in T. cruzi and Leishmania spp., and the AB-thiolase only in T. cruzi. Each of the trypanosomatid thiolases clusters with its orthologues from other organisms in a phylogenetic analysis and shares with them the isoform-specific sequence fingerprints. The single T. brucei SCP2-thiolase has been expressed in Escherichia coli and characterized. It shows activity in both the degradative and synthetic directions. Transcripts of this thiolase were detected in both bloodstream- and procyclic-form trypanosomes, but the protein was found only in the procyclic form. The encoded protein has both a predicted N-terminal mitochondrial signal peptide and a C-terminal candidate type 1 peroxisomal-targeting signal for sorting it into glycosomes. However experimentally, only a mitochondrial localization was found for both procyclic trypanosomes grown with glucose and cells cultured with amino acids as an energy source. When the thiolase expression in procyclic cells was knocked down by RNA interference, no important change in growth rate occurred, irrespective of whether the cells were grown with or without glucose, indicating that the metabolic pathway(s) involving this enzyme is/are not essential for the parasite under either of these growth conditions.},
}
@article {pmid21914666,
year = {2011},
author = {Guastella, AM and Zuccaro, A and Criscione, A and Marletta, D and Bordonaro, S},
title = {Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers.},
journal = {The Journal of heredity},
volume = {102},
number = {6},
pages = {753-758},
doi = {10.1093/jhered/esr091},
pmid = {21914666},
issn = {1465-7333},
mesh = {Animals ; Breeding ; Cluster Analysis ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/*genetics ; Endangered Species ; Female ; Genetic Markers ; Genetic Variation ; Haplotypes ; Horses/*genetics ; Male ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Sicily ; },
abstract = {Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes.},
}
@article {pmid21921696,
year = {2011},
author = {Bashir, K and Ishimaru, Y and Nishizawa, NK},
title = {Identification and characterization of the major mitochondrial Fe transporter in rice.},
journal = {Plant signaling &amp; behavior},
volume = {6},
number = {10},
pages = {1591-1593},
pmid = {21921696},
issn = {1559-2324},
mesh = {Gene Expression Regulation, Plant ; Glucuronidase/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Oryza/cytology/genetics/growth &amp; development/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; },
abstract = {The uptake, translocation, and compartmentalization of Fe are essential for plant cell function and life cycle. Despite rapid progress in our understanding of Fe homeostasis in plants, Fe transport from the cytoplasm to mitochondria was, until recently, poorly understood. The screening of 3,993 mutant lines for symptoms of Fe deficiency resulted in the identification and characterization of a major mitochondrial Fe transporter (MIT) in rice. MIT was found to localize to mitochondria and to complement the growth of a yeast strain defective in mitochondrial Fe transport. The knock-out of MIT resulted in a lethal phenotype, and in knock-down plants, several agronomic characteristics were compromised, such as plant height, average number of tillers, days to flower, fertility, and yield. Changes in the expression of genes involved in Fe transport suggested a disturbance of cellular Fe transport. Furthermore, the mitochondrial Fe concentration and the activity of the mitochondrial Fe-S enzyme aconitase were significantly reduced compared with wild-type plants. The identification of MIT is a significant advance in the field of plant Fe nutrition and should facilitate the cloning of paralogs from other plant species.},
}
@article {pmid21933443,
year = {2011},
author = {Slade, KM and Freggiaro, S and Cottrell, KA and Smith, JJ and Wiley, EA},
title = {Sirtuin-mediated nuclear differentiation and programmed degradation in Tetrahymena.},
journal = {BMC cell biology},
volume = {12},
number = {},
pages = {40},
pmid = {21933443},
issn = {1471-2121},
mesh = {Active Transport, Cell Nucleus/drug effects ; Amino Acid Sequence ; Apoptosis/drug effects ; Cell Nucleus/*metabolism ; Cells, Cultured ; Chromatin Assembly and Disassembly/drug effects ; Conjugation, Genetic/drug effects ; DNA Fragmentation ; Meiosis/drug effects ; Mitochondria/*metabolism ; Molecular Sequence Data ; Niacinamide/pharmacology ; Phylogeny ; Protein Multimerization/drug effects ; Protein Transport ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Sirtuins/antagonists &amp; inhibitors/genetics/*metabolism ; Tetrahymena/*physiology ; },
abstract = {BACKGROUND: The NAD(+)-dependent histone deacetylases, known as "sirtuins", participate in a variety of processes critical for single- and multi-cellular life. Recent studies have elucidated the importance of sirtuin activity in development, aging, and disease; yet, underlying mechanistic pathways are not well understood. Specific sirtuins influence chromatin structure and gene expression, but differences in their pathways as they relate to distinct chromatin functions are just beginning to emerge. To further define the range of global chromatin changes dependent on sirtuins, unique biological features of the ciliated protozoan Tetrahymena thermophila can be exploited. This system offers clear spatial and temporal separation of multiple whole genome restructuring events critical for the life cycle.<br><br>RESULTS: Inhibition with nicotinamide revealed that sirtuin deacetylase activity in Tetrahymena cells promotes chromatin condensation during meiotic prophase, differentiation of heterochromatin from euchromatin during development, and chromatin condensation/degradation during programmed nuclear death. We identified a class I sirtuin, called Thd14, that resides in mitochondria and nucleoli during vegetative growth, and forms a large sub-nuclear aggregate in response to prolonged cell starvation that may be peripherally associated with nucleoli. During sexual conjugation and development Thd14 selectively concentrates in the parental nucleus prior to its apoptotic-like degradation.<br><br>CONCLUSIONS: Sirtuin activity is important for several functionally distinct events requiring global chromatin condensation. Our findings suggest a novel role for sirtuins in promoting programmed pycnosis by acting on chromatin destined for degradation. The sirtuin Thd14, which displays physiological-dependent differential localization within the nucleus, is a candidate for a chromatin condensation enzyme that is coupled to nuclear degradation.},
}
@article {pmid21945877,
year = {2011},
author = {Feng, J and Zhang, J and Liu, M and Wan, G and Qi, K and Zheng, C and Lv, Z and Hu, C and Zeng, Y and Gregory, SG and Yang, Z},
title = {Association of mtDNA haplogroup F with healthy longevity in the female Chuang population, China.},
journal = {Experimental gerontology},
volume = {46},
number = {12},
pages = {987-993},
doi = {10.1016/j.exger.2011.09.001},
pmid = {21945877},
issn = {1873-6815},
mesh = {Aged ; Aged, 80 and over ; Aging/*genetics/physiology ; Asian People/*genetics ; China/epidemiology ; DNA, Mitochondrial/*genetics ; Female ; Gene Frequency ; Genotype ; Haplotypes/*genetics ; Humans ; Longevity/*genetics/physiology ; Middle Aged ; Phenotype ; Phylogeny ; },
abstract = {Human longevity is a complex heritable genetic trait. Based on substantial evidence from model organisms, it is clear that mitochondria play a pivotal role in aging and lifespan. However, the effects that mitochondrial genome variations have upon longevity and longevity-related phenotypes in Chuang people in China have yet to be established. By genotyping 15 variants for 10 haplogroups in 738 Chuang subjects, including 367 long-lived individuals and 371 controls, we found that haplogroup F was significantly associated with longevity in females of Zhuang population of China (p=0.003, OR: 2.01, 95%CI: 1.263-3.197). Additionally, haplogroup F was related to higher HDL levels (p<0.05) in long-lived individuals. Further analysis suggests that the non-synonymous variant m.13928G>C in haplogroup F was also associated with longevity in female Zhuang Chinese which might account for the beneficial effect of F.},
}
@article {pmid21947849,
year = {2012},
author = {Zifa, E and Daniil, Z and Skoumi, E and Stavrou, M and Papadimitriou, K and Terzenidou, M and Kostikas, K and Bagiatis, V and Gourgoulianis, KI and Mamuris, Z},
title = {Mitochondrial genetic background plays a role in increasing risk to asthma.},
journal = {Molecular biology reports},
volume = {39},
number = {4},
pages = {4697-4708},
pmid = {21947849},
issn = {1573-4978},
mesh = {Adult ; Asthma/*genetics ; Base Sequence ; Case-Control Studies ; DNA Mutational Analysis ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex I/chemistry ; Female ; Genes, Mitochondrial/genetics ; *Genetic Predisposition to Disease ; Haplotypes/genetics ; Humans ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/genetics ; Risk Factors ; },
abstract = {A number of studies suggest that mitochondrial dysfunction plays a role in the pathogenesis of asthma. To shed light for the first time on the role of the mitochondrial genome in the etiology of asthma we analyzed the mitochondrial tRNA genes and part of their flanking regions in patients with asthma compared with a set of healthy controls. We found a total of 10 mutations in 56 out of 76 asthmatic patients. Four of these mutations were not found in the control group, five were observed at a significantly lower frequency in controls, but none of the combinations of mutations detected in asthma patients was observed in the controls. Furthermore, we observed that 27.6% of the asthma patients (vs. 4% of the controls) belonged to the haplogroup U (Fisher test P = 0.00) and a positive significant correlation was found between the occurrence of the haplogroup U and the severity of the disease (Fisher test P = 0.02). Whereas further studies in larger cohorts are needed to confirm these observations we suggest that the mitochondrial genetic background plays a key role in asthma development.},
}
@article {pmid21950843,
year = {2012},
author = {Ducluzeau, AL and Wamboldt, Y and Elowsky, CG and Mackenzie, SA and Schuurink, RC and Basset, GJ},
title = {Gene network reconstruction identifies the authentic trans-prenyl diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in Arabidopsis.},
journal = {The Plant journal : for cell and molecular biology},
volume = {69},
number = {2},
pages = {366-375},
doi = {10.1111/j.1365-313X.2011.04796.x},
pmid = {21950843},
issn = {1365-313X},
mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Arabidopsis/*enzymology/genetics/metabolism/ultrastructure ; Chloroplasts/enzymology ; Cloning, Molecular ; Gene Knockout Techniques ; Gene Regulatory Networks/*genetics ; Genetic Complementation Test ; Green Fluorescent Proteins ; Mitochondria/enzymology ; Mutation ; Phylogeny ; Plants, Genetically Modified ; Plastoquinone/metabolism ; RNA Interference ; Saccharomyces cerevisiae/genetics/metabolism ; Terpenes/chemistry/metabolism ; Ubiquinone/chemistry/*metabolism ; },
abstract = {Ubiquinone (coenzyme Q) is the generic name of a class of lipid-soluble electron carriers formed of a redox active benzoquinone ring attached to a prenyl side chain. The length of the latter varies among species, and depends upon the product specificity of a trans-long-chain prenyl diphosphate synthase that elongates an allylic diphosphate precursor. In Arabidopsis, this enzyme is assumed to correspond to an endoplasmic reticulum-located solanesyl diphosphate synthase, although direct genetic evidence was lacking. In this study, the reconstruction of the functional network of Arabidopsis genes linked to ubiquinone biosynthesis singled out an unsuspected solanesyl diphosphate synthase candidate--product of gene At2g34630--that, extraordinarily, had been shown previously to be targeted to plastids and to contribute to the biosynthesis of gibberellins. Green fluorescent protein (GFP) fusion experiments in tobacco and Arabidopsis, and complementation of a yeast coq1 knockout lacking mitochondrial hexaprenyl diphosphate synthase demonstrated that At2g34630 is also targeted to mitochondria. At2g34630 is the main--if not sole--contributor to solanesyl diphosphate synthase activity required for the biosynthesis of ubiquinone, as demonstrated by the dramatic (75-80%) reduction of the ubiquinone pool size in corresponding RNAi lines. Overexpression of At2g34630 gave up to a 40% increase in ubiquinone content compared to wild-type plants. None of the silenced or overexpressing lines, in contrast, displayed altered levels of plastoquinone. Phylogenetic analyses revealed that At2g34630 is the only Arabidopsis trans-long-chain prenyl diphosphate synthase that clusters with the Coq1 orthologs involved in the biosynthesis of ubiquinone in other eukaryotes.},
}
@article {pmid21966477,
year = {2011},
author = {Verma, S and Mehta, A and Shaha, C},
title = {CYP5122A1, a novel cytochrome P450 is essential for survival of Leishmania donovani.},
journal = {PloS one},
volume = {6},
number = {9},
pages = {e25273},
pmid = {21966477},
issn = {1932-6203},
mesh = {Adenosine Triphosphate/metabolism ; Animals ; Blotting, Western ; Cricetinae ; Cytochrome P-450 Enzyme System/classification/genetics/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Ergosterol/metabolism ; Genome, Protozoan/genetics ; Immunohistochemistry ; Leishmania donovani/genetics/*metabolism/*pathogenicity ; Leishmaniasis, Visceral/parasitology ; Mesocricetus ; Mitochondria/drug effects/metabolism ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; },
abstract = {BACKGROUND: Cytochrome P450s (CYP450s) are hemoproteins catalysing diverse biochemical reactions important for metabolism of xenobiotics and synthesis of physiologically important compounds such as sterols. Therefore, they are functionally important for survival of invading pathogens. One such opportunistic pathogen Leishmania donovani causes visceral leishmaniasis worldwide, which is an important public health problem due to significant disease burden. The parasite genome database, Gene DB, annotates 3 CYP450s in Leishmania, however, the functional role of cytochrome P450 enzymes in Leishmania spp. remains elusive.<br><br>A CYP450-like gene cloned from Leishmania donovani was identified as a novel CYP450, the CYP5122A1. Upon co-localization with organelle specific markers, CYP5122A1 distribution was shown to be localized in the promastigote ER, mitochondria and the glycosomes. Replacement of one allele of CYP5122A1 with either neomycin or hygromycin gene by homologous recombination in Leishmania promastigotes induced substantial reduction of CYP5122A1 expression. These parasites showed impaired growth, lower mitochondrial Ca(2+) and membrane potential resulting in low ATP generation. Also, these parasites were less infective in vitro and in vivo than their wild-type counterparts as assessed by incubation of Leishmania promastigotes with macrophages in vitro as well as through administration of parasites into hamsters. The HKOs were more susceptible to drugs like miltefosine and antimony, but showed reduced sensitivity to amphotericin B. Removal of two alleles of CYP5122A1 did not allow the parasites to survive. The mutant parasites showed 3.5 times lower ergosterol level as compared to the wild-type parasites when estimated by Gas chromatography/mass spectrometry. Complementation of CYP5122A1 through episomal expression of protein by using pXG-GFP+2 vector partially rescued CYP5122A1 expression and restored ergosterol levels by 1.8 times. Phenotype reversal included restored growth pattern and lesser drug susceptibility.<br><br>CONCLUSIONS/SIGNIFICANCE: In summary, this study establishes CYP5122A1 as an important molecule linked to processes like cell growth, infection and ergosterol biosynthesis in Leishmania donovani.},
}
@article {pmid21974833,
year = {2012},
author = {Naidu, A and Fitak, RR and Munguia-Vega, A and Culver, M},
title = {Novel primers for complete mitochondrial cytochrome b gene sequencing in mammals.},
journal = {Molecular ecology resources},
volume = {12},
number = {2},
pages = {191-196},
doi = {10.1111/j.1755-0998.2011.03078.x},
pmid = {21974833},
issn = {1755-0998},
mesh = {Animals ; Cytochromes b/*genetics ; DNA Primers/*genetics ; Mammals/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.},
}
@article {pmid21984653,
year = {2012},
author = {Waller, JC and Ellens, KW and Alvarez, S and Loizeau, K and Ravanel, S and Hanson, AD},
title = {Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron-sulphur cluster metabolism.},
journal = {Journal of experimental botany},
volume = {63},
number = {1},
pages = {403-411},
pmid = {21984653},
issn = {1460-2431},
support = {UL1 TR000064/TR/NCATS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Arabidopsis Proteins/chemistry/*metabolism ; Iron/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Sequence Homology, Amino Acid ; Sulfur/*metabolism ; },
abstract = {COG0354 proteins have been implicated in synthesis or repair of iron/sulfur (Fe/S) clusters in all domains of life, and those of bacteria, animals, and protists have been shown to require a tetrahydrofolate to function. Two COG0354 proteins were identified in Arabidopsis and many other plants, one (At4g12130) related to those of α-proteobacteria and predicted to be mitochondrial, the other (At1g60990) related to those of cyanobacteria and predicted to be plastidial. Grasses and poplar appear to lack the latter. The predicted subcellular locations of the Arabidopsis proteins were validated by in vitro import assays with purified pea organelles and by targeting assays in Arabidopsis and tobacco protoplasts using green fluorescent protein fusions. The At4g12130 protein was shown to be expressed mainly in flowers, siliques, and seeds, whereas the At1g60990 protein was expressed mainly in young leaves. The folate dependence of both Arabidopsis proteins was established by functional complementation of an Escherichia coli COG0354 (ygfZ) deletant; both plant genes restored in vivo activity of the Fe/S enzyme MiaB but restoration was abrogated when folates were eliminated by deleting folP. Insertional inactivation of At4g12130 was embryo lethal; this phenotype was reversed by genetic complementation of the mutant. These data establish that COG0354 proteins have a folate-dependent function in mitochondria and plastids, and that the mitochondrial protein is essential. That plants retain mitochondrial and plastidial COG0354 proteins with distinct phylogenetic origins emphasizes how deeply the extant Fe/S cluster assembly machinery still reflects the ancient endosymbioses that gave rise to plants.},
}
@article {pmid21986531,
year = {2011},
author = {Nozawa, A and Fujimoto, R and Matsuoka, H and Tsuboi, T and Tozawa, Y},
title = {Cell-free synthesis, reconstitution, and characterization of a mitochondrial dicarboxylate-tricarboxylate carrier of Plasmodium falciparum.},
journal = {Biochemical and biophysical research communications},
volume = {414},
number = {3},
pages = {612-617},
doi = {10.1016/j.bbrc.2011.09.130},
pmid = {21986531},
issn = {1090-2104},
mesh = {Carrier Proteins/biosynthesis/*chemistry/classification/genetics ; Cell-Free System/chemistry ; Dicarboxylic Acid Transporters/biosynthesis/*chemistry/classification/genetics ; Mitochondria/*metabolism ; Phylogeny ; Plasmodium falciparum/genetics/*metabolism ; Protozoan Proteins/biosynthesis/*chemistry/classification/genetics ; Tricarboxylic Acids/*metabolism ; },
abstract = {The malaria parasite, Plasmodium falciparum, was recently shown to operate a branched pathway of tricarboxylic acid (TCA) metabolism. To identify and characterize membrane transporters required for such TCA metabolism in the parasite, we isolated a cDNA for a dicarboxylate-tricarboxylate carrier homolog (PfDTC), synthesized the encoded protein with the use of a cell-free translation system, and determined the substrate specificity of its transport activity with a proteoliposome reconstitution system. PfDTC was found to mediate efficient oxoglutarate-malate, oxoglutarate-oxaloacetate, or oxoglutarate-oxoglutarate exchange across the liposome membrane. Our results suggest that PfDTC may mediate the oxoglutarate-malate exchange across the inner mitochondrial membrane required for the branched pathway of TCA metabolism in the malaria parasite.},
}
@article {pmid21988877,
year = {2011},
author = {Ito, K and Ogata, T and Kakizaki, Y and Elliott, C and Albury, MS and Moore, AL},
title = {Identification of a gene for pyruvate-insensitive mitochondrial alternative oxidase expressed in the thermogenic appendices in Arum maculatum.},
journal = {Plant physiology},
volume = {157},
number = {4},
pages = {1721-1732},
pmid = {21988877},
issn = {1532-2548},
support = {BB/E015328/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arum/drug effects/*enzymology/genetics ; Base Sequence ; Cell Respiration ; Chromatography, Liquid ; DNA, Complementary/genetics ; DNA, Plant/chemistry/genetics ; Flowers/*enzymology/genetics ; Hot Temperature ; Mitochondrial Proteins/drug effects/genetics/*metabolism ; Molecular Sequence Data ; Organ Specificity ; Oxidoreductases/drug effects/genetics/*metabolism ; Phylogeny ; Plant Proteins/drug effects/genetics/*metabolism ; Pyruvic Acid/*pharmacology ; Schizosaccharomyces/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Tandem Mass Spectrometry ; Alternative Oxidase ; },
abstract = {Heat production in thermogenic plants has been attributed to a large increase in the expression of the alternative oxidase (AOX). AOX acts as an alternative terminal oxidase in the mitochondrial respiratory chain, where it reduces molecular oxygen to water. In contrast to the mitochondrial terminal oxidase, cytochrome c oxidase, AOX is nonprotonmotive and thus allows the dramatic drop in free energy between ubiquinol and oxygen to be dissipated as heat. Using reverse transcription-polymerase chain reaction-based cloning, we reveal that, although at least seven cDNAs for AOX exist (AmAOX1a, -1b, -1c, -1d, -1e, -1f, and -1g) in Arum maculatum, the organ and developmental regulation for each is distinct. In particular, the expression of AmAOX1e transcripts appears to predominate in thermogenic appendices among the seven AmAOXs. Interestingly, the amino acid sequence of AmAOX1e indicates that the ENV element found in almost all other AOX sequences, including AmAOX1a, -1b, -1c, -1d, and -1f, is substituted by QNT. The existence of a QNT motif in AmAOX1e was confirmed by nano-liquid chromatography-tandem mass spectrometry analysis of mitochondrial proteins from thermogenic appendices. Further functional analyses with mitochondria prepared using a yeast heterologous expression system demonstrated that AmAOX1e is insensitive to stimulation by pyruvate. These data suggest that a QNT type of pyruvate-insensitive AOX, AmAOX1e, plays a crucial role in stage- and organ-specific heat production in the appendices of A. maculatum.},
}
@article {pmid21998669,
year = {2011},
author = {De Barro, P and Ahmed, MZ},
title = {Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.},
journal = {PloS one},
volume = {6},
number = {10},
pages = {e25579},
pmid = {21998669},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/genetics ; Genes, Insect/*genetics ; Genetic Variation/genetics ; Haplotypes/genetics ; Hemiptera/*classification/*genetics ; *Introduced Species ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally.<br><br>Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010). Only two species proposed in Dinsdale et al. (2010) departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED) and Middle East - Asia Minor 1 (MEAM1), showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region.<br><br>CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of the available genetic diversity.},
}
@article {pmid22001261,
year = {2012},
author = {Yang, EC and Boo, GH and Kim, HJ and Cho, SM and Boo, SM and Andersen, RA and Yoon, HS},
title = {Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles.},
journal = {Protist},
volume = {163},
number = {2},
pages = {217-231},
doi = {10.1016/j.protis.2011.08.001},
pmid = {22001261},
issn = {1618-0941},
mesh = {Cell Nucleus/genetics ; *Genes, Chloroplast ; Genes, Mitochondrial ; Mitochondria/genetics ; Photosynthesis ; *Phylogeny ; Plastids/genetics ; RNA, Ribosomal/genetics ; Ribosomes/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Stramenopiles/*classification/genetics ; },
abstract = {Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.},
}
@article {pmid22004680,
year = {2011},
author = {Coyne, RS and Hannick, L and Shanmugam, D and Hostetler, JB and Brami, D and Joardar, VS and Johnson, J and Radune, D and Singh, I and Badger, JH and Kumar, U and Saier, M and Wang, Y and Cai, H and Gu, J and Mather, MW and Vaidya, AB and Wilkes, DE and Rajagopalan, V and Asai, DJ and Pearson, CG and Findly, RC and Dickerson, HW and Wu, M and Martens, C and Van de Peer, Y and Roos, DS and Cassidy-Hanley, DM and Clark, TG},
title = {Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.},
journal = {Genome biology},
volume = {12},
number = {10},
pages = {R100},
pmid = {22004680},
issn = {1474-760X},
support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM099820/GM/NIGMS NIH HHS/United States ; R01 GM077402/GM/NIGMS NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; R01 AI028398/AI/NIAID NIH HHS/United States ; SC1 GM081068/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Antigens, Protozoan/genetics ; Base Composition ; Chromosome Mapping ; Ciliophora Infections/*prevention &amp; control ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Databases, Genetic ; Genes, Protozoan ; Genome Size ; Genomics/*methods ; Host-Parasite Interactions ; Hymenostomatida/classification/*genetics/growth &amp; development/pathogenicity ; Ictaluridae/parasitology ; *Life Cycle Stages ; Macronucleus/genetics ; Membrane Transport Proteins/genetics ; Metabolic Networks and Pathways ; Mitochondria/enzymology/genetics ; Mitochondrial Proton-Translocating ATPases/genetics ; Molecular Sequence Annotation ; Phylogeny ; Protein Kinases/classification/genetics ; Protozoan Proteins/genetics ; RNA, Protozoan/genetics ; Zebrafish/genetics/*parasitology ; },
abstract = {BACKGROUND: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism.<br><br>RESULTS: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.<br><br>CONCLUSIONS: Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.},
}
@article {pmid22008015,
year = {2012},
author = {Schuhmann, H and Adamska, I},
title = {Deg proteases and their role in protein quality control and processing in different subcellular compartments of the plant cell.},
journal = {Physiologia plantarum},
volume = {145},
number = {1},
pages = {224-234},
doi = {10.1111/j.1399-3054.2011.01533.x},
pmid = {22008015},
issn = {1399-3054},
mesh = {Arabidopsis/enzymology ; Arabidopsis Proteins/*metabolism ; Cell Nucleus/enzymology ; Chloroplast Proteins/metabolism ; Chloroplasts/*enzymology ; Mitochondria/enzymology ; Oxidation-Reduction ; Peroxisomes/*enzymology/physiology ; Photosynthesis ; Phylogeny ; Plant Cells/*enzymology/physiology ; Proteolysis ; Serine Endopeptidases/*metabolism ; },
abstract = {Degradation of periplasmic proteins (Deg)/high temperature requirement A (HtrA) proteases are ATP-independent serine endopeptidases found in almost every organism. Database searches revealed that 16 Deg paralogues are encoded by the genome of Arabidopsis thaliana, six of which were experimentally shown to be located in chloroplasts, one in peroxisomes, one in mitochondria and one in the nucleus. Two more Deg proteases are predicted to reside in chloroplasts, five in mitochondria (one of them with a dual chloroplastidial/mitochondrial localization) and the subcellular location of one protein is uncertain. This review summarizes the current knowledge on the role of Deg proteases in maintaining protein homeostasis and protein processing in various subcompartments of the plant cell. The chloroplast Deg proteases are the best examined so far, especially with respect to their role in the degradation of photodamaged photosynthetic proteins and in biogenesis of photosystem II (PSII). A combined action of thylakoid lumen and stroma Deg proteases in the primary cleavage of photodamaged D1 protein from PSII reaction centre is discussed on the basis of a recently resolved crystal structure of plant Deg1. The peroxisomal Deg protease is a processing enzyme responsible for the cleavage of N-terminal peroxisomal targeting signals (PTSs). A. thaliana mutants lacking this enzyme show reduced peroxisomal β-oxidation, indicating for the first time the impact of protein processing on peroxisomal functions in plants. Much less data is available for mitochondrial and nuclear Deg proteases. Based on the available expression data we hypothesize a role in general protein quality control and during acquired heat resistance.},
}
@article {pmid22012225,
year = {2011},
author = {Bourke, BP and Nagaki, SS and Bergo, ES and Cardoso, Jda C and Sallum, MA},
title = {Molecular phylogeny of the Myzorhynchella Section of Anopheles (Nyssorhynchus) (Diptera: Culicidae): genetic support for recently described and resurrected species.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {106},
number = {6},
pages = {705-715},
doi = {10.1590/s0074-02762011000600010},
pmid = {22012225},
issn = {1678-8060},
mesh = {Animals ; Anopheles/classification/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Female ; Genes, Insect/*genetics ; Mitochondria/enzymology ; Phylogeny ; Species Specificity ; },
abstract = {Phylogenetic relationships among species of the Myzorhynchella Section of Anopheles (Nyssorhynchus) were investigated using the nuclear ribosomal DNA second internal transcribed spacer (ITS2), the nuclear whitegene and mitochondrial cytochrome oxidase subunit I (COI) regions. The recently described Anopheles pristinus and resurrected Anopheles guarani were also included in the study. Bayesian phylogenetic analyses found Anopheles parvus to be the most distantly related species within the Section, a finding that is consistent with morphology. An. pristinus and An. guarani were clearly resolved from Anopheles antunesi and Anopheles lutzii, respectively. An. lutzii collected in the same mountain range as the type locality were found within a strongly supported clade, whereas individuals from the southern state of Rio Grande do Sul, tentatively identified as An. lutzii based on adult female external morphology, were distinct from An. lutzii, An. antunesi and from each other, and may therefore represent two new sympatric species. A more detailed examination of An. lutzii sensu latoalong its known geographic range is recommended to resolve these anomalous relationships.},
}
@article {pmid22013080,
year = {2012},
author = {Costa-Urrutia, P and Abud, C and Secchi, ER and Lessa, EP},
title = {Population genetic structure and social kin associations of franciscana dolphin, Pontoporia blainvillei.},
journal = {The Journal of heredity},
volume = {103},
number = {1},
pages = {92-102},
doi = {10.1093/jhered/esr103},
pmid = {22013080},
issn = {1465-7333},
mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Brazil ; Dolphins/*genetics ; Endangered Species ; Female ; Genetic Structures ; *Genetic Variation ; Haplotypes ; Male ; Markov Chains ; Microsatellite Repeats ; Mitochondria/genetics ; Monte Carlo Method ; Multilocus Sequence Typing ; Phylogeny ; Phylogeography ; Sexual Behavior, Animal ; Social Behavior ; Uruguay ; },
abstract = {We investigated population and social structure of the franciscana dolphin, Pontoporia blainvillei, an endemic and the most endangered cetacean of the southwestern Atlantic Ocean. We analyzed samples from the Rio de la Plata estuary obtained in Uruguayan waters and from the Atlantic Ocean obtained in both Uruguayan and Brazilian waters. Mitochondrial and microsatellite DNA markers were used to study differentiation between the estuary and the ocean and the association between kinship and social group structure. Although multilocus analyses suggested that franciscanas are structured into 2 subpopulations (K = 2, divergence among clusters: F(ST) = 0.06, P = 0.002; R(ST) = 0.3, P = 0.001), mitochondrial markers did not support such divergence (F(ST) = 0.02, P = 0.12; Ф(ST) = 0.06, P =0.06). However, these units are not entirely segregated geographically. Regarding social structure, some groups are composed by first-order related individuals (R ≥ 0.5, P < 0.5). Overall, the data suggest that matrilines could be the social unit in this species. We argue that the divergence found could be associated to local adaptation and social structure, resulting from either feature leading to a recent divergence or reflecting equilibrium between local differentiation and gene flow. This evidence supports considering franciscanas from the Rio de la Plata estuary a discrete management unit.},
}
@article {pmid22022283,
year = {2011},
author = {Bratic, A and Wredenberg, A and Grönke, S and Stewart, JB and Mourier, A and Ruzzenente, B and Kukat, C and Wibom, R and Habermann, B and Partridge, L and Larsson, NG},
title = {The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster.},
journal = {PLoS genetics},
volume = {7},
number = {10},
pages = {e1002324},
pmid = {22022283},
issn = {1553-7404},
mesh = {Animals ; Body Weight/genetics ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster/*genetics/*growth &amp; development/physiology ; Fertility/genetics ; Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; Mitochondria/*genetics/physiology ; Mitochondrial Proteins/genetics/metabolism ; Oxidative Phosphorylation ; Phylogeny ; Polyadenylation/*genetics ; Protein Biosynthesis ; RNA Interference ; RNA, Messenger/*genetics ; RNA-Binding Proteins/*genetics/metabolism ; },
abstract = {The bicoid stability factor (BSF) of Drosophila melanogaster has been reported to be present in the cytoplasm, where it stabilizes the maternally contributed bicoid mRNA and binds mRNAs expressed from early zygotic genes. BSF may also have other roles, as it is ubiquitously expressed and essential for survival of adult flies. We have performed immunofluorescence and cell fractionation analyses and show here that BSF is mainly a mitochondrial protein. We studied two independent RNAi knockdown fly lines and report that reduced BSF protein levels lead to a severe respiratory deficiency and delayed development at the late larvae stage. Ubiquitous knockdown of BSF results in a severe reduction of the polyadenylation tail lengths of specific mitochondrial mRNAs, accompanied by an enrichment of unprocessed polycistronic RNA intermediates. Furthermore, we observed a significant reduction in mRNA steady state levels, despite increased de novo transcription. Surprisingly, mitochondrial de novo translation is increased and abnormal mitochondrial translation products are present in knockdown flies, suggesting that BSF also has a role in coordinating the mitochondrial translation in addition to its role in mRNA maturation and stability. We thus report a novel function of BSF in flies and demonstrate that it has an important intra-mitochondrial role, which is essential for maintaining mtDNA gene expression and oxidative phosphorylation.},
}
@article {pmid22036291,
year = {2011},
author = {Hafez, M and Hausner, G},
title = {The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus.},
journal = {Fungal biology},
volume = {115},
number = {11},
pages = {1122-1137},
doi = {10.1016/j.funbio.2011.07.007},
pmid = {22036291},
issn = {1878-6146},
mesh = {Base Sequence ; *Genetic Variation ; Introns ; Mitochondria/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Ophiostoma/chemistry/classification/*genetics ; Phylogeny ; RNA, Fungal/chemistry/genetics ; RNA, Ribosomal/chemistry/*genetics ; Ribosome Subunits, Small/chemistry/*genetics ; },
abstract = {Mitochondrial genomes in the true fungi are highly variable both in size and organization. Most of this size variation is due to the presence of introns and intron-encoded open reading frames (ORFs). The objectives for this work were to examine the mitochondrial small-subunit ribosomal RNA (rns) gene of strains of Ophiostoma minus for the presence of introns and to characterize such introns and their encoded ORFs. DNA sequence analysis showed that among different strains of O. minus various rns gene exon/intron configurations can be observed. Based on comparative sequence analysis and RNA secondary structure modeling group I introns with LAGLIDADG ORFs were uncovered at positions mS569 and mS1224 and group II introns were present at positions mS379 and mS952. The mS379 group II intron encoded a fragmented reverse transcriptase (RT)-like ORF and the mS952 group II intron encoded a LAGLIDADG-type ORF. Examples of intron ORF degeneration due to frameshift mutations were observed. The mS379 group II intron is the first mitochondrial group II intron to have an ORF inserted within domain II, typically RT-like ORFs are inserted in domain IV. The evolutionary dynamics of the intron-encoded ORFs have also been examined.},
}
@article {pmid22041769,
year = {2011},
author = {Fong, MY and Lau, YL and Chin, LC and Al-Mekhlafi, AM},
title = {Sequence analysis on the mitochondrial COXI gene of recent clinical isolates of Plasmodium knowlesi in Klang Valley, peninsular Malaysia.},
journal = {Tropical biomedicine},
volume = {28},
number = {2},
pages = {457-463},
pmid = {22041769},
issn = {2521-9855},
mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Humans ; Malaria/parasitology ; Malaysia ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plasmodium knowlesi/*enzymology/*genetics/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The cytochrome oxidase subunit I (COXI) gene sequences of three recent (2007-2008) clinical Plasmodium knowlesi isolates from Klang Valley, peninsular Malaysia, were determined and compared with those of older (1960's) peninsular Malaysia, recent isolates from Sarawak (on Borneo Island), and an isolate from Thailand. Multiple alignment of the sequences showed that the three clinical isolates were more similar to the older peninsular Malaysia isolates than to those from Sarawak and Thailand. Phylogenetic tree based on the COXI sequences revealed three distinct clusters of P. knowlesi. The first cluster consisted of isolates from peninsular Malaysia, the second consisted of Sarawak isolates and the third composed of the Thailand isolate. The findings of this study highlight the usefulness of mitochondrial COXI gene as a suitable marker for phylogeographic studies of P. knowlesi.},
}
@article {pmid22062157,
year = {2011},
author = {Stael, S and Rocha, AG and Robinson, AJ and Kmiecik, P and Vothknecht, UC and Teige, M},
title = {Arabidopsis calcium-binding mitochondrial carrier proteins as potential facilitators of mitochondrial ATP-import and plastid SAM-import.},
journal = {FEBS letters},
volume = {585},
number = {24},
pages = {3935-3940},
doi = {10.1016/j.febslet.2011.10.039},
pmid = {22062157},
issn = {1873-3468},
support = {MC_U105674181/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Arabidopsis/*cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/metabolism ; Calcium/metabolism ; Calcium Signaling ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; EF Hand Motifs ; Genome, Plant/genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Protein Transport ; S-Adenosylmethionine/*metabolism ; Substrate Specificity ; },
abstract = {Chloroplasts and mitochondria are central to crucial cellular processes in plants and contribute to a whole range of metabolic pathways. The use of calcium ions as a secondary messenger in and around organelles is increasingly appreciated as an important mediator of plant cell signaling, enabling plants to develop or to acclimatize to changing environmental conditions. Here, we have studied the four calcium-dependent mitochondrial carriers that are encoded in the Arabidopsis genome. An unknown substrate carrier, which was previously found to localize to chloroplasts, is proposed to present a calcium-dependent S-adenosyl methionine carrier. For three predicted ATP/phosphate carriers, we present experimental evidence that they can function as mitochondrial ATP-importers.},
}
@article {pmid22066495,
year = {2011},
author = {San Francisco, B and Bretsnyder, EC and Rodgers, KR and Kranz, RG},
title = {Heme ligand identification and redox properties of the cytochrome c synthetase, CcmF.},
journal = {Biochemistry},
volume = {50},
number = {50},
pages = {10974-10985},
pmid = {22066495},
issn = {1520-4995},
support = {R01 GM047909/GM/NIGMS NIH HHS/United States ; R15 AI072719/AI/NIAID NIH HHS/United States ; AI072719/AI/NIAID NIH HHS/United States ; GM47909/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Binding Sites ; Biocatalysis ; Enzyme Activation/drug effects ; Escherichia coli Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Heme/chemistry/*metabolism ; Histidine/chemistry ; Holoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; Imidazoles/pharmacology ; Indicators and Reagents/pharmacology ; Ligands ; Lyases/chemistry/genetics/isolation &amp; purification/*metabolism ; Models, Molecular ; Mutant Proteins/chemistry/isolation &amp; purification/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Protein Subunits/chemistry/genetics/isolation &amp; purification/metabolism ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Spectrum Analysis, Raman ; },
abstract = {Cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein CcmF, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. We previously reported that the E. coli CcmF protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. Here, we show that mutation of either of two conserved transmembrane histidines (His261 or His491) impairs stoichiometric b-heme binding in CcmF and results in spectral perturbations in the remaining heme. Exogeneous imidazole is able to correct cytochrome c maturation for His261 and His491 substitutions with small side chains (Ala or Gly), suggesting that a "cavity" is formed in these CcmF mutants in which imidazole binds and acts as a functional ligand to the b-heme. The results of resonance Raman spectroscopy on wild-type CcmF are consistent with a hexacoordinate low-spin b-heme with at least one endogeneous axial His ligand. Analysis of purified recombinant CcmF proteins from diverse prokaryotes reveals that the b-heme in CcmF is widely conserved. We have also determined the reduction potential of the CcmF b-heme (E(m,7) = -147 mV). We discuss these results in the context of CcmF structure and functions as a heme reductase and cytochrome c synthetase.},
}
@article {pmid22066674,
year = {2012},
author = {Martin, FN and Coffey, MD},
title = {Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi.},
journal = {Phytopathology},
volume = {102},
number = {2},
pages = {229-239},
doi = {10.1094/PHYTO-04-11-0115},
pmid = {22066674},
issn = {0031-949X},
mesh = {Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genetic Loci/*genetics ; Genome, Mitochondrial/*genetics ; Geography ; Haplotypes/*genetics ; Mitochondria/*classification/genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Phytophthora/*classification/genetics/isolation &amp; purification ; Polymorphism, Genetic/*genetics ; Sequence Analysis, DNA ; },
abstract = {Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.},
}
@article {pmid22069449,
year = {2011},
author = {Jimenez-Morales, D and Liang, J},
title = {Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e26400},
pmid = {22069449},
issn = {1932-6203},
support = {R01 GM081682/GM/NIGMS NIH HHS/United States ; P50 GM086145/GM/NIGMS NIH HHS/United States ; GM079804/GM/NIGMS NIH HHS/United States ; GM081682/GM/NIGMS NIH HHS/United States ; R01 GM079804/GM/NIGMS NIH HHS/United States ; GM086145/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution ; Bacteria/*metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Bayes Theorem ; Genome, Bacterial ; Membrane Proteins/*chemistry/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Protein Structure, Secondary ; },
abstract = {β-barrel membrane proteins play an important role in controlling the exchange and transport of ions and organic molecules across bacterial and mitochondrial outer membranes. They are also major regulators of apoptosis and are important determinants of bacterial virulence. In contrast to β-helical membrane proteins, their evolutionary pattern of residue substitutions has not been quantified, and there are no scoring matrices appropriate for their detection through sequence alignment. Using a Bayesian Monte Carlo estimator, we have calculated the instantaneous substitution rates of transmembrane domains of bacterial β-barrel membrane proteins. The scoring matrices constructed from the estimated rates, called bbTM for β-barrel Transmembrane Matrices, improve significantly the sensitivity in detecting homologs of β-barrel membrane proteins, while avoiding erroneous selection of both soluble proteins and other membrane proteins of similar composition. The estimated evolutionary patterns are general and can detect β-barrel membrane proteins very remote from those used for substitution rate estimation. Furthermore, despite the separation of 2-3 billion years since the proto-mitochondrion entered the proto-eukaryotic cell, mitochondria outer membrane proteins in eukaryotes can also be detected accurately using these scoring matrices derived from bacteria. This is consistent with the suggestion that there is no eukaryote-specific signals for translocation. With these matrices, remote homologs of β-barrel membrane proteins with known structures can be reliably detected at genome scale, allowing construction of high quality structural models of their transmembrane domains, at the rate of 131 structures per template protein. The scoring matrices will be useful for identification, classification, and functional inference of membrane proteins from genome and metagenome sequencing projects. The estimated substitution pattern will also help to identify key elements important for the structural and functional integrity of β-barrel membrane proteins, and will aid in the design of mutagenesis studies.},
}
@article {pmid22079833,
year = {2011},
author = {Schneider, RE and Brown, MT and Shiflett, AM and Dyall, SD and Hayes, RD and Xie, Y and Loo, JA and Johnson, PJ},
title = {The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes.},
journal = {International journal for parasitology},
volume = {41},
number = {13-14},
pages = {1421-1434},
pmid = {22079833},
issn = {1879-0135},
support = {T32 AI007323/AI/NIAID NIH HHS/United States ; 2-T32-AI-007323/AI/NIAID NIH HHS/United States ; F32 AI080084/AI/NIAID NIH HHS/United States ; R37 AI027857/AI/NIAID NIH HHS/United States ; R37 AI027587/AI/NIAID NIH HHS/United States ; F32-AI080084/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Mass Spectrometry ; Mitochondria/chemistry/genetics/*metabolism ; Organelles/chemistry/genetics/*metabolism ; Phylogeny ; Proteome/chemistry/genetics/*metabolism ; Proteomics ; Protozoan Proteins/chemistry/genetics/*metabolism ; Trichomonas vaginalis/chemistry/classification/genetics/*metabolism ; },
abstract = {The human pathogen Trichomonas vaginalis lacks conventional mitochondria and instead contains divergent mitochondrial-related organelles. These double-membrane bound organelles, called hydrogenosomes, produce molecular hydrogen. Phylogenetic and biochemical analyses of hydrogenosomes indicate a common origin with mitochondria; however identification of hydrogenosomal proteins and studies on its metabolism have been limited. Here we provide a detailed proteomic analysis of the T. vaginalis hydrogenosome. The proteome of purified hydrogenosomes consists of 569 proteins, a number substantially lower than the 1,000-1,500 proteins reported for fungal and animal mitochondrial proteomes, yet considerably higher than proteins assigned to mitosomes. Pathways common to and distinct from both mitochondria and mitosomes were revealed by the hydrogenosome proteome. Proteins known to function in amino acid and energy metabolism, Fe-S cluster assembly, flavin-mediated catalysis, oxygen stress response, membrane translocation, chaperonin functions, proteolytic processing and ATP hydrolysis account for ∼30% of the hydrogenosome proteome. Of the 569 proteins in the hydrogenosome proteome, many appear to be associated with the external surface of hydrogenosomes, including large numbers of GTPases and ribosomal proteins. Glycolytic proteins were also found to be associated with the hydrogenosome proteome, similar to that previously observed for mitochondrial proteomes. Approximately 18% of the hydrogenosomal proteome is composed of hypothetical proteins of unknown function, predictive of multiple activities and properties yet to be uncovered for these highly adapted organelles.},
}
@article {pmid22114710,
year = {2011},
author = {Foury, F and Szczepanowska, K},
title = {Antimutator alleles of yeast DNA polymerase gamma modulate the balance between DNA synthesis and excision.},
journal = {PloS one},
volume = {6},
number = {11},
pages = {e27847},
pmid = {22114710},
issn = {1932-6203},
mesh = {Alleles ; DNA Polymerase I/genetics/metabolism ; DNA Polymerase gamma ; *DNA Replication ; DNA, Mitochondrial/*genetics/*metabolism ; DNA-Directed DNA Polymerase/chemistry/*genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Exonucleases/metabolism ; Humans ; Mutation/*genetics ; Mutation Rate ; Phenotype ; Protein Conformation ; Saccharomyces cerevisiae/*enzymology/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Mutations in mitochondrial DNA (mtDNA) are an important cause of disease and perhaps aging in human. DNA polymerase gamma (pol γ), the unique replicase inside mitochondria, plays a key role in the fidelity of mtDNA replication through selection of the correct nucleotide and 3'-5' exonuclease proofreading. For the first time, we have isolated and characterized antimutator alleles in the yeast pol γ (Mip1). These mip1 mutations, localised in the 3'-5' exonuclease and polymerase domains, elicit a 2-15 fold decrease in the frequency of mtDNA point mutations in an msh1-1 strain which is partially deficient in mtDNA mismatch-repair. In vitro experiments show that in all mutants the balance between DNA synthesis and exonucleolysis is shifted towards excision when compared to wild-type, suggesting that in vivo more opportunity is given to the editing function for removing the replicative errors. This results in partial compensation for the mismatch-repair defects and a decrease in mtDNA point mutation rate. However, in all mutants but one the antimutator trait is lost in the wild-type MSH1 background. Accordingly, the polymerases of selected mutants show reduced oligonucleotide primed M13 ssDNA synthesis and to a lesser extent DNA binding affinity, suggesting that in mismatch-repair proficient cells efficient DNA synthesis is required to reach optimal accuracy. In contrast, the Mip1-A256T polymerase, which displays wild-type like DNA synthesis activity, increases mtDNA replication fidelity in both MSH1 and msh1-1 backgrounds. Altogether, our data show that accuracy of wild-type Mip1 is probably not optimal and can be improved by specific (often conservative) amino acid substitutions that define a pol γ area including a loop of the palm subdomain, two residues near the ExoII motif and an exonuclease helix-coil-helix module in close vicinity to the polymerase domain. These elements modulate in a subtle manner the balance between DNA polymerization and excision.},
}
@article {pmid22116655,
year = {2012},
author = {Chigri, F and Flosdorff, S and Pilz, S and Kölle, E and Dolze, E and Gietl, C and Vothknecht, UC},
title = {The Arabidopsis calmodulin-like proteins AtCML30 and AtCML3 are targeted to mitochondria and peroxisomes, respectively.},
journal = {Plant molecular biology},
volume = {78},
number = {3},
pages = {211-222},
pmid = {22116655},
issn = {1573-5028},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism/ultrastructure ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Transport, Active ; Calmodulin/chemistry/genetics/*metabolism ; Intracellular Calcium-Sensing Proteins/chemistry/genetics/*metabolism ; Luminescent Proteins/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Peroxisomes/metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Conformation ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Signal Transduction ; Nicotiana/genetics/metabolism/ultrastructure ; },
abstract = {Calmodulin (CaM) is a ubiquitous sensor/transducer of calcium signals in eukaryotic organisms. While CaM mediated calcium regulation of cytosolic processes is well established, there is growing evidence for the inclusion of organelles such as chloroplasts, mitochondria and peroxisomes into the calcium/calmodulin regulation network. A number of CaM-binding proteins have been identified in these organelles and processes such as protein import into chloroplasts and mitochondria have been shown to be governed by CaM regulation. What have been missing to date are the mediators of this regulation since no CaM or calmodulin-like protein (CML) has been identified in any of these organelles. Here we show that two Arabidopsis CMLs, AtCML3 and AtCML30, are localized in peroxisomes and mitochondria, respectively. AtCML3 is targeted via an unusual C-terminal PTS1-like tripeptide while AtCML30 utilizes an N-terminal, non-cleavable transit peptide. Both proteins possess the typical structure of CaMs, with two pairs of EF-hand motifs separated by a short linker domain. They furthermore display common characteristics, such as calcium-dependent alteration of gel mobility and calcium-dependent exposure of a hydrophobic surface. This indicates that they can function in a similar manner as canonical CaMs. The presence of close homologues to AtCML3 and AtCML30 in other plants further indicates that organellar targeting of these CMLs is not a specific feature of Arabidopsis. The identification of peroxisomal and mitochondrial CMLs is an important step in the understanding how these organelles are integrated into the cellular calcium/calmodulin signaling pathways.},
}
@article {pmid22117417,
year = {2011},
author = {ZvychaĬnaia, EIu and Danilkin, AA and Kholodova, MV and Sipko, TP and Berber, AP},
title = {[Analysis of the variability of the control region and cytochrome b gene of mtDNA of Capreolus pygargus Pall].},
journal = {Izvestiia Akademii nauk. Seriia biologicheskaia},
volume = {},
number = {5},
pages = {511-517},
pmid = {22117417},
issn = {1026-3470},
mesh = {Animals ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; *Genetic Variation ; Haplotypes/genetics ; Kazakhstan ; Mitochondria/genetics ; Phylogeny ; *Polymorphism, Genetic ; Russia ; },
abstract = {Analysis the of cytochrome b gene (1140 b.p.) polymorphism and polymorphism of 79 specimens of the control region (934 b.p.) of mtDNA of the Siberian roe deer Capreolus pygargus from 23 regions of Russia and Kazakhstan has been carried out. The combined alignment of two fragments ofmitochondrial DNA revealed 36 haplotypes, which are distributed in three haplogroups. The net distance was 0.8, 1.3, and 1.3%. The specific pattern of haplogroups was described for roe deer of each region (Ural, trans-Ural, Eastern Siberia, Far East, Northeastern China). Unrelated haplogroups were found in populations of the Urals and Siberia. The variation pattern and spatial distribution of mitochondrial lines allowed us to suggest that a haplogroup that initially belongs to C. p. tianschanicus occurs secondarily in C. p. pygargus.},
}
@article {pmid22124893,
year = {2012},
author = {Rupwate, SD and Rajasekharan, R},
title = {C2 domain is responsible for targeting rice phosphoinositide specific phospholipase C.},
journal = {Plant molecular biology},
volume = {78},
number = {3},
pages = {247-258},
pmid = {22124893},
issn = {1573-5028},
mesh = {Amino Acid Sequence ; Base Sequence ; Calcium Signaling ; Catalytic Domain/genetics ; Conserved Sequence ; DNA, Plant/genetics ; Genes, Plant ; Models, Molecular ; Molecular Sequence Data ; Oryza/*enzymology/genetics ; Phosphoinositide Phospholipase C/*chemistry/genetics/*metabolism ; Phylogeny ; Plant Proteins/*chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Structural Homology, Protein ; },
abstract = {Phosphoinositide-specific phospholipase C (PLC) is involved in Ca[2+] mediated signalling events that lead to altered cellular status. Using various sequence-analysis methods, we identified two conserved motifs in known PLC sequences. The identified motifs are located in the C2 domain of plant PLCs and are not found in any other protein. These motifs are specifically found in the Ca[2+] binding loops and form adjoining beta strands. Further, we identified certain conserved residues that are highly distinct from corresponding residues of animal PLCs. The motifs reported here could be used to annotate plant-specific phospholipase C sequences. Furthermore, we demonstrated that the C2 domain alone is capable of targeting PLC to the membrane in response to a Ca[2+] signal. We also showed that the binding event results from a change in the hydrophobicity of the C2 domain upon Ca[2+] binding. Bioinformatic analyses revealed that all PLCs from Arabidopsis and rice lack a transmembrane domain, myristoylation and GPI-anchor protein modifications. Our bioinformatic study indicates that plant PLCs are located in the cytoplasm, the nucleus and the mitochondria. Our results suggest that there are no distinct isoforms of plant PLCs, as have been proposed to exist in the soluble and membrane associated fractions. The same isoform could potentially be present in both subcellular fractions, depending on the calcium level of the cytosol. Overall, these data suggest that the C2 domain of PLC plays a vital role in calcium signalling.},
}
@article {pmid22140228,
year = {2012},
author = {Burstein, D and Gould, SB and Zimorski, V and Kloesges, T and Kiosse, F and Major, P and Martin, WF and Pupko, T and Dagan, T},
title = {A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis.},
journal = {Eukaryotic cell},
volume = {11},
number = {2},
pages = {217-228},
pmid = {22140228},
issn = {1535-9786},
mesh = {Amino Acid Sequence ; *Artificial Intelligence ; Genes, Protozoan ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Protozoan Proteins/*chemistry/genetics/metabolism ; Sequence Alignment ; Trichomonas vaginalis/*metabolism ; },
abstract = {The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, the most widespread nonviral sexually transmitted disease in humans. It possesses hydrogenosomes-anaerobic mitochondria that generate H(2), CO(2), and acetate from pyruvate while converting ADP to ATP via substrate-level phosphorylation. T. vaginalis hydrogenosomes lack a genome and translation machinery; hence, they import all their proteins from the cytosol. To date, however, only 30 imported proteins have been shown to localize to the organelle. A total of 226 nuclear-encoded proteins inferred from the genome sequence harbor a characteristic short N-terminal presequence, reminiscent of mitochondrial targeting peptides, which is thought to mediate hydrogenosomal targeting. Recent studies suggest, however, that the presequences might be less important than previously thought. We sought to identify new hydrogenosomal proteins within the 59,672 annotated open reading frames (ORFs) of T. vaginalis, independent of the N-terminal targeting signal, using a machine learning approach. Our training set included 57 gene and protein features determined for all 30 known hydrogenosomal proteins and 576 nonhydrogenosomal proteins. Several classifiers were trained on this set to yield an import score for all proteins encoded by T. vaginalis ORFs, predicting the likelihood of hydrogenosomal localization. The machine learning results were tested through immunofluorescence assay and immunodetection in isolated cell fractions of 14 protein predictions using hemagglutinin constructs expressed under the homologous SCSα promoter in transiently transformed T. vaginalis cells. Localization of 6 of the 10 top predicted hydrogenosome-localized proteins was confirmed, and two of these were found to lack an obvious N-terminal targeting signal.},
}
@article {pmid22143034,
year = {2012},
author = {Kang, GZ and Peng, HF and Han, QX and Wang, YH and Guo, TC},
title = {Identification and expression pattern of ribosomal L5 gene in common wheat (Triticum aestivum L.).},
journal = {Gene},
volume = {493},
number = {1},
pages = {62-68},
doi = {10.1016/j.gene.2011.11.023},
pmid = {22143034},
issn = {1879-0038},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Genes, Plant ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; Stress, Psychological ; Triticum/*genetics ; },
abstract = {The full-length cDNA sequence (1158 bp) encoding a ribosomal L5 protein, designated as TaL5, was firstly isolated from common wheat (Triticum aestivum L.) using the rapid amplification of cDNA ends method (RACE). The open reading frame (ORF) of TaL5 gene was 906 bp, and its deduced amino acid sequence (301 residues) shared high similarity to those of other higher plant L5 proteins. TaL5 protein contained a putative 5S binding region (74 amino acids). TaL5 DNA sequence was further cloned, and sequence analysis showed that it contained 7 introns and 8 exons. Predicated using TargetP software, TaL5 protein was putatively located in mitochondria and contains a transit peptide of 12 amino acids. During grain filling period, temporal expression pattern of TaL5 gene was approximately consistent with the rates of starch accumulation in grains. Additionally, TaL5 gene was dramatically induced by salt, drought and freezing stresses, exogenous abscisic acid (ABA) and salicylic acid (SA) in wheat seedlings. These implied that TaL5 gene could function in growth, development and abiotic stresses in wheat plants.},
}
@article {pmid22173057,
year = {2012},
author = {M Santos, J and Graindorge, A and Soldati-Favre, D},
title = {New insights into parasite rhomboid proteases.},
journal = {Molecular and biochemical parasitology},
volume = {182},
number = {1-2},
pages = {27-36},
doi = {10.1016/j.molbiopara.2011.11.010},
pmid = {22173057},
issn = {1872-9428},
mesh = {Animals ; Apicomplexa/chemistry/classification/*enzymology ; Catalytic Domain ; Cell Membrane/chemistry/enzymology ; Enzyme Activation ; Membrane Proteins/chemistry ; Mitochondria/chemistry ; Mitochondrial Proteins/chemistry ; Peptide Hydrolases/*chemistry ; Phylogeny ; Protozoan Proteins/*chemistry/classification ; *Signal Transduction ; Substrate Specificity ; },
abstract = {The rhomboid-like proteins constitute a large family of intramembrane serine proteases that are present in all branches of life. First studied in Drosophila, these enzymes catalyse the release of the active forms of proteins from the membrane and hence trigger signalling events. In protozoan parasites, a limited number of rhomboid-like proteases have been investigated and some of them are associated to pathogenesis. In Apicomplexans, rhomboid-like protease activity is involved in shedding adhesins from the surface of the zoites during motility and host cell entry. Recently, a Toxoplasma gondii rhomboid was also implicated in an intracellular signalling mechanism leading to parasite proliferation. In Entamoeba histolytica, the capacity to adhere to host cells and to phagocytose cells is potentiated by a rhomboid-like protease. Survey of a small number of protozoan parasite genomes has uncovered species-specific rhomboid-like protease genes, many of which are predicted to encode inactive enzymes. Functional investigation of the rhomboid-like proteases in other protozoan parasites will likely uncover novel and unexpected implications for this family of proteases.},
}
@article {pmid22174774,
year = {2011},
author = {Hirst, MB and Kita, KN and Dawson, SC},
title = {Uncultivated microbial eukaryotic diversity: a method to link ssu rRNA gene sequences with morphology.},
journal = {PloS one},
volume = {6},
number = {12},
pages = {e28158},
pmid = {22174774},
issn = {1932-6203},
support = {R01 AI077571/AI/NIAID NIH HHS/United States ; T32 GM007377/GM/NIGMS NIH HHS/United States ; 3R01AI077571-01A1S1/AI/NIAID NIH HHS/United States ; },
mesh = {Actin Cytoskeleton/metabolism ; Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Cilia/metabolism ; Eukaryota/*cytology/*genetics ; Genes, rRNA/*genetics ; Hydrogen/metabolism ; In Situ Hybridization, Fluorescence ; Microtubules/metabolism ; Mitochondria/metabolism ; Phylogeny ; RNA, Ribosomal/*genetics ; Ribosome Subunits, Small/*genetics ; Staining and Labeling ; },
abstract = {Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA "phylotypes" from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH) with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of novel lineages, identified in diverse environments.},
}
@article {pmid22174833,
year = {2011},
author = {Sokolowski, B and Orchard, S and Harvey, M and Sridhar, S and Sakai, Y},
title = {Conserved BK channel-protein interactions reveal signals relevant to cell death and survival.},
journal = {PloS one},
volume = {6},
number = {12},
pages = {e28532},
pmid = {22174833},
issn = {1932-6203},
support = {R01 DC004295/DC/NIDCD NIH HHS/United States ; FP7-HEALTH-2007-223411/FP/OFP OASH HHS/United States ; R01DC004295/DC/NIDCD NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Cell Death ; Cell Survival ; Chickens ; Cochlea/*cytology ; Conserved Sequence ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Immunoprecipitation ; Large-Conductance Calcium-Activated Potassium Channels/chemistry/*metabolism ; Mice ; Molecular Sequence Data ; Phylogeny ; Prohibitins ; Protein Binding ; Protein Interaction Maps ; Protein Transport ; RNA, Small Interfering/metabolism ; *Signal Transduction ; Species Specificity ; Subcellular Fractions/metabolism ; },
abstract = {The large-conductance Ca(2+)-activated K(+) (BK) channel and its β-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and to reveal putative BK functions, we undertook a systems analysis of BK and BK-Associated Proteins (BKAPS) in the chicken cochlea and compared these results to other species. We identified 110 putative partners from cytoplasmic and membrane/cytoskeletal fractions, using a combination of coimmunoprecipitation, 2-D gel, and LC-MS/MS. Partners included 14-3-3γ, valosin-containing protein (VCP), stathmin (STMN), cortactin (CTTN), and prohibitin (PHB), of which 16 partners were verified by reciprocal coimmunoprecipitation. Bioinformatics revealed binary partners, the resultant interactome, subcellular localization, and cellular processes. The interactome contained 193 proteins involved in 190 binary interactions in subcellular compartments such as the ER, mitochondria, and nucleus. Comparisons with mice showed shared hub proteins that included N-methyl-D-aspartate receptor (NMDAR) and ATP-synthase. Ortholog analyses across six species revealed conserved interactions involving apoptosis, Ca(2+) binding, and trafficking, in chicks, mice, and humans. Functional studies using recombinant BK and RNAi in a heterologous expression system revealed that proteins important to cell death/survival, such as annexinA5, γ-actin, lamin, superoxide dismutase, and VCP, caused a decrease in BK expression. This revelation led to an examination of specific kinases and their effectors relevant to cell viability. Sequence analyses of the BK C-terminus across 10 species showed putative binding sites for 14-3-3, RAC-α serine/threonine-protein kinase 1 (Akt), glycogen synthase kinase-3β (GSK3β) and phosphoinositide-dependent kinase-1 (PDK1). Knockdown of 14-3-3 and Akt caused an increase in BK expression, whereas silencing of GSK3β and PDK1 had the opposite effect. This comparative systems approach suggests conservation in BK function across different species in addition to novel functions that may include the initiation of signals relevant to cell death/survival.},
}
@article {pmid22178219,
year = {2012},
author = {Skonieczna, K and Malyarchuk, BA and Grzybowski, T},
title = {The landscape of mitochondrial DNA variation in human colorectal cancer on the background of phylogenetic knowledge.},
journal = {Biochimica et biophysica acta},
volume = {1825},
number = {2},
pages = {153-159},
doi = {10.1016/j.bbcan.2011.11.004},
pmid = {22178219},
issn = {0006-3002},
mesh = {Colorectal Neoplasms/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Neoplasm/*genetics ; Genetic Variation ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/pathology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Recently, an increasing number of studies indicate that mutations in mitochondrial genome may contribute to cancer development or metastasis. Hence, it is important to determine whether the mitochondrial DNA might be a good, clinically applicable marker of cancer. This review describes hereditary as well as somatic mutations reported in mitochondrial DNA of colorectal cancer cells. We showed here that the entire mitochondrial genome mutational spectra are different in colorectal cancer and non-tumor cells. We also placed the described mutations on the phylogenetic context, which highlighted the recurrent problem of data quality. Therefore, the most important rules for adequately assessing the quality of mitochondrial DNA sequence analysis in cancer have been summarized. As follows from this review, neither the reliable spectrum of mtDNA somatic mutations nor the association between hereditary mutations and colorectal cancer risk have been resolved. This indicates that only high resolution studies on mtDNA variability, followed by a proper data interpretation employing phylogenetic knowledge may finally verify the utility of mtDNA sequence (if any) in clinical practice.},
}
@article {pmid22187346,
year = {2012},
author = {Mao, HT and Wang, DH and Lan, Z and Zhou, H and Yang, WX},
title = {Gene expression profiles of prohibitin in testes of Octopus tankahkeei (ot-phb) revealing its possible role during spermiogenesis.},
journal = {Molecular biology reports},
volume = {39},
number = {5},
pages = {5519-5528},
pmid = {22187346},
issn = {1573-4978},
mesh = {Animals ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Male ; Models, Molecular ; Molecular Sequence Data ; Octopodiformes/*genetics/growth &amp; development ; Phylogeny ; Prohibitins ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Spermatogenesis/*genetics ; Testis/*metabolism ; Time Factors ; Xenopus Proteins ; },
abstract = {Prohibitin is essential for intracellular homeostasis and stabilization of mitochondrial respiratory chain complexes. To explore its functions during spermiogenesis of Octopus tankahkeei (O. tankahkeei), we have cloned and sequenced the cDNA of this mammalian PHB homologue (termed ot-PHB) from the testes of O. tankahkeei. The 1165 bp ot-phb cDNA contains a 100 bp 5' UTR, a 882 bp open reading frame and a 183 bp 3' UTR. The putative ot-PHB protein owns a transmembrane domain from 6 to 31 amino acid (aa) and a putative PHB domain from 26 to 178 aa. Protein alignment demonstrated that ot-PHB had 73.3, 73.6, 74.0, 75.1, and 45.4% identity with its homologues in Homo sapiens, Mus muculus, Danio rerio, Xenopus tropicalis and Trypanosoma brucei, respectively. Tissue distribution profile analysis revealed its presence in all the tissues examined. In situ hybridization in spermiogenic cells demonstrated that ot-phb was expressed moderately at the beginning of the spermiogenesis. The abundance of transcripts increased in intermediate spermatids and in drastically remodeling final spermatids. In mature spermatozoa, the residuary transcripts concentrated around the chondriosomal mantle where mitochondria assemble around. In summary, the expression of ot-phb during spermiogenesis implicates a potential function of this protein during mitochondrial ubiquitination. It is the first time to implicate the role of prohibitin in cephalopod spermiogenesis.},
}
@article {pmid22192748,
year = {2011},
author = {Li, S and Rousseau, D},
title = {[ATAD3, a vital membrane-bound mitochondrial ATPase involved in tumor progression].},
journal = {Medecine sciences : M/S},
volume = {27},
number = {12},
pages = {1089-1095},
doi = {10.1051/medsci/20112712015},
pmid = {22192748},
issn = {0767-0974},
mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/genetics/metabolism/*physiology ; Animals ; Disease Progression ; Humans ; Membrane Proteins/genetics/metabolism/*physiology ; Mitochondrial Membranes/enzymology/metabolism/physiology ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Models, Biological ; Neoplasms/*genetics/metabolism/*pathology ; Phylogeny ; Primates ; },
abstract = {ATAD3 (ATPase family AAA domain-containing protein 3) is a mitochondrial membrane bound ATPase whose function has not yet been discovered but its role is essential for the embryonic development. The ATAD3 gene exists since the pluri-cellular organisms with specialized tissues and remains unique until vertebrates. In primates and humans, two other genes have appeared (called ATAD3B and ATAD3C versus ATAD3A the ancestral gene). ATAD3 knock down in different non-transformed cell lines is associated with drastic changes in the mitochondrial network, inhibition of proliferation and modification of the functional interactions between mitochondria and endoplasmic reticulum. However, the analysis of the functions of ATAD3A and ATAD3B in different human cancer cell lines shows on the contrary that they can have anti-proliferative effects and induce chemoresistant properties. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular -organization and involved in tumorigenesis.},
}
@article {pmid22203571,
year = {2011},
author = {Choi, YJ and Thines, M and Han, JG and Shin, HD},
title = {Mitochondrial phylogeny reveals intraspecific variation in Peronospora effusa, the spinach downy mildew pathogen.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {49},
number = {6},
pages = {1039-1043},
pmid = {22203571},
issn = {1976-3794},
mesh = {*Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; Peronospora/*classification/genetics/*isolation &amp; purification ; *Phylogeny ; Plant Diseases/*parasitology ; Spinacia oleracea/*parasitology ; },
abstract = {Since about two hundred years, downy mildew caused by Peronospora effusa is probably the most economically important disease of spinach (Spinacia oleracea). However, there is no information on the global phylogeographic structure of the pathogen and thus it is unclear whether a single genotype occurs worldwide or whether some local genetic variation exists. To investigate the genetic variability of this pathogen, a sequence analysis of two partial mitochondrial DNA genes, cox2 and nad1, was carried out. Thirty-three specimens of Peronospora effusa from four continents were analyzed, including samples from Australia, China, Japan, Korea, Mexico, Russia, Sweden, and the USA. Despite the potential anthropogenic admixture of genotypes, a phylogeographic pattern was observed, which corresponds to two major groups, an Asian/Oceanian clade and another group, which includes American/European specimens. Notably, two of six Japanese specimens investigated did not belong to the Asian/Oceanian clade, but were identical to three of the specimens from the USA, suggestive of a recent introduction from the USA to Japan. As similar introduction events may be occurring as a result of the globalised trade with plant and seed material, a better knowledge of the phylogeographic distribution of pathogens is highly warranted for food security purposes.},
}
@article {pmid22209780,
year = {2012},
author = {Halsne, R and Esbensen, Y and Wang, W and Scheffler, K and Suganthan, R and Bjørås, M and Eide, L},
title = {Lack of the DNA glycosylases MYH and OGG1 in the cancer prone double mutant mouse does not increase mitochondrial DNA mutagenesis.},
journal = {DNA repair},
volume = {11},
number = {3},
pages = {278-285},
doi = {10.1016/j.dnarep.2011.12.001},
pmid = {22209780},
issn = {1568-7856},
mesh = {Animals ; Cell Respiration/genetics ; DNA Damage/genetics ; DNA Glycosylases/*deficiency/metabolism ; DNA, Mitochondrial/*genetics ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Mutagenesis/*genetics ; Mutation/*genetics ; Mutation Rate ; Neoplasms/*enzymology/*genetics ; Organ Specificity/genetics ; },
abstract = {Reactive oxygen species (ROS) are formed as natural byproducts during aerobic metabolism and readily induce premutagenic base lesions in the DNA. The 8-oxoguanine DNA glycosylase (OGG1) and MutY homolog 1 (MYH) synergistically prevent mutagenesis and cancer formation in mice. Their localization in the mitochondria as well as in the nucleus suggests that mutations in mitochondrial DNA (mtDNA) contribute to the carcinogenesis in the myh[-]/[-]/ogg1[-]/[-] double knockout mouse. In order to test this hypothesis, we analyzed mtDNA mutagenesis and mitochondrial function in young (1month) and adult (6months) wt and myh[-]/[-]/ogg1[-]/[-] mice. To our surprise, the absence of OGG1 and MYH had no impact on mtDNA mutation rates in these mice, even at the onset of cancer. This indicates that mtDNA mutagenesis is not responsible for the carcinogenesis of myh[-]/[-]/ogg1[-]/[-] mice. In line with these results, mitochondrial function was unaffected in the cancerous tissues liver and lung, whereas a significant reduction in respiration capacity was observed in brain mitochondria from the adult myh[-]/[-]/ogg1[-]/[-] mouse. The reduced respiration capacity correlated with a specific reduction (-25%) in complex I biochemical activity in brain mitochondria. Our results demonstrate that mtDNA mutations are not associated with cancer development in myh[-]/[-]/ogg1[-]/[-] mice, and that impairment of mitochondrial function in brain could be linked to nuclear DNA mutations in this strain. OGG1 and MYH appear to be dispensable for antimutator function in mitochondria.},
}
@article {pmid22214610,
year = {2012},
author = {Kalifa, L and Quintana, DF and Schiraldi, LK and Phadnis, N and Coles, GL and Sia, RA and Sia, EA},
title = {Mitochondrial genome maintenance: roles for nuclear nonhomologous end-joining proteins in Saccharomyces cerevisiae.},
journal = {Genetics},
volume = {190},
number = {3},
pages = {951-964},
pmid = {22214610},
issn = {1943-2631},
support = {F31 GM078700/GM/NIGMS NIH HHS/United States ; },
mesh = {Antigens, Nuclear/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair/*physiology ; DNA Repair ; DNA, Mitochondrial/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Endodeoxyribonucleases/genetics/metabolism ; Exodeoxyribonucleases/genetics/metabolism ; Gene Order ; Genome, Mitochondrial ; Ku Autoantigen ; Mitochondria/genetics/metabolism ; Models, Genetic ; Mutation Rate ; Nuclear Proteins/*metabolism ; Phenotype ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Deletion ; Signal Transduction ; },
abstract = {Mitochondrial DNA (mtDNA) deletions are associated with sporadic and inherited diseases and age-associated neurodegenerative disorders. Approximately 85% of mtDNA deletions identified in humans are flanked by short directly repeated sequences; however, mechanisms by which these deletions arise are unknown. A limitation in deciphering these mechanisms is the essential nature of the mitochondrial genome in most living cells. One exception is budding yeast, which are facultative anaerobes and one of the few organisms for which directed mtDNA manipulation is possible. Using this model system, we have developed a system to simultaneously monitor spontaneous direct-repeat-mediated deletions (DRMDs) in the nuclear and mitochondrial genomes. In addition, the mitochondrial DRMD reporter contains a unique KpnI restriction endonuclease recognition site that is not present in otherwise wild-type (WT) mtDNA. We have expressed KpnI fused to a mitochondrial localization signal to induce a specific mitochondrial double-strand break (mtDSB). Here we report that loss of the MRX (Mre11p, Rad50p, Xrs2p) and Ku70/80 (Ku70p, Ku80p) complexes significantly impacts the rate of spontaneous deletion events in mtDNA, and these proteins contribute to the repair of induced mtDSBs. Furthermore, our data support homologous recombination (HR) as the predominant pathway by which mtDNA deletions arise in yeast, and suggest that the MRX and Ku70/80 complexes are partially redundant in mitochondria.},
}
@article {pmid22222877,
year = {2012},
author = {Peris, D and Belloch, C and Lopandić, K and Álvarez-Pérez, JM and Querol, A and Barrio, E},
title = {The molecular characterization of new types of Saccharomyces cerevisiae×S. kudriavzevii hybrid yeasts unveils a high genetic diversity.},
journal = {Yeast (Chichester, England)},
volume = {29},
number = {2},
pages = {81-91},
doi = {10.1002/yea.2891},
pmid = {22222877},
issn = {1097-0061},
mesh = {Base Sequence ; Chimera ; DNA, Fungal/genetics ; Electron Transport Complex IV/genetics ; Fungal Proteins/genetics ; *Genetic Variation ; Genome, Fungal/*genetics ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Saccharomyces/*genetics ; Saccharomyces cerevisiae/classification/*genetics ; Sequence Analysis, DNA ; Wine/microbiology ; },
abstract = {New double- and triple-hybrid Saccharomyces yeasts were characterized using PCR-restriction fragment length polymorphism of 35 nuclear genes, located on different chromosome arms, and the sequencing of one nuclear and one mitochondrial gene. Most of these new hybrids were originally isolated from fermentations; however, two of them correspond to clinical and dietary supplement isolates. This is the first time that the presence of double-hybrid S. cerevisiae×S. kudriavzevii in non-fermentative substrates has been reported and investigated. Phylogenetic analysis of the MET6 nuclear gene confirmed the double or triple parental origin of the new hybrids. Restriction analysis of gene regions in these hybrids revealed a high diversity of genome types. From these molecular characterizations, a reduction of the S. kudriavzevii fraction of the hybrid genomes is observed in most hybrids. Mitochondrial inheritance in hybrids was deduced from the analysis of mitochondrial COX2 gene sequences, which showed that most hybrids received the mitochondrial genome from the S. kudriavzevii parent. However, two strains inherited a S. cerevisiae COX2, being the first report of S. cerevisiae×S. kudriavzevii hybrids with S. cerevisiae mitochondrial genomes. These two strains are those showing a higher S. kudriavzevii nuclear genome reduction, especially in the wine hybrid AMH. This may be due to the release of selective pressures acting on the other hybrids to maintain kudriavzevii mitochondria-interacting genes.},
}
@article {pmid22227114,
year = {2012},
author = {Otranto, D and Latrofa, MS and Brianti, E and Annoscia, G and Parisi, A and Dantas-Torres, F and Bain, O and Gasser, RB},
title = {An assessment of genetic variability in the mitochondrial cytochrome c oxidase subunit 1 gene of Cercopithifilaria sp. (Spirurida, Onchocercidae) from dog and Rhipicephalus sanguineus populations.},
journal = {Molecular and cellular probes},
volume = {26},
number = {2},
pages = {81-89},
doi = {10.1016/j.mcp.2011.12.002},
pmid = {22227114},
issn = {1096-1194},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Dog Diseases/*parasitology ; Dogs ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Greece ; Haplotypes ; Italy ; Mediterranean Region ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Onchocerca/enzymology/*genetics ; Onchocerciasis/parasitology/*veterinary ; Phylogeny ; Phylogeography ; Protein Subunits/*genetics ; Rhipicephalus sanguineus/*parasitology ; Sequence Analysis, DNA ; Skin/parasitology ; Spain ; },
abstract = {This study investigates sequence variation in mitochondrial cytochrome c oxidase subunit 1 gene within Cercopithifilaria sp. recorded recently in Italy. Fourteen sequence types (haplotypes) were characterized for 163 (7.7%) amplicons from 2111 Genomic DNA samples prepared from skin samples from dogs and from Rhipicephalus sanguineus (ticks) from different geographical areas of the Mediterranean basin (i.e., Italy, Spain and Greece). The most prevalent sequence types represented haplotypes I (70.5%) and X (16.0%), followed by haplotype VIII (4.9%) and other 11 haplotypes (8.6%). Three haplotypes (II, V and VI) were found exclusively in ticks. The overall intraspecific nucleotide variation among pcox1 haplotypes ranged from 0.4 to 3.5% (mean = 1.6%), whereas a mean interspecific difference of 9.5% was detected as compared with other onchocercids. Phylogenetic analysis of the nucleotide sequence data showed a clustering of Cercopithifilaria sp. with the other Cercopithifilaria species (with strong statistical support) to the exclusion of other onchocercids. The number of haplotypes identified here might be explained by complex ecology and transmission patterns as well as the high mutation rate of mitochondrial DNA and/or inbreeding associated with hosts and their vectors.},
}
@article {pmid22236206,
year = {2012},
author = {Luévano-Martínez, LA and Barba-Ostria, C and Araiza-Olivera, D and Chiquete-Félix, N and Guerrero-Castillo, S and Rial, E and Georgellis, D and Uribe-Carvajal, S},
title = {A critical tyrosine residue determines the uncoupling protein-like activity of the yeast mitochondrial oxaloacetate carrier.},
journal = {The Biochemical journal},
volume = {443},
number = {1},
pages = {317-325},
doi = {10.1042/BJ20110992},
pmid = {22236206},
issn = {1470-8728},
mesh = {Amino Acid Motifs ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Hydrogen-Ion Concentration ; Linoleic Acid/pharmacology/physiology ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Oxaloacetic Acid/metabolism ; Phylogeny ; Point Mutation ; Protons ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Sulfates/metabolism ; Yarrowia/*genetics ; },
abstract = {The mitochondrial Oac (oxaloacetate carrier) found in some fungi and plants catalyses the uptake of oxaloacetate, malonate and sulfate. Despite their sequence similarity, transport specificity varies considerably between Oacs. Indeed, whereas ScOac (Saccharomyces cerevisiae Oac) is a specific anion-proton symporter, the YlOac (Yarrowia lipolytica Oac) has the added ability to transport protons, behaving as a UCP (uncoupling protein). Significantly, we identified two amino acid changes at the matrix gate of YlOac and ScOac, tyrosine to phenylalanine and methionine to leucine. We studied the role of these amino acids by expressing both wild-type and specifically mutated Oacs in an Oac-null S. cerevisiae strain. No phenotype could be associated with the methionine to leucine substitution, whereas UCP-like activity was dependent on the presence of the tyrosine residue normally expressed in the YlOac, i.e. Tyr-ScOac mediated proton transport, whereas Phe-YlOac lost its protonophoric activity. These findings indicate that the UCP-like activity of YlOac is determined by the tyrosine residue at position 146.},
}
@article {pmid22237536,
year = {2012},
author = {Horn, S},
title = {Case study: enrichment of ancient mitochondrial DNA by hybridization capture.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {840},
number = {},
pages = {189-195},
doi = {10.1007/978-1-61779-516-9_22},
pmid = {22237536},
issn = {1940-6029},
mesh = {Animals ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; *Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {In ancient DNA studies focusing on estimating population histories, genetic markers are sequenced from a large number of samples belonging to the same species. Targeting loci of interest using traditional PCR can be time-consuming, in particular when samples are not well preserved and multiple overlapping fragments are required. Here, I describe the process of generating DNA libraries from ancient DNA (aDNA) extracts for high-throughput sequencing. I use a serial in-solution DNA hybridization approach with subsequent bead capture to enrich libraries for the target locus, in this case the mitochondrial control region of ancient beavers (Castor fiber). The resulting sequencing reads are run through quality control filters to obtain reliable consensus sequences. Using these sequences, I construct a phylogenetic tree, which agrees with previously published data regarding phylogeographic relationships among beavers.},
}
@article {pmid22238375,
year = {2012},
author = {Wanschers, BF and Szklarczyk, R and Pajak, A and van den Brand, MA and Gloerich, J and Rodenburg, RJ and Lightowlers, RN and Nijtmans, LG and Huynen, MA},
title = {C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation.},
journal = {Nucleic acids research},
volume = {40},
number = {9},
pages = {4040-4051},
pmid = {22238375},
issn = {1362-4962},
support = {096919/WT_/Wellcome Trust/United Kingdom ; BB/F011520/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Cell Line, Tumor ; Gene Knockdown Techniques ; Genes, Bacterial ; HEK293 Cells ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/chemistry/genetics/*physiology ; Molecular Sequence Data ; Nucleotides/metabolism ; Operon ; Phylogeny ; *Protein Biosynthesis ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/genetics/*physiology ; Ribosome Subunits, Large, Eukaryotic/*chemistry ; Sequence Analysis, DNA ; },
abstract = {In a comparative genomics study for mitochondrial ribosome-associated proteins, we identified C7orf30, the human homolog of the plant protein iojap. Gene order conservation among bacteria and the observation that iojap orthologs cannot be transferred between bacterial species predict this protein to be associated with the mitochondrial ribosome. Here, we show colocalization of C7orf30 with the large subunit of the mitochondrial ribosome using isokinetic sucrose gradient and 2D Blue Native polyacrylamide gel electrophoresis (BN-PAGE) analysis. We co-purified C7orf30 with proteins of the large subunit, and not with proteins of the small subunit, supporting interaction that is specific to the large mitoribosomal complex. Consistent with this physical association, a mitochondrial translation assay reveals negative effects of C7orf30 siRNA knock-down on mitochondrial gene expression. Based on our data we propose that C7orf30 is involved in ribosomal large subunit function. Sequencing the gene in 35 patients with impaired mitochondrial translation did not reveal disease-causing mutations in C7orf30.},
}
@article {pmid22248533,
year = {2012},
author = {Umasuthan, N and Revathy, KS and Lee, Y and Whang, I and Lee, J},
title = {Mitochondrial thioredoxin-2 from Manila clam (Ruditapes philippinarum) is a potent antioxidant enzyme involved in antibacterial response.},
journal = {Fish &amp; shellfish immunology},
volume = {32},
number = {4},
pages = {513-523},
doi = {10.1016/j.fsi.2011.12.010},
pmid = {22248533},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Antioxidants ; Base Sequence ; Bivalvia/*enzymology/*immunology/microbiology ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Enzymologic/*immunology ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Thioredoxins/genetics/*metabolism ; Transcription, Genetic/immunology ; },
abstract = {Thioredoxin (TRx) is a ubiquitous protein involved in the regulation of multiple biological processes. The TRx-2 isoform is exclusively expressed in mitochondria, where it contributes to mitochondrial redox state maintenance. In the present study, a novel thioredoxin-2 gene was identified in the Manila clam, Ruditapes philippinarum. The full-length sequence of RpTRx-2 (1561 bp) consists of a 498 bp coding region encoding a 166 amino acid protein. The N-terminal region of RpTRx-2 harbors a mitochondrial localization signal (56 amino acids), while the C-terminal portion contains the characteristic (89)WCGPC(93) catalytic active site. Phylogenetic analysis revealed that RpTRx-2 is closest to its ortholog from abalone. The broad distribution pattern of RpTRx-2 mRNA in healthy animal tissues implicates a generally significant function in normal clam physiology. The transcription level of RpTRx-2, however, is highest in hemocytes. Lipopolysaccharide and Vibrio tapetis bacterium caused up-regulation of the RpTrx-2 transcript levels in gill and hemocytes. Interestingly, clam manganese superoxide dismutase (MnSOD) mRNA levels in hemocytes elicited a corresponding response to these immune challenges. RpTRx-2 was recombinantly expressed in Escherichia coli BL21 (DE3) and used in insulin disulfide reduction assay as well as metal-catalyzed oxidation assay to elucidate its antioxidant property by reducing substrate and protecting super-coiled DNA from oxidative damage through free radical scavenging, respectively. Collectively, our data indicated that RpTRx-2, a mitochondrial TRx-2 family member, is an antioxidant enzyme that may be involved in antibacterial defense of clams.},
}
@article {pmid22275765,
year = {2012},
author = {Liu, Y and Moskwa, NL and Goffinet, B},
title = {Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses.},
journal = {American journal of botany},
volume = {99},
number = {2},
pages = {e62-5},
doi = {10.3732/ajb.1100402},
pmid = {22275765},
issn = {1537-2197},
mesh = {Base Sequence ; Bryophyta/classification/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Databases, Genetic ; Genetic Loci ; Genetic Markers ; INDEL Mutation ; Mitochondria/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {PREMISE OF THE STUDY: In comparison to the wide use of chloroplast markers, few mitochondrial markers are available for phylogenetic studies in bryophytes. We investigated the phylogenetic suitability of several mtDNA markers within the Funariaceae and across mosses.<br><br>METHODS AND RESULTS: By comparing mitochondrial genomes of two mosses, eight regions with higher substitution rates were identified and sequenced for three species in the Funariaceae and one outgroup taxon. Variations in the substitution rate of these new loci were compared to previously used markers. Thirty-four samples representing all major moss lineages were targeted to assess the universality of the newly designed primers.<br><br>CONCLUSIONS: The new markers provided similar or more sequence variations in Funariaceae compared to previously developed mtDNA markers. Five out of eight loci were amplified in 70% of other taxa, indicating that these markers may be suitable for phylogenetic studies in other moss lineages.},
}
@article {pmid22293155,
year = {2012},
author = {Nakajima, Y and Nishikawa, A and Iguchi, A and Sakai, K},
title = {The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals.},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {2},
pages = {527-531},
doi = {10.1016/j.ympev.2012.01.006},
pmid = {22293155},
issn = {1095-9513},
mesh = {Animals ; Anthozoa/*classification/*genetics ; Genetic Variation ; Genetics, Population ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species boundary of Acropora at the population level. These species are morphologically and ecologically similar but are reproductively isolated by differences of a few months in their spawning seasons. We could not distinguish these species using a phylogenetic analysis of the mitochondrial control region, as previously reported in other Acropora species. In contrast, a population genetic approach clearly distinguished these species both sympatrically and allopatrically. Our results suggest that recent speciation and shared ancestral polymorphisms could partly explain the para- and polyphyly of several Acropora species.},
}
@article {pmid22301089,
year = {2012},
author = {Yamane, K and Suzuki, Y and Tachi, E and Li, T and Chen, X and Nakao, M and Nkouawa, A and Yanagida, T and Sako, Y and Ito, A and Sato, H and Okamoto, M},
title = {Recent hybridization between Taenia asiatica and Taenia saginata.},
journal = {Parasitology international},
volume = {61},
number = {2},
pages = {351-355},
doi = {10.1016/j.parint.2012.01.005},
pmid = {22301089},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Genotype ; Heterozygote ; Humans ; Hybridization, Genetic/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Taenia/*classification/genetics/isolation &amp; purification ; Taenia saginata/*classification/genetics/isolation &amp; purification ; Taeniasis/*parasitology ; Tibet ; },
abstract = {Five Taenia tapeworms collected from humans in Tibetan Plateau, Sichuan, China, where three species of human Taenia are sympatrically endemic, were examined for the mitochondrial cox1 gene and two nuclear genes, ef1 and elp. Phylogenetic analyses of these genes revealed that two adult worms showed nuclear-mitochondrial discordance, suggesting that they originated from hybridization between Taenia saginata and Taenia asiatica. One of two worms had T. asiatica-type mtDNA, whereas another worm had T. saginata-type mtDNA, indicating that reciprocal hybridization between T. saginata and T. asiatica could occur. The worm having T. asiatica-type mtDNA was heterozygous at both nuclear loci with T. saginata-type alleles and T. asiatica-type alleles. In another worm, the ef1 locus was heterozygous with a T. saginata-type alleles and T. asiatica-type alleles, while the elp locus was homozygous with T. saginata-type alleles. Self-fertilization is the main reproductive method of the genus Taenia. Since self-fertilization represents a type of inbreeding, each locus in the offspring would become homozygous over generations with genetic drift. The fact that some nuclear loci are still heterozygous means that hybridization might have occurred recently. Hybridization between T. asiatica and T. saginata is probably an ongoing event in many areas in which they are sympatrically endemic.},
}
@article {pmid22306043,
year = {2012},
author = {Gaya, E and Högnabba, F and Holguin, A and Molnar, K and Fernández-Brime, S and Stenroos, S and Arup, U and Søchting, U and Van den Boom, P and Lücking, R and Sipman, HJ and Lutzoni, F},
title = {Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {2},
pages = {374-387},
doi = {10.1016/j.ympev.2012.01.012},
pmid = {22306043},
issn = {1095-9513},
mesh = {Ascomycota/*classification/*genetics ; Base Sequence ; Genetic Variation ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA/genetics ; RNA Polymerase II/genetics ; RNA, Fungal/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity--the Megalosporaceae--which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data.},
}
@article {pmid22309213,
year = {2012},
author = {Scott, I and Webster, BR and Li, JH and Sack, MN},
title = {Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1.},
journal = {The Biochemical journal},
volume = {443},
number = {3},
pages = {655-661},
pmid = {22309213},
issn = {1470-8728},
support = {ZIA HL006047/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Acetylation ; Acetyltransferases/*metabolism ; Animals ; Gene Knockdown Techniques ; Humans ; Immunoprecipitation ; Mice ; Mitochondria/*enzymology ; Nerve Tissue Proteins/genetics/metabolism/*physiology ; Oxidative Stress ; Phylogeny ; Sirtuin 3/physiology ; },
abstract = {SIRT3 (sirtuin 3) modulates respiration via the deacetylation of lysine residues in electron transport chain proteins. Whether mitochondrial protein acetylation is controlled by a counter-regulatory program has remained elusive. In the present study we identify an essential component of this previously undefined mitochondrial acetyltransferase system. We show that GCN5L1 [GCN5 (general control of amino acid synthesis 5)-like 1; also known as Bloc1s1] counters the acetylation and respiratory effects of SIRT3. GCN5L1 is mitochondrial-enriched and displays significant homology with a prokaryotic acetyltransferase. Genetic knockdown of GCN5L1 blunts mitochondrial protein acetylation, and its reconstitution in intact mitochondria restores protein acetylation. GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain targets and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics. The results of the present study identify GCN5L1 as a critical prokaryote-derived component of the mitochondrial acetyltransferase programme.},
}
@article {pmid22311013,
year = {2012},
author = {Zhang, M and Nie, X and Cao, T and Wang, J and Li, T and Zhang, X and Guo, Y and Ma, E and Zhong, Y},
title = {The complete mitochondrial genome of the butterfly Apatura metis (Lepidoptera: Nymphalidae).},
journal = {Molecular biology reports},
volume = {39},
number = {6},
pages = {6529-6536},
pmid = {22311013},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Butterflies/*genetics ; Gene Order ; Genes, Insect ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Likelihood Functions ; Locus Control Region ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer's purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif 'ATAGA' and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.},
}
@article {pmid22315334,
year = {2012},
author = {Takeuchi, T and Kawashima, T and Koyanagi, R and Gyoja, F and Tanaka, M and Ikuta, T and Shoguchi, E and Fujiwara, M and Shinzato, C and Hisata, K and Fujie, M and Usami, T and Nagai, K and Maeyama, K and Okamoto, K and Aoki, H and Ishikawa, T and Masaoka, T and Fujiwara, A and Endo, K and Endo, H and Nagasawa, H and Kinoshita, S and Asakawa, S and Watabe, S and Satoh, N},
title = {Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {19},
number = {2},
pages = {117-130},
pmid = {22315334},
issn = {1756-1663},
mesh = {Alleles ; Animals ; Chromosome Mapping ; Chromosomes/genetics ; DNA, Complementary/genetics/*isolation &amp; purification ; Expressed Sequence Tags ; *Genome ; Mitochondria/genetics ; Multigene Family ; Phylogeny ; Pinctada/classification/*genetics ; Sequence Analysis, DNA ; Tandem Repeat Sequences ; Transcription Factors/genetics ; Transcriptome ; },
abstract = {The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ~1150-Mb genome at ~40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.},
}
@article {pmid22317974,
year = {2012},
author = {Chen, H and Zheng, J and Xue, L and Meng, Y and Wang, Y and Zheng, B and Fang, F and Shi, S and Qiu, Q and Jiang, P and Lu, Z and Mo, JQ and Lu, J and Guan, MX},
title = {The 12S rRNA A1555G mutation in the mitochondrial haplogroup D5a is responsible for maternally inherited hypertension and hearing loss in two Chinese pedigrees.},
journal = {European journal of human genetics : EJHG},
volume = {20},
number = {6},
pages = {607-612},
pmid = {22317974},
issn = {1476-5438},
support = {R01 DC007696/DC/NIDCD NIH HHS/United States ; R01DC07696/DC/NIDCD NIH HHS/United States ; },
mesh = {Adult ; Aged ; Asian People/genetics ; Base Sequence ; DNA, Mitochondrial/chemistry ; Female ; Hearing Loss/*ethnology/*genetics ; Humans ; Hypertension/*ethnology/*genetics ; Male ; Middle Aged ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Mutation ; Pedigree ; Phenotype ; Phylogeny ; RNA, Ribosomal/*genetics/metabolism ; },
abstract = {We reported here clinical, genetic evaluations and molecular analysis of mitochondrial DNA (mtDNA) in two Han Chinese families carrying the known mitochondrial 12S rRNA A1555G mutation. In contrast with the previous data that hearing loss as a sole phenotype was present in the maternal lineage of other families carrying the A1555G mutation, matrilineal relatives among these two Chinese families exhibited both hearing loss and hypertension. Of 21 matrilineal relatives, 9 subjects exhibited both hearing loss and hypertension, 2 individuals suffered from only hypertension and 1 member had only hearing loss. The average age at onset of hypertension in the affected matrilineal relatives of these families was 60 and 46 years, respectively, whereas those of hearing loss in these two families were 33 and 55 years, respectively. Molecular analysis of their mtDNA identified distinct sets of variants belonging to the Eastern Asian haplogroup D5a. In contrast, the A1555G mutation occurred among other mtDNA haplogroups D, B, R, F, G, Y, M and N, respectively. Our data further support that the A1555G mutation is necessary but by itself insufficient to produce the clinical phenotype. The other modifiers are responsible for the phenotypic variability of matrilineal relatives within and among these families carrying the A1555G mutation. Our investigation provides the first evidence that the 12S rRNA A1555G mutation leads to both of hearing loss and hypertension. Thus, our findings may provide the new insights into the understanding of pathophysiology and valuable information for management and treatment of maternally inherited hearing loss and hypertension.},
}
@article {pmid22318359,
year = {2012},
author = {Li, S and Rousseau, D},
title = {ATAD3, a vital membrane bound mitochondrial ATPase involved in tumor progression.},
journal = {Journal of bioenergetics and biomembranes},
volume = {44},
number = {1},
pages = {189-197},
pmid = {22318359},
issn = {1573-6881},
mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/*genetics/*metabolism ; Amino Acid Sequence ; Base Sequence ; Cell Line, Tumor ; Cell Transformation, Neoplastic/*genetics ; Enzyme-Linked Immunosorbent Assay ; Fluorescent Antibody Technique ; Gene Components ; Humans ; Membrane Proteins/*genetics/*metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology ; Species Specificity ; },
abstract = {ATAD3 (ATPase family AAA Domain-containing protein 3) is a mitochondrial membrane bound ATPase whose function has not yet been discovered but its role is essential for embryonic development. The ATAD3 gene has existed since the pluri-cellular organisms with specialized tissues and has remained unique until vertebrates. In primates and human, two other genes have appeared (called ATAD3B and ATAD3C versus ATAD3A the ancestral gene). ATAD3 knock-down in different non-transformed cell lines is associated with drastic changes in the mitochondrial network, inhibition of proliferation and modification of the functional interactions between mitochondria and endoplasmic reticulum. However, the analysis of the cellular properties of ATAD3A and ATAD3B in different human cancer cell lines shows on the contrary that they can present anti-proliferative and chemoresistant properties. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular organization and involved in tumorigenesis.},
}
@article {pmid22326838,
year = {2012},
author = {Doucet-Beaupré, H and Blier, PU and Chapman, EG and Piontkivska, H and Dufresne, F and Sietman, BE and Mulcrone, RS and Hoeh, WR},
title = {Pyganodon (Bivalvia: Unionoida: Unionidae) phylogenetics: a male- and female-transmitted mitochondrial DNA perspective.},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {2},
pages = {430-444},
doi = {10.1016/j.ympev.2012.01.017},
pmid = {22326838},
issn = {1095-9513},
mesh = {Animals ; Base Sequence ; Cyclooxygenase 1/genetics ; Cyclooxygenase 2/genetics ; DNA, Mitochondrial/*genetics ; Female ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genetic Variation ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sex Determination Processes/genetics ; Unionidae/*classification/*genetics ; },
abstract = {Species boundaries, evolutionary relationships and geographic distributions of many unionoid bivalve species, like those in the genus Pyganodon, remain unresolved in Eastern North America. Because unionoid bivalves are one of the most imperiled groups of animals in the world, understanding the genetic variation within and among populations as well as among species is crucial for effective conservation planning. Conservation of unionoid species is indispensable from a freshwater habitat perspective but also because they possess a unique mitochondrial inheritance system where distinct gender-associated mitochondrial DNA lineages coexist: a female-transmitted (F) mt genome and a male-transmitted (M) mt genome that are involved in the maintenance of separate sexes (=dioecy). In this study, 42 populations of Pyganodon sp. were sampled across a large geographical range and fragments of two mitochondrial genes (cox1 and cox2) were sequenced from both the M- and F-transmitted mtDNA genomes. Our results support the recency of the divergence between P. cataracta and P. fragilis. We also found two relatively divergent F and M lineages within P. grandis. Surprisingly, the relationships among the P. grandis specimens in the F and M sequence trees are not congruent. We found that a single haplotype in P. lacustris has recently swept throughout the M genotype space leading to an unexpectedly low diversity in the M lineage in that species. Our survey put forward some challenging results that force us to rethink hybridization and species boundaries in the genus Pyganodon. As the M and F genomes do not always display the same phylogeographic story in each species, we also discuss the importance of being careful in the interpretation of molecular data based solely on maternal transmitted mtDNA genomes. The involvement of F and M genomes in unionoid bivalve sex determination likely played a role in the genesis of the unorthodox phylogeographic patterns reported herein.},
}
@article {pmid22331485,
year = {2012},
author = {Dubey, B and Meganathan, PR and Haque, I},
title = {Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).},
journal = {Molecular biology reports},
volume = {39},
number = {7},
pages = {7403-7412},
pmid = {22331485},
issn = {1573-4978},
mesh = {Adenosine Triphosphate/genetics ; Animals ; Base Sequence ; Boidae/*genetics ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Electron Transport Complex I/genetics ; Endangered Species ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.},
}
@article {pmid22337505,
year = {2012},
author = {Egan, SP and Hood, GR and Feder, JL and Ott, JR},
title = {Divergent host-plant use promotes reproductive isolation among cynipid gall wasp populations.},
journal = {Biology letters},
volume = {8},
number = {4},
pages = {605-608},
pmid = {22337505},
issn = {1744-957X},
mesh = {Adaptation, Biological ; Animals ; Body Size ; Copulation ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Female ; *Genetic Speciation ; Genetics, Population/methods ; Host-Parasite Interactions ; Male ; Mitochondria/genetics ; Plant Tumors/parasitology ; Quercus/*parasitology ; Reproduction ; *Reproductive Isolation ; Wasps/anatomy &amp; histology/genetics/*pathogenicity ; },
abstract = {Ecological speciation occurs when reproductive isolation evolves as a consequence of divergent natural selection among environments. A direct prediction of this process is that ecologically divergent pairs of populations will exhibit greater reproductive isolation than ecologically similar pairs of populations. By comparing allopatric populations of the cynipid gall wasp Belonocnema treatae infesting Quercus virginiana and Quercus geminata, we tested the role that divergent host use plays in generating ecological divergence and sexual isolation. We found differences in body size and gall structure associated with divergent host use, but no difference in neutral genetic divergence between populations on the same or different host plant. We observed significant assortative mating between populations from alternative host plants but not between allopatric populations on the same host plant. Thus, we provide evidence that divergent host use promotes speciation among gall wasp populations.},
}
@article {pmid22361213,
year = {2012},
author = {Päckert, M and Martens, J and Wink, M and Feigl, A and Tietze, DT},
title = {Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers.},
journal = {Molecular phylogenetics and evolution},
volume = {63},
number = {3},
pages = {606-616},
doi = {10.1016/j.ympev.2012.02.002},
pmid = {22361213},
issn = {1095-9513},
mesh = {Animals ; Avian Proteins/genetics ; Bayes Theorem ; Birds/classification/*genetics ; Cell Nucleus/*genetics ; Cytochromes b/genetics ; Genetic Markers ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Multilocus Sequence Typing ; *Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b, 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda, (2) African-Asian clade of A. caffer, A. batesi, A. horus, A. affinis and A. nipalensis, (3) African-Palearctic clade of eight currently accepted species among which sequences of A. apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus, Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus, A. barbatus, A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome-b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis/A. nipalensis and A. apus/A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results.},
}
@article {pmid22363720,
year = {2012},
author = {Kawafune, K and Hongoh, Y and Hamaji, T and Nozaki, H},
title = {Molecular identification of rickettsial endosymbionts in the non-phagotrophic volvocalean green algae.},
journal = {PloS one},
volume = {7},
number = {2},
pages = {e31749},
pmid = {22363720},
issn = {1932-6203},
mesh = {Base Sequence ; Cell Size ; Chlorophyta/cytology/growth &amp; development/*microbiology ; Host-Pathogen Interactions ; Humans ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Molecular Sequence Data ; Nucleotides/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsiaceae/*genetics ; Species Specificity ; Staining and Labeling ; Symbiosis/*genetics ; },
abstract = {BACKGROUND: The order Rickettsiales comprises gram-negative obligate intracellular bacteria (also called rickettsias) that are mainly associated with arthropod hosts. This group is medically important because it contains human-pathogenic species that cause dangerous diseases. Until now, there has been no report of non-phagotrophic photosynthetic eukaryotes, such as green plants, harboring rickettsias.<br><br>We examined the bacterial endosymbionts of two freshwater volvocalean green algae: unicellular Carteria cerasiformis and colonial Pleodorina japonica. Epifluorescence microscopy using 4'-6-deamidino-2-phenylindole staining revealed the presence of endosymbionts in all C. cerasiformis NIES-425 cells, and demonstrated a positive correlation between host cell size and the number of endosymbionts. Strains both containing and lacking endosymbionts of C. cerasiformis (NIES-425 and NIES-424) showed a >10-fold increase in cell number and typical sigmoid growth curves over 192 h. A phylogenetic analysis of 16 S ribosomal (r)RNA gene sequences from the endosymbionts of C. cerasiformis and P. japonica demonstrated that they formed a robust clade (hydra group) with endosymbionts of various non-arthropod hosts within the family Rickettsiaceae. There were significantly fewer differences in the 16 S rRNA sequences of the rickettsiacean endosymbionts between C. cerasiformis and P. japonica than in the chloroplast 16 S rRNA or 18 S rRNA of the host volvocalean cells. Fluorescence in situ hybridization demonstrated the existence of the rickettsiacean endosymbionts in the cytoplasm of two volvocalean species.<br><br>CONCLUSIONS/SIGNIFICANCE: The rickettsiacean endosymbionts are likely not harmful to their volvocalean hosts and may have been recently transmitted from other non-arthropod organisms. Because rickettsias are the closest relatives of mitochondria, incipient stages of mitochondrial endosymbiosis may be deduced using both strains with and without C. cerasiformis endosymbionts.},
}
@article {pmid22366764,
year = {2012},
author = {Morita, M and Imanaka, T},
title = {Peroxisomal ABC transporters: structure, function and role in disease.},
journal = {Biochimica et biophysica acta},
volume = {1822},
number = {9},
pages = {1387-1396},
doi = {10.1016/j.bbadis.2012.02.009},
pmid = {22366764},
issn = {0006-3002},
mesh = {ATP-Binding Cassette Transporters/genetics/metabolism/*physiology ; Acyl Coenzyme A/metabolism ; Adrenoleukodystrophy/metabolism/pathology ; Animals ; Biological Transport, Active ; Humans ; Lipid Metabolism ; Neurons/metabolism ; Peroxisomes/*metabolism ; Phylogeny ; Protein Conformation ; Protein Transport ; },
abstract = {ATP-binding cassette (ABC) transporters belong to one of the largest families of membrane proteins, and are present in almost all living organisms from eubacteria to mammals. They exist on plasma membranes and intracellular compartments such as the mitochondria, peroxisomes, endoplasmic reticulum, Golgi apparatus and lysosomes, and mediate the active transport of a wide variety of substrates in a variety of different cellular processes. These include the transport of amino acids, polysaccharides, peptides, lipids and xenobiotics, including drugs and toxins. Three ABC transporters belonging to subfamily D have been identified in mammalian peroxisomes. The ABC transporters are half-size and assemble mostly as a homodimer after posttranslational transport to peroxisomal membranes. ABCD1/ALDP and ABCD2/ALDRP are suggested to be involved in the transport of very long chain acyl-CoA with differences in substrate specificity, and ABCD3/PMP70 is involved in the transport of long and branched chain acyl-CoA. ABCD1 is known to be responsible for X-linked adrenoleukodystrophy (X-ALD), an inborn error of peroxisomal β-oxidation of very long chain fatty acids. Here, we summarize recent advances and important points in our advancing understanding of how these ABC transporters target and assemble to peroxisomal membranes and perform their functions in physiological and pathological processes, including the neurodegenerative disease, X-ALD.},
}
@article {pmid22368181,
year = {2012},
author = {Kabran, P and Rossignol, T and Gaillardin, C and Nicaud, JM and Neuvéglise, C},
title = {Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {19},
number = {3},
pages = {231-244},
pmid = {22368181},
issn = {1756-1663},
mesh = {Alternative Splicing/*genetics ; Citric Acid Cycle/genetics ; Cytosol/enzymology ; Fungal Proteins/*genetics/metabolism ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Introns/genetics ; Malate Dehydrogenase/classification/*genetics/metabolism ; Mitochondria/enzymology ; Peroxisomes/enzymology ; Phylogeny ; RNA Precursors/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Yarrowia/enzymology/*genetics ; },
abstract = {Alternative pre-mRNA splicing is a major mechanism contributing to the proteome complexity of most eukaryotes, especially mammals. In less complex organisms, such as yeasts, the numbers of genes that contain introns are low and cases of alternative splicing (AS) with functional implications are rare. We report the first case of AS with functional consequences in the yeast Yarrowia lipolytica. The splicing pattern was found to govern the cellular localization of malate dehydrogenase, an enzyme of the central carbon metabolism. This ubiquitous enzyme is involved in the tricarboxylic acid cycle in mitochondria and in the glyoxylate cycle, which takes place in peroxisomes and the cytosol. In Saccharomyces cerevisiae, three genes encode three compartment-specific enzymes. In contrast, only two genes exist in Y. lipolytica. One gene (YlMDH1, YALI0D16753g) encodes a predicted mitochondrial protein, whereas the second gene (YlMDH2, YALI0E14190g) generates the cytosolic and peroxisomal forms through the alternative use of two 3'-splice sites in the second intron. Both splicing variants were detected in cDNA libraries obtained from cells grown under different conditions. Mutants expressing the individual YlMdh2p isoforms tagged with fluorescent proteins confirmed that they localized to either the cytosolic or the peroxisomal compartment.},
}
@article {pmid22373076,
year = {2012},
author = {Pereira-da-Conceicoa, LL and Price, BW and Barber-James, HM and Barker, NP and de Moor, FC and Villet, MH},
title = {Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {26},
pmid = {22373076},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; *Genetic Variation ; Insecta/*classification/cytology/*genetics ; Mitochondria/genetics ; Phylogeny ; South Africa ; },
abstract = {BACKGROUND: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.<br><br>RESULTS: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1&#x3b1;] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1&#x3b1; gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1&#x3b1; gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya).<br><br>CONCLUSIONS: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.},
}
@article {pmid22395773,
year = {2012},
author = {Houtkooper, RH and Pirinen, E and Auwerx, J},
title = {Sirtuins as regulators of metabolism and healthspan.},
journal = {Nature reviews. Molecular cell biology},
volume = {13},
number = {4},
pages = {225-238},
pmid = {22395773},
issn = {1471-0080},
support = {231138/ERC_/European Research Council/International ; },
mesh = {Aging/genetics/*metabolism ; Animals ; Energy Metabolism ; Glucose/metabolism ; Histones/genetics/metabolism ; Homeostasis ; Humans ; Insulin/metabolism ; Insulin Secretion ; Lipid Metabolism ; Longevity/genetics ; Multigene Family ; NAD/metabolism ; Phylogeny ; Protein Processing, Post-Translational ; Resveratrol ; Sirtuins/*physiology ; Stilbenes/pharmacology ; },
abstract = {Since the beginning of the century, the mammalian sirtuin protein family (comprising SIRT1-SIRT7) has received much attention for its regulatory role, mainly in metabolism and ageing. Sirtuins act in different cellular compartments: they deacetylate histones and several transcriptional regulators in the nucleus, but also specific proteins in other cellular compartments, such as in the cytoplasm and in mitochondria. As a consequence, sirtuins regulate fat and glucose metabolism in response to physiological changes in energy levels, thereby acting as crucial regulators of the network that controls energy homeostasis and as such determines healthspan.},
}
@article {pmid22397374,
year = {2012},
author = {He, W and Lu, WH and Li, XG and Lu, NN and Sun, DF and Li, YZ},
title = {Taxonomic status of Chinese bahaba (Bahaba taipingensis) and its phylogenetic relationship with other species in the family Sciaenidae.},
journal = {Mitochondrial DNA},
volume = {23},
number = {2},
pages = {53-61},
doi = {10.3109/19401736.2011.653797},
pmid = {22397374},
issn = {1940-1744},
mesh = {Animals ; Bayes Theorem ; China ; Cytochromes b/genetics ; Genes, rRNA ; Mitochondria/enzymology ; Perciformes/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Sciaenidae is one of the largest fish families, but the phylogeny and taxonomy of these fishes are still being disputed. Furthermore, the taxonomic status of the Chinese bahaba (Bahaba taipingensis), which is an endemic species to China, had never been studied through molecular method. In this study, phylogenetic relationships among sciaenid species were reconstructed using DNA sequence data from the mitochondrial cytochrome b (cyt b) gene and the 16S ribosomal RNA (16S rRNA) gene through Bayesian inference (BI) analyses. The phylogenetic trees indicated that the Chinese bahaba closely related to Collichthys and Pseudosciaena. Previous studies (Meng et al. 2004. Prog Nat Sci 14(5):514-521, [in Chinese]) showed that the subfamily Pseudosciaeninae represented the latest evolutionary sort, which was more suitable with the current environment. Based on our 16S rRNA, the Chinese bahaba showed close relationship with Pseudosciaena, thus the divergence of the Chinese bahaba maybe also very late within the family Sciaenidae. It was probably that the oceanographic or ecological discontinuities of these species vary considerably causing particularly strong breaks. Furthermore, combined with previous studies, we suggested that there was only one genus, Otolithes, within the subfamily Otolithinae. Nevertheless, the taxonomic status of the Chinese bahaba and the phylogeny of the whole family were not completely solved. Additional samples of more species are required to develop a clearer picture of the evolutionary history of Sciaenidae.},
}
@article {pmid22399435,
year = {2012},
author = {Grzybowski, T and Rogalla, U},
title = {Mitochondria in anthropology and forensic medicine.},
journal = {Advances in experimental medicine and biology},
volume = {942},
number = {},
pages = {441-453},
doi = {10.1007/978-94-007-2869-1_20},
pmid = {22399435},
issn = {0065-2598},
mesh = {*Anthropology ; DNA, Mitochondrial/genetics ; *Forensic Medicine ; Humans ; Mitochondria/*physiology ; Phylogeny ; },
abstract = {Mitochondria's role in crucial metabolic pathways is probably the first answer which comes to our minds for the question: what do these tiny organelles serve for? However, specific features of their DNA made them extremely useful also in the field of anthropology and forensics. MtDNA analyses became a milestone in the complex task of unraveling earliest human migrations. Evidence provided by these experiments left no doubts on modern humans origins pointing to Africa being our cradle. It also contributed to interpretation of putative ways of our dispersal around Asia and Americas thousands years ago. On the other hand, analysis of mtDNA is well established and valuable tool in forensic genetics. When other definitely more popular markers give no answer on identity, it is the time to employ information carried by mitochondria. This chapter summarizes not only current reports on the role of mitochondria in forensics and reconstruction of modern humans phylogeny, but also calls one's attention to a broad range of difficulties and constraints associated with mtDNA analyses.},
}
@article {pmid22409411,
year = {2012},
author = {Ovchinnikov, S and Masta, SE},
title = {Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias.},
journal = {BMC evolutionary biology},
volume = {12},
number = {},
pages = {31},
pmid = {22409411},
issn = {1471-2148},
mesh = {Animals ; Arachnida/*genetics ; Base Composition ; DNA, Mitochondrial/chemistry/genetics ; Gene Order ; *Gene Rearrangement ; Genes, rRNA/genetics ; Genome/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/*genetics ; RNA, Transfer/chemistry/genetics ; },
abstract = {BACKGROUND: Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.<br><br>RESULTS: We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.<br><br>CONCLUSION: The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.},
}
@article {pmid22426856,
year = {2012},
author = {Frelin, O and Agrimi, G and Laera, VL and Castegna, A and Richardson, LG and Mullen, RT and Lerma-Ortiz, C and Palmieri, F and Hanson, AD},
title = {Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize.},
journal = {Functional &amp; integrative genomics},
volume = {12},
number = {2},
pages = {317-326},
pmid = {22426856},
issn = {1438-7948},
mesh = {Acetolactate Synthase/metabolism ; Arabidopsis/*genetics ; Cell Line ; Genetic Complementation Test ; Mitochondria/enzymology/metabolism ; Mitochondrial Membrane Transport Proteins/biosynthesis/*genetics ; Phylogeny ; Plant Proteins/biosynthesis/*genetics ; Protein Transport ; Saccharomyces cerevisiae/genetics ; Thiamine Monophosphate/metabolism ; Thiamine Pyrophosphate/*metabolism ; Zea mays/*genetics ; },
abstract = {It is currently held that thiamin is made in chloroplasts and converted in the cytosol to the active cofactor thiamin diphosphate (ThDP), and that mitochondria and plastids import ThDP. The organellar transporters that mediate ThDP import in plants have not been identified. Comparative genomic analysis indicated that two members of the mitochondrial carrier family (MCF) in Arabidopsis (At5g48970 and At3g21390) and two in maize (GRMZM2G118515 and GRMZM2G124911) are related to the ThDP carriers of animals and Saccharomyces cerevisiae. Expression of each of these plant proteins in a S. cerevisiae ThDP carrier (TPC1) null mutant complemented the growth defect on fermentable carbon sources and restored the level of mitochondrial ThDP and the activity of the mitochondrial ThDP-dependent enzyme acetolactate synthase. The plant proteins were targeted to mitochondria as judged by dual import assays with purified pea mitochondria and chloroplasts, and by microscopic analysis of the subcellular localization of green fluorescent protein fusions in transiently transformed tobacco suspension cells. Both maize genes were shown to be expressed throughout the plant, which is consistent with the known ubiquity of mitochondrial ThDP-dependent enzymes. Collectively, these data establish that plants have mitochondrially located MCF carriers for ThDP, and indicate that these carriers are highly evolutionarily conserved. Our data provide a firm basis to propagate the functional annotation of mitochondrial ThDP carriers to other angiosperm genomes.},
}
@article {pmid22439812,
year = {2012},
author = {Ladner, JT and Palumbi, SR},
title = {Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes.},
journal = {Molecular ecology},
volume = {21},
number = {9},
pages = {2224-2238},
doi = {10.1111/j.1365-294X.2012.05528.x},
pmid = {22439812},
issn = {1365-294X},
mesh = {Animals ; Anthozoa/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetic Variation ; Geography ; Hybridization, Genetic ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; *Sympatry ; },
abstract = {The identification of species is one of the most basic, and yet critically important, issues in biology with far-reaching potential implications for fields such as biodiversity conservation, population ecology and epidemiology. Morphology has long been the primary tool biologists have used to categorize life. However, we now know that a significant portion of natural diversity is morphologically hidden, and therefore, we must integrate nonmorphological tools into the description of biodiversity. Here, we demonstrate the utility of multilocus population genetic data for identifying and characterizing cryptic species complexes, even when species share large amounts of genetic variability. Specifically, we have used DNA sequence data from 12 genomic regions to characterize two widespread species complexes in the coral genus Acropora: A. cytherea and A. hyacinthus. These two morphospecies have each been sampled from 5 to 7 locations throughout their Indo-Pacific distributions, and with the use of structure and hierarchical clustering, we demonstrate the presence of at least six widespread cryptic species within these two morphospecies complexes. After identifying cryptic lineages, we then utilize the genetic data to examine the history of introgressive hybridization within and between these morphospecies complexes. Our data indicate that these two complexes form a global syngameon with consistent patterns of introgression between species across large geographic distributions.},
}
@article {pmid22457064,
year = {2012},
author = {Atkinson, GC and Kuzmenko, A and Kamenski, P and Vysokikh, MY and Lakunina, V and Tankov, S and Smirnova, E and Soosaar, A and Tenson, T and Hauryliuk, V},
title = {Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae.},
journal = {Nucleic acids research},
volume = {40},
number = {13},
pages = {6122-6134},
pmid = {22457064},
issn = {1362-4962},
mesh = {Amino Acid Sequence ; Conserved Sequence ; Eukaryotic Initiation Factor-2/chemistry/classification/genetics ; Eukaryotic Initiation Factor-3/chemistry/classification/*genetics ; Genetic Complementation Test ; Mitochondrial Proteins/chemistry/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry/classification/*genetics ; Sequence Alignment ; },
abstract = {Mitochondrial translation is essentially bacteria-like, reflecting the bacterial endosymbiotic ancestry of the eukaryotic organelle. However, unlike the translation system of its bacterial ancestors, mitochondrial translation is limited to just a few mRNAs, mainly coding for components of the respiratory complex. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in bacteria, but only IF2 is universal in mitochondria (mIF2). We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae. Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3. Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.},
}
@article {pmid22471645,
year = {2012},
author = {Ding, Y and Leng, J},
title = {Is mitochondrial tRNA Leu(UUR) 3291T&gt;C mutation pathogenic?.},
journal = {Mitochondrial DNA},
volume = {23},
number = {4},
pages = {323-326},
doi = {10.3109/19401736.2012.674119},
pmid = {22471645},
issn = {1940-1744},
mesh = {Aged ; Asian People/genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Family ; Female ; *Genetic Predisposition to Disease ; Humans ; Male ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics/pathology ; Mitochondrial Myopathies/genetics ; Molecular Sequence Data ; *Mutation ; Phylogeny ; RNA, Transfer, Leu/chemistry/*genetics/metabolism ; Sequence Alignment ; Thermodynamics ; },
abstract = {According to a recent report by Sunami et al., a maternally inherited Japanese family with variable phenotypes including mitochondrial myopathy, recurrent headache, and myoclonus and epilepsy had been described to be associated with mitochondrial tRNA(Leu(UUR)) 3291T>C mutation. In order to verify this association, we reanalyzed the clinical and molecular datasets obtained from Sunami's work; in addition, a phylogenetic approach was employed to evaluate the conservation index of this mutation among different species. We further utilized RNA Fold Web Server to predict the minimum free energy (MFE) of tRNA(Leu(UUR)) gene with and without this mutation. Most strikingly, a low level of conservation was found regarding 3291T>C mutation and a slight change in MFE had been observed between the wild type and the mutant. Our negative results gave no support for an active role for this mutation on the clinical expression of mitochondrial disorders.},
}
@article {pmid22486892,
year = {2012},
author = {Lin, L and Pan, G and Li, T and Dang, X and Deng, Y and Ma, C and Chen, J and Luo, J and Zhou, Z},
title = {The protein import pore Tom40 in the microsporidian Nosema bombycis.},
journal = {The Journal of eukaryotic microbiology},
volume = {59},
number = {3},
pages = {251-257},
doi = {10.1111/j.1550-7408.2012.00618.x},
pmid = {22486892},
issn = {1550-7408},
mesh = {Computational Biology ; Fungal Proteins/genetics/*metabolism ; Microsporidia/classification/metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Membranes/metabolism ; Nosema/classification/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; },
abstract = {Microsporidia, an unusual group of unicellular parasites related to fungi, possess a highly reduced mitochondrion known as the mitosome. Since mitosomes lack an organellar genome, their proteins must be translated in the cytosol before being imported into the mitosome via translocases. We have identified a Tom40 gene (NbTom40), the main component of the translocase of the outer mitochondrial membrane, in the genome of the microsporidian Nosema bombycis. NbTom40 is reduced in size, but it is predicted to form a β-barrel structure composed of 19 β-strands. Phylogenetic analysis confirms that NbTom40 forms a clade with Tom40 sequences from other species, distinct from a related clade of voltage-dependent anion channels (VDACs). The NbTom40 contains a β-signal motif that the polar residue is substituted by glycine. Furthermore, we show that expression of NbTom40, as a GFP fusion protein within yeast cells, directs GFP to mitochondria of yeast. These findings suggest that NbTom40 may serve as an import channel of the microsporidian mitosome and facilitate protein translocation into this organelle.},
}
@article {pmid22487608,
year = {2012},
author = {Quicke, DL and Smith, MA and Janzen, DH and Hallwachs, W and Fernandez-Triana, J and Laurenne, NM and Zaldívar-Riverón, A and Shaw, MR and Broad, GR and Klopfstein, S and Shaw, SR and Hrcek, J and Hebert, PD and Miller, SE and Rodriguez, JJ and Whitfield, JB and Sharkey, MJ and Sharanowski, BJ and Jussila, R and Gauld, ID and Chesters, D and Vogler, AP},
title = {Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence.},
journal = {Molecular ecology resources},
volume = {12},
number = {4},
pages = {676-685},
doi = {10.1111/j.1755-0998.2012.03143.x},
pmid = {22487608},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Wasps/*classification/*genetics ; },
abstract = {The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.},
}
@article {pmid22491760,
year = {2012},
author = {Koblmüller, S and Wayne, RK and Leonard, JA},
title = {Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote.},
journal = {Biology letters},
volume = {8},
number = {4},
pages = {644-647},
pmid = {22491760},
issn = {1744-957X},
mesh = {Animals ; Bayes Theorem ; Canada ; Carnivory/*physiology ; *Climate Change ; Competitive Behavior/*physiology ; Coyotes/classification/genetics/*physiology ; Ecosystem ; Genetics, Population/methods ; Geography ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; United States ; },
abstract = {Recurrent cycles of climatic change during the Quaternary period have dramatically affected the population genetic structure of many species. We reconstruct the recent demographic history of the coyote (Canis latrans) through the use of Bayesian techniques to examine the effects of Late Quaternary climatic perturbations on the genetic structure of a highly mobile generalist species. Our analysis reveals a lack of phylogeographic structure throughout the range but past population size changes correlated with climatic changes. We conclude that even generalist carnivorous species are very susceptible to environmental changes associated with climatic perturbations. This effect may be enhanced in coyotes by interspecific competition with larger carnivores.},
}
@article {pmid22497212,
year = {2012},
author = {Koban, E and Denizci, M and Aslan, O and Aktoprakligil, D and Aksu, S and Bower, M and Balcioglu, BK and Ozdemir Bahadir, A and Bilgin, R and Erdag, B and Bagis, H and Arat, S},
title = {High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia.},
journal = {Animal genetics},
volume = {43},
number = {4},
pages = {401-409},
doi = {10.1111/j.1365-2052.2011.02285.x},
pmid = {22497212},
issn = {1365-2052},
mesh = {Animals ; Asia ; Breeding ; DNA, Mitochondrial/*genetics/metabolism ; Europe ; *Genetic Variation ; Genotype ; Horses/*genetics ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Statistics as Topic ; },
abstract = {The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.},
}
@article {pmid22503399,
year = {2012},
author = {Zhang, B and Dai, W},
title = {Ultrastructure of the spermatozoa of Cicadella viridis (Linnaeus) and its bearing on the phylogeny of Auchenorrhyncha.},
journal = {Micron (Oxford, England : 1993)},
volume = {43},
number = {9},
pages = {978-984},
doi = {10.1016/j.micron.2012.03.022},
pmid = {22503399},
issn = {1878-4291},
mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Hemiptera/*genetics/*ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; },
abstract = {The ultrastructure of mature spermatozoa of the leafhopper Cicadella viridis (Linnaeus) was investigated using light and transmission electron microscopy. The spermatozoon is composed of a head containing an acrosome and an elongated nucleus, and a long tail, which consists of a flagellum. The acrosome is conical and invaginated to form a subacrosomal space, and the acrosomal contents are filled with electron-dense tubular substructures. The nucleus is linear and filled with homogeneously condensed chromatin. The centriolar adjunct is parallel to the nucleus and connects the nucleus with the mid-piece/flagellum. The flagellum is formed by a 9+9+2 axoneme, two mitochondrial derivatives and two accessory bodies. The mitochondrial derivatives with an orderly array of peripheral cristae are symmetrical. The accessory bodies are small and slightly elliptical. The end of the axoneme shows progressive loss of microtubules. Comparison of sperm ultrastructure of C. viridis with those of other Auchenorrhyncha families supports the major relationships within Cicadomorpha as (Membracoidea (Cicadoidea, Cercopoidea)).},
}
@article {pmid22512685,
year = {2012},
author = {Kakizaki, Y and Moore, AL and Ito, K},
title = {Different molecular bases underlie the mitochondrial respiratory activity in the homoeothermic spadices of Symplocarpus renifolius and the transiently thermogenic appendices of Arum maculatum.},
journal = {The Biochemical journal},
volume = {445},
number = {2},
pages = {237-246},
pmid = {22512685},
issn = {1470-8728},
support = {BB/E015328/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Araceae/genetics/*metabolism ; Arum/genetics/*metabolism ; Blotting, Western ; Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Flowers ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; NADPH Dehydrogenase/genetics/metabolism ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; *Thermogenesis ; Alternative Oxidase ; },
abstract = {Symplocarpus renifolius and Arum maculatum are known to produce significant heat during the course of their floral development, but they use different regulatory mechanisms, i.e. homoeothermic compared with transient thermogenesis. To further clarify the molecular basis of species-specific thermogenesis in plants, in the present study we have analysed the native structures and expression patterns of the mitochondrial respiratory components in S. renifolius and A. maculatum. Our comparative analysis using Blue native PAGE combined with nano LC (liquid chromatography)-MS/MS (tandem MS) has revealed that the constituents of the respiratory complexes in both plants were basically similar, but that several mitochondrial components appeared to be differently expressed in their thermogenic organs. Namely, complex II in S. renifolius was detected as a 340 kDa product, suggesting an oligomeric or supramolecular structure in vivo. Moreover, the expression of an external NAD(P)H dehydrogenase was found to be higher in A. maculatum than in S. renifolius, whereas an internal NAD(P)H dehydrogenase was expressed at a similar level in both species. Alternative oxidase was detected as smear-like signals that were elongated on the first dimension with a peak at around 200 kDa in both species. The significance and implication of these data are discussed in terms of thermoregulation in plants.},
}
@article {pmid22513280,
year = {2012},
author = {Gómez-Díaz, E and Morris-Pocock, JA and González-Solís, J and McCoy, KD},
title = {Trans-oceanic host dispersal explains high seabird tick diversity on Cape Verde islands.},
journal = {Biology letters},
volume = {8},
number = {4},
pages = {616-619},
pmid = {22513280},
issn = {1744-957X},
mesh = {Animals ; Bird Diseases/epidemiology/parasitology ; Birds/*parasitology ; Cabo Verde/epidemiology ; *Genes, Mitochondrial ; Genes, rRNA ; *Genetic Variation ; Genetics, Population/methods ; Haplotypes ; Mitochondria/genetics ; Ornithodoros/classification/*genetics/growth &amp; development ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/analysis/genetics ; Tick Infestations/epidemiology/parasitology/veterinary ; },
abstract = {Parasites represent ideal models for unravelling biogeographic patterns and mechanisms of diversification on islands. Both host-mediated dispersal and within-island adaptation can shape parasite island assemblages. In this study, we examined patterns of genetic diversity and structure of Ornithodoros seabird ticks within the Cape Verde Archipelago in relation to their global phylogeography. Contrary to expectations, ticks from multiple, geographically distant clades mixed within the archipelago. Trans-oceanic colonization via host movements probably explains high local tick diversity, contrasting with previous research that suggests little large-scale dispersal in these birds. Although host specificity was not obvious at a global scale, host-associated genetic structure was found within Cape Verde colonies, indicating that post-colonization adaptation to specific hosts probably occurs. These results highlight the role of host metapopulation dynamics in the evolutionary ecology and epidemiology of avian parasites and pathogens.},
}
@article {pmid22523123,
year = {2012},
author = {Ewers, C and Wares, JP},
title = {Examining an outlier: molecular diversity in the cirripedia.},
journal = {Integrative and comparative biology},
volume = {52},
number = {3},
pages = {410-417},
doi = {10.1093/icb/ics047},
pmid = {22523123},
issn = {1557-7023},
mesh = {Alleles ; Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gene Frequency ; *Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population/methods ; Mitochondria/genetics ; Phylogeny ; Population Density ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; Thoracica/classification/*genetics/physiology ; },
abstract = {Despite the typical assumption in studies of mitochondrial diversity that such data are useful for approximating population size and demography, studies of sequence diversity in mitochondrial DNA across the Metazoa have shown a surprising excess of rare alleles, a pattern associated either with strong selection or population growth. Previous work has shown that this bias toward an excess of rare alleles is typical across the Crustacea, and in particular, in the Cirripedia (barnacles). Here, we directly evaluate sequence data from studies of barnacle populations to ensure that inclusion of cryptic species is not the cause of this pattern. The results shown here reinforce previous studies that suggest caution in interpreting such patterns of allele frequencies, as they are likely to be influenced both by demographic changes and selection.},
}
@article {pmid22523127,
year = {2012},
author = {Tsang, LM and Wu, TH and Shih, HT and Williams, GA and Chu, KH and Chan, BK},
title = {Genetic and morphological differentiation of the Indo-West Pacific intertidal barnacle Chthamalus malayensis.},
journal = {Integrative and comparative biology},
volume = {52},
number = {3},
pages = {388-409},
pmid = {22523127},
issn = {1557-7023},
mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetics, Population/methods ; Indian Ocean ; Mitochondria/genetics ; Oceans and Seas ; Pacific Ocean ; Phylogeny ; Phylogeography ; Population Density ; Reproductive Isolation ; Species Specificity ; Temperature ; Thoracica/*anatomy &amp; histology/classification/*genetics/growth &amp; development ; },
abstract = {Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.},
}
@article {pmid22558439,
year = {2012},
author = {Lin, LH and Qu, YF and Li, H and Zhou, KY and Ji, X},
title = {Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence.},
journal = {PloS one},
volume = {7},
number = {4},
pages = {e36334},
pmid = {22558439},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/genetics ; Conservation of Natural Resources/*methods ; Elapidae/classification/*genetics ; Genetic Markers/genetics ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; },
abstract = {An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a "star" cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.},
}
@article {pmid22560092,
year = {2012},
author = {Pala, M and Olivieri, A and Achilli, A and Accetturo, M and Metspalu, E and Reidla, M and Tamm, E and Karmin, M and Reisberg, T and Hooshiar Kashani, B and Perego, UA and Carossa, V and Gandini, F and Pereira, JB and Soares, P and Angerhofer, N and Rychkov, S and Al-Zahery, N and Carelli, V and Sanati, MH and Houshmand, M and Hatina, J and Macaulay, V and Pereira, L and Woodward, SR and Davies, W and Gamble, C and Baird, D and Semino, O and Villems, R and Torroni, A and Richards, MB},
title = {Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia.},
journal = {American journal of human genetics},
volume = {90},
number = {5},
pages = {915-924},
pmid = {22560092},
issn = {1537-6605},
mesh = {DNA, Mitochondrial/*genetics/*metabolism ; Europe ; Europe, Eastern/epidemiology ; Genetic Variation ; Genetics, Population ; Humans ; Middle East ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; White People/*genetics ; },
abstract = {Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19-12 thousand years (ka) ago.},
}
@article {pmid22567162,
year = {2012},
author = {Smith, MA and Bertrand, C and Crosby, K and Eveleigh, ES and Fernandez-Triana, J and Fisher, BL and Gibbs, J and Hajibabaei, M and Hallwachs, W and Hind, K and Hrcek, J and Huang, DW and Janda, M and Janzen, DH and Li, Y and Miller, SE and Packer, L and Quicke, D and Ratnasingham, S and Rodriguez, J and Rougerie, R and Shaw, MR and Sheffield, C and Stahlhut, JK and Steinke, D and Whitfield, J and Wood, M and Zhou, X},
title = {Wolbachia and DNA barcoding insects: patterns, potential, and problems.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36514},
pmid = {22567162},
issn = {1932-6203},
mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Insecta/classification/*genetics/*microbiology ; Phylogeny ; Wolbachia/*genetics ; },
abstract = {Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.},
}
@article {pmid22567860,
year = {2012},
author = {Torgunakova, OA and Khrisanfov, VE and Prizenko, VK and Bogeruk, AK and Egorova, TA and Semenova, SK},
title = {[Polymorphism of the cytochrome oxidase b gene (cyt b) in Russian populations of common carp and wild common carp (Cyprinus carpio L.)].},
journal = {Genetika},
volume = {48},
number = {1},
pages = {104-111},
pmid = {22567860},
issn = {0016-6758},
mesh = {Animals ; Carps/*genetics ; Cytochromes b/*genetics ; Haplotypes/*genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Population/genetics ; Russia ; Sequence Analysis, DNA ; },
abstract = {Polymorphism of the mitochondrial cyt b gene was examined in 35 individuals of common carp and wild common carp (Cyprinus carpio L.). The fish examined represented two natural populations from Khabarovsk krai (Ac and Am), Volga wild common carp, Don wild common carp, and two common carp breeds, Ropsha (strains BB and MM) common carp and Hungarian common carp. The highest level of nucleotide (pi) and haplotype (h) diversity was detected in two strains of Ropsha common carp (MM, pi = 0.67%, h = 0.7; and BB, pi = 0.21%, h = 0.9) and in one population (Am) of Amur wild common carp (pi = 0.26%; h = 0.6). The second population of Amur wild common carp (Ac) and Hungarian common carp were characterized by lower variation estimates (pi = 0.035%, h = 0.4; and pi = 0.09%, h = 0.7, respectively). Genetic homogeneity was demonstrated for the populations of Volga and Don wild common carp (pi = 0, h = 0). In the sample of the cyt b sequences examined, three lineages were identified. Lineages I and II united all haplotypes of the Am Amur wild common carp along with two haplotypes of Ropsha common carp, strain MM. The third lineage (III) was formed by the haplotypes of three individuals of Ropsha common carp strain MM, all representatives of Ropsha common carp strain BB, Hungarian common carp, Ac Amur wild common carp, and Don and Volga wild common carps. Statistically significant amino acid differences were observed only for the sequences, corresponding to haplotypes of lineage III, and the sum of sequences of lineages I and II. Effectiveness of different types of markers to differentiate the two subspecies of European and Amur wild common carp (C. c. carpio and C. c. haematopterus) is discussed, as well as the issues of the origin and dispersal of Russian common carp and wild common carp breeds.},
}
@article {pmid22569235,
year = {2012},
author = {Huynen, MA and Duarte, I and Chrzanowska-Lightowlers, ZM and Nabuurs, SB},
title = {Structure based hypothesis of a mitochondrial ribosome rescue mechanism.},
journal = {Biology direct},
volume = {7},
number = {},
pages = {14},
pmid = {22569235},
issn = {1745-6150},
support = {096919/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Carboxylic Ester Hydrolases/metabolism ; Codon, Terminator ; Conserved Sequence ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; *Models, Biological ; Peptide Chain Termination, Translational ; Peptide Termination Factors/*genetics ; Phylogeny ; *Protein Biosynthesis ; RNA, Bacterial/genetics ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomes/*metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Thermus thermophilus/genetics ; Vertebrates/*genetics ; },
abstract = {BACKGROUND: mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions that are conserved among mtRF1 sequences but that are different in their mtRF1a paralogs. We subsequently modeled the 3D structure of mtRF1a and mtRF1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtRF1.<br><br>RESULTS: Our model predicts, in agreement with the experimental data, that the 3D structure of mtRF1a allows it to recognize the stop codons UAA and UAG in the A-site of the ribosome. In contrast, we show that mtRF1 likely can only bind the ribosome when the A-site is devoid of mRNA. Furthermore, while mtRF1a will adopt its catalytic conformation, in which it functions as a peptidyl-tRNA hydrolase in the ribosome, only upon binding of a stop codon in the A-site, mtRF1 appears specifically adapted to assume this extended, peptidyl-tRNA hydrolyzing conformation in the absence of mRNA in the A-site.<br><br>CONCLUSIONS: We predict that mtRF1 specifically recognizes ribosomes with an empty A-site and is able to function as a peptidyl-tRNA hydrolase in those situations. Stalled ribosomes with empty A-sites that still contain a tRNA bound to a peptide chain can result from the translation of truncated, stop-codon less mRNAs. We hypothesize that mtRF1 recycles such stalled ribosomes, performing a function that is analogous to that of tmRNA in bacteria.},
}
@article {pmid22574125,
year = {2012},
author = {Mallet, S and Weiss, S and Jacques, N and Leh-Louis, V and Sacerdot, C and Casaregola, S},
title = {Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the Millerozyma (Pichia) farinosa species complex.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e35842},
pmid = {22574125},
issn = {1932-6203},
mesh = {Aneuploidy ; Animals ; Cattle ; Chimera ; Chromosomes, Fungal/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Genome, Fungal/genetics ; Haploidy ; Humans ; Life Cycle Stages ; *Phylogeny ; Reproducibility of Results ; Reproduction/genetics ; Saccharomycetales/*classification/genetics/*growth &amp; development ; Spores, Fungal/growth &amp; development ; },
abstract = {Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004(T) (= CLIB 1230(T)) and Candida pseudofarinosa sp. nov.NCYC 386(T)(= CLIB 1231(T)). Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strains from distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.},
}
@article {pmid22578654,
year = {2012},
author = {Shi, H and Liu, R and Sha, Z and Ma, J},
title = {Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster.},
journal = {Marine genomics},
volume = {6},
number = {},
pages = {7-15},
doi = {10.1016/j.margen.2011.11.002},
pmid = {22578654},
issn = {1876-7478},
mesh = {Animals ; Base Composition ; Base Sequence ; Codon ; DNA, Mitochondrial/*chemistry/genetics ; Decapoda/classification/*genetics ; Gene Order ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/*genetics ; Species Specificity ; Translocation, Genetic ; },
abstract = {As a phylogenetically valuable decapoda, a complete mitochondrial genome from Stenopodidea has not been reported to date. Here, we determined the complete mitochondrial DNA sequence of Stenopus hispidus (Olivier, 1811). The 15,528 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs) and two ribosomal RNA (rRNA) genes plus the putative control region (CR). This finding is similar to other metazoan animals but with the exception of 23 transfer RNA (tRNA) genes, which contain an additional tRNA-Gln compared with other crustaceans. With respect to the pancrustacean ground pattern mitochondria gene order, 5 tRNAs appear to be rearranged (tRNAs-Leu (CUN), Arg, Glu, Gln, and Met), one of which has also undergone inversion (tRNA-Leu (CUN)). Phylogenetic analyses reveal Stenopodidea and Reptantia form a clade sister to Caridea, which agrees with Abele and Felgenhauer's (1986) hypothesis. This topology contrasts with previous results based on morphological and some molecular data.},
}
@article {pmid22606033,
year = {2012},
author = {Liu, CC and Liu, BG and Yang, ZW and Li, CM and Wang, BC and Yang, CP},
title = {Genome-wide identification and in silico analysis of poplar peptide deformylases.},
journal = {International journal of molecular sciences},
volume = {13},
number = {4},
pages = {5112-5124},
pmid = {22606033},
issn = {1422-0067},
mesh = {Amidohydrolases/*genetics/metabolism ; Amino Acid Sequence ; Arabidopsis/enzymology/genetics ; Arabidopsis Proteins/metabolism ; Base Sequence ; Genome, Plant ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Populus/*enzymology/*genetics ; Sequence Alignment ; },
abstract = {Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them.},
}
@article {pmid22606053,
year = {2012},
author = {Rout, PK and Thangraj, K and Mandal, A and Roy, R},
title = {Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.},
journal = {TheScientificWorldJournal},
volume = {2012},
number = {},
pages = {618909},
pmid = {22606053},
issn = {1537-744X},
mesh = {Alleles ; Animals ; Breeding ; DNA, Mitochondrial/*genetics ; Genetic Carrier Screening/methods ; Genetic Drift ; Genetic Loci ; *Genetic Variation ; Genetics, Population/*methods ; Goats/*genetics ; Heterozygote ; India ; Linkage Disequilibrium ; Male ; *Microsatellite Repeats ; Milk Proteins/*genetics ; Mitochondria/genetics ; Population Density ; Selection, Genetic ; Y Chromosome/genetics ; },
abstract = {Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.},
}
@article {pmid22614282,
year = {2012},
author = {Özdil, F and İlhan, F},
title = {Phylogenetic relationship of Turkish Apis mellifera subspecies based on sequencing of mitochondrial cytochrome C oxidase I region.},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {2},
pages = {1130-1141},
doi = {10.4238/2012.April.27.12},
pmid = {22614282},
issn = {1676-5680},
mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Turkey ; },
abstract = {Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees.},
}
@article {pmid22615898,
year = {2012},
author = {Shi, W and Kerdelhué, C and Ye, H},
title = {Genetic structure and inferences on potential source areas for Bactrocera dorsalis (Hendel) based on mitochondrial and microsatellite markers.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e37083},
pmid = {22615898},
issn = {1932-6203},
mesh = {Animal Migration ; Animal Population Groups/genetics ; Animals ; Asia, Southeastern ; Gene Flow ; Genetic Structures ; Genetic Variation ; Geography ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Pilot Projects ; Tephritidae/*genetics ; },
abstract = {Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan.},
}
@article {pmid22629338,
year = {2012},
author = {Papura, D and Burban, C and van Helden, M and Giresse, X and Nusillard, B and Guillemaud, T and Kerdelhué, C},
title = {Microsatellite and mitochondrial data provide evidence for a single major introduction for the Neartic leafhopper Scaphoideus titanus in Europe.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e36882},
pmid = {22629338},
issn = {1932-6203},
mesh = {Animals ; Europe ; Genetic Loci ; Genetic Variation ; Genetics, Population ; Haplotypes ; Hemiptera/*genetics ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {Scaphoideus titanus, a leafhopper native to North America and invasive in Europe, is the vector of the Flavescence dorée phytoplasma, the causal agent of the most important form of grapevine yellows in European vineyards. We studied 10 polymorphic microsatellite loci and a 623 bp fragment of the mitochondrial cytochrome oxidase II gene in native S. titanus from north-eastern America and introduced European populations, to elucidate the colonization scenario. Consistent with their recent history, invasive European populations were less genetically diverse than American populations for both types of markers, suggesting a recent bottleneck. Significant isolation by distance was detected between American populations but not between European populations. None of the European mitochondrial haplotypes was found in the American vineyards, from which they are assumed to have originated. The precise source of the invasive S. titanus populations therefore remains unclear. Nevertheless, the high heterozygosity of North-East American populations (which contained 92% of the observed alleles) suggests that this region is part of the native range of S. titanus. Clustering population genetics analyses with microsatellite and mitochondrial data suggested that European populations originated from a single introduction event. Most of the introduced populations clustered with populations from Long Island, the Atlantic Coast winegrowing region in which Vitis aestivalis occurs.},
}
@article {pmid22651232,
year = {2012},
author = {Marín, MA and López, A and Uribe, SI},
title = {Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.},
journal = {Mitochondrial DNA},
volume = {23},
number = {3},
pages = {208-215},
doi = {10.3109/19401736.2012.668895},
pmid = {22651232},
issn = {1940-1744},
mesh = {Animals ; Base Sequence ; Butterflies/classification/*genetics ; *Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer, Ser/chemistry/*genetics ; *Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.},
}
@article {pmid22655034,
year = {2012},
author = {Fang, Y and Wu, H and Zhang, T and Yang, M and Yin, Y and Pan, L and Yu, X and Zhang, X and Hu, S and Al-Mssallem, IS and Yu, J},
title = {A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome.},
journal = {PloS one},
volume = {7},
number = {5},
pages = {e37164},
pmid = {22655034},
issn = {1932-6203},
mesh = {Arecaceae/*genetics ; DNA, Mitochondrial/genetics ; *Gene Expression Profiling ; *Genome, Mitochondrial ; Genome, Plant ; Phylogeny ; Plant Proteins/genetics ; Polymorphism, Single Nucleotide ; RNA Editing ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; },
abstract = {Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.},
}
@article {pmid22659201,
year = {2012},
author = {Sheehy, CM and Solórzano, A and Pfaller, JB and Lillywhite, HB},
title = {Preliminary insights into the phylogeography of the yellow-bellied sea snake, Pelamis platurus.},
journal = {Integrative and comparative biology},
volume = {52},
number = {2},
pages = {321-330},
doi = {10.1093/icb/ics088},
pmid = {22659201},
issn = {1557-7023},
mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Elapidae/classification/*genetics/physiology ; Gene Flow ; Genes, RAG-1 ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; *Phylogeography ; Population Growth ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The yellow-bellied sea snake, Pelamis platurus (Elapidae, Hydrophiinae), has the largest distribution of any snake species, and patterns related to its distribution and regional color variation suggest there is population structuring in this species. Here, we use mitochondrial (ND4, Cyt-b) and nuclear (RAG-1) DNA to (1) test whether genetic variation is associated with local variation in color pattern, and (2) assess whether large-scale patterns of genetic variation are correlated with geographic distribution across the Pacific Ocean. We found low levels of genetic variation and shallow population structure that are correlated with local variation in color pattern and with geographic distribution. The low levels of genetic divergence indicate a relatively high rate of gene flow throughout the Pacific region and/or a recent expansion of range, both of which could be attributable to the passive drifting of these snakes on oceanic surface currents. The mtDNA data conform closely to a model of past exponential population growth, and this may have been associated with the species' large eastward and westward expansion of range. The pattern of low nucleotide and high haplotype diversity suggests that this population growth occurred in the relatively recent past. Data from drifting buoys can potentially act as informative models for predicting patterns of drifting in Pelamis and for generating additional testable hypotheses relating to its population structure and biogeography. Future studies should employ nuclear microsatellite markers to investigate population structure in this species at a finer scale. The exploitation of oceanic currents as a novel and highly efficient dispersal mechanism has likely facilitated gene flow throughout the Pacific Ocean in this uniquely pelagic species of sea snake, resulting in a distribution spanning over half of the earth's circumference.},
}
@article {pmid22661327,
year = {2012},
author = {Goyal, S and Balick, DJ and Jerison, ER and Neher, RA and Shraiman, BI and Desai, MM},
title = {Dynamic mutation-selection balance as an evolutionary attractor.},
journal = {Genetics},
volume = {191},
number = {4},
pages = {1309-1319},
pmid = {22661327},
issn = {1943-2631},
support = {260686/ERC_/European Research Council/International ; R01 GM086793/GM/NIGMS NIH HHS/United States ; GM086793/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Computer Simulation ; Genetic Fitness ; Genetics, Population ; *Models, Genetic ; *Mutation ; Mutation Rate ; Population Density ; Reproduction, Asexual/genetics ; *Selection, Genetic ; },
abstract = {The vast majority of mutations are deleterious and are eliminated by purifying selection. Yet in finite asexual populations, purifying selection cannot completely prevent the accumulation of deleterious mutations due to Muller's ratchet: once lost by stochastic drift, the most-fit class of genotypes is lost forever. If deleterious mutations are weakly selected, Muller's ratchet can lead to a rapid degradation of population fitness. Evidently, the long-term stability of an asexual population requires an influx of beneficial mutations that continuously compensate for the accumulation of the weakly deleterious ones. Hence any stable evolutionary state of a population in a static environment must involve a dynamic mutation-selection balance, where accumulation of deleterious mutations is on average offset by the influx of beneficial mutations. We argue that such a state can exist for any population size N and mutation rate U and calculate the fraction of beneficial mutations, ε, that maintains the balanced state. We find that a surprisingly low ε suffices to achieve stability, even in small populations in the face of high mutation rates and weak selection, maintaining a well-adapted population in spite of Muller's ratchet. This may explain the maintenance of mitochondria and other asexual genomes.},
}
@article {pmid22688299,
year = {2012},
author = {Kontro, H and Hulmi, JJ and Rahkila, P and Kainulainen, H},
title = {Cellular and tissue expression of DAPIT, a phylogenetically conserved peptide.},
journal = {European journal of histochemistry : EJH},
volume = {56},
number = {2},
pages = {e18},
pmid = {22688299},
issn = {2038-8306},
mesh = {Animals ; Antibodies ; Gene Expression Regulation/*physiology ; HEK293 Cells ; Human Umbilical Vein Endothelial Cells ; Humans ; Lysosomes/*metabolism ; Membrane Proteins/*biosynthesis ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis ; Organ Specificity ; Phylogeny ; Proton Pumps/metabolism ; Rats ; },
abstract = {DAPIT (Diabetes Associated Protein in Insulin-sensitive Tissues) is a small, phylogenetically conserved, 58 amino acid peptide that was previously shown to be down-regulated at mRNA level in insulin-sensitive tissues of type 1 diabetes rats. In this study we characterize a custom made antibody against DAPIT and confirm the mitochondrial presence of DAPIT on cellular level. We also show that DAPIT is localized in lysosomes of HUVEC and HEK 293T cells. In addition, we describe the histological expression of DAPIT in several tissues of rat and man and show that it is highly expressed especially in cells with high aerobic metabolism and epithelial cells related to active transport of nutrients and ions. We propose that DAPIT, in addition to indicated subunit of mitochondrial F-ATPase, is also a subunit of lysosomal V-ATPase suggesting that it is a common component in different proton pumps.},
}
@article {pmid22701687,
year = {2012},
author = {van de Sande, WW},
title = {Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e38654},
pmid = {22701687},
issn = {1932-6203},
mesh = {Base Sequence ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Genome, Mitochondrial/*genetics ; Humans ; Likelihood Functions ; Madurella/*classification/*genetics ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mycetoma/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sudan ; },
abstract = {BACKGROUND: Madurella mycetomatis is the most common cause of human eumycetoma. The genus Madurella has been characterized by overall sterility on mycological media. Due to this sterility and the absence of other reliable morphological and ultrastructural characters, the taxonomic classification of Madurella has long been a challenge. Mitochondria are of monophyletic origin and mitochondrial genomes have been proven to be useful in phylogenetic analyses.<br><br>RESULTS: The first complete mitochondrial DNA genome of a mycetoma-causative agent was sequenced using 454 sequencing. The mitochondrial genome of M. mycetomatis is a circular DNA molecule with a size of 45,590 bp, encoding for the small and the large subunit rRNAs, 27 tRNAs, 11 genes encoding subunits of respiratory chain complexes, 2 ATP synthase subunits, 5 hypothetical proteins, 6 intronic proteins including the ribosomal protein rps3. In phylogenetic analyses using amino acid sequences of the proteins involved in respiratory chain complexes and the 2 ATP synthases it appeared that M. mycetomatis clustered together with members of the order Sordariales and that it was most closely related to Chaetomium thermophilum. Analyses of the gene order showed that within the order Sordariales a similar gene order is found. Furthermore also the tRNA order seemed mostly conserved.<br><br>CONCLUSION: Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.},
}
@article {pmid22723492,
year = {2012},
author = {Lease, HM and Klok, CJ and Kaiser, A and Harrison, JF},
title = {Body size is not critical for critical PO2 in scarabaeid and tenebrionid beetles.},
journal = {The Journal of experimental biology},
volume = {215},
number = {Pt 14},
pages = {2524-2533},
doi = {10.1242/jeb.057141},
pmid = {22723492},
issn = {1477-9145},
mesh = {Anaerobiosis ; Animals ; *Body Size ; Body Weight ; Carbon Dioxide/metabolism ; Coleoptera/*anatomy &amp; histology/genetics/*metabolism ; Flight, Animal/physiology ; Oxygen/*metabolism ; Partial Pressure ; Phylogeny ; Sample Size ; Species Specificity ; Tenebrio/*anatomy &amp; histology/genetics/*metabolism ; },
abstract = {Constraints on oxygen delivery potentially limit animal body size. Because diffusion rates are highly distance dependent, and because tracheal length increases with size, gas exchange was traditionally thought to be more difficult for larger insects. As yet the effect of body size on critical oxygen partial pressure (P(crit)) has not been measured for any clade of insect species for which there are interspecific data on tracheal scaling. We addressed this deficiency by measuring P(crit) over a 4150-fold mass range (ratio of largest to smallest species mean) of two families of Coleoptera (Tenebrionidae and Scarabaeidae). We exposed adult beetles to progressively lower oxygen levels and measured their ability to maintain CO(2) release rates. Absolute metabolic rates increased hypometrically with beetle body mass (M) at both normoxic (M(0.748)) and hypoxic (M(0.846)) conditions. P(crit), however, was independent of body size. Maximum overall conductances for oxygen from air to mitochondria (G(O(2),max)) matched metabolic rates as insects became larger, likely enabling the similar P(crit) values observed in large and small beetles. These data suggest that current atmospheric oxygen levels do not limit body size of insects because of limitations on gas exchange. However, increasing relative investment in the tracheal system in larger insects may produce trade-offs or meet spatial limits that constrain insect size.},
}
@article {pmid22747896,
year = {2012},
author = {Ruegg, K and Anderson, EC and Slabbekoorn, H},
title = {Differences in timing of migration and response to sexual signalling drive asymmetric hybridization across a migratory divide.},
journal = {Journal of evolutionary biology},
volume = {25},
number = {9},
pages = {1741-1750},
doi = {10.1111/j.1420-9101.2012.02554.x},
pmid = {22747896},
issn = {1420-9101},
mesh = {Amplified Fragment Length Polymorphism Analysis ; Animal Migration/*physiology ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Ecotype ; Female ; Gene Flow ; *Genetic Speciation ; Genetics, Population ; Hybridization, Genetic/genetics/*physiology ; Male ; Mating Preference, Animal/physiology ; Mitochondria/genetics ; Reproductive Isolation ; Seasons ; Singing/*physiology ; Songbirds/genetics/*physiology ; Sympatry ; Time Factors ; },
abstract = {Ecological traits and sexual signals may both contribute to the process of ecological speciation. Here we investigate the roles of an ecological trait, seasonal migratory behaviour and a sexual trait, song, in restricting or directing gene flow across a migratory divide in the Swainson's thrush (Catharus ustulatus). We show that short-distance migratory ecotypes wintering in Central America arrive earlier at the breeding grounds than long-distance migratory ecotypes wintering primarily in South America, providing the potential for some premating isolation. Playback experiments suggest that early- and late-arriving forms recognize each other as competitors, but that the early-arriving form responds more aggressively to a broader spectrum of stimuli. Genetic analysis suggests that hybridization occurs more often between males of the early-arriving ecotype and females of the late-arriving ecotype. Together our results suggest that differences in arrival times may reduce the temporal coincidence of mate choice, but asymmetry in response to heterotypic song may hinder complete divergence. These data provide further insight into the roles of ecological traits and sexual signals during the incipient stages of speciation.},
}
@article {pmid22768139,
year = {2012},
author = {Konrad, C and Kiss, G and Torocsik, B and Adam-Vizi, V and Chinopoulos, C},
title = {Absence of Ca2+-induced mitochondrial permeability transition but presence of bongkrekate-sensitive nucleotide exchange in C. crangon and P. serratus.},
journal = {PloS one},
volume = {7},
number = {6},
pages = {e39839},
pmid = {22768139},
issn = {1932-6203},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Bongkrekic Acid/*pharmacology ; Calcium/*pharmacology ; Crangonidae/drug effects/*metabolism ; Ligands ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Mitochondria/drug effects/metabolism/ultrastructure ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Permeability Transition Pore ; Molecular Sequence Data ; Nucleotides/*metabolism ; Palaemonidae/drug effects/*metabolism ; Permeability/drug effects ; Phylogeny ; Sequence Alignment ; },
abstract = {Mitochondria from the embryos of brine shrimp (Artemia franciscana) do not undergo Ca(2+)-induced permeability transition in the presence of a profound Ca(2+) uptake capacity. Furthermore, this crustacean is the only organism known to exhibit bongkrekate-insensitive mitochondrial adenine nucleotide exchange, prompting the conjecture that refractoriness to bongkrekate and absence of Ca(2+)-induced permeability transition are somehow related phenomena. Here we report that mitochondria isolated from two other crustaceans, brown shrimp (Crangon crangon) and common prawn (Palaemon serratus) exhibited bongkrekate-sensitive mitochondrial adenine nucleotide transport, but lacked a Ca(2+)-induced permeability transition. Ca(2+) uptake capacity was robust in the absence of adenine nucleotides in both crustaceans, unaffected by either bongkrekate or cyclosporin A. Transmission electron microscopy images of Ca(2+)-loaded mitochondria showed needle-like formations of electron-dense material strikingly similar to those observed in mitochondria from the hepatopancreas of blue crab (Callinectes sapidus) and the embryos of Artemia franciscana. Alignment analysis of the partial coding sequences of the adenine nucleotide translocase (ANT) expressed in Crangon crangon and Palaemon serratus versus the complete sequence expressed in Artemia franciscana reappraised the possibility of the 208-214 amino acid region for conferring sensitivity to bongkrekate. However, our findings suggest that the ability to undergo Ca(2+)-induced mitochondrial permeability transition and the sensitivity of adenine nucleotide translocase to bongkrekate are not necessarily related phenomena.},
}
@article {pmid22773745,
year = {2012},
author = {Manavski, N and Guyon, V and Meurer, J and Wienand, U and Brettschneider, R},
title = {An essential pentatricopeptide repeat protein facilitates 5' maturation and translation initiation of rps3 mRNA in maize mitochondria.},
journal = {The Plant cell},
volume = {24},
number = {7},
pages = {3087-3105},
pmid = {22773745},
issn = {1532-298X},
mesh = {5' Untranslated Regions/*genetics ; Amino Acid Sequence ; Base Sequence ; Endosperm/metabolism ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Organ Specificity ; Phenotype ; Phylogeny ; Plant Leaves/cytology/embryology/genetics/metabolism ; Plant Proteins/genetics/isolation &amp; purification/*metabolism ; Plants, Genetically Modified ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins ; Ribosomal Proteins/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Zea mays/cytology/embryology/genetics/*metabolism ; },
abstract = {Pentatricopeptide repeat (PPR) proteins are members of one of the largest nucleus-encoded protein families in plants. Here, we describe the previously uncharacterized maize (Zea mays) PPR gene, MPPR6, which was isolated from a Mutator-induced collection of maize kernel mutants by a cDNA-based forward genetic approach. Identification of a second mutant allele and cosegregation analysis confirmed correlation with the mutant phenotype. Histological investigations revealed that the mutation coincides with abnormities in the transfer cell layer, retardation of embryo development, and a considerable reduction of starch level. The function of MPPR6 is conserved across a wide phylogenetic distance as revealed by heterologous complementation of the Arabidopsis thaliana mutant in the orthologous APPR6 gene. MPPR6 appeared to be exclusively present in mitochondria. RNA coimmunoprecipitation and in vitro binding studies revealed a specific physical interaction of MPPR6 with the 5' untranslated region of ribosomal protein S3 (rps3) mRNA. Mapping of transcript termini showed specifically extended rps3 5' ends in the mppr6 mutant. Considerable reduction of mitochondrial translation was observed, indicating loss of RPS3 function. This is consistent with the appearance of truncated RPS3 protein lacking the N terminus in mppr6. Our results suggest that MPPR6 is directly involved in 5' maturation and translation initiation of rps3 mRNA.},
}
@article {pmid22797472,
year = {2012},
author = {Melonek, J and Matros, A and Trösch, M and Mock, HP and Krupinska, K},
title = {The core of chloroplast nucleoids contains architectural SWIB domain proteins.},
journal = {The Plant cell},
volume = {24},
number = {7},
pages = {3060-3073},
pmid = {22797472},
issn = {1532-298X},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Chromosomes, Plant/genetics/metabolism ; DNA-Binding Proteins/genetics/isolation &amp; purification/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Escherichia coli/cytology/genetics/metabolism ; Green Fluorescent Proteins ; Luminescent Proteins ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/*genetics/isolation &amp; purification/metabolism ; Protein Structure, Tertiary ; Proteomics ; Recombinant Fusion Proteins ; Sequence Alignment ; Spinacia oleracea/cytology/*genetics/metabolism ; Nicotiana/cytology/genetics/metabolism ; Red Fluorescent Protein ; },
abstract = {A highly enriched fraction of the transcriptionally active chromosome from chloroplasts of spinach (Spinacia oleracea) was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. Among such plastid nucleoid-associated candidate proteins a 12-kD SWIB (SWI/SNF complex B) domain-containing protein was identified. It belongs to a subgroup of low molecular mass SWIB domain proteins, which in Arabidopsis thaliana has six members (SWIB-1 to SWIB-6) with predictions for localization in the two DNA-containing organelles. Green/red fluorescent protein fusions of four of them were shown to be targeted to chloroplasts, where they colocalize with each other as well as with the plastid envelope DNA binding protein in structures corresponding to plastid nucleoids. For SWIB-6 and SWIB-4, a second localization in mitochondria and nucleus, respectively, could be observed. SWIB-4 has a histone H1 motif next to the SWIB domain and was shown to bind to DNA. Moreover, the recombinant SWIB-4 protein was shown to induce compaction and condensation of nucleoids and to functionally complement a mutant of Escherichia coli lacking the histone-like nucleoid structuring protein H-NS.},
}
@article {pmid22815925,
year = {2012},
author = {Gonçalves, RL and Oliveira, JH and Oliveira, GA and Andersen, JF and Oliveira, MF and Oliveira, PL and Barillas-Mury, C},
title = {Mitochondrial reactive oxygen species modulate mosquito susceptibility to Plasmodium infection.},
journal = {PloS one},
volume = {7},
number = {7},
pages = {e41083},
pmid = {22815925},
issn = {1932-6203},
support = {//Intramural NIH HHS/United States ; },
mesh = {Aedes/metabolism/*parasitology ; Animals ; Anopheles/metabolism/*parasitology ; Anti-Bacterial Agents/chemistry ; Cloning, Molecular ; Gene Silencing ; Hydrogen Peroxide/chemistry ; Malaria/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Models, Biological ; Molecular Conformation ; Oxidation-Reduction ; Oxidative Phosphorylation ; Oxygen Consumption ; Phylogeny ; Plasmodium berghei/*metabolism ; Protons ; Protozoan Proteins/genetics/*metabolism ; RNA, Double-Stranded/metabolism ; *Reactive Oxygen Species ; },
abstract = {BACKGROUND: Mitochondria perform multiple roles in cell biology, acting as the site of aerobic energy-transducing pathways and as an important source of reactive oxygen species (ROS) that modulate redox metabolism.<br><br>We demonstrate that a novel member of the mitochondrial transporter protein family, Anopheles gambiae mitochondrial carrier 1 (AgMC1), is required to maintain mitochondrial membrane potential in mosquito midgut cells and modulates epithelial responses to Plasmodium infection. AgMC1 silencing reduces mitochondrial membrane potential, resulting in increased proton-leak and uncoupling of oxidative phosphorylation. These metabolic changes reduce midgut ROS generation and increase A. gambiae susceptibility to Plasmodium infection.<br><br>CONCLUSION: We provide direct experimental evidence indicating that ROS derived from mitochondria can modulate mosquito epithelial responses to Plasmodium infection.},
}
@article {pmid22829778,
year = {2012},
author = {Häuser, R and Pech, M and Kijek, J and Yamamoto, H and Titz, B and Naeve, F and Tovchigrechko, A and Yamamoto, K and Szaflarski, W and Takeuchi, N and Stellberger, T and Diefenbacher, ME and Nierhaus, KH and Uetz, P},
title = {RsfA (YbeB) proteins are conserved ribosomal silencing factors.},
journal = {PLoS genetics},
volume = {8},
number = {7},
pages = {e1002815},
pmid = {22829778},
issn = {1553-7404},
support = {R01 GM079710/GM/NIGMS NIH HHS/United States ; R01GM79710/GM/NIGMS NIH HHS/United States ; },
mesh = {*Bacteria/genetics/growth &amp; development/metabolism ; Bacterial Proteins/genetics/metabolism ; Binding Sites ; Conserved Sequence ; *Eukaryota/genetics/growth &amp; development/metabolism ; HeLa Cells ; Humans ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Biosynthesis/genetics ; Ribosomal Proteins/*chemistry/metabolism ; Ribosome Subunits, Large/*chemistry/metabolism ; Sequence Homology, Amino Acid ; Transcription Factors/genetics/metabolism ; },
abstract = {The YbeB (DUF143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. While they have been shown to be associated with ribosomes, their molecular function remains unclear. Here we show that YbeB is a ribosomal silencing factor (RsfA) in the stationary growth phase and during the transition from rich to poor media. A knock-out of the rsfA gene shows two strong phenotypes: (i) the viability of the mutant cells are sharply impaired during stationary phase (as shown by viability competition assays), and (ii) during transition from rich to poor media the mutant cells adapt slowly and show a growth block of more than 10 hours (as shown by growth competition assays). RsfA silences translation by binding to the L14 protein of the large ribosomal subunit and, as a consequence, impairs subunit joining (as shown by molecular modeling, reporter gene analysis, in vitro translation assays, and sucrose gradient analysis). This particular interaction is conserved in all species tested, including Escherichia coli, Treponema pallidum, Streptococcus pneumoniae, Synechocystis PCC 6803, as well as human mitochondria and maize chloroplasts (as demonstrated by yeast two-hybrid tests, pull-downs, and mutagenesis). RsfA is unrelated to the eukaryotic ribosomal anti-association/60S-assembly factor eIF6, which also binds to L14, and is the first such factor in bacteria and organelles. RsfA helps cells to adapt to slow-growth/stationary phase conditions by down-regulating protein synthesis, one of the most energy-consuming processes in both bacterial and eukaryotic cells.},
}
@article {pmid22830417,
year = {2012},
author = {Evans, ML and Bernatchez, L},
title = {Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence.},
journal = {Journal of evolutionary biology},
volume = {25},
number = {9},
pages = {1823-1834},
doi = {10.1111/j.1420-9101.2012.02570.x},
pmid = {22830417},
issn = {1420-9101},
mesh = {Adaptation, Biological ; Adenosine Triphosphate/genetics/metabolism ; Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Genes, Mitochondrial ; Genetic Speciation ; Genetics, Population/methods ; Lakes ; Maine ; Mitochondria/genetics ; *Oxidative Phosphorylation ; Salmonidae/*genetics/metabolism/*physiology ; Species Specificity ; Statistics, Nonparametric ; Sympatry ; *Transcription, Genetic ; Up-Regulation ; },
abstract = {Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved 'dwarf' and 'normal' sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with the five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further studies are now needed to evaluate the contribution of genetically vs. plasticity driven variation in transcription associated with this critical physiological pathway.},
}
@article {pmid22840995,
year = {2012},
author = {Asensio, AC and Gil-Monreal, M and Pires, L and Gogorcena, Y and Aparicio-Tejo, PM and Moran, JF},
title = {Two Fe-superoxide dismutase families respond differently to stress and senescence in legumes.},
journal = {Journal of plant physiology},
volume = {169},
number = {13},
pages = {1253-1260},
doi = {10.1016/j.jplph.2012.04.019},
pmid = {22840995},
issn = {1618-1328},
mesh = {Antibodies/analysis ; Cytosol/*enzymology ; Fabaceae/*enzymology/growth &amp; development ; Isoenzymes ; Phylogeny ; Plant Leaves/enzymology ; Plant Roots/enzymology ; Plastids/*enzymology ; Glycine max/enzymology/growth &amp; development ; Stress, Physiological/*physiology ; Superoxide Dismutase/classification/immunology/*metabolism ; Time ; },
abstract = {Three main families of SODs in plants may be distinguished according to the metal in the active center: CuZnSODs, MnSOD, and FeSOD. CuZnSODs have two sub-families localized either in plant cell cytosol or in plastids, the MnSOD family is essentially restricted to mitochondria, and the FeSOD enzyme family has been typically localized into the plastid. Here, we describe, based on a phylogenetic tree and experimental data, the existence of two FeSOD sub-families: a plastidial localized sub-family that is universal to plants, and a cytosolic localized FeSOD sub-family observed in determinate-forming nodule legumes. Anti-cytosolic FeSOD (cyt_FeSOD) antibodies were employed, together with a novel antibody raised against plastidial FeSOD (p_FeSOD). Stress conditions, such as nitrate excess or drought, markedly increased cyt_FeSOD contents in soybean tissues. Also, cyt_FeSOD content and activity increased with age in both soybean and cowpea plants, while the cyt_CuZnSOD isozyme was predominant during early stages. p_FeSOD in leaves decreased with most of the stresses applied, but this isozyme markedly increased with abscisic acid in roots. The great differences observed for p_FeSOD and cyt_FeSOD contents in response to stress and aging in plant tissues reveal distinct functionality and confirm the existence of two immunologically differentiated FeSOD sub-families. The in-gel FeSOD activity patterns showed a good correlation to cyt_FeSOD contents but not to those of p_FeSOD. This indicates that cyt_FeSOD is the main active FeSOD in soybean and cowpea tissues. The diversity of functions associated with the complexity of FeSOD isoenzymes depending of the location is discussed.},
}
@article {pmid22841711,
year = {2012},
author = {Kluth, J and Schmidt, A and März, M and Krupinska, K and Lorbiecke, R},
title = {Arabidopsis Zinc Ribbon 3 is the ortholog of yeast mitochondrial HSP70 escort protein HEP1 and belongs to an ancient protein family in mitochondria and plastids.},
journal = {FEBS letters},
volume = {586},
number = {19},
pages = {3071-3076},
doi = {10.1016/j.febslet.2012.07.052},
pmid = {22841711},
issn = {1873-3468},
mesh = {Amino Acid Sequence ; Animals ; Arabidopsis Proteins/*genetics/metabolism ; Chloroplast Proteins/genetics/metabolism ; Genetic Complementation Test ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Humans ; Mitochondrial Proteins/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {ZR proteins belong to a phylogenetically conserved family of small zinc-ribbon proteins in plastids and mitochondria of higher plants. The function of these proteins is so far unclear. The mitochondrial proteins share sequence similarities with mitochondrial Hsp70 escort proteins (HEP) from Saccharomyces cerevisiae (HEP1) and human. Expression of the mitochondrial ZR protein from Arabidopsis, ZR3, rescued a hep1 knockout mutant from yeast. Accordingly, ZR3 was found to physically interact with mitochondrial Hsp70 from Arabidopsis. Our findings support the idea that mitochondrial and plastidic ZR proteins from higher plants are orthologs of HEP proteins.},
}
@article {pmid22876320,
year = {2012},
author = {Prole, DL and Taylor, CW},
title = {Identification and analysis of cation channel homologues in human pathogenic fungi.},
journal = {PloS one},
volume = {7},
number = {8},
pages = {e42404},
pmid = {22876320},
issn = {1932-6203},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Calcium Channels/chemistry/genetics/metabolism ; Cations/metabolism ; Fungi/*genetics/metabolism ; Humans ; Ion Channels/chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Potassium Channels/chemistry/genetics/metabolism ; Sequence Alignment ; Transient Receptor Potential Channels/chemistry/genetics/metabolism ; },
abstract = {Fungi are major causes of human, animal and plant disease. Human fungal infections can be fatal, but there are limited options for therapy, and resistance to commonly used anti-fungal drugs is widespread. The genomes of many fungi have recently been sequenced, allowing identification of proteins that may become targets for novel therapies. We examined the genomes of human fungal pathogens for genes encoding homologues of cation channels, which are prominent drug targets. Many of the fungal genomes examined contain genes encoding homologues of potassium (K(+)), calcium (Ca(2+)) and transient receptor potential (Trp) channels, but not sodium (Na(+)) channels or ligand-gated channels. Some fungal genomes contain multiple genes encoding homologues of K(+) and Trp channel subunits, and genes encoding novel homologues of voltage-gated K(v) channel subunits are found in Cryptococcus spp. Only a single gene encoding a homologue of a plasma membrane Ca(2+) channel was identified in the genome of each pathogenic fungus examined. These homologues are similar to the Cch1 Ca(2+) channel of Saccharomyces cerevisiae. The genomes of Aspergillus spp. and Cryptococcus spp., but not those of S. cerevisiae or the other pathogenic fungi examined, also encode homologues of the mitochondrial Ca(2+) uniporter (MCU). In contrast to humans, which express many K(+), Ca(2+) and Trp channels, the genomes of pathogenic fungi encode only very small numbers of K(+), Ca(2+) and Trp channel homologues. Furthermore, the sequences of fungal K(+), Ca(2+), Trp and MCU channels differ from those of human channels in regions that suggest differences in regulation and susceptibility to drugs.},
}
@article {pmid22884976,
year = {2012},
author = {Liesa, M and Qiu, W and Shirihai, OS},
title = {Mitochondrial ABC transporters function: the role of ABCB10 (ABC-me) as a novel player in cellular handling of reactive oxygen species.},
journal = {Biochimica et biophysica acta},
volume = {1823},
number = {10},
pages = {1945-1957},
pmid = {22884976},
issn = {0006-3002},
support = {R01 DK074778/DK/NIDDK NIH HHS/United States ; R01 HL071629/HL/NHLBI NIH HHS/United States ; R01HL071629-03/HL/NHLBI NIH HHS/United States ; R01DK074778/DK/NIDDK NIH HHS/United States ; },
mesh = {ATP-Binding Cassette Transporters/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Structure-Activity Relationship ; },
abstract = {Mitochondria are one of the major sources of reactive oxygen species (ROS) in the cell. When exceeding the capacity of antioxidant mechanisms, ROS production may lead to different pathologies, such as ischemia-reperfusion injury, neurodegeneration, anemia and ageing. As a consequence of the endosymbiotic origin of mitochondria, eukaryotic cells have developed different transport mechanisms that coordinate mitochondrial function with other cellular compartments. Four mitochondrial ATP-binding cassette (ABC) transporters have been described to date in mammals: ABCB6, ABCB8, ABCB7 and ABCB10. ABCB10 is located in the inner mitochondrial membrane forming homodimers, with the ATP binding domain facing the mitochondrial matrix. ABCB10 expression is highly induced during erythroid differentiation and its overexpression increases hemoglobin synthesis in erythroid cells. However, ABCB10 is also expressed in nonerythroid tissues, suggesting a role not directly related to hemoglobin synthesis. Recent evidence points toward ABCB10 as an important player in the protection from oxidative stress in mammals. In this regard, ABCB10 is required for normal erythropoiesis and cardiac recovery after ischemia-reperfusion, processes intimately related to mitochondrial ROS generation. Here, we review the current knowledge on mitochondrial ABC transporters and ABCB10 and discuss the potential mechanisms by which ABCB10 and its transport activity may regulate oxidative stress. We discuss ABCB10 as a potential therapeutic target for diseases in which increased mitochondrial ROS production and oxidative stress play a major role.},
}
@article {pmid22903087,
year = {2013},
author = {Pichrtová, M and Remias, D and Lewis, LA and Holzinger, A},
title = {Changes in phenolic compounds and cellular ultrastructure of arctic and antarctic strains of Zygnema (Zygnematophyceae, Streptophyta) after exposure to experimentally enhanced UV to PAR ratio.},
journal = {Microbial ecology},
volume = {65},
number = {1},
pages = {68-83},
pmid = {22903087},
issn = {1432-184X},
support = {P 24242/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Antarctic Regions ; Arctic Regions ; Chlorophyll/analysis ; Chlorophyll A ; Chromatography, High Pressure Liquid ; DNA, Plant/genetics ; Microscopy, Electron, Transmission ; Phenols/*analysis ; Photosynthesis/radiation effects ; Photosystem II Protein Complex/radiation effects ; Phylogeny ; Streptophyta/chemistry/*radiation effects/*ultrastructure ; *Ultraviolet Rays ; Xanthophylls/analysis ; },
abstract = {Ultraviolet (UV) radiation has become an important stress factor in polar regions due to anthropogenically induced ozone depletion. Although extensive research has been conducted on adaptations of polar organisms to this stress factor, few studies have focused on semi-terrestrial algae so far, in spite of their apparent vulnerability. This study investigates the effect of UV on two semi-terrestrial arctic strains (B, G) and one Antarctic strain (E) of the green alga Zygnema, isolated from Arctic and Antarctic habitats. Isolates of Zygnema were exposed to experimentally enhanced UV A and B (predominant UV A) to photosynthetic active radiation (PAR) ratio. The pigment content, photosynthetic performance and ultrastructure were studied by means of high-performance liquid chromatography (HPLC), chlorophyll a fluorescence and transmission electron microscopy (TEM). In addition, phylogenetic relationships of the investigated strains were characterised using rbcL sequences, which determined that the Antarctic isolate (E) and one of the Arctic isolates (B) were closely related, while G is a distinct lineage. The production of protective phenolic compounds was confirmed in all of the tested strains by HPLC analysis for both controls and UV-exposed samples. Moreover, in strain E, the content of phenolics increased significantly (p = 0.001) after UV treatment. Simultaneously, the maximum quantum yield of photosystem II photochemistry significantly decreased in UV-exposed strains E and G (p < 0.001), showing a clear stress response. The phenolics were most probably stored at the cell periphery in vacuoles and cytoplasmic bodies that appear as electron-dense particles when observed by TEM after high-pressure freeze fixation. While two strains reacted moderately on UV exposure in their ultrastructure, in strain G, damage was found in chloroplasts and mitochondria. Plastidal pigments and xanthophyll cycle pigments were investigated by HPLC analysis; UV A- and UV B-exposed samples had a higher deepoxidation state as controls, particularly evident in strain B. The results indicate that phenolics are involved in UV protection of Zygnema and also revealed different responses to UV stress across the three strains, suggesting that other protection mechanisms may be involved in these organisms.},
}
@article {pmid22917911,
year = {2012},
author = {Cao, LF and Niu, DF and He, SY and Kuang, HO and Hu, FL},
title = {[Phylogenetic relationships of honey bees (Hymenoptera: Apinae) inferred from mitochondrial and nuclear DNA sequences].},
journal = {Yi chuan = Hereditas},
volume = {34},
number = {8},
pages = {1057-1063},
doi = {10.3724/sp.j.1005.2012.01057},
pmid = {22917911},
issn = {0253-9772},
mesh = {Animals ; *Base Sequence ; Bees/*genetics ; DNA, Mitochondrial/*genetics ; *Genes, Insect ; Insect Proteins/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Species Specificity ; },
abstract = {The sequences of mitochondrial ND2, CO2, and 16S rRNA genes and nuclear ITPR gene were obtained from 22 samples of 5 Apis species from China. The characteristics of the sequences and the pairwise distances among species were analyzed. Phylogenetic trees were reconstructed for Apis species using maximum parsimony, neighbor-joining and maximum likelihood methods together with the sequences of the other 4 Apis species downloaded from GenBank. Results supported that Apis species were divided into three major clusters: dwarf bees (A. florea and A. andreniformis), giant bees (A. dorsata and A. laboriosa), and cavity-nesting bees (A. mellifera, A. cerana, A. koschevnikovi, A. nigrocinta, and A. nuluensis). The dwarf honey bees were confirmed as basal lineage. Our study also revealed a high level of genetic divergence between A. dorsata from Hainan Island and China mainland.},
}
@article {pmid22920973,
year = {2012},
author = {Hooks, KB and Turner, JE and Graham, IA and Runions, J and Hooks, MA},
title = {GFP-tagging of Arabidopsis acyl-activating enzymes raises the issue of peroxisome-chloroplast import competition versus dual localization.},
journal = {Journal of plant physiology},
volume = {169},
number = {16},
pages = {1631-1638},
doi = {10.1016/j.jplph.2012.05.026},
pmid = {22920973},
issn = {1618-1328},
support = {P19408//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/genetics/radiation effects/ultrastructure ; Arabidopsis Proteins/metabolism ; Chloroplasts/enzymology/*metabolism ; Coenzyme A Ligases/*metabolism ; Cytosol/enzymology/metabolism ; Green Fluorescent Proteins ; Light ; Luminescent Agents ; Microscopy, Confocal ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; Mutation ; Peroxisomes/enzymology/*metabolism ; Phenotype ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Seedlings/enzymology/genetics/radiation effects/ultrastructure ; Sequence Alignment ; },
abstract = {Protein sequence analysis of a subfamily of 18 Arabidopsis acyl-activating enzymes (AAE) for organelle targeting signals revealed that eight of them possessed putative peroxisomal targeting signals (PTS1), five of which belonged to Clade VI of the AAE superfamily. Peroxisomal localization was confirmed by confocal microscopy of green fluorescent protein (GFP)-AAE fusion proteins co-localizing with peroxisomal RFP. The sequence analysis also revealed that all enzymes of Clade VI possess N-terminal regions indicative of chloroplast transit peptides (cTP). Among the five Clade VI peroxisomal enzymes tested, masking the PTS1 signal with GFP redirected three to plastids. In addition, three other peroxisomal AAEs appeared to be redirected to plastids in AAE-GFP fusion constructs. Due to the lack of evidence supporting plastid localization, we propose that competition dictates the exclusive localization to peroxisomes. AAE2 of Clade VI was the only enzyme with a putative mitochondrial targeting sequence, and it appeared to be targeted to mitochondria. The remainder of the AAEs appeared to be localized to plastids or cytosol. The AAE9-GFP fusion protein appeared to be located within discreet structures within plastids that may be plastoglobules. AAE15-GFP, but not AAE16-GFP appeared to be located in the chloroplast envelope. The number of examples is increasing whereby proteins located within other compartments contribute to plastid function. We provide an example of this through the light-sensitive phenotype of mutants of AAE2.},
}
@article {pmid22923044,
year = {2012},
author = {Anderson, MZ and Baller, JA and Dulmage, K and Wigen, L and Berman, J},
title = {The three clades of the telomere-associated TLO gene family of Candida albicans have different splicing, localization, and expression features.},
journal = {Eukaryotic cell},
volume = {11},
number = {10},
pages = {1268-1275},
pmid = {22923044},
issn = {1535-9786},
support = {R01 AI075096/AI/NIAID NIH HHS/United States ; AI075096-03S1/AI/NIAID NIH HHS/United States ; },
mesh = {Candida albicans/*genetics/metabolism ; Cell Nucleus/metabolism ; Fungal Proteins/*genetics/metabolism ; Introns ; Mediator Complex/genetics/metabolism ; Mitochondria/metabolism ; *Multigene Family ; Phylogeny ; Protein Subunits/genetics/metabolism ; RNA Splicing ; Telomere-Binding Proteins/*genetics/metabolism ; Transcription, Genetic ; },
abstract = {Candida albicans grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated TLO gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in C. albicans. This correlates with increased virulence and clinical prevalence relative to those of other Candida clade species. The 14 expressed TLO gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally, TLOα genes are generally expressed at much higher levels than are TLOγ genes. We propose that expansion of the TLO gene family and the predicted role of Tlo proteins in transcription regulation provide C. albicans with the ability to adapt rapidly to the broad range of different environmental niches within the human host.},
}
@article {pmid22962606,
year = {2012},
author = {Wang, Z and Zheng, J and Zhang, X and Peng, J and Liu, J and Huang, Y},
title = {Identification and sequence analysis of metazoan tRNA 3'-end processing enzymes tRNase Zs.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e44264},
pmid = {22962606},
issn = {1932-6203},
mesh = {Alternative Splicing ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Nucleus/*enzymology/genetics ; Endoribonucleases/*chemistry/genetics/metabolism ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; *RNA 3' End Processing ; RNA Precursors/metabolism ; RNA, Transfer/*metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; },
abstract = {tRNase Z is the endonuclease responsible for removing the 3'-trailer sequences from precursor tRNAs, a prerequisite for the addition of the CCA sequence. It occurs in the short (tRNase Z(S)) and long (tRNase Z(L)) forms. Here we report the identification and sequence analysis of candidate tRNase Zs from 81 metazoan species. We found that the vast majority of deuterostomes, lophotrochozoans and lower metazoans have one tRNase Z(S) and one tRNase Z(L) genes, whereas ecdysozoans possess only a single tRNase Z(L) gene. Sequence analysis revealed that in metazoans, a single nuclear tRNase Z(L) gene is likely to encode both the nuclear and mitochondrial forms of tRNA 3'-end processing enzyme through mechanisms that include alternative translation initiation from two in-frame start codons and alternative splicing. Sequence conservation analysis revealed a variant PxKxRN motif, PxPxRG, which is located in the N-terminal region of tRNase Z(S)s. We also identified a previously unappreciated motif, AxDx, present in the C-terminal region of both tRNase Z(S)s and tRNase Z(L)s. The AxDx motif consisting mainly of a very short loop is potentially close enough to form hydrogen bonds with the loop containing the PxKxRN or PxPxRG motif. Through complementation analysis, we demonstrated the likely functional importance of the AxDx motif. In conclusion, our analysis supports the notion that in metazoans a single tRNase Z(L) has evolved to participate in both nuclear and mitochondrial tRNA 3'-end processing, whereas tRNase Z(S) may have evolved new functions. Our analysis also unveils new evolutionarily conserved motifs in tRNase Zs, including the C-terminal AxDx motif, which may have functional significance.},
}
@article {pmid22968790,
year = {2012},
author = {Zilberg, D and Jones, JB and Burger, MA and Nicholls, PK and Nolan, D and Crockford, M and Stephens, F},
title = {New pathological condition in cultured mulloway Argyrosomus japonicus: histopathological, ultrastructural and molecular studies.},
journal = {Diseases of aquatic organisms},
volume = {100},
number = {3},
pages = {219-230},
doi = {10.3354/dao02495},
pmid = {22968790},
issn = {0177-5103},
mesh = {Animals ; Aquaculture ; Fish Diseases/*pathology ; Kidney/pathology ; Kidney Diseases/pathology/*veterinary ; Myxozoa/classification/genetics/isolation &amp; purification ; Parasitic Diseases, Animal/*parasitology/pathology ; *Perciformes ; Phylogeny ; },
abstract = {Mulloway Argyrosomus japonicus is a native fish species in Western Australia, for which aquaculture production has recently been developed. A single cohort was stocked in a cage offshore at Geraldton, Western Australia, at a water depth of 6 m. Fish appeared healthy before stocking. Routine histological analysis was carried out from 10 mo post stocking and until completion of harvest (about 2.5 yr post stocking). No gross pathology was evident. Microscopically, however, granulomatous lesions were present in the kidneys of almost 100% of the fish examined. Enclosed in the granuloma was an aggregate of organisms, 4.2 to 5.4 µm in diameter. Kidney granulomas appeared as multi-focal aggregates. Granulomas at different stages of formation and finally fibrosing granulomas were observed. Granulomas also appeared infrequently in other organs: a few granulomas were found in the liver and spleen and a single granuloma in the heart of one fish. Transmission electron microscopy (TEM) revealed that the organism was composed of 2 cells, an outer cell enclosing an inner cell. The inner cell was surrounded by a double membrane and the outer cell by a single membrane. Cellular material, presumably of parasitic nature, surrounded the outer cell. The organism contained primitive mitochondria and abundant free ribosomes. Small subunit ribosomal DNA (SSU rDNA) sequence obtained by PCR revealed an 84% sequence identity with the myxosporean Latyspora scomberomori. Based on TEM and preliminary molecular results, we suggest that the organism is the extrasporogonic developmental stage of a myxozoan parasite, which failed to form spores in the mulloway host.},
}
@article {pmid22970129,
year = {2012},
author = {de Saint Pierre, M and Bravi, CM and Motti, JM and Fuku, N and Tanaka, M and Llop, E and Bonatto, SL and Moraga, M},
title = {An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups.},
journal = {PloS one},
volume = {7},
number = {9},
pages = {e43486},
pmid = {22970129},
issn = {1932-6203},
mesh = {Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; Ethnicity/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes/*genetics ; Humans ; Mitochondria/genetics ; *Models, Biological ; Molecular Sequence Data ; Mutation Rate ; Nucleic Acid Conformation ; Phylogeny ; South America ; Time Factors ; },
abstract = {After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.},
}
@article {pmid22982315,
year = {2012},
author = {Ma, HZ and Liu, GQ and Li, CW and Kang, GZ and Guo, TC},
title = {Identification of the TaBTF3 gene in wheat (Triticum aestivum L.) and the effect of its silencing on wheat chloroplast, mitochondria and mesophyll cell development.},
journal = {Biochemical and biophysical research communications},
volume = {426},
number = {4},
pages = {608-614},
doi = {10.1016/j.bbrc.2012.08.137},
pmid = {22982315},
issn = {1090-2104},
mesh = {Amino Acid Sequence ; Chloroplasts/genetics/*physiology ; Gene Expression Regulation, Plant ; Gene Silencing ; Genes, Mitochondrial ; Mesophyll Cells/metabolism/*physiology/ultrastructure ; Mitochondria/genetics/*physiology ; Molecular Sequence Data ; Nuclear Proteins/classification/genetics/*physiology ; Phylogeny ; Transcription Factors/classification/genetics/*physiology ; Transcription, Genetic ; Triticum/genetics/*growth &amp; development/ultrastructure ; },
abstract = {The full-length cDNA (882bp) and DNA (1742bp) sequences encoding a basic transcription factor 3, designated as TaBTF3, were first isolated from common wheat (Triticum aestivum L.). Subcellular localization studies revealed that the TaBTF3 protein was mainly located in the cytoplasm and nucleus. In TaBTF3-silenced transgenic wheat seedlings obtained using the Virus-induced gene silencing (VIGS) method, the chlorophyll pigment content was markedly reduced. However, the malonaldehyde (MDA) and H(2)O(2) contents were enhanced, and the structure of the wheat mesophyll cell was seriously damaged. Furthermore, transcripts of the chloroplast- and mitochondrial-encoded genes were significantly reduced in TaBTF3-silenced transgenic wheat plants. These results suggest that the TaBTF3 gene might function in the development of the wheat chloroplast, mitochondria and mesophyll cell. This paper is the first report to describe the involvement of TaBTF3 in maintaining the normal plant mesophyll cell structure.},
}
@article {pmid23046553,
year = {2012},
author = {Zhang, Y and Lin, J and Gao, Y},
title = {In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria.},
journal = {BMC systems biology},
volume = {6 Suppl 1},
number = {Suppl 1},
pages = {S20},
pmid = {23046553},
issn = {1752-0509},
mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; DNA, Bacterial/genetics/*metabolism ; DNA, Cruciform/genetics/*metabolism ; Genomics/*methods ; Homologous Recombination ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; },
abstract = {BACKGROUND: Homologous recombination is a fundamental cellular process that is most widely used by cells to rearrange genes and accurately repair DNA double-strand breaks. It may result in the formation of a critical intermediate named Holliday junction, which is a four-way DNA junction and needs to be resolved to allow chromosome segregation. Different Holliday junction resolution systems and enzymes have been characterized from all three domains of life. In bacteria, the RuvABC complex is the most important resolution system.<br><br>RESULTS: In this study, we conducted comparative genomics studies to identify a novel DNA-binding protein, YebC, which may serve as a key transcriptional regulator that mainly regulates the gene expression of RuvABC resolvasome in bacteria. On the other hand, the presence of YebC orthologs in some organisms lacking RuvC implied that it might participate in other biological processes. Further phylogenetic analysis of YebC protein sequences revealed two functionally different subtypes: YebC_I and YebC_II. Distribution of YebC_I is much wider than YebC_II. Only YebC_I proteins may play an important role in regulating RuvABC gene expression in bacteria. Investigation of YebC-like proteins in eukaryotes suggested that they may have originated from YebC_II proteins and evolved a new function as a specific translational activator in mitochondria. Finally, additional phylum-specific genes associated with Holliday junction resolution were predicted.<br><br>CONCLUSIONS: Overall, our data provide new insights into the basic mechanism of Holliday junction resolution and homologous recombination in bacteria.},
}
@article {pmid23069387,
year = {2013},
author = {Jeelani, G and Husain, A and Sato, D and Soga, T and Suematsu, M and Nozaki, T},
title = {Biochemical and functional characterization of novel NADH kinase in the enteric protozoan parasite Entamoeba histolytica.},
journal = {Biochimie},
volume = {95},
number = {2},
pages = {309-319},
doi = {10.1016/j.biochi.2012.09.034},
pmid = {23069387},
issn = {1638-6183},
mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Cations, Divalent ; Conserved Sequence ; Entamoeba histolytica/drug effects/*enzymology/genetics ; Gene Expression/drug effects ; Hydrogen Peroxide/pharmacology ; Kinetics ; Magnesium/chemistry ; Molecular Sequence Data ; NAD/*metabolism ; NADP/*metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism ; Phylogeny ; Polyphosphates/chemistry ; Protozoan Proteins/genetics/*metabolism ; Reactive Oxygen Species ; Sequence Alignment ; Substrate Specificity ; },
abstract = {NAD(H) kinase catalyzes the phosphorylation of NAD(H) to form NADP(H) using ATP or inorganic polyphosphate as a phosphoryl donor. While the enzyme is conserved throughout prokaryotes and eukaryotes, remarkable differences in kinetic parameters including substrate preference, cation dependence, and physiological roles exist among the organisms. In the present study, we biochemically characterized NAD(H) kinase from the anaerobic/microaerophilic fermentative protozoan parasite Entamoeba histolytica, which lacks the conventional mitochondria capable of oxidative phosphorylation, leading to ATP. The kinetic properties of E. histolytica NAD(H) kinase recombinantly produced in Escherichia coli showed remarkable differences from those in bacteria and higher eukaryotes. Entamoeba NAD(H) kinase preferred NADH to NAD+ as the phosphoryl acceptor, utilized nucleoside triphosphates including ATP, GTP and deoxyATP, but not nucleoside di-, mono-phosphates, or inorganic polyphosphates, as the phosphoryl donor. To further understand the physiological roles in E. histolytica, we generated a stable transformant overexpressing NAD(H) kinase. Overexpression of NAD(H) kinase resulted in a 1.6-2 fold increase in the NADPH and NADP+ concentrations, a 40% reduction of the intracellular concentration of reactive oxygen species, and also led to increased tolerance toward hydrogen peroxide. These data, together with the essentially of NAD(H) kinase gene, underscore its significance as an NADP(H)-producing enzyme in this organism, and should help in designing of drugs targeting this enzyme.},
}
@article {pmid23072391,
year = {2012},
author = {Hsu, CY and Huang, PL and Chen, CM and Mao, CT and Chaw, SM},
title = {Tangy scent in Toona sinensis (Meliaceae) leaflets: isolation, functional characterization, and regulation of TsTPS1 and TsTPS2, two key terpene synthase genes in the biosynthesis of the scent compound.},
journal = {Current pharmaceutical biotechnology},
volume = {13},
number = {15},
pages = {2721-2732},
doi = {10.2174/138920112804724864},
pmid = {23072391},
issn = {1873-4316},
mesh = {Alkyl and Aryl Transferases/*genetics ; Amino Acid Sequence ; Genes, Plant/*genetics ; Meliaceae/*genetics/metabolism ; Molecular Sequence Data ; Odorants ; Phylogeny ; Plant Leaves/metabolism ; Plant Roots/metabolism ; Terpenes/isolation &amp; purification ; },
abstract = {Toona sinensis (Chinese Mahogany; Meliaceae), a subtropical deciduous tree, has a tangy scent resembling a mix of shallots and garlic. T. sinensis has long been known for its medicinal efficacy for treating enteritis, dysentery, itch and some cancers. However, its volatile components and their biosynthesis remain unexamined. In this study, we identified the spectrum of volatile compounds, isolated and functionally characterized two terpene synthase genes, Tstps1 and Tstps2, responsible for terpenoid synthesis in T. sinensis leaflets. TsTPS1 and TsTPS2 afford multiple products upon incubation with geranyl and farnesyl diphosphate respectively and mainly regulate the biosynthesis of (+) limonene and β- elemene in vitro, respectively. Headspace analyses show that 98% of leaflet volatiles were sesquiterpenoids and the developing leaflets released a greater diversity and quantity of volatiles than the mature leaflets did, and that β-elemene was the dominant component in both of them. These data suggested that tangy scent of T. sinensis consists of a combination of terpenoids and that Tstps2 was the major gene involved in the terpenoid biosynthesis in T. sinensis. In situ hybridization revealed that glandular cells of the leaf rachises accumulated abundant Tstps1 mRNA transcripts. Our GFP-based assay further unprecedentedly demonstrated that the transit-peptide of TsTPS1 targets specifically to the mitochondria.},
}
@article {pmid23090476,
year = {2012},
author = {Wanrooij, S and Miralles Fusté, J and Stewart, JB and Wanrooij, PH and Samuelsson, T and Larsson, NG and Gustafsson, CM and Falkenberg, M},
title = {In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication.},
journal = {EMBO reports},
volume = {13},
number = {12},
pages = {1130-1137},
pmid = {23090476},
issn = {1469-3178},
mesh = {Animals ; Conserved Sequence ; DNA/genetics ; DNA Helicases/genetics/metabolism ; DNA Replication/*genetics ; *DNA, Mitochondrial/biosynthesis/genetics ; Humans ; Mice ; Mitochondria/genetics ; Mitochondrial Proteins/genetics/metabolism ; Models, Genetic ; *Mutagenesis ; Phylogeny ; Replication Origin/*genetics ; Sequence Analysis, DNA ; },
abstract = {The mechanisms of mitochondrial DNA replication have been hotly debated for a decade. The strand-displacement model states that lagging-strand DNA synthesis is initiated from the origin of light-strand DNA replication (OriL), whereas the strand-coupled model implies that OriL is dispensable. Mammalian mitochondria cannot be transfected and the requirements of OriL in vivo have therefore not been addressed. We here use in vivo saturation mutagenesis to demonstrate that OriL is essential for mtDNA maintenance in the mouse. Biochemical and bioinformatic analyses show that OriL is functionally conserved in vertebrates. Our findings strongly support the strand-displacement model for mtDNA replication.},
}
@article {pmid23091033,
year = {2012},
author = {Beinart, RA and Sanders, JG and Faure, B and Sylva, SP and Lee, RW and Becker, EL and Gartman, A and Luther, GW and Seewald, JS and Fisher, CR and Girguis, PR},
title = {Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {47},
pages = {E3241-50},
pmid = {23091033},
issn = {1091-6490},
mesh = {Animals ; Bayes Theorem ; Carbon Isotopes ; *Ecosystem ; Electrochemical Techniques ; Electron Transport Complex IV/genetics ; Epsilonproteobacteria/*genetics ; Gammaproteobacteria/*genetics ; Gastropoda/*genetics/*microbiology ; Geography ; Haplotypes/genetics ; Hydrothermal Vents/*microbiology ; Isotope Labeling ; Mitochondria/genetics ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Protein Subunits/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; Temperature ; },
abstract = {Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus Alviniconcha) in the Lau Basin. We extensively surveyed Alviniconcha holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one ε-proteobacteria and two γ-proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with ε-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with γ-proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.},
}
@article {pmid23091644,
year = {2012},
author = {Biacchesi, S and Mérour, E and Lamoureux, A and Bernard, J and Brémont, M},
title = {Both STING and MAVS fish orthologs contribute to the induction of interferon mediated by RIG-I.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e47737},
pmid = {23091644},
issn = {1932-6203},
mesh = {Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Cell Line ; DEAD-box RNA Helicases/*metabolism ; DNA Viruses/immunology ; Endoplasmic Reticulum/metabolism ; Fish Diseases/genetics/immunology/virology ; Fishes/genetics/immunology/*metabolism ; Gene Expression ; Gene Expression Regulation ; Interferons/*biosynthesis ; Membrane Proteins/chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Binding ; Protein Transport ; RNA Viruses/immunology ; Sequence Alignment ; Virus Diseases/genetics/immunology/virology ; },
abstract = {Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR), the sensors for pathogen-associated molecular patterns (PAMPs), which induce the production of cytokines, such as type I interferons (IFN). Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs), and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS) protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER) adaptor: the stimulator of interferon genes (STING) protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs). STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING (HE856619); EPC STING (HE856620); EPC IRF3 (HE856621); EPC IFN promoter (HE856618).},
}
@article {pmid23096487,
year = {2013},
author = {Regalado, A and Pierri, CL and Bitetto, M and Laera, VL and Pimentel, C and Francisco, R and Passarinho, J and Chaves, MM and Agrimi, G},
title = {Characterization of mitochondrial dicarboxylate/tricarboxylate transporters from grape berries.},
journal = {Planta},
volume = {237},
number = {3},
pages = {693-703},
pmid = {23096487},
issn = {1432-2048},
mesh = {Amino Acid Sequence ; Carrier Proteins/chemistry/*metabolism ; Cloning, Molecular ; Dicarboxylic Acid Transporters/chemistry/*metabolism ; Escherichia coli/metabolism ; Fruit/enzymology/genetics/growth &amp; development/*metabolism ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Kinetics ; Malates/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Alignment ; Substrate Specificity ; Vitis/enzymology/genetics/growth &amp; development/*metabolism ; },
abstract = {Grape berries (Vitis vinifera L fruit) exhibit a double-sigmoid pattern of development that results from two successive periods of vacuolar swelling during which the nature of accumulated solutes changes significantly. Throughout the first period, called green or herbaceous stage, berries accumulate high levels of organic acids, mainly malate and tartrate. At the cellular level fruit acidity comprises both metabolism and vacuolar storage. Malic acid compartmentation is critical for optimal functioning of cytosolic enzymes. Therefore, the identification and characterization of the carriers involved in malate transport across sub-cellular compartments is of great importance. The decrease in acid content during grape berry ripening has been mainly associated to mitochondrial malate oxidation. However, no Vitis vinifera mitochondrial carrier involved in malate transport has been reported to date. Here we describe the identification of three V. vinifera mitochondrial dicarboxylate/tricarboxylate carriers (VvDTC1-3) putatively involved in mitochondrial malate, citrate and other di/tricarboxylates transport. The three VvDTCs are very similar, sharing a percentage of identical residues of at least 83 %. Expression analysis of the encoding VvDTC genes in grape berries shows that they are differentially regulated exhibiting a developmental pattern of expression. The simultaneous high expression of both VvDTC2 and VvDTC3 in grape berry mesocarp close to the onset of ripening suggests that these carriers might be involved in the transport of malate into mitochondria.},
}
@article {pmid23097428,
year = {2012},
author = {Chujo, T and Suzuki, T},
title = {Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs.},
journal = {RNA (New York, N.Y.)},
volume = {18},
number = {12},
pages = {2269-2276},
pmid = {23097428},
issn = {1469-9001},
mesh = {Adenosine/*analogs &amp; derivatives/metabolism ; Amino Acid Sequence ; Bacterial Proteins/genetics ; HeLa Cells ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Quaternary ; RNA/chemistry/genetics/*metabolism ; RNA, Mitochondrial ; RNA, Transfer/chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; tRNA Methyltransferases/chemistry/genetics/*metabolism ; },
abstract = {In human mitochondria, 1-methyladenosine (m[1]A) occurs at position 58 of tRNA(Leu(UUR)). In addition, partial m[1]A58 modifications have been found in human mitochondrial tRNA(Lys) and tRNA(Ser(UCN)). We identified human Trmt61B, which encodes a mitochondria-specific tRNA methyltransferase responsible for m[1]A58 in these three tRNAs. Trmt61B is dominantly localized to the mitochondria. m[1]A58 formation in human mitochondrial tRNA(Leu(UUR)) could be reconstituted in vitro using recombinant Trmt61B in the presence of Ado-Met as a methyl donor. Unlike the cytoplasmic tRNA m[1]A58 methyltransferase that consists of an α2β2 heterotetramer formed by Trmt61A and Trmt6, Trmt61B formed a homo-oligomer (presumably a homotetramer) that resembled the bacterial homotetrameric m[1]A58 methyltransferase. The bacterial origin of Trmt61B is supported by the results of the phylogenetic analysis.},
}
@article {pmid23106560,
year = {2012},
author = {Yu, JN and Han, SH and Kim, BH and Kryukov, AP and Kim, S and Lee, BY and Kwak, M},
title = {Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.},
journal = {Zoological science},
volume = {29},
number = {11},
pages = {753-760},
doi = {10.2108/zsj.29.753},
pmid = {23106560},
issn = {0289-0003},
mesh = {Animals ; Base Sequence ; Cytochromes b/genetics/*metabolism ; Demography ; Asia, Eastern ; Foxes/*genetics/physiology ; Gene Expression Regulation, Enzymologic ; Genetic Variation ; Mitochondria/*enzymology ; Phylogeny ; Republic of Korea ; },
abstract = {The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.},
}
@article {pmid23109865,
year = {2012},
author = {Mipam, TD and Wen, Y and Fu, C and Li, S and Zhao, H and Ai, Y and Li, L and Zhang, L and Zou, D},
title = {Maternal phylogeny of a newly-found yak population in china.},
journal = {International journal of molecular sciences},
volume = {13},
number = {9},
pages = {11455-11470},
pmid = {23109865},
issn = {1422-0067},
mesh = {Animals ; Base Sequence ; Cattle/anatomy &amp; histology/*genetics ; China ; DNA, Mitochondrial/*genetics ; Female ; Haplotypes/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length/*genetics ; Sequence Analysis, DNA/*veterinary ; },
abstract = {The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced for the whole mtDNA genome with a length of 16,371-bp. To compare with the data from other yaks, we extracted sequence data from Genebank, including D-loop of 398 yaks (from 12 breeds) and 55 wild yaks, and whole mitochondrial genomes of 53 yaks (from 12 breeds) and 21 wild yaks. A total of 127 haplotypes were defined, based on the D-loop data. Thirteen haplotypes were defined from 23 mtDNA D-loop sequences of Jinchuan yaks, six of which were shared only by Jinchuan, and one was shared by Jinchuan and wild yaks. The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively. It was also suggested that the Jinchuan population has no distinct different phylogenetic relationship in maternal inheritance with other breeds of yak. The highly haplotype diversity of the Pali breed, Jinchuan population, Maiwa breed and Jiulong breed suggested that the yak was first domesticated from wild yaks in the middle Himalayan region and the northern Hengduan Mountains. The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.},
}
@article {pmid23129619,
year = {2012},
author = {Sung, W and Tucker, AE and Doak, TG and Choi, E and Thomas, WK and Lynch, M},
title = {Extraordinary genome stability in the ciliate Paramecium tetraurelia.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {109},
number = {47},
pages = {19339-19344},
pmid = {23129619},
issn = {1091-6490},
support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Substitution/genetics ; DNA-Directed DNA Polymerase/metabolism ; Genome, Protozoan/*genetics ; Genomic Instability/*genetics ; Mitochondria/genetics ; Mutation Rate ; Paramecium tetraurelia/enzymology/*genetics ; Reproduction/genetics ; },
abstract = {Mutation plays a central role in all evolutionary processes and is also the basis of genetic disorders. Established base-substitution mutation rates in eukaryotes range between ∼5 × 10(-10) and 5 × 10(-8) per site per generation, but here we report a genome-wide estimate for Paramecium tetraurelia that is more than an order of magnitude lower than any previous eukaryotic estimate. Nevertheless, when the mutation rate per cell division is extrapolated to the length of the sexual cycle for this protist, the measure obtained is comparable to that for multicellular species with similar genome sizes. Because Paramecium has a transcriptionally silent germ-line nucleus, these results are consistent with the hypothesis that natural selection operates on the cumulative germ-line replication fidelity per episode of somatic gene expression, with the germ-line mutation rate per cell division evolving downward to the lower barrier imposed by random genetic drift. We observe ciliate-specific modifications of widely conserved amino acid sites in DNA polymerases as one potential explanation for unusually high levels of replication fidelity.},
}
@article {pmid23133520,
year = {2012},
author = {Micheletti, S and Parra, E and Routman, EJ},
title = {Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.},
journal = {PloS one},
volume = {7},
number = {10},
pages = {e47694},
pmid = {23133520},
issn = {1932-6203},
mesh = {Alleles ; Animals ; Base Sequence ; Color ; Cytochromes b/genetics ; DNA, Mitochondrial/metabolism ; Genetic Markers/genetics ; *Genetic Variation ; Genetics, Population ; Lizards/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; Receptor, Melanocortin, Type 1/genetics ; Sequence Analysis, DNA ; },
abstract = {Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.},
}
@article {pmid23135986,
year = {2013},
author = {Oner, Y and Calvo, JH and Elmaci, C},
title = {Investigation of the genetic diversity among native Turkish sheep breeds using mtDNA polymorphisms.},
journal = {Tropical animal health and production},
volume = {45},
number = {4},
pages = {947-951},
pmid = {23135986},
issn = {1573-7438},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; Female ; Genetic Variation ; Haplotypes/genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; Sheep/*genetics ; Turkey ; },
abstract = {A total of 135 unrelated sheep from nine Turkish native sheep breeds (Daglıc, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 ± 0.011, 0.01407 ± 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.},
}
@article {pmid23143325,
year = {2013},
author = {Kabashima, Y and Sone, N and Kusumoto, T and Sakamoto, J},
title = {Purification and characterization of malate:quinone oxidoreductase from thermophilic Bacillus sp. PS3.},
journal = {Journal of bioenergetics and biomembranes},
volume = {45},
number = {1-2},
pages = {131-136},
pmid = {23143325},
issn = {1573-6881},
mesh = {Bacillus/*enzymology/genetics ; Bacterial Proteins/*chemistry/genetics/*isolation &amp; purification/metabolism ; Geobacillus/enzymology/genetics ; Kinetics ; Membrane Proteins/*chemistry/genetics/*isolation &amp; purification/metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/genetics/*isolation &amp; purification/metabolism ; Phylogeny ; Vitamin K 2/chemistry ; },
abstract = {Several bacteria possess membrane-bound dehydrogenases other than cytosolic dehydrogenases in their respiratory chains. In many cases, the membrane-bound malate:quinone oxidoreductases (MQOs) are essential for growth. However, these MQOs are absent in mammalian mitochondria, and therefore may be a potential drug target for pathogenic bacteria. To characterize the kinetic properties of MQOs, we purified MQO from Bacillus sp. PS3, which is a gram-positive and thermophilic bacterium, and cloned the gene encoding MQO based on the obtained partial N-terminus sequence. Purified MQOs showed a molecular mass of ~90 kDa, which was estimated using gel filtration, and it consists of two subunits with a molecular mass of ~50 kDa. Phylogenetic analysis showed a high similarity to the MQO of the Geobacillus group rather than the Bacillus group. Additionally, the purified enzyme was thermostable and it retained menaquinol reduction activity at high temperatures. Although it is difficult to conduct experiments using menaquinol because of its instability, we were able to measure the oxidase activity of cytochrome bd-type quinol oxidase by using menaquinol-1 by coupling this molecule with the menaquinol reduction reaction using purified MQOs.},
}
@article {pmid23171165,
year = {2012},
author = {Wylezich, C and Karpov, SA and Mylnikov, AP and Anderson, R and Jürgens, K},
title = {Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae.},
journal = {BMC microbiology},
volume = {12},
number = {},
pages = {271},
pmid = {23171165},
issn = {1471-2180},
mesh = {Anaerobiosis ; Choanoflagellata/*classification/isolation &amp; purification/physiology/*ultrastructure ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Mitochondria/*ultrastructure ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Seawater/*parasitology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities.<br><br>RESULTS: Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches.<br><br>CONCLUSIONS: Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.},
}
@article {pmid23178692,
year = {2013},
author = {Shi, Y and Zhao, Z and Zhu, X and Chen, K and Zhang, Q},
title = {Expression and functional characterization of a gene associated with retinoid-interferon-induced mortality 19 (GRIM-19) from orange-spotted grouper (Epinephelus coioides).},
journal = {Fish &amp; shellfish immunology},
volume = {34},
number = {1},
pages = {273-279},
doi = {10.1016/j.fsi.2012.11.017},
pmid = {23178692},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Bass/*genetics/*metabolism ; Caspases/metabolism ; Cloning, Molecular ; DNA, Complementary/genetics ; Fish Proteins/*genetics/*metabolism ; HeLa Cells ; Humans ; Interferon-beta/metabolism ; Lipopolysaccharides/pharmacology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; RNA/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Transfection ; Tretinoin/metabolism ; },
abstract = {GRIM-19 is a nuclear encoded subunit of complex I that has been implicated in apoptosis. The protein participates in multiple functions including the innate immune response. GRIM-19 has been studied in humans and other mammals; however, fish GRIM-19 has not been well characterized. In this study, a new GRIM-19 gene, EcGRIM-19, was isolated from the orange-spotted grouper (Epinephelus coioides) cDNA library, which was constructed following LPS treatment. EcGRIM-19 is a 582-bp gene that encodes a 144-amino acid protein. The gene is a true ortholog of mammalian GRIM-19. EcGRIM-19 exhibits ubiquitous and constitutive expression in the different tissues of the orange-spotted grouper. The expression levels of EcGRIM-19 are altered in the gill, spleen, kidney and liver after induction with LPS. The subcellular localization analysis demonstrated that the EcGRIM-19 protein is localized predominantly in the mitochondria. In addition, amino acids 30-50 of the protein are responsible for the mitochondrial localization of EcGRIM-19. The caspase assay demonstrated that the overexpression of GRIM-19 enhanced the cellular sensitivity to interferon(IFN)-β- and retinoic acid (RA)-induced death in HeLa cells. The data presented in this study are important for further understanding the EcGRIM-19 gene function in fish.},
}
@article {pmid23199478,
year = {2013},
author = {Bertucci, A and Moya, A and Tambutté, S and Allemand, D and Supuran, CT and Zoccola, D},
title = {Carbonic anhydrases in anthozoan corals-A review.},
journal = {Bioorganic &amp; medicinal chemistry},
volume = {21},
number = {6},
pages = {1437-1450},
doi = {10.1016/j.bmc.2012.10.024},
pmid = {23199478},
issn = {1464-3391},
mesh = {Animals ; Anthozoa/*enzymology ; Calcium Carbonate/chemistry/metabolism ; Carbonic Anhydrase Inhibitors/chemistry/metabolism ; Carbonic Anhydrases/chemistry/classification/*metabolism ; Humans ; Isoenzymes/chemistry/metabolism ; Mitochondria/enzymology ; Photosynthesis ; Phylogeny ; Symbiosis ; },
abstract = {Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. The deposition of massive calcium carbonate skeletons (biomineralization or calcification) by scleractinian corals forms the coral reef framework/architecture that serves as habitat for a large diversity of organisms. This process would not be possible without the intimate symbiosis between corals and photosynthetic dinoflagellates, commonly called zooxanthellae. Carbonic anhydrases play major roles in those two essential processes of coral's physiology: they are involved in the carbon supply for calcium carbonate precipitation as well as in carbon-concentrating mechanisms for symbiont photosynthesis. Here, we review the current understanding of diversity and function of carbonic anhydrases in corals and discuss the perspective of theses enzymes as a key to understanding impacts of environmental changes on coral reefs.},
}
@article {pmid23199630,
year = {2012},
author = {Fadhlaoui-Zid, K and Knittweis, L and Aurelle, D and Nafkha, C and Ezzeddine, S and Fiorentino, F and Ghmati, H and Ceriola, L and Jarboui, O and Maltagliati, F},
title = {Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene.},
journal = {Comptes rendus biologies},
volume = {335},
number = {10-11},
pages = {625-636},
doi = {10.1016/j.crvi.2012.10.004},
pmid = {23199630},
issn = {1768-3238},
mesh = {Algorithms ; Analysis of Variance ; Animals ; DNA/biosynthesis/genetics ; DNA, Mitochondrial/genetics ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Variation ; Mediterranean Sea ; Mitochondria/*enzymology/*genetics ; Molecular Biology ; Octopodiformes/*enzymology/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {The polymorphism of the mitochondrial gene cytochrome oxidase III was studied in the Mediterranean octopus, Octopus vulgaris Cuvier, 1797. A total of 202 specimens from seven sampling sites were analysed with the aim of elucidating patterns of genetic structure in the central Mediterranean Sea and to give an insight into the phylogeny of the Octopus genus. Phylogenetic analyses showed that individuals from the central Mediterranean belong to the O. vulgaris species whose limits should nevertheless be clarified. Concerning genetic structure, two high-frequency haplotypes were present in all locations. The overall genetic divergence (Φ(ST)=0.05, P<0.05) indicated a significant genetic structuring in the study area and an AMOVA highlighted a significant break between western and eastern Mediterranean basins (Φ(CT)=0.094, P<0.05). Possible explanations for the observed patterns of genetic structuring are discussed with reference to their relevance for fisheries management.},
}
@article {pmid23199631,
year = {2012},
author = {Kacem, H and Bakhoum, AJ and Eira, C and Neifar, L and Miquel, J},
title = {Ultrastructural characters of the spermatozoon of the digenean Hypocreadium caputvadum Kacem et al., 2011 (Lepocreadioidea: Lepocreadiidae), an intestinal parasite of Balistes capriscus in Tunisia.},
journal = {Comptes rendus biologies},
volume = {335},
number = {10-11},
pages = {637-644},
doi = {10.1016/j.crvi.2012.10.002},
pmid = {23199631},
issn = {1768-3238},
mesh = {Animals ; Axoneme/ultrastructure ; Cell Membrane/ultrastructure ; Glycogen/metabolism ; Indicators and Reagents ; Intestines/*parasitology ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Parasites ; Phylogeny ; Spermatozoa/*ultrastructure ; Tetraodontiformes/*parasitology ; Trematoda/*physiology ; Tunisia ; },
abstract = {The ultrastructural organization of the spermatozoon of the digenean Hypocreadium caputvadum (Lepocreadioidea: Lepocreadiidae) is described. Live digeneans were collected from Balistes capriscus (Teleostei: Balistidae) from the Gulf of Gabès, Tunisia (Eastern Mediterranean Sea). The mature spermatozoon of H. caputvadum shows several ultrastructural characters such as two axonemes of different lengths exhibiting the classical 9+"1" trepaxonematan pattern, a nucleus, two mitochondria, granules of glycogen, external ornamentation of the plasma membrane and two bundles of parallel cortical microtubules. Moreover, in the anterior extremity, the second axoneme is partly surrounded by a discontinuous and submembranous layer of electron-dense material. Our study provides new data on the spermatozoon of H. caputvadum in order to improve the understanding of phylogenetic relationships in the Digenea, particularly in the superfamily Lepocreadioidea. In this context, the electron-dense material surrounding one of the axonemes in the anterior spermatozoon extremity constitutes the unique distinguishing ultrastructural character of lepocreadioideans, and it is present in spermatozoa of lepocreadiids, aephnidiogenids and gyliauchenids.},
}
@article {pmid23199637,
year = {2012},
author = {Durand, JD and Chen, WJ and Shen, KN and Fu, C and Borsa, P},
title = {Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae).},
journal = {Comptes rendus biologies},
volume = {335},
number = {10-11},
pages = {687-697},
doi = {10.1016/j.crvi.2012.09.005},
pmid = {23199637},
issn = {1768-3238},
mesh = {Animals ; Classification ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics/*physiology ; Molecular Biology ; Phylogeny ; Sequence Analysis, DNA ; Smegmamorpha/*classification/*genetics ; Species Specificity ; },
abstract = {A comprehensive mitochondrial phylogeny of the family Mugilidae (Durand et al., Mol. Phylogenet. Evol. 64 (2012) 73-92) demonstrated the polyphyly or paraphyly of a proportion of the 20 genera in the family. Based on these results, here we propose a revised classification with 25 genera, including 15 genera currently recognized as valid (Agonostomus, Aldrichetta, Cestraeus, Chaenomugil, Chelon, Crenimugil, Ellochelon, Joturus, Mugil, Myxus, Neomyxus, Oedalechilus, Rhinomugil, Sicamugil and Trachystoma), 7 resurrected genera [Dajaus (for Agonostomus monticola), Gracilimugil (for Liza argentea), Minimugil (for Sicamugil cascasia), Osteomugil (for several species currently under Moolgarda and Valamugil, including M. cunnesius, M. engeli, M. perusii, and V. robustus), Planiliza (for Indo-Pacific Chelon spp., Indo-Pacific Liza spp., and Paramugil parmatus), Plicomugil (for Oedalechilus labiosus), and Squalomugil (for Rhinomugil nasutus)] and 3 new genera: Neochelon gen. nov. (for Liza falcipinnis), Parachelon gen. nov. (for L. grandisquamis) and Pseudomyxus gen. nov. (for Myxus capensis). Genus Chelon was shown to include exclusively Chelon spp. and Liza spp. from the Atlantic and the Mediterranean, and Liza spp. species endemic to eastern southern Africa. Genus Crenimugil should now include C. crenilabis, Moolgarda seheli and V. buchanani. Genus names Liza, Moolgarda, Paramugil, Valamugil and Xenomugil should be abandoned because they are no longer valid. Further genetic evidence is required to confirm or infirm the validity of the genus Paracrenimugil Senou 1988. The mitochondrial phylogeny of the 25 genera from the present revision is the following: [(Sicamugil, (Minimugil, Rhinomugil)); Trachystoma; ((Myxus, Neomyxus), (Cestraeus, Chaenomugil, (Agonostomus, Dajaus, Joturus), Mugil)); (Aldrichetta, Gracilimugil); Neochelon gen. nov.; (Pseudomyxus gen. nov., (Chelon, Oedalechilus, Planiliza, Parachelon gen. nov.)); ((Squalomugil, (Ellochelon, Plicomugil)), (Crenimugil, Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level.},
}
@article {pmid23209127,
year = {2013},
author = {Chauton, MS and Winge, P and Brembu, T and Vadstein, O and Bones, AM},
title = {Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles.},
journal = {Plant physiology},
volume = {161},
number = {2},
pages = {1034-1048},
pmid = {23209127},
issn = {1532-2548},
mesh = {Acclimatization/genetics/radiation effects ; Carbohydrate Metabolism/genetics/radiation effects ; Carbon/*metabolism ; Carbon Cycle/*genetics ; Diatoms/genetics/metabolism/*radiation effects ; Gene Expression Profiling ; Gene Expression Regulation/*radiation effects ; Gluconeogenesis/genetics/radiation effects ; Glycolysis/genetics/radiation effects ; Lipid Metabolism/genetics/radiation effects ; Membrane Transport Proteins/classification/genetics ; Mitochondria/genetics/metabolism/radiation effects ; Mitosis/genetics/radiation effects ; Monocarboxylic Acid Transporters ; Oligonucleotide Array Sequence Analysis ; *Photoperiod ; Phylogeny ; Plastids/genetics/metabolism/radiation effects ; Pyruvate Dehydrogenase Complex/classification/genetics ; },
abstract = {The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.},
}
@article {pmid23212402,
year = {2012},
author = {Hao, XL and Yao, HF and Cheng, YZ and Wang, RX},
title = {Homology cloning, sequence characterization, and expression analysis of cDNA encoding electron transfer flavoprotein beta polypeptide in mud crab (Scylla paramamosain).},
journal = {Genetics and molecular research : GMR},
volume = {11},
number = {4},
pages = {4316-4322},
doi = {10.4238/2012.November.12.11},
pmid = {23212402},
issn = {1676-5680},
mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Brachyura/*genetics/metabolism ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary/genetics ; Electron-Transferring Flavoproteins/chemistry/*genetics/metabolism ; Gene Expression ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Electron transfer flavoproteins (ETFs) are αβ-heterodimers found in eukaryotic mitochondria and bacteria. Herein we report a full-length complementary DNA of a mud crab (Scylla paramamosain) ETF β subunit (Scpa-ETFB) isolated with a homology cloning strategy. The complete complementary DNA of the Scpa-ETFB contains a 17-nt 5'-untranslated region, a 765-nt open reading frame encoding 254 amino acids, and a 248-nt 3'-untranslated region. The high identity of Scpa-ETFB with ETFB in other organisms indicated that Scpa-ETFB is a new member of the ETFB family. Although the conserved motif associated with flavin adenine dinucleotide binding is absent in Scpa-ETFB, the signature sequences of the ETF superfamily were identified. Using reverse transcriptase polymerase chain reaction, we detected the messenger RNA transcript of Scpa-ETFB in high levels in the tissues of the hepatopancreas, ovary, heart, and muscle. Phylogenetic analysis showed that Scpa-ETFB is most closely related to the ETFB genes of Caligus rogercresseyi and Lepeophtheirus salmonis. These results provided basic information for elucidating the molecular mechanism of energy production in the mud crab.},
}
@article {pmid23220190,
year = {2013},
author = {Yao, P and Lu, W and Meng, F and Wang, X and Xu, B and Guo, X},
title = {Molecular cloning, expression and oxidative stress response of a mitochondrial thioredoxin peroxidase gene (AccTpx-3) from Apis cerana cerana.},
journal = {Journal of insect physiology},
volume = {59},
number = {3},
pages = {273-282},
doi = {10.1016/j.jinsphys.2012.11.005},
pmid = {23220190},
issn = {1879-1611},
mesh = {Amino Acid Sequence ; Animals ; Bees/classification/*enzymology/genetics/*metabolism ; *Cloning, Molecular ; Insect Proteins/chemistry/*genetics/metabolism ; Mitochondria/chemistry/*enzymology/metabolism ; Molecular Sequence Data ; Oxidative Stress ; Peroxiredoxins/chemistry/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; },
abstract = {Thioredoxin peroxidase (Tpxs) plays an important role in maintaining redox homeostasis and in protecting organisms from the accumulation of toxic reactive oxygen species (ROS). Here, we isolated a mitochondrial thioredoxin peroxidase gene from Apis cerana cerana, AccTpx-3. The open reading frame (ORF) of AccTpx-3 is 729 bp in length and encodes a predicted protein of 242 amino acids, 27.084 kDa and an isoelectric point of 8.70. Furthermore, the 980 bp 5' flanking region was cloned, and the transcription factor binding sites were predicted. A quantitative RT-PCR (Q-PCR) analysis indicated that AccTpx-3 was expressed higher in muscle than other tissues, with its highest expression occurring on the fourth day of the larval stage, followed by the fifteenth day of the adult stage. Moreover, the expression of the AccTpx-3 transcript was upregulated by such abiotic stresses as 4°C, 42°C, H(2)O(2), cyhalothrin, acaricide and phoxime treatments. In contrast, AccTpx-3 transcription was downregulated by other abiotic stresses, including 16°C, 25°C, ultraviolet light and HgCl(2). Recombinant AccTpx-3 protein acted as a potent antioxidant that resisted paraquat-induced oxidative stress and protected DNA from oxidative damage. Taken together, these results suggest that the AccTpx-3 protein is an antioxidant enzyme that may protect organisms from oxidative stress.},
}
@article {pmid23227215,
year = {2012},
author = {Schmidt-Roach, S and Miller, KJ and Woolsey, E and Gerlach, G and Baird, AH},
title = {Broadcast spawning by Pocillopora species on the Great Barrier Reef.},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e50847},
pmid = {23227215},
issn = {1932-6203},
mesh = {Animals ; Anthozoa/*physiology ; Australia ; *Coral Reefs ; Female ; Islands ; Male ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; Reproduction/physiology ; Species Specificity ; },
abstract = {The coral genus Pocillopora is one of the few to include some species that broadcast spawn gametes and some species that brood larvae, although reports of reproductive mode and timing vary within and among species across their range. Notably, the ubiquitous Pocillopora damicornis has been described as both a brooder and spawner, although evidence of broadcast spawning is rare. Here, we report observations of broadcast-spawning in four species of Pocillopora on the Great Barrier Reef (GBR), including P. damicornis. All species spawned predictably during the early morning, two days following the full moon, and spawning was observed in multiple months over the summer period (November to February). Eggs and sperm were free-spawned concurrently. Eggs were negatively buoyant and contained Symbiodinium. This newfound knowledge on the mode, timing and regularity of broadcast spawning in Pocillopora spp. on the GBR brings us one step closer to elucidating the complex reproductive ecology of these species.},
}
@article {pmid23251637,
year = {2012},
author = {Alex, A and Vasconcelos, V and Tamagnini, P and Santos, A and Antunes, A},
title = {Unusual symbiotic cyanobacteria association in the genetically diverse intertidal marine sponge Hymeniacidon perlevis (Demospongiae, Halichondrida).},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e51834},
pmid = {23251637},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; Cyanobacteria/classification/*genetics ; Ecosystem ; Genetic Variation ; Microscopy, Electron, Transmission/methods ; Mitochondria/genetics ; Phylogeny ; Porifera/*genetics/*microbiology ; Portugal ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; },
abstract = {Cyanobacteria represent one of the most common members of the sponge-associated bacterial community and are abundant symbionts of coral reef ecosystems. In this study we used Transmission Electron Microscopy (TEM) and molecular techniques (16S rRNA gene marker) to characterize the spatial distribution of cyanobionts in the widely dispersed marine intertidal sponge Hymeniacidon perlevis along the coast of Portugal (Atlantic Ocean). We described new sponge associated cyanobacterial morphotypes (Xenococcus-like) and we further observed Acaryochloris sp. as a sponge symbiont, previously only reported in association with ascidians. Besides these two unique cyanobacteria, H. perlevis predominantly harbored Synechococcus sp. and uncultured marine cyanobacteria. Our study supports the hypothesis that the community of sponge cyanobionts varies irrespective of the geographical location and is likely influenced by seasonal fluctuations. The observed multiple cyanobacterial association among sponges of the same host species over a large distance may be attributed to horizontal transfer of symbionts. This may explain the absence of a co-evolutionary pattern between the sponge host and its symbionts. Finally, in spite of the short geographic sampling distance covered, we observed an unexpected high intra-specific genetic diversity in H. perlevis using the mitochondrial genes ATP6 (π = 0.00177), COI (π = 0.00241) and intergenic spacer SP1 (π = 0.00277) relative to the levels of genetic variation of marine sponges elsewhere. Our study suggests that genotypic variation among the sponge host H. perlevis and the associated symbiotic cyanobacteria diversity may be larger than previously recognized.},
}
@article {pmid23266212,
year = {2013},
author = {Daugbjerg, N and Jensen, MH and Hansen, PJ},
title = {Using nuclear-encoded LSU and SSU rDNA sequences to identify the eukaryotic endosymbiont in Amphisolenia bidentata (Dinophyceae).},
journal = {Protist},
volume = {164},
number = {3},
pages = {411-422},
doi = {10.1016/j.protis.2012.10.001},
pmid = {23266212},
issn = {1618-0941},
mesh = {Alveolata/classification/*genetics ; Animals ; Chloroplasts/genetics ; DNA, Ribosomal/*analysis ; Eukaryota/*classification/*genetics ; Indian Ocean ; Microscopy, Fluorescence ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; },
abstract = {The marine dinoflagellate Amphisolenia bidentata possesses complete intracellular symbionts of prokaryotic and eukaryotic origin. This was confirmed ultrastructurally little over 20 years ago when it was showed that the eukaryotic endosymbiont had a nucleus, a chloroplast and mitochondria. We collected Amphisolenia bidentata cells in the Indian Ocean and the identity of the eukaryotic endosymbionts was investigated using both microscopical and molecular methods. Individual specimens of Amphisolenia bidentata were identified by light microscopy and selected for single-cell PCR. Host and endosymbiont nuclear-encoded LSU and SSU rDNA sequences were determined by PCR cloning. Blast searches showed the endosymbiont LSU sequence to have affinity to Pelagophyceae, an algal class within Chromalveolata that also includes dinoflagellates. Since more SSU rDNA sequences from pelagophytes are available we performed a SSU based phylogeny of chromalveolates. The eukaryotic endosymbiont clustered within a clade comprising flagellated and coccoid pelagophytes whereas Amphisolenia bidentata formed a sister taxon to other dinophysioids. Molecular data therefore resolved the endosymbiont in A. bidentata being a pelagophyte and thus identified the ninth novel chloroplast type in dinoflagellates and a new species association. Based on sequence divergence estimates and phylogenetic inference the endosymbiont in A. bidentata likely represents an undescribed genus of pelagophytes.},
}
@article {pmid23269202,
year = {2013},
author = {Silveira, P and Belo, NO and Lacorte, GA and Kolesnikovas, CK and Vanstreels, RE and Steindel, M and Catão-Dias, JL and Valkiūnas, G and Braga, EM},
title = {Parasitological and new molecular-phylogenetic characterization of the malaria parasite Plasmodium tejerai in South American penguins.},
journal = {Parasitology international},
volume = {62},
number = {2},
pages = {165-171},
doi = {10.1016/j.parint.2012.12.004},
pmid = {23269202},
issn = {1873-0329},
mesh = {Animals ; Base Sequence ; Brazil ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/genetics ; Endothelial Cells/parasitology ; Fatal Outcome ; Macrophages/parasitology ; Malaria, Avian/blood/*parasitology/pathology ; Mitochondria/metabolism ; Molecular Sequence Data ; Myocardium/pathology ; Parasitemia ; Phylogeny ; Plasmodium/classification/cytology/genetics/*isolation &amp; purification ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spheniscidae/*parasitology ; },
abstract = {This study is the first report on mortality of Spheniscus magellanicus, penguin of South America, caused by Plasmodium tejerai, which was identified using morphological and molecular analyses. Blood stages (trophozoites, meronts and gametocytes) were reported and illustrated. The necropsy revealed marked splenomegaly and pulmonary edema, as well as moderate hepatomegaly and hydropericardium. The histopathology revealed the presence of tissue meronts in the macrophages and endothelial cells of multiple organs. The molecular analyses showed 5.6% of genetic divergence in cytochrome b gene between P. tejerai and Plasmodium relictum. Morphology of blood and tissue stages of P. tejerai is similar to P. relictum; the distinction between these two species requires experience in the identification of avian Plasmodium species. Molecular studies associated with reliably identified morphological species are useful for barcoding and comparisons with previous studies of wildlife malaria infections as well as for posterior phylogenetic and phylogeographic studies. S. magellanicus is a new host record of P. tejerai, which is the virulent parasite and worth more attention in avian conservation and veterinary medicine projects in South America.},
}
@article {pmid23269854,
year = {2013},
author = {Payo, DA and Leliaert, F and Verbruggen, H and D'hondt, S and Calumpong, HP and De Clerck, O},
title = {Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines.},
journal = {Proceedings. Biological sciences},
volume = {280},
number = {1753},
pages = {20122660},
pmid = {23269854},
issn = {1471-2954},
mesh = {Algal Proteins/genetics/metabolism ; *Biodiversity ; Cell Nucleus/genetics ; Conservation of Natural Resources ; Mitochondria/genetics ; Molecular Sequence Data ; Philippines ; Phylogeny ; Plastids/genetics ; Polymerase Chain Reaction ; Rhodophyta/*classification/cytology/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {We investigated species diversity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-West Pacific (Portieria hornemannii), DNA-based species delimitation resulted in the recognition of 21 species within the Philippines. Species distributions were found to be highly structured with most species restricted to island groups within the archipelago. These extremely narrow species ranges and high levels of intra-archipelagic endemism contrast with the wide-held belief that marine organisms generally have large geographical ranges and that endemism is at most restricted to the archipelagic level. Our results indicate that speciation in the marine environment may occur at spatial scales smaller than 100 km, comparable with some terrestrial systems. Our finding of fine-scale endemism has important consequences for marine conservation and management.},
}
@article {pmid23272130,
year = {2012},
author = {Jin, L and Zhang, M and Ma, J and Zhang, J and Zhou, C and Liu, Y and Wang, T and Jiang, AA and Chen, L and Wang, J and Jiang, Z and Zhu, L and Shuai, S and Li, R and Li, M and Li, X},
title = {Mitochondrial DNA evidence indicates the local origin of domestic pigs in the upstream region of the Yangtze River.},
journal = {PloS one},
volume = {7},
number = {12},
pages = {e51649},
pmid = {23272130},
issn = {1932-6203},
mesh = {Animals ; Bayes Theorem ; Breeding ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Models, Genetic ; Models, Statistical ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; Sus scrofa/genetics ; },
abstract = {Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.},
}
@article {pmid23279335,
year = {2013},
author = {Limenitakis, J and Oppenheim, RD and Creek, DJ and Foth, BJ and Barrett, MP and Soldati-Favre, D},
title = {The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii.},
journal = {Molecular microbiology},
volume = {87},
number = {4},
pages = {894-908},
pmid = {23279335},
issn = {1365-2958},
support = {/WT_/Wellcome Trust/United Kingdom ; 085349/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Acyl Coenzyme A/metabolism/toxicity ; Animals ; Carbon-Carbon Lyases/genetics/metabolism ; Citrates/*metabolism ; Humans ; Mice ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Propionates/*metabolism/toxicity ; Protozoan Proteins/genetics/metabolism ; Toxoplasma/classification/enzymology/genetics/*metabolism ; Toxoplasmosis/*parasitology ; },
abstract = {Toxoplasma gondii belongs to the coccidian subgroup of the Apicomplexa phylum. The Coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. These parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (BCAA) as a possible pathway to generate acetyl-CoA. Importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-CoA, a toxic metabolite that inhibits cell growth. Like fungi and bacteria, the Coccidia possess the complete set of enzymes necessary to metabolize and detoxify propionate by oxidation to pyruvate via the 2-methylcitrate cycle (2-MCC). Phylogenetic analysis provides evidence that the 2-MCC was acquired via horizontal gene transfer. In T. gondii tachyzoites, this pathway is split between the cytosol and the mitochondrion. Although the rate-limiting enzyme 2-methylisocitrate lyase is dispensable for parasite survival, its substrates accumulate in parasites deficient in the enzyme and its absence confers increased sensitivity to propionic acid. BCAA is also dispensable in tachyzoites, leaving unresolved the source of mitochondrial acetyl-CoA.},
}
@article {pmid23296446,
year = {2013},
author = {Boscaro, V and Petroni, G and Ristori, A and Verni, F and Vannini, C},
title = {"Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii", two novel ciliate endosymbionts belonging to the "Midichloria clade".},
journal = {Microbial ecology},
volume = {65},
number = {2},
pages = {302-310},
pmid = {23296446},
issn = {1432-184X},
mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Euplotes/*microbiology ; In Situ Hybridization, Fluorescence ; Paramecium/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; },
abstract = {The "Midichloria clade" is a recently discovered but well-established evolutionary lineage clustering inside the order Rickettsiales (Alphaproteobacteria). Not much is known about the biology of these organisms. The best characterized ones are endocellular symbionts of very different eukaryotic hosts, ranging from arthropods to protists. "Candidatus Midichloria mitochondrii", the most studied organism of the group, is an interesting object of study because of its unique capability to infect metazoans' mitochondria and the presence of flagellar genes in its genome. With this work, we aim at increasing the knowledge on the biodiversity and phylogeny of the "Midichloria group". We characterized according to the "full cycle rRNA approach" two novel endosymbionts of ciliated protozoa, i.e. Paramecium nephridiatum and Euplotes aediculatus. According to the nomenclatural rules for uncultivated prokaryotes, we established the novel taxa "Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii" for the two bacterial symbionts. Our phylogenetic analysis based on 16S rRNA gene sequences confirms that the evolutionary histories of "Midichloria clade" representatives and of their hosts are very different. This suggests that the symbiotic processes arose many times independently, perhaps through ways of transmission still not described in Rickettsiales.},
}
@article {pmid23304069,
year = {2012},
author = {Bi, R and Zhang, AM and Jia, X and Zhang, Q and Yao, YG},
title = {Complete mitochondrial DNA genome sequence variation of Chinese families with mutation m.3635G&gt;A and Leber hereditary optic neuropathy.},
journal = {Molecular vision},
volume = {18},
number = {},
pages = {3087-3094},
pmid = {23304069},
issn = {1090-0535},
mesh = {Adolescent ; Adult ; *Asian People ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genome, Mitochondrial ; Haplotypes ; Humans ; Male ; Mitochondria/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {PURPOSE: The majority of Leber hereditary optic neuropathy (LHON) cases are caused by one of three mitochondrial DNA (mtDNA) primary mutations (m.3460G>A, m.11778G>A, and m.14484T>C). In recent studies, we and others have shown that mutation m.3635G>A is a primary LHON mutation, particularly in Chinese. The purpose of this study was to perform a thorough analysis for the complete mtDNA genome sequence variation in Chinese patients with m.3635G>A and to identify potentially functional variants cosegregated with m.3635G>A.<br><br>METHODS: The complete mtDNA genomes of five Chinese patients with LHON carrying m.3635G>A were determined. A phylogenetic tree was constructed to distinguish the private and ancestral mtDNA variants in each lineage. Previously unreported variants in each mtDNA were defined with a web-based and database search. mtDNA variants that changed the structure of the membrane-spanning region of the protein were also evaluated, together with evolutionary conservation analysis, to predict their potential pathogenicity.<br><br>RESULTS: The five patients with LHON sequenced in this study belonged to haplogroups M7b4 (Le131), F1a (Le329 and Le337), B5b (Le569), and M7b6 (Le834), which suggested multiple origins of m.3635G>A. Private variants m.12811T>C, m.14063T>C, m.15237T>C, and m.9071C>T in these patients were predicted to change the structure of the membrane-spanning region of the respective proteins.<br><br>CONCLUSIONS: Mutation m.3635G>A had multiple origins in Chinese patients with LHON. We also identified several potentially functional variants cosegregated with m.3635G>A.},
}
@article {pmid23327366,
year = {2013},
author = {Chen, HN and Høeg, JT and Chan, BK},
title = {Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species.},
journal = {Biofouling},
volume = {29},
number = {2},
pages = {133-145},
doi = {10.1080/08927014.2012.753061},
pmid = {23327366},
issn = {1029-2454},
mesh = {Animals ; *Biofouling ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Genetic Variation ; Introduced Species ; Larva/classification/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Mitochondria/genetics ; Multivariate Analysis ; Phylogeny ; Species Specificity ; Taiwan ; Thoracica/anatomy &amp; histology/*classification/genetics ; },
abstract = {The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.},
}
@article {pmid23344321,
year = {2013},
author = {Tumonggor, MK and Karafet, TM and Hallmark, B and Lansing, JS and Sudoyo, H and Hammer, MF and Cox, MP},
title = {The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific.},
journal = {Journal of human genetics},
volume = {58},
number = {3},
pages = {165-173},
doi = {10.1038/jhg.2012.154},
pmid = {23344321},
issn = {1435-232X},
mesh = {Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/genetics ; Female ; *Genetic Variation ; Genetics, Population/*methods ; Haplotypes ; Humans ; Indonesia ; Male ; Mitochondria/genetics ; Pacific Islands ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; },
abstract = {Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date-2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement.},
}
@article {pmid23358826,
year = {2013},
author = {Szczesny, RJ and Hejnowicz, MS and Steczkiewicz, K and Muszewska, A and Borowski, LS and Ginalski, K and Dziembowski, A},
title = {Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.},
journal = {Nucleic acids research},
volume = {41},
number = {5},
pages = {3144-3161},
pmid = {23358826},
issn = {1362-4962},
mesh = {Amino Acid Substitution ; Catalytic Domain ; DNA Cleavage ; DNA, Mitochondrial/*metabolism ; DNA, Single-Stranded/chemistry ; Exodeoxyribonucleases/chemistry/*genetics/metabolism ; Gene Expression ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Mitochondria/*enzymology/genetics ; Models, Molecular ; Molecular Sequence Annotation ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Structure, Secondary ; Protein Transport ; RNA, Small Interfering/genetics ; Sequence Analysis, DNA ; },
abstract = {Although the human mitochondrial genome has been investigated for several decades, the proteins responsible for its replication and expression, especially nucleolytic enzymes, are poorly described. Here, we characterized a novel putative PD-(D/E)XK nuclease encoded by the human C20orf72 gene named Ddk1 for its predicted catalytic residues. We show that Ddk1 is a mitochondrially localized metal-dependent DNase lacking detectable ribonuclease activity. Ddk1 degrades DNA mainly in a 3'-5' direction with a strong preference for single-stranded DNA. Interestingly, Ddk1 requires free ends for its activity and does not degrade circular substrates. In addition, when a chimeric RNA-DNA substrate is provided, Ddk1 can slide over the RNA fragment and digest DNA endonucleolytically. Although the levels of the mitochondrial DNA are unchanged on RNAi-mediated depletion of Ddk1, the mitochondrial single-stranded DNA molecule (7S DNA) accumulates. On the other hand, overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation. We propose a structural model of Ddk1 and discuss its similarity to other PD-(D/E)XK superfamily members.},
}
@article {pmid23365671,
year = {2013},
author = {Jacobson, AL and Booth, W and Vargo, EL and Kennedy, GG},
title = {Thrips tabaci population genetic structure and polyploidy in relation to competency as a vector of tomato spotted wilt virus.},
journal = {PloS one},
volume = {8},
number = {1},
pages = {e54484},
pmid = {23365671},
issn = {1932-6203},
mesh = {Animals ; Electron Transport Complex IV/classification/*genetics ; *Genetics, Population ; Host-Pathogen Interactions ; Insect Vectors/*genetics/virology ; Microsatellite Repeats ; Mitochondria/enzymology/genetics ; North Carolina ; Phylogeny ; Plant Diseases/prevention &amp; control/virology ; Polyploidy ; Protein Subunits/classification/*genetics ; Reproduction/*genetics ; Sequence Analysis, DNA ; Thysanoptera/*genetics/virology ; Tospovirus/*physiology ; },
abstract = {Knowledge of population-level genetic differences can help explain variation among populations of insect vectors in their role in the epidemiology of specific viruses. Variation in competency to transmit Tomato spotted wilt virus (TSWV) that exists among populations of Thrips tabaci has been associated with the presence of cryptic species that exhibit different modes of reproduction and host ranges. However, recent findings suggest that vector competency of T. tabaci at any given location depends on the thrips and virus populations that are present. This study characterizes the population genetic structure of T. tabaci collected from four locations in North Carolina and examines the relationship between population genetic structure and variation in TSWV transmission by T. tabaci. Mitochondrial COI sequence analysis revealed the presence of two genetically distinct groups with one characterized by thelytokous, parthenogenetic reproduction and the other by arrhenotokous, sexual reproduction. Using a set of 11 microsatellite markers that we developed to investigate T. tabaci population genetic structure, we identified 17 clonal groups and found significant genetic structuring among the four NC populations that corresponded to the geographic locations where the populations were collected. Application of microsatellite markers also led to the discovery of polyploidy in this species. All four populations contained tetraploid individuals, and three contained both diploid and tetraploid individuals. Analysis of variation in transmission ofTSWV among isofemale lines initiated with individuals used in this study revealed that 'clone assignment,' 'virus isolate' and their interaction significantly influenced vector competency. These results highlight the importance of interactions between specific T. tabaci clonal types and specific TSWV isolates underlying transmission of TSWV by T. tabaci.},
}
@article {pmid23394930,
year = {2013},
author = {Ambrosio, AB and do Nascimento, LC and Oliveira, BV and Teixeira, PJ and Tiburcio, RA and Toledo Thomazella, DP and Leme, AF and Carazzolle, MF and Vidal, RO and Mieczkowski, P and Meinhardt, LW and Pereira, GA and Cabrera, OG},
title = {Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome.},
journal = {BMC genomics},
volume = {14},
number = {},
pages = {91},
pmid = {23394930},
issn = {1471-2164},
mesh = {Ascomycota/classification/*genetics/pathogenicity ; Cacao/genetics/microbiology ; Computational Biology ; DNA, Mitochondrial/*genetics ; Gene Expression Regulation, Fungal ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics ; Phylogeny ; Plant Diseases/genetics/microbiology ; Proteome/analysis/genetics ; },
abstract = {BACKGROUND: The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated "omics" approaches.<br><br>RESULTS: The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization.<br><br>CONCLUSIONS: The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.},
}
@article {pmid23411694,
year = {2013},
author = {Xu, J and Yang, J and Wu, Z and Liu, H and Huang, F and Wu, Y and Carrie, C and Narsai, R and Murcha, M and Whelan, J and Wu, P},
title = {Identification of a dual-targeted protein belonging to the mitochondrial carrier family that is required for early leaf development in rice.},
journal = {Plant physiology},
volume = {161},
number = {4},
pages = {2036-2048},
pmid = {23411694},
issn = {1532-2548},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Arabidopsis/genetics/metabolism ; Chloroplasts/metabolism/ultrastructure ; Cloning, Molecular ; Escherichia coli/metabolism ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Complementation Test ; Kinetics ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Mutation/genetics ; Oryza/genetics/*growth &amp; development/*metabolism ; Phenotype ; Phylogeny ; Plant Leaves/*growth &amp; development/*metabolism ; Plant Proteins/*metabolism ; Protein Transport ; RNA Interference ; Subcellular Fractions/metabolism ; Time Factors ; },
abstract = {A dual-targeted protein belonging to the mitochondrial carrier family was characterized in rice (Oryza sativa) and designated 3'-Phosphoadenosine 5'-Phosphosulfate Transporter1 (PAPST1). The papst1 mutant plants showed a defect in thylakoid development, resulting in leaf chlorosis at an early leaf developmental stage, while normal leaf development was restored 4 to 6 d after leaf emergence. OsPAPST1 is highly expressed in young leaves and roots, while the expression is reduced in mature leaves, in line with the recovery of chloroplast development seen in the older leaves of papst1 mutant plants. OsPAPST1 is located on the outer mitochondrial membrane and chloroplast envelope. Whole-genome transcriptomic analysis reveals reduced expression of genes encoding photosynthetic components (light reactions) in papst1 mutant plants. In addition, sulfur metabolism is also perturbed in papst1 plants, and it was seen that PAPST1 can act as a nucleotide transporter when expressed in Escherichia coli that can be inhibited significantly by 3'-phosphoadenosine 5'-phosphosulfate. Given these findings, together with the altered phenotype seen only when leaves are first exposed to light, it is proposed that PAPST1 may act as a 3'-phosphoadenosine 5'-phosphosulfate carrier that has been shown to act as a retrograde signal between chloroplasts and the nucleus.},
}
@article {pmid23437098,
year = {2013},
author = {Letcher, PM and Lopez, S and Schmieder, R and Lee, PA and Behnke, C and Powell, MJ and McBride, RC},
title = {Characterization of Amoeboaphelidium protococcarum, an algal parasite new to the cryptomycota isolated from an outdoor algal pond used for the production of biofuel.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e56232},
pmid = {23437098},
issn = {1932-6203},
mesh = {Animals ; *Biofuels ; Eukaryota/classification/growth &amp; development/*isolation &amp; purification/ultrastructure ; Life Cycle Stages ; Parasites/cytology/growth &amp; development/*isolation &amp; purification/ultrastructure ; Phylogeny ; Ponds/*parasitology ; Scenedesmus/growth &amp; development/*parasitology ; Sequence Analysis, DNA ; },
abstract = {Mass culture of algae for the production of biofuels is a developing technology designed to offset the depletion of fossil fuel reserves. However, large scale culture of algae in open ponds can be challenging because of incidences of infestation with algal parasites. Without knowledge of the identity of the specific parasite and how to control these pests, algal-based biofuel production will be limited. We have characterized a eukaryotic parasite of Scenedesmus dimorphus growing in outdoor ponds used for biofuel production. We demonstrated that as the genomic DNA of parasite FD01 increases, the concentration of S. dimorphus cells decreases; consequently, this is a highly destructive pathogen. Techniques for culture of the parasite and host were developed, and the endoparasite was identified as the Aphelidea, Amoeboaphelidium protococcarum. Phylogenetic analysis of ribosomal sequences revealed that parasite FD01 placed within the recently described Cryptomycota, a poorly known phylum based on two species of Rozella and environmental samples. Transmission electron microscopy demonstrated that aplanospores of the parasite produced filose pseudopodia, which contained fine fibers the diameter of actin microfilaments. Multiple lipid globules clustered and were associated with microbodies, mitochondria and a membrane cisternae, an arrangement characteristic of the microbody-lipid globule complex of chytrid zoospores. After encystment and attachment to the host cells, the parasite injected its protoplast into the host between the host cell wall and plasma membrane. At maturity the unwalled parasite occupied the entire host cell. After cleavage of the protoplast into aplanospores, a vacuole and lipids remained in the host cell. Amoeboaphelidium protococcarum isolate FD01 is characteristic of the original description of this species and is different from strain X-5 recently characterized. Our results help put a face on the Cryptomycota, revealing that the phylum is more diverse than previously understood and include some of the Aphelidea as well as Rozella species and potentially Microsporidia.},
}
@article {pmid23437234,
year = {2013},
author = {Jackson, CJ and Waller, RF},
title = {A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e56777},
pmid = {23437234},
issn = {1932-6203},
mesh = {Dinoflagellida/enzymology/*genetics ; Electron Transport Complex IV/*genetics ; Exons ; Genome, Mitochondrial ; Mitochondria/enzymology/*genetics ; Phylogeny ; RNA, Messenger/*genetics ; RNA, Spliced Leader/genetics ; Trans-Splicing/*genetics ; },
abstract = {Cytochrome oxidase subunit 3 (Cox3) is a mitochondrion-encoded core membrane protein of complex IV of the mitochondrial respiratory chain, and consists of seven trans-membrane helices. Here we show that in diverse later-branching dinoflagellates, cox3 is consistently split into two exons in the mitochondrial genome between helices six and seven. Gene exons are transcribed as two discrete oligoadenylated precursor RNAs, and these are subsequently trans-spliced to form a complete coding mRNA. This trans-splicing is highly unusual in that some of the oligoadenylated tail is incorporated at the splice site, such that a short string of adenosines links the two coding exons. This feature is consistently represented in diverse dinoflagellates, however the number of adenosines added varies according to the size of the coding gap between the two exons. Thus we observed between zero (Amphidinium carterae) and 10 (Symbiodinium sp.) adenosines added in different taxa, but the final coding sequence length is identical with the reading frame maintained. Northern analyses show that precursor cox3 transcripts are approximately equally abundant as mature cox3 mRNAs, suggesting a slow or regulated maturation process. These data indicate that the splicing mechanism in dinoflagellate mitochondria is tolerant of variations in the length of the precursor coding sequence, and implicates the use of a splicing template, or guide molecule, during splicing that controls mature mRNA length.},
}
@article {pmid23451266,
year = {2013},
author = {Phillips, MJ and Haouchar, D and Pratt, RC and Gibb, GC and Bunce, M},
title = {Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes.},
journal = {PloS one},
volume = {8},
number = {2},
pages = {e57745},
pmid = {23451266},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Genes, Mitochondrial ; Macropodidae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.},
}
@article {pmid23463613,
year = {2013},
author = {Tang, S and Wang, J and Zhang, VW and Li, FY and Landsverk, M and Cui, H and Truong, CK and Wang, G and Chen, LC and Graham, B and Scaglia, F and Schmitt, ES and Craigen, WJ and Wong, LJ},
title = {Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects.},
journal = {Human mutation},
volume = {34},
number = {6},
pages = {882-893},
doi = {10.1002/humu.22307},
pmid = {23463613},
issn = {1098-1004},
mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Follow-Up Studies ; Gene Deletion ; *Genome, Mitochondrial ; Genomics ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Male ; Middle Aged ; Mitochondria/genetics/metabolism ; Mitochondrial Diseases/*diagnosis/*genetics ; Mutation ; Mutation Rate ; Young Adult ; },
abstract = {The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity. Conventional analysis of the mitochondrial genome often starts with a screening panel for common mitochondrial DNA (mtDNA) point mutations and large deletions (mtScreen). If negative, it has been traditionally followed by Sanger sequencing of the entire mitochondrial genome (mtWGS). The recently developed "Next-Generation Sequencing" (NGS) technology offers a robust high-throughput platform for comprehensive mtDNA analysis. Here, we summarize the results of the past 6 years of clinical practice using the mtScreen and mtWGS tests on 9,261 and 2,851 unrelated patients, respectively. A total of 344 patients (3.7%) had mutations identified by mtScreen and 99 (3.5%) had mtDNA mutations identified by mtWGS. The combinatorial analyses of mtDNA and POLG revealed a diagnostic yield of 6.7% in patients with suspected mitochondrial disorders but no recognizable syndromes. From the initial mtWGS-NGS cohort of 391 patients, 21 mutation-positive cases (5.4%) have been identified. The mtWGS-NGS provides a one-step approach to detect common and uncommon point mutations, as well as deletions. Additionally, NGS provides accurate, sensitive heteroplasmy measurement, and the ability to map deletion breakpoints. A new era of more efficient molecular diagnosis of mtDNA mutations has arrived.},
}
@article {pmid23463776,
year = {2013},
author = {Liu, YJ and Xiu, ZH and Meeley, R and Tan, BC},
title = {Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize.},
journal = {The Plant cell},
volume = {25},
number = {3},
pages = {868-883},
pmid = {23463776},
issn = {1532-298X},
mesh = {Alleles ; Amino Acid Sequence ; Cloning, Molecular ; Electron Transport Complex IV/genetics/metabolism ; Genes, Plant ; Heterozygote ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics/metabolism ; Oryza/genetics/growth &amp; development/metabolism ; Phylogeny ; Plants, Genetically Modified/genetics/metabolism ; Protein Structure, Tertiary ; RNA/genetics/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Plant/genetics/metabolism ; Seeds/genetics/*growth &amp; development/metabolism ; Zea mays/genetics/growth &amp; development/*metabolism ; },
abstract = {In flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.},
}
@article {pmid23480379,
year = {2013},
author = {Zhang, HL and Zhao, L and Zheng, ZM and Huang, Y},
title = {Complete mitochondrial genome of Gomphocerus sibiricus (Orthoptera: Acrididae) and comparative analysis in four Gomphocerinae mitogenomes.},
journal = {Zoological science},
volume = {30},
number = {3},
pages = {192-204},
doi = {10.2108/zsj.30.192},
pmid = {23480379},
issn = {0289-0003},
mesh = {Animals ; Base Sequence ; Gene Expression Regulation ; Genome, Insect/*genetics ; Insect Proteins/genetics/metabolism ; Mitochondria/*genetics ; Orthoptera/*genetics ; Phylogeny ; RNA/chemistry/genetics ; Species Specificity ; },
abstract = {The complete mitochondrial genome (mitogenome) of Gomphocerus sibiricus, consisting of 15,590 bp, was determined and analyzed. It displays typical genome organization found in other Caelifera mitogenomes: 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one A+T rich region. In this paper, we focused on the comparative analyses of mitogenomes from four Gomphocerinae taxa to find characteristics of nucleotide composition and overlapping and non-coding regions. In addition, we compared variable sites in the structure of 22 tRNAs and two rRNAs, and differences in some common conserved elements of A+T rich regions. Furthermore, we analyzed phylogenetic relationships of 12 Caelifera species using maximum likelihood (ML) and Bayesian inference (BI) based on two different datasets from mitogenomes. Our results reveal that G. sibiricus has a close relationship with Gomphocerus licenti of the four Gomphocerinae taxa examined in these analyses.},
}
@article {pmid23496286,
year = {2014},
author = {Constenla, M and Padrós, F and Palenzuela, O},
title = {Endolimax piscium sp. nov. (Amoebozoa), causative agent of systemic granulomatous disease of cultured sole, Solea senegalensis Kaup.},
journal = {Journal of fish diseases},
volume = {37},
number = {3},
pages = {229-240},
doi = {10.1111/jfd.12097},
pmid = {23496286},
issn = {1365-2761},
mesh = {Amebiasis/immunology/parasitology/*veterinary ; Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Endolimax/*classification/*physiology/ultrastructure ; Fish Diseases/immunology/*parasitology ; Fisheries ; *Flatfishes ; Microscopy, Electron, Transmission/veterinary ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Spain ; Species Specificity ; },
abstract = {A new amoeba species pathogenic for Senegalese sole is described based on ultrastructural analysis and SSU rDNA phylogenetic inference. The parasite presents round to ovoid trophozoites (<5 μm) with a high degree of intracellular simplification. No mitochondria were observed, but mitosome-like organelles were present. No cysts could be detected. Phylogenetic analysis confirmed the Senegalese sole parasite as an amitochondriate Archamoeba related to Endolimax nana and Iodamoeba spp., and we tentatively describe it as a new species in the genus Endolimax, Endolimax piscium. However, the genetic distance with E. nana is quite large, with only 60% pairwise identity between both SSU rDNA genotypes. Although the overall topology of the Archamoebae cladograms containing E. piscium was consistent, the support for the branching of Endolimax spp. relative to its closest neighbours was variable, being higher with distance or parsimony-based inference methods than with ML or Bayesian trees. The use of stringent alignment sampling masks also caused instability and reduced support for some branches, including the monophyly of Endolimax spp. in the most conservative data sets. The characterization of other Archamoebae parasitizing fish could help to clarify the status of E. piscium and to interpret the large genetic distance observed between Endolimax species.},
}
@article {pmid23516901,
year = {2012},
author = {Torgunakova, OA and Egorova, TA and Semenova, SK},
title = {[Comparative analysis of variability of three mitochondrial genes of cytochrome oxidase complex (cox1, cox2, and cox3) in wild and domestic carp (Cyprinus carpio L.)].},
journal = {Genetika},
volume = {48},
number = {12},
pages = {1401-1409},
pmid = {23516901},
issn = {0016-6758},
mesh = {Animals ; Animals, Domestic/genetics ; Animals, Wild/genetics ; Carps/classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Genes, Mitochondrial ; Haplotypes ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {For the first time, we studied the polymorphism of three mitochondrial genes of the cytochrome oxidase complex (cox1, cox2, and cox3) in natural populations of wild carp living in the Volga, Amur, and Don River Basins, as well as in European Hungarian carp and two pedigree lines of Ropsha carp of domestic breeding. The highest level of nucleotide and haplotype diversity in the studied samples was detected for the cox1 gene (pi = 0.61, h = 100%). Two lines of the Ropsha carp (pi = 0.61, h = 100%) and the Far East population of Amur wild carp from Shershikh strait (Am: pi = 0.20, h = 70%) were the most polymorphic for three genes. The second sample of Amur wild carp from the Amur River (Ac), as well as the samples of Volga and Don wild carp and Hungarian carp had lower values of variability. The presence of two main genealogical lines of the wild carp and carp was demonstrated based on the total sequence of three genes, as well as the corresponding amino acid sequences in the studied area. One of these lines (line I) is typical of the sample of Amur wild carp (Am) and three members of the Ropsha carp. Line II is developed by sequences of Volga, Don, and Amur wild carp (Ac), as well as European Hungarian carp and seven other members of the Ropsha carp. Three to four sublines, which differ in nucleotide and amino acid substitutions, were found within the lines. Possible reasons for the origin of genomic variability in wild carp, as well as in European and Russian breeds of carp, are discussed.},
}
@article {pmid23533597,
year = {2013},
author = {Soares, P and Abrantes, D and Rito, T and Thomson, N and Radivojac, P and Li, B and Macaulay, V and Samuels, DC and Pereira, L},
title = {Evaluating purifying selection in the mitochondrial DNA of various mammalian species.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e58993},
pmid = {23533597},
issn = {1932-6203},
mesh = {Animals ; Cattle ; DNA, Mitochondrial/*genetics ; Dogs ; Mammals ; Mice ; Phylogeny ; Sus scrofa ; Whale, Killer ; },
abstract = {Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.},
}
@article {pmid23535017,
year = {2013},
author = {Kou, Q and Li, X and Chan, TY and Chu, KH and Huang, H and Gan, Z},
title = {Phylogenetic relationships among genera of the Periclimenes complex (Crustacea: Decapoda: Pontoniinae) based on mitochondrial and nuclear DNA.},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {1},
pages = {14-22},
doi = {10.1016/j.ympev.2013.03.010},
pmid = {23535017},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/chemistry/*genetics ; DNA, Mitochondrial/*classification/genetics ; Decapoda/*classification/genetics ; Genetic Speciation ; Mitochondria/chemistry/*genetics ; Phosphoenolpyruvate Carboxykinase (ATP)/classification/genetics ; Phosphopyruvate Hydratase/classification/genetics ; *Phylogeny ; Protein Serine-Threonine Kinases/classification/genetics ; RNA, Ribosomal, 16S/*classification/genetics ; Sequence Analysis, DNA ; },
abstract = {The genus Periclimenes Costa, 1844 is the most species-rich genus in the subfamily Pontoniinae. Recent studies have suggested that it might be a polyphyletic taxon and could be further subdivided. In this study, three protein-coding nuclear genes and one mitochondrial ribosomal gene were used to analyze the phylogenetic relationships among the genera of the Periclimenes complex, includes the genus Periclimenes and 15 related genera, viz. Ancylomenes, Brucecaris, Crinotonia, Cuapetes, Harpiliopsis, Harpilius, Laomenes, Leptomenaeus, Manipontonia, Palaemonella, Periclimenella, Philarius, Phycomenes, Unguicaris and Vir. Based on both independent and combined data analyses, the results support that the genus Periclimenes is a polyphyletic group. Furthermore, the studied Periclimenes species could be divided into several independent groups, and the taxonomic status of P. commensalis, P. brevicarpalis and P. digitalis may need to be reconsidered. Besides, the majority of the related genera of Periclimenes are suggested to be monophyletic. Our analyses also reveal that these genera approximately form two main clades, despite some deep relationships are still obscure.},
}
@article {pmid23538482,
year = {2013},
author = {Elrod, JW and Molkentin, JD},
title = {Physiologic functions of cyclophilin D and the mitochondrial permeability transition pore.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {77},
number = {5},
pages = {1111-1122},
pmid = {23538482},
issn = {1347-4820},
support = {/HHMI/Howard Hughes Medical Institute/United States ; F32 HL092737/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Apoptosis ; Peptidyl-Prolyl Isomerase F ; Cyclophilins/genetics/*metabolism ; Energy Metabolism ; Humans ; Mitochondria, Heart/*metabolism/pathology ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Membranes/*metabolism/pathology ; Mitochondrial Permeability Transition Pore ; Myocardial Reperfusion Injury/metabolism/mortality ; Myocytes, Cardiac/*metabolism/pathology ; Necrosis ; Phylogeny ; Protein Processing, Post-Translational ; },
abstract = {This review focuses on the role of cyclophilin D (CypD) as a prominent mediator of the mitochondrial permeability transition pore (MPTP) and subsequent effects on cardiovascular physiology and pathology. Although a great number of reviews have been written on the MPTP and its effects on cell death, we focus on the biology surrounding CypD itself and the non-cell death physiologic functions of the MPTP. A greater understanding of the physiologic functions of the MPTP and its regulation by CypD will likely suggest novel therapeutic approaches for cardiovascular disease, both dependent and independent of programmed necrotic cell death mechanisms.},
}
@article {pmid23541082,
year = {2013},
author = {Khalifa, ME and Pearson, MN},
title = {Molecular characterization of three mitoviruses co-infecting a hypovirulent isolate of Sclerotinia sclerotiorum fungus.},
journal = {Virology},
volume = {441},
number = {1},
pages = {22-30},
doi = {10.1016/j.virol.2013.03.002},
pmid = {23541082},
issn = {1096-0341},
mesh = {Ascomycota/isolation &amp; purification/*virology ; Cluster Analysis ; Mitochondria/ultrastructure/virology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Double-Stranded/genetics ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Viral Proteins/genetics ; },
abstract = {Three double-stranded RNAs (dsRNAs) of 2438 nts (A), 2588 nts (B), and 2744 nts (C), from a single isolate of Sclerotinia sclerotiorum were sequenced. All three sequences showed similarity to known mitoviruses, consisting of a single open reading frame (ORF) with the characteristic conserved motifs of RNA-dependent RNA polymerase (RdRp). Mitochondrial malformations and reduced virulence and growth were associated with the presence of the dsRNAs. The terminal sequences of the (+) strand of the three dsRNAs could be folded into stem-loop structures and the inverted terminal complimentary sequences of dsRNA-A potentially form a panhandle structure. Sequence A showed 91.6% aa similarity to the previously described Sclerotinia sclerotiorum mitovirus 2 and was tentatively assigned the acronym SsMV2/NZ1. Sequences B and C showed only 16.4% similarity to each other and 15-48% aa similarity to the previously described mitoviruses and consequently appear to be new mitoviruses.},
}
@article {pmid23541838,
year = {2013},
author = {Mariguela, TC and Ortí, G and Avelino, GS and Abe, KT and Oliveira, C},
title = {Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): a case study based on mitochondrial and nuclear DNA sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {1},
pages = {23-34},
doi = {10.1016/j.ympev.2013.03.011},
pmid = {23541838},
issn = {1095-9513},
mesh = {Animals ; Cell Nucleus/chemistry/*genetics ; Characidae/*classification/genetics ; Cytochromes b/classification/genetics ; DNA, Mitochondrial/*classification/genetics ; DNA-Binding Proteins/classification/genetics ; Fresh Water ; Genetic Speciation ; Homeodomain Proteins/classification/genetics ; Mitochondria/chemistry/*genetics ; Myosin Heavy Chains/classification/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*classification/genetics ; },
abstract = {Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient.},
}
@article {pmid23542002,
year = {2013},
author = {Dunz, AR and Schliewen, UK},
title = {Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as "Tilapia".},
journal = {Molecular phylogenetics and evolution},
volume = {68},
number = {1},
pages = {64-80},
doi = {10.1016/j.ympev.2013.03.015},
pmid = {23542002},
issn = {1095-9513},
mesh = {Africa, Eastern ; Africa, Western ; Animals ; Cell Nucleus/chemistry/genetics ; DNA, Mitochondrial/*classification/genetics ; Genetic Speciation ; Mitochondria/chemistry/genetics ; NADH Dehydrogenase/*classification/genetics ; Nuclear Proteins/*classification/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/*classification/genetics ; Tilapia/*classification/genetics ; },
abstract = {African cichlids formerly referred to as "Tilapia" represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important "Tilapia" or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for "Tilapia" joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.},
}
@article {pmid23545131,
year = {2013},
author = {Conceição, PA and Crainey, JL and Almeida, TP and Shelley, AJ and Luz, SL},
title = {New molecular identifiers for Simulium limbatum and Simulium incrustatum s.l. and the detection of genetic substructure with potential implications for onchocerciasis epidemiology in the Amazonia focus of Brazil.},
journal = {Acta tropica},
volume = {127},
number = {2},
pages = {118-125},
doi = {10.1016/j.actatropica.2013.03.012},
pmid = {23545131},
issn = {1873-6254},
mesh = {Animals ; Brazil/epidemiology ; Cytochromes/genetics ; Female ; Gene Expression Regulation ; Genetic Markers ; Humans ; Insect Vectors/genetics/parasitology ; Mitochondria/genetics ; Onchocerciasis/*epidemiology ; Phylogeny ; Simuliidae/*genetics ; Species Specificity ; },
abstract = {The Amazonia onchocerciasis focus of southern Venezuela and northern Brazil is the larger of the two remaining Latin American onchocerciasis foci where disease transmission still occurs and is often regarded as the most challenging of all the Latin American foci to eliminate onchocerciasis. The site is home to a population of over 20,000 semi-nomadic, hunter-gatherer Yanomami people and is made-up of a mosaic of rainforest and savannah ecologies, which are influenced by the area's undulating terrain and rich geological diversity. At least six blackfly vectors have been implicated in onchocerciasis transmission in this focus; however, because of the difficulty in their routine identification the relative importance of each has been obscured. Simulium limbatum and Simulium incrustatum s.l. have both been recorded as vectors in the Amazonia focus, but they are difficult to discriminate morphologically and thus the ecological range of these species, and indeed the presence of S. limbatum in the Amazonia focus at all, have remained controversial. In the work described here, we report 15 S. incrustatum s.l. CO1 sequences and 27 S. limbatum sequences obtained from field-caught adult female blackflies collected from forest and savannah localities, inside and just outside the Amazonia focus. Phylogenetic analysis with the sequences generated in this study, showed that both the S. limbatum and the S. incrustatum s.l. CO1 sequences obtained (even from specimens living in sympatry) all fell into discrete species-specific bootstrap-supported monophyletic groups and thus confirmed the utility of the CO1 gene for identifying both these species inside the Amazonia focus. As the S. limbatum-exclusive cluster included CO1 sequences obtained from forest-caught and morphologically identified specimens these results provide the clearest evidence yet of the presence of S. limbatum inside the Amazonia focus. The question, however, of whether S. limbatum is actually a vector in the focus still remains unanswered as the data presented here also suggest that S. limbatum found in the savannahs adjacent to, but outside the Amazonia focus (and which represent the only S. limbatum population to be unambiguously incriminated as a host of Onchocerca volvulus), are genetically distinct from those living inside the focus. These findings highlight the need for a clearer picture of the vector taxonomy inside the Amazonia onchocerciasis focus.},
}
@article {pmid23551461,
year = {2013},
author = {Lambert, SM and Geneva, AJ and Luke Mahler, D and Glor, RE},
title = {Using genomic data to revisit an early example of reproductive character displacement in Haitian Anolis lizards.},
journal = {Molecular ecology},
volume = {22},
number = {15},
pages = {3981-3995},
doi = {10.1111/mec.12292},
pmid = {23551461},
issn = {1365-294X},
mesh = {Adaptation, Biological/genetics ; Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Mitochondrial/analysis ; Gene Flow/*genetics ; Genetic Speciation ; *Genetic Variation ; Haiti ; Lizards/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; *Reproductive Isolation ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The pattern of reproductive character displacement (RCD)-in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation-is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example, Anolis caudalis appears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNA sequence data, information on dewlap phenotypes and GIS data on environmental variation to test the hypothesis of RCD generated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent with RCD at the southern and northern limits of the range of A. caudalis. We evaluate the evidence for reinforcement as the explanation for RCD in Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation in Haitian trunk anoles.},
}
@article {pmid23555709,
year = {2013},
author = {Seenivasan, R and Sausen, N and Medlin, LK and Melkonian, M},
title = {Picomonas judraskeda gen. et sp. nov.: the first identified member of the Picozoa phylum nov., a widespread group of picoeukaryotes, formerly known as 'picobiliphytes'.},
journal = {PloS one},
volume = {8},
number = {3},
pages = {e59565},
pmid = {23555709},
issn = {1932-6203},
mesh = {Cell Movement ; Eukaryota/cytology/genetics/*isolation &amp; purification/ultrastructure ; Flow Cytometry ; Microscopy, Electron ; Mitochondria/metabolism ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; },
abstract = {In 2007, a novel, putatively photosynthetic picoeukaryotic lineage, the 'picobiliphytes', with no known close eukaryotic relatives, was reported from 18S environmental clone library sequences and fluorescence in situ hybridization. Although single cell genomics later showed these organisms to be heterotrophic rather than photosynthetic, until now this apparently widespread group of pico-(or nano-)eukaryotes has remained uncultured and the organisms could not be formally recognized. Here, we describe Picomonas judraskeda gen. et sp. nov., from marine coastal surface waters, which has a 'picobiliphyte' 18S rDNA signature. Using vital mitochondrial staining and cell sorting by flow cytometry, a single cell-derived culture was established. The cells are biflagellate, 2.5-3.8×2-2.5 µm in size, lack plastids and display a novel stereotypic cycle of cell motility (described as the "jump, drag, and skedaddle"-cycle). They consist of two hemispherical parts separated by a deep cleft, an anterior part that contains all major cell organelles including the flagellar apparatus, and a posterior part housing vacuoles/vesicles and the feeding apparatus, both parts separated by a large vacuolar cisterna. From serial section analyses of cells, fixed at putative stages of the feeding cycle, it is concluded that cells are not bacterivorous, but feed on small marine colloids of less than 150 nm diameter by fluid-phase, bulk flow endocytosis. Based on the novel features of cell motility, ultrastructure and feeding, and their isolated phylogenetic position, we establish a new phylum, Picozoa, for Picomonas judraskeda, representing an apparently widespread and ecologically important group of heterotrophic picoeukaryotes, formerly known as 'picobiliphytes'.},
}
@article {pmid23557683,
year = {2013},
author = {Palinauskas, V and Iezhova, TA and Križanauskienė, A and Markovets, MY and Bensch, S and Valkiūnas, G},
title = {Molecular characterization and distribution of Haemoproteus minutus (Haemosporida, Haemoproteidae): a pathogenic avian parasite.},
journal = {Parasitology international},
volume = {62},
number = {4},
pages = {358-363},
doi = {10.1016/j.parint.2013.03.006},
pmid = {23557683},
issn = {1873-0329},
mesh = {Animals ; Bird Diseases/epidemiology/*parasitology ; Birds/blood/*parasitology ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; Haemosporida/classification/*genetics ; Mitochondria/genetics ; Phylogeny ; *Protozoan Infections, Animal ; },
abstract = {Recently, the lineage hTURDUS2 of Haemoproteus minutus (Haemosporida, Haemoproteidae) was reported to cause mortality in captive parrots. This parasite lineage is widespread and prevalent in the blackbird Turdus merula throughout its entire distribution range. Species identity of other closely related lineages recently reported in dead parrots remains unclear, but will be important to determine for a better understanding of the epidemiology of haemoproteosis. Using polymerase chain reaction (PCR)-based and microscopic methods, we analyzed 265 blood samples collected from 52 species of wild birds in Eurasia (23 samples from Kamchatka Peninsula, 73 from Sakhalin Island, 150 from Ekaterinburg and 19 from Irkutsk regions of Russia). Single infections of the lineages hTURDUS2 (hosts are redwing Turdus iliacus and fieldfare Turdus pilaris), hTUPHI1 (song thrush Turdus philomelos) and hTUCHR01 (fieldfare, redwing, song thrush and brown-headed thrush Turdus chysolaus) were detected. We identified species of these haemoproteids based on morphology of their blood stages and conclude that these lineages belong to H. minutus, a widespread parasite of different species of thrushes (genus Turdus), which serve as reservoir hosts of this haemoproteid infection. Phylogenetic analysis shows that the lineages hTURDUS2, hTUCHR01 and hTUPHI1 of H. minutus are closely related to Haemoproteus pallidus (lineages hPFC1 and hCOLL2), Haemoproteus pallidulus (hSYAT03), and Haemoproteus sp. (hMEUND3); genetic distance among their mitochondrial cytochrome b (cyt b) lineages is small (<1% or<4 nucleotides). All these blood parasites are different in many morphological characters, but are similar due to one feature, which is the pale staining of their macrogametocytes' cytoplasm with Giemsa. Because of the recent publications about mortality caused by the lineages hTUPHI1 and hTURDUS2 of H. minutus in captive parrots in Europe, H. minutus and the closely related H. pallidus and H. pallidulus are worth more attention as these are possible agents of haemoproteosis in exotic birds. The present study provides barcodes for molecular detection of different lineages of H. minutus, and extends information about the distribution of this blood parasite.},
}
@article {pmid23572355,
year = {2013},
author = {Xu, L and Fan, Y and Jiang, XL and Yao, YG},
title = {[Molecular evidence on the phylogenetic position of tree shrews].},
journal = {Dong wu xue yan jiu = Zoological research},
volume = {34},
number = {2},
pages = {70-76},
doi = {10.3724/SP.J.1141.2013.02070},
pmid = {23572355},
issn = {0254-5853},
mesh = {Animals ; Humans ; *Phylogeny ; Primates/classification/genetics/growth &amp; development/physiology ; Tupaiidae/*classification/*genetics/growth &amp; development/physiology ; },
abstract = {The tree shrew is currently located in the Order Scandentia and is widely distributed in Southeast Asia, South Asia, and South China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, the tree shrew has been proposed as an alternative experimental animal to primates in biomedical research. However, there is unresolved debate regarding the phylogenetic affinity of tree shrews to primates and their phylogenetic position in Euarchontoglires. To help settle this debate, we summarized the available molecular evidence on the phylogenetic position of the tree shrew. Most nuclear DNA data, including recent genome data, suggested that the tree shrew belongs to the Euarchonta clade harboring primates and flying lemurs (colugos). However, analyses of mitochondrial DNA (mtDNA) data suggested a close relationship to lagomorphs and rodents. These different clustering patterns could be explained by nuclear gene data and mtDNA data discrepancies, as well as the different phylogenetic approaches used in previous studies. Taking all available conclusions together, the robust data from whole genome of this species supports tree shrews being genetically closely related to primates.},
}
@article {pmid23575541,
year = {2013},
author = {Zhang, CQ and Chen, BB and Chen, YY and Liu, XJ and Zheng, J and Gao, JJ and Huang, SY and Nan, BY and Zhang, YY and Yu, X and Guan, MX},
title = {[Prevalence of common genetic mutations and clinical characteristics analysis in patients at different ages with nonsyndromic hearing impairment].},
journal = {Yi chuan = Hereditas},
volume = {35},
number = {3},
pages = {352-358},
doi = {10.3724/sp.j.1005.2013.00352},
pmid = {23575541},
issn = {0253-9772},
mesh = {Adolescent ; Adult ; Age Factors ; Child ; Child, Preschool ; Connexin 26 ; Connexins/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Testing ; Hearing Loss, Sensorineural/*diagnosis/*genetics ; Humans ; Infant ; Male ; Middle Aged ; *Mutation ; Mutation Rate ; Young Adult ; },
abstract = {To evaluate the correlation between genetic mutations and the age in nonsyndromic hearing impairment (NSHI) and the clinical characteristics of NSHI, 215 patients with NSHI were enrolled between April 2006 and April 2012. All patients were divided into four groups according to ages of hearing loss onset and clinic presentation (0-3, 3-6, 6-18 and 18+ years). The mutations of GJB2 and mitochondria DNA (mtDNA) 1555G/C1494T were screened from peripheral blood samples in each age group. The prevalence of mutations and the age ratio were obtained. The study showed that 18.14% of all patients were found to have GJB2 mutations and 11.16% were found to have mtDNA A1555G/C1494T mutations. The prevalence of GJB2 mutation in adult group (5.26%) was lower than juvenile group who sought medical attention at 0-18 years of age (22.36%), while the prevalence of mtDNA A1555G/C1494T in adult group (31.48%) was higher than juvenile group (4.97%). Significant differences in the prevalence of GJB2 (χ2=7.108, P=0.008) and mtDNA A1555G/C1494T (χ2=20.852, P=0.000) were observed in both of two groups. The prevalence of GJB2 mutations between adult and juvenile groups according to ages of hearing loss onset was statistically significant different (0%, 20.10%, respectively, and P=0.023), while the prevalence of mtDNA A1555G/C1494T mutations was not different (14.29%, 11.34%, respectively, and P=0.698). The onset age of 66.67% of patients with GJB2 mutations was less than 1 year old, while the onset of patients with mtDNA A1555G/C1494T mutations could be found at any age group. Different standardizations of hearing loss could also show different results. These data strongly suggest that most of GJB2 mutations are found in congenital deafness and mtDNA A1555G/C1494T mutations mainly represent acquired deafness, which can be induced or aggravated by aminoglycoside antibiotics in all age groups and should be tested mainly ranging from 4 kHz to 8 kHz. Both newborn hearing screening and genetic testing are important to find early deafness.},
}
@article {pmid23610429,
year = {2013},
author = {Wu, B and Novelli, J and Jiang, D and Dailey, HA and Landmann, F and Ford, L and Taylor, MJ and Carlow, CK and Kumar, S and Foster, JM and Slatko, BE},
title = {Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {110},
number = {19},
pages = {7748-7753},
pmid = {23610429},
issn = {1091-6490},
support = {L30 DK096501/DK/NIDDK NIH HHS/United States ; R01 DK096051/DK/NIDDK NIH HHS/United States ; DK96501/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Animals, Genetically Modified ; Bayes Theorem ; Brugia malayi/*enzymology/genetics ; Caenorhabditis elegans/genetics ; Cloning, Molecular ; Escherichia coli/metabolism ; Exons ; Female ; Ferrochelatase/*genetics ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome ; Green Fluorescent Proteins/metabolism ; In Situ Hybridization ; Male ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; },
abstract = {Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function. Herein, we report functional lateral gene transfer in animal parasitic nematodes. Members of the Nematoda are heme auxotrophs, lacking the ability to synthesize heme; however, the human filarial parasite Brugia malayi has acquired a bacterial gene encoding ferrochelatase (BmFeCH), the terminal step in heme biosynthesis. BmFeCH, encoded by a 9-exon gene, is a mitochondrial-targeted, functional ferrochelatase based on enzyme assays, complementation, and inhibitor studies. Homologs have been identified in several filariae and a nonfilarial nematode. RNAi and ex vivo inhibitor experiments indicate that BmFeCH is essential for viability, validating it as a potential target for filariasis control.},
}
@article {pmid23658748,
year = {2013},
author = {Sauer, J and Oldeland, J and Hausdorf, B},
title = {Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete.},
journal = {PloS one},
volume = {8},
number = {5},
pages = {e62569},
pmid = {23658748},
issn = {1932-6203},
mesh = {Amplified Fragment Length Polymorphism Analysis ; *Animal Distribution ; Animals ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetic Markers ; Greece ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Multigene Family ; Phylogeny ; Phylogeography ; Selection, Genetic ; Snails/*genetics ; },
abstract = {The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.},
}
@article {pmid23663090,
year = {2013},
author = {Jezkova, T and Leal, M and Rodríguez-Robles, JA},
title = {Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi).},
journal = {Journal of evolutionary biology},
volume = {26},
number = {7},
pages = {1458-1471},
doi = {10.1111/jeb.12149},
pmid = {23663090},
issn = {1420-9101},
mesh = {Animals ; Caribbean Region ; DNA, Mitochondrial ; *Genetic Drift ; *Genetics, Population ; *Hybridization, Genetic ; Likelihood Functions ; Lizards/*genetics ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Puerto Rico ; },
abstract = {Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly or completely replaced the native mtDNA of A. pulchellus on this part of the island. We proposed two not mutually exclusive scenarios to account for the interspecific matings between A. pulchellus and A. krugi. We inferred that hybridization events occurred independently in several populations, and determined that k-mtDNA haplotypes harboured in individuals of A. pulchellus can be assigned to four of the five major mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA clades in the two species is largely congruent. Based on this evidence, we concluded that natural selection was the probable driving mechanism for the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear data sets yielded different results. DNAH3 showed reciprocal monophyly of A. pulchellus and A. krugi, indicating no effect of hybridization on this marker. In contrast, the two species shared nine NKTR alleles, probably due to incomplete lineage sorting. Our study system will provide an excellent opportunity to experimentally assess the behavioural and ecological mechanisms that can lead to hybridization in closely related taxa.},
}
@article {pmid23665487,
year = {2013},
author = {Zhang, J and Zhao, F and Fu, Q and Liang, M and Tong, Y and Liu, X and Lin, B and Mi, H and Zhang, M and Wei, QP and Xue, L and Jiang, P and Zhou, X and Mo, JQ and Huang, T and Qu, J and Guan, MX},
title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the LHON-associated m.14484T&gt;C (MT-ND6) mutation in Chinese families.},
journal = {Mitochondrion},
volume = {13},
number = {6},
pages = {772-781},
doi = {10.1016/j.mito.2013.05.002},
pmid = {23665487},
issn = {1872-8278},
mesh = {China ; Female ; Genome, Mitochondrial ; *Haplotypes ; Humans ; Male ; Mitochondria/*genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber ; Pedigree ; Phenotype ; Phylogeny ; },
abstract = {Mitochondrial m.14484T>C (MT-ND6) mutation has been associated with Leber's hereditary optic neuropathy. Previous investigations revealed that the m.14484T>C mutation is a primary factor underlying the development of optic neuropathy but is not sufficient to produce a clinical phenotype. However, mitochondrial haplogroups have been proposed to modulate the phenotypic manifestation of the m.14484T>C mutation. Here, we performed the clinical, genetic evaluation and complete mitochondrial genome sequence analysis of 41 Han Chinese pedigrees carrying the m.14484T>C mutation. These families exhibited a wide range of penetrances and expressivities of optic neuropathy. The average ratio between affected male/female matrilineal relatives from 41 families was 2:1. The penetrance of optic neuropathy in these Chinese pedigrees ranged from 5.6% to 100%, with the average of 23.8%. Furthermore, the age-of-onset for optic neuropathy varied from 4 to 44 years, with the average of 19.3 years. Sequence analysis of their mitochondrial genomes identified distinct sets of polymorphisms belonging to ten Eastern Asian haplogroups, indicating that the m.14484T>C mutation occurred through recurrent origins and founder events. We showed that mitochondrial haplogroups M9, M10 and N9 increased the penetrance of optic neuropathy in these Chinese families. In particular, these mitochondrial haplogroup specific variants: m.3394T>C (MT-ND1), m.14502T>C (MT-ND4) and m.14693A>G (MT-TE) enhanced the penetrance of visual loss in these Chinese families. These data provided the direct evidence that mitochondrial modifiers modulate the variable penetrance and expressivity of optic neuropathy among Chinese pedigrees carrying the m.14484T>C mutation.},
}
@article {pmid23673559,
year = {2013},
author = {Voelter-Mahlknecht, S and Mahlknecht, U},
title = {Cloning, chromosomal characterization and FISH mapping of the NAD(+)-dependent histone deacetylase gene sirtuin 5 in the mouse.},
journal = {International journal of oncology},
volume = {43},
number = {1},
pages = {237-245},
doi = {10.3892/ijo.2013.1939},
pmid = {23673559},
issn = {1791-2423},
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; *Cloning, Molecular ; Group III Histone Deacetylases/*genetics ; In Situ Hybridization, Fluorescence ; Mice ; NAD/genetics/*metabolism ; Phylogeny ; Sequence Alignment ; Sirtuins/*genetics/metabolism ; },
abstract = {Sirtuin 5 (SIRT5) is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, belonging to the silent information regulator 2 (Sir2) family of sirtuin histone deacetylases (sirtuins). The yeast Sir2 protein and its mammalian derivatives are important in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization and in the regulation of aging. In mammals, 7 sirtuin isoforms have been identified to date of which three (SIRT3, SIRT4 and SIRT5) are localized in the mitochondria, which serve as the center of energy management and the initiation of cellular apoptosis. In the study presented herein, we report the genomic organization and chromosomal localization of the murine sirt5 gene. We have isolated and characterized the murine sirt5 genomic sequence, which spans a region of 24,449 bp and which has one single genomic locus. The murine sirt5 gene consists of 8 exons and encodes a 310-aa protein with a predictive mo-lecular weight of 34.1 kDa and an isoelectric point of 8.90. For the murine sirt5 gene only one single genomic locus has been identified. The gene has been localized to mouse chromosome 13A4 and is flanked by STS-marker 164522 (synonymous WI MRC-RH: 506859).},
}
@article {pmid23685010,
year = {2013},
author = {Zhao, C and Feng, B and Cao, Y and Xie, P and Xu, J and Pang, Y and Liu, X and Li, Q},
title = {Identification and characterisation of ROS modulator 1 in Lampetra japonica.},
journal = {Fish &amp; shellfish immunology},
volume = {35},
number = {2},
pages = {278-283},
doi = {10.1016/j.fsi.2013.04.039},
pmid = {23685010},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Exocrine Glands/metabolism ; Fish Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation ; Lampreys/*genetics/*immunology/metabolism ; Lipopolysaccharides/physiology ; Membrane Proteins/chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Real-Time Polymerase Chain Reaction/veterinary ; Sequence Alignment ; },
abstract = {Reactive oxygen species (ROS) are a heterogeneous group of highly reactive molecules that oxidise targets in biological systems. ROS are also considered important immune regulators. In this study, we identified a homologue of reactive oxygen species modulator 1 (Romo1) in the Japanese lamprey (Lampetra japonica). The L japonica Romo1 (Lj-Romo1) gene shares high sequence homology with the Romo1 genes of jawed vertebrates. Real-time quantitative PCR demonstrated the wide distribution of Lj-Romo1 in lamprey tissues. Furthermore, after the lampreys were stimulated with lipopolysaccharide (LPS), the level of Lj-Romo1 mRNA was markedly up-regulated in the liver, gill, kidney, and intestine tissues. Lj-Romo1 was localised to the mitochondria and has the capacity to increase the ROS level in cells. The results obtained in the present study will help us to understand the roles of Romo1 in ROS production and innate immune responses in jawless vertebrates.},
}
@article {pmid23696374,
year = {2013},
author = {Vianello, D and Sevini, F and Castellani, G and Lomartire, L and Capri, M and Franceschi, C},
title = {HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment.},
journal = {Human mutation},
volume = {34},
number = {9},
pages = {1189-1194},
doi = {10.1002/humu.22356},
pmid = {23696374},
issn = {1098-1004},
mesh = {Algorithms ; DNA, Mitochondrial/*classification/*genetics ; *Databases, Nucleic Acid ; Genetic Variation ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Software ; },
abstract = {Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the "postgenomic era": the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it.},
}
@article {pmid23742009,
year = {2013},
author = {Kowald, A and Kirkwood, TB},
title = {Mitochondrial mutations and aging: random drift is insufficient to explain the accumulation of mitochondrial deletion mutants in short-lived animals.},
journal = {Aging cell},
volume = {12},
number = {4},
pages = {728-731},
doi = {10.1111/acel.12098},
pmid = {23742009},
issn = {1474-9726},
support = {MR/K006312/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Aging ; Animals ; Computer Simulation ; DNA, Mitochondrial/genetics/*metabolism ; *Genetic Drift ; Longevity ; Mitochondria/genetics/metabolism ; Models, Biological ; Mutation Rate ; *Sequence Deletion ; Species Specificity ; Time Factors ; },
abstract = {Mitochondrial DNA deletions accumulate over the life course in post-mitotic cells of many species and may contribute to aging. Often a single mutant expands clonally and finally replaces the wild-type population of a whole cell. One proposal to explain the driving force behind this accumulation states that random drift alone, without any selection advantage, is sufficient to explain the clonal accumulation of a single mutant. Existing mathematical models show that such a process might indeed work for humans. However, to be a general explanation for the clonal accumulation of mtDNA mutants, it is important to know whether random drift could also explain the accumulation process in short-lived species like rodents. To clarify this issue, we modelled this process mathematically and performed extensive computer simulations to study how different mutation rates affect accumulation time and the resulting degree of heteroplasmy. We show that random drift works for lifespans of around 100 years, but for short-lived animals, the resulting degree of heteroplasmy is incompatible with experimental observations.},
}
@article {pmid23781066,
year = {2013},
author = {Maddocks, OD and Scanlon, KM and Donnenberg, MS},
title = {An Escherichia coli effector protein promotes host mutation via depletion of DNA mismatch repair proteins.},
journal = {mBio},
volume = {4},
number = {3},
pages = {e00152-13},
pmid = {23781066},
issn = {2150-7511},
support = {R01 AI032074/AI/NIAID NIH HHS/United States ; R21 CA141038/CA/NCI NIH HHS/United States ; R01 AI32074/AI/NIAID NIH HHS/United States ; },
mesh = {Carrier Proteins/*metabolism ; *DNA Mismatch Repair ; DNA Repair Enzymes/*metabolism ; Enteropathogenic Escherichia coli/*genetics/*metabolism ; Escherichia coli Proteins/*metabolism ; *Host-Pathogen Interactions ; Humans ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; *Mutation ; Mutation Rate ; Protein Transport ; Virulence Factors/metabolism ; },
abstract = {Enteropathogenic Escherichia coli (EPEC) is an attaching and effacing (A/E) human pathogen that causes diarrhea during acute infection, and it can also sustain asymptomatic colonization. A/E E. coli depletes host cell DNA mismatch repair (MMR) proteins in colonic cell lines and has been detected in colorectal cancer (CRC) patients. However, until now, a direct link between infection and host mutagenesis has not been fully demonstrated. Here we show that the EPEC-secreted effector protein EspF is critical for complete EPEC-induced depletion of MMR proteins. The mechanism of EspF activity on MMR protein was posttranscriptional and dependent on EspF mitochondrial targeting. EPEC infection also induced EspF-independent elevation of host reactive oxygen species levels. Moreover, EPEC infection significantly increased spontaneous mutation frequency in host cells, and this effect was dependent on mitochondrially targeted EspF. Taken together, these results support the hypothesis that A/E E. coli can promote colorectal carcinogenesis in humans.},
}
@article {pmid23782532,
year = {2013},
author = {Du, Y and Zhang, H and Hong, L and Wang, J and Zheng, X and Zhang, Z},
title = {Acetolactate synthases MoIlv2 and MoIlv6 are required for infection-related morphogenesis in Magnaporthe oryzae.},
journal = {Molecular plant pathology},
volume = {14},
number = {9},
pages = {870-884},
pmid = {23782532},
issn = {1364-3703},
mesh = {Acetolactate Synthase/chemistry/*metabolism ; Amino Acids/biosynthesis/pharmacology ; Biosynthetic Pathways/drug effects ; Fungal Proteins/chemistry/*metabolism ; Hyphae/drug effects/growth &amp; development ; Magnaporthe/drug effects/*enzymology/*growth &amp; development/pathogenicity ; Molecular Sequence Data ; *Morphogenesis/drug effects ; Mutation/genetics ; Phylogeny ; Pigmentation/drug effects ; Plant Diseases/*microbiology ; Protein Binding/drug effects ; Protein Structure, Tertiary ; Spores, Fungal/drug effects/growth &amp; development ; Structure-Activity Relationship ; },
abstract = {Amino acids are important components in the metabolism of a variety of pathogens, plants and animals. Acetolactate synthase (ALS) catalyses the first common step in leucine, isoleucine and valine biosynthesis, and is the target of several classes of inhibitors. Here, MoIlv2, an orthologue of the Saccharomyces cerevisiae ALS catalytic subunit Ilv2, and MoIlv6, an orthologue of the S. cerevisiae ALS regulatory subunit Ilv6, were identified. To characterize MoILV2 and MoILV6 functions, we generated the deletion mutants ΔMoilv2 and ΔMoilv6. Phenotypic analysis showed that both mutants were auxotrophic for leucine, isoleucine and valine, and were defective in conidial morphogenesis, appressorial penetration and pathogenicity. Further studies suggested that MoIlv2 and MoIlv6 play a critical role in maintaining the balance of intracellular amino acid levels. MoIlv2 and MoIlv6 are both localized to the mitochondria and the signal peptide of MoIlv6 is critical for its localization. In summary, our evidence indicates that MoIlv2 plays a crucial role in isoleucine and valine biosynthesis, whereas MoIlv6 contributes to isoleucine and leucine biosynthesis; both genes are required for fungal pathogenicity. This study indicates the potential of targeting branched-chain amino acid biosynthesis for anti-rice blast management.},
}
@article {pmid23782838,
year = {2013},
author = {Chauvigné, F and Boj, M and Vilella, S and Finn, RN and Cerdà, J},
title = {Subcellular localization of selectively permeable aquaporins in the male germ line of a marine teleost reveals spatial redistribution in activated spermatozoa.},
journal = {Biology of reproduction},
volume = {89},
number = {2},
pages = {37},
doi = {10.1095/biolreprod.113.110783},
pmid = {23782838},
issn = {1529-7268},
mesh = {Animals ; Aquaporins/genetics/*metabolism ; Germ Cells/*metabolism ; Male ; Phylogeny ; Sea Bream ; Sperm Motility/genetics ; Spermatogenesis/genetics ; Spermatozoa/*metabolism ; },
abstract = {In oviparous vertebrates such as the marine teleost gilthead seabream, water and fluid homeostasis associated with testicular physiology and the external activation of spermatozoa is potentially mediated by multiple aquaporins. To test this hypothesis, we isolated five novel members of the aquaporin superfamily from gilthead seabream and developed paralog-specific antibodies to localize the cellular sites of protein expression in the male reproductive tract. Together with phylogenetic classification, functional characterization of four of the newly isolated paralogs, Aqp0a, -7, -8b, and -9b, demonstrated that they were water permeable, while Aqp8b was also permeable to urea, and Aqp7 and -9b were permeable to glycerol and urea. Immunolocalization experiments indicated that up to seven paralogous aquaporins are differentially expressed in the seabream testis: Aqp0a and -9b in Sertoli and Leydig cells, respectively; Aqp1ab, -7, and -10b from spermatogonia to spermatozoa; and Aqp1aa and -8b in spermatids and sperm. In the efferent duct, only Aqp10b was found in the luminal epithelium. Ejaculated spermatozoa showed a segregated spatial distribution of five aquaporins: Aqp1aa and -7 in the entire flagellum or the head, respectively, and Aqp1ab, -8b, and -10b both in the head and the anterior tail. The combination of immunofluorescence microscopy and biochemical fractionation of spermatozoa indicated that Aqp10b and phosphorylated Aqp1ab are rapidly translocated to the head plasma membrane upon activation, whereas Aqp8b accumulates in the mitochondrion of the spermatozoa. In contrast, Aqp1aa and -7 remained unchanged. These data reveal that aquaporin expression in the teleost testis shares conserved features of the mammalian system, and they suggest that the piscine channels may play different roles in water and solute transport during spermatogenesis, sperm maturation and nutrition, and the initiation and maintenance of sperm motility.},
}
@article {pmid23783412,
year = {2013},
author = {Wu, TM and Lin, WR and Kao, YT and Hsu, YT and Yeh, CH and Hong, CY and Kao, CH},
title = {Identification and characterization of a novel chloroplast/mitochondria co-localized glutathione reductase 3 involved in salt stress response in rice.},
journal = {Plant molecular biology},
volume = {83},
number = {4-5},
pages = {379-390},
pmid = {23783412},
issn = {1573-5028},
mesh = {Amino Acid Sequence ; Chloroplasts/*enzymology ; Conserved Sequence ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Plant/*drug effects ; Glutathione Reductase/drug effects/*genetics/metabolism ; Isoenzymes ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oryza/drug effects/*enzymology/genetics/ultrastructure ; Phylogeny ; Plant Growth Regulators/pharmacology ; Plant Proteins/drug effects/genetics/metabolism ; Plant Roots/drug effects/enzymology/genetics/ultrastructure ; Plant Shoots/drug effects/enzymology/genetics/ultrastructure ; Plants, Genetically Modified ; Recombinant Fusion Proteins ; Salicylic Acid/pharmacology ; Salinity ; Seedlings/drug effects/enzymology/genetics/ultrastructure ; Sequence Alignment ; Sodium Chloride/pharmacology ; Stress, Physiological/*drug effects ; },
abstract = {Glutathione reductases (GRs) are important components of the antioxidant machinery that plants use to respond against abiotic stresses. In rice, one cytosolic and two chloroplastic GR isoforms have been identified. In this work, we describe the cloning and characterization of the full-length cDNA encoding OsGR3, a chloroplast-localized GR that up to now was considered as a non-functional enzyme because of assumed lack of N-terminal conserved domains. The expression of OsGR3 in E. coli validated that it can be translated as a protein with GR activity. OsGR3 shows 76 and 53 % identity with OsGR1 (chloroplastic) and OsGR2 (cytosolic), respectively. Phylogenetic analysis revealed 2 chloroplastic GRs in Poaceae species, including rice, sorghum and brachypodium, but only one chloroplastic GR in dicots. A plastid transit peptide is located at the N terminus of OsGR3, and genetic transformation of rice with a GR3-GFP fusion construct further confirmed its localization in chloroplasts. Furthermore, OsGR1 and OsGR3 are also targeted to mitochondria, which suggest a combined antioxidant mechanism in both chloroplasts and mitochondria. However, both isoforms showed a distinct response to salinity: the expression of OsGR3 but not OsGR1 was induced by salt stress. In addition, the transcript level of OsGR3 was greatly increased with salicylic acid treatment but was not significantly affected by methyl jasmonate, dehydration or heat shock stress. Our results provide new clues about the possible roles of functional OsGR3 in salt stress and biotic stress tolerance.},
}
@article {pmid23792080,
year = {2013},
author = {Flipphi, M and Fekete, E and Ag, N and Scazzocchio, C and Karaffa, L},
title = {Spliceosome twin introns in fungal nuclear transcripts.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {57},
number = {},
pages = {48-57},
doi = {10.1016/j.fgb.2013.06.003},
pmid = {23792080},
issn = {1096-0937},
mesh = {Alternative Splicing/genetics ; Chloroplasts/chemistry/genetics ; Conserved Sequence ; Introns ; *Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry/*genetics ; RNA Splicing/*genetics ; RNA, Messenger/genetics ; Spliceosomes/*genetics ; },
abstract = {The spliceosome is an RNA/protein complex, responsible for intron excision from eukaryotic nuclear transcripts. In bacteria, mitochondria and plastids, intron excision does not involve the spliceosome, but occurs through mechanisms dependent on intron RNA secondary and tertiary structure. For group II/III chloroplast introns, "twintrons" (introns within introns) have been described. The excision of the external intron, and thus proper RNA maturation, necessitates prior removal of the internal intron, which interrupts crucial sequences of the former. We have here predicted analogous instances of spliceosomal twintrons ("stwintrons") in filamentous fungi. In two specific cases, where the internal intron interrupts the donor of the external intron after the first or after the second nucleotide, respectively, we show that intermediates with the sequence predicted by the "stwintron" hypothesis, are produced in the splicing process. This implies that two successive rounds of RNA scanning by the spliceosome are necessary to produce the mature mRNA. The phylogenetic distributions of the stwintrons we have identified suggest that they derive from "late" events, subsequent to the appearance of the host intron. They may well not be limited to fungal nuclear transcripts, and their generation and eventual disappearance in the evolutionary process are relevant to hypotheses of intron origin and alternative splicing.},
}
@article {pmid23804672,
year = {2013},
author = {Chung-Davidson, YW and Priess, MC and Yeh, CY and Brant, CO and Johnson, NS and Li, K and Nanlohy, KG and Bryan, MB and Brown, CT and Choi, J and Li, W},
title = {A thermogenic secondary sexual character in male sea lamprey.},
journal = {The Journal of experimental biology},
volume = {216},
number = {Pt 14},
pages = {2702-2712},
pmid = {23804672},
issn = {1477-9145},
support = {R24 GM083982/GM/NIGMS NIH HHS/United States ; 5R24GM83982/GM/NIGMS NIH HHS/United States ; },
mesh = {Adenosine Triphosphate/metabolism ; Adipose Tissue/*physiology/ultrastructure ; Animals ; Electron Transport Complex IV/metabolism ; Fatty Acids/metabolism ; Gas Chromatography-Mass Spectrometry ; Gene Expression Regulation/*physiology ; Immunohistochemistry ; Male ; Microscopy, Electron, Transmission ; Petromyzon/*physiology ; Phylogeny ; Real-Time Polymerase Chain Reaction ; *Sex Characteristics ; Sexual Behavior, Animal/*physiology ; Thermogenesis/*physiology ; Transcriptome ; },
abstract = {Secondary sexual characters in animals are exaggerated ornaments or weapons for intrasexual competition. Unexpectedly, we found that a male secondary sexual character in sea lamprey (Petromyzon marinus) is a thermogenic adipose tissue that instantly increases its heat production during sexual encounters. This secondary sexual character, developed in front of the anterior dorsal fin of mature males, is a swollen dorsal ridge known as the 'rope' tissue. It contains nerve bundles, multivacuolar adipocytes and interstitial cells packed with small lipid droplets and mitochondria with dense and highly organized cristae. The fatty acid composition of the rope tissue is rich in unsaturated fatty acids. The cytochrome c oxidase activity is high but the ATP concentration is very low in the mitochondria of the rope tissue compared with those of the gill and muscle tissues. The rope tissue temperature immediately rose up to 0.3°C when the male encountered a conspecific. Mature males generated more heat in the rope and muscle tissues when presented with a mature female than when presented with a male (paired t-test, P<0.05). On average, the rope generated 0.027±0.013 W cm(-3) more heat than the muscle in 10 min. Transcriptome analyses revealed that genes involved in fat cell differentiation are upregulated whereas those involved in oxidative-phosphorylation-coupled ATP synthesis are downregulated in the rope tissue compared with the gill and muscle tissues. Sexually mature male sea lamprey possess the only known thermogenic secondary sexual character that shows differential heat generation toward individual conspecifics.},
}
@article {pmid23804750,
year = {2013},
author = {Giacomotto, J and Brouilly, N and Walter, L and Mariol, MC and Berger, J and Ségalat, L and Becker, TS and Currie, PD and Gieseler, K},
title = {Chemical genetics unveils a key role of mitochondrial dynamics, cytochrome c release and IP3R activity in muscular dystrophy.},
journal = {Human molecular genetics},
volume = {22},
number = {22},
pages = {4562-4578},
doi = {10.1093/hmg/ddt302},
pmid = {23804750},
issn = {1460-2083},
mesh = {Animals ; Animals, Genetically Modified ; Binding Sites ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Cell Death ; Cyclophilins/antagonists &amp; inhibitors/*metabolism ; Cyclosporine/*pharmacology ; Cytochromes c/genetics/*metabolism ; Gene Knockdown Techniques ; Humans ; Inositol 1,4,5-Trisphosphate Receptors/genetics/*metabolism ; Methazolamide/pharmacology ; *Mitochondrial Dynamics/drug effects/genetics ; Mitochondrial Proteins/genetics/metabolism ; Muscular Dystrophy, Animal/*drug therapy/pathology ; Muscular Dystrophy, Duchenne/genetics/*metabolism/pathology ; Phylogeny ; Sequence Homology ; Zebrafish/embryology/genetics ; },
abstract = {Duchenne muscular dystrophy (DMD) is a neuromuscular disease caused by mutations in the dystrophin gene. The subcellular mechanisms of DMD remain poorly understood and there is currently no curative treatment available. Using a Caenorhabditis elegans model for DMD as a pharmacologic and genetic tool, we found that cyclosporine A (CsA) reduces muscle degeneration at low dose and acts, at least in part, through a mitochondrial cyclophilin D, CYN-1. We thus hypothesized that CsA acts on mitochondrial permeability modulation through cyclophilin D inhibition. Mitochondrial patterns and dynamics were analyzed, which revealed dramatic mitochondrial fragmentation not only in dystrophic nematodes, but also in a zebrafish model for DMD. This abnormal mitochondrial fragmentation occurs before any obvious sign of degeneration can be detected. Moreover, we demonstrate that blocking/delaying mitochondrial fragmentation by knocking down the fission-promoting gene drp-1 reduces muscle degeneration and improves locomotion abilities of dystrophic nematodes. Further experiments revealed that cytochrome c is involved in muscle degeneration in C. elegans and seems to act, at least in part, through an interaction with the inositol trisphosphate receptor calcium channel, ITR-1. Altogether, our findings reveal that mitochondria play a key role in the early process of muscle degeneration and may be a target of choice for the design of novel therapeutics for DMD. In addition, our results provide the first indication in the nematode that (i) mitochondrial permeability transition can occur and (ii) cytochrome c can act in cell death.},
}
@article {pmid23815330,
year = {2015},
author = {Ma, Z and Huang, Z and Zhang, S and Xie, L and Yang, X and Zhang, X and Yang, R},
title = {The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {116-117},
doi = {10.3109/19401736.2013.809446},
pmid = {23815330},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {For understanding the phylogenetic position of Micropercops swinhonis within the family Odontobutidae, the complete nucleotide sequence of M. swinhonis mitochondrial genome was firstly determined. The genome is 16,493 bp in length, and consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and 2 main noncoding regions (the control region and the origin of the light strand replication). The gene composition and order of which were similar to most other vertebrates. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified.},
}
@article {pmid23826813,
year = {2013},
author = {Wei, Q and Wang, S and Yao, J and Lu, Y and Chen, Z and Xing, G and Cao, X},
title = {Genetic mutations of GJB2 and mitochondrial 12S rRNA in nonsyndromic hearing loss in Jiangsu Province of China.},
journal = {Journal of translational medicine},
volume = {11},
number = {},
pages = {163},
pmid = {23826813},
issn = {1479-5876},
mesh = {Adolescent ; Adult ; Case-Control Studies ; Child ; Child, Preschool ; China ; Connexin 26 ; Connexins/*genetics ; DNA, Mitochondrial/genetics ; Deafness/genetics ; Female ; Heterozygote ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Nucleic Acid Conformation ; Phylogeny ; RNA, Messenger/genetics ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {BACKGROUND: Hearing loss is caused by several environmental and genetic factors and the proportion attributed to inherited causes is assumed at 50 ~ 60% . Mutations in GJB2 and mitochondrial DNA (mtDNA) 12S rRNA are the most common molecular etiology for nonsyndromic sensorineural hearing loss (NSHL). The mutation spectra of these genes vary among different ethnic groups.<br><br>METHODS: To add the molecular etiologic information of hearing loss in the Chinese population, a total of 658 unrelated patients with NSHL from Jiangsu Province of China were selected for mutational screening including GJB2 and mtDNA 12S rRNA genes using PCR and DNA sequencing technology. As for controls, 462 normal-hearing individuals were collected.<br><br>RESULTS: A total of 9 pathogenic mutations in the GJB2 and 7 pathogenic mutations in the 12S rRNA gene were identified. Of all patients, 70 had monoallelic GJB2 coding region mutation in the heterozygous state, 94 carried two confirmed pathogenic mutations including 79 homozygotes and 15 compound heterozygotes. The 235delC appears to be the most common deafness-causing GJB2 mutation (102/658, 15.50%). No mutations or variants in the GJB2 exon1 and basal promoter region were found. In these patients, 4 subjects carried the m.1494C&#x2009;>&#x2009;T mutation (0.61%) and 39 subjects harbored the m.1555A&#x2009;>&#x2009;G mutation (5.93%) in mtDNA 12S rRNA gene. A novel sequence variant at m.1222A&#x2009;>&#x2009;G in the 12S rRNA gene was identified, which could alter the secondary structure of the 12S rRNA.<br><br>CONCLUSION: The mutation spectrum and prevalence of GJB2 and mtDNA 12S rRNA genes in Jiangsu population are similar to other areas of China. There are in total 31.46% of the patients with NSHL carry deafness-causing mutation in GJB2 or mtDNA 12S rRNA genes. Mutation in GJB2 gene is the most common factor, mtDNA 12S rRNA also plays an important part in the pathogenesis of hearing loss in Jiangsu Province areas. The m.1222A&#x2009;>&#x2009;G was found to be a new candidate mutation associated with hearing loss. Our results indicated the necessity of genetic screening for mutations of these genes in Jiangsu patients with NSHL.},
}
@article {pmid23829495,
year = {2013},
author = {Rondeau, EB and Messmer, AM and Sanderson, DS and Jantzen, SG and von Schalburg, KR and Minkley, DR and Leong, JS and Macdonald, GM and Davidsen, AE and Parker, WA and Mazzola, RS and Campbell, B and Koop, BF},
title = {Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene.},
journal = {BMC genomics},
volume = {14},
number = {},
pages = {452},
pmid = {23829495},
issn = {1471-2164},
mesh = {Animals ; *Chromosome Mapping ; Female ; Fishes/*genetics/physiology ; Genetic Markers/genetics ; Genome, Mitochondrial/genetics ; *Genomics ; Genotyping Techniques ; Male ; Mitochondria/*genetics ; Phenotype ; *Phylogeny ; *Sex Characteristics ; Sex Determination Processes/*genetics ; Smegmamorpha/genetics ; Synteny/genetics ; },
abstract = {BACKGROUND: The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable.<br><br>RESULTS: A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis.<br><br>CONCLUSIONS: The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.},
}
@article {pmid23831752,
year = {2013},
author = {Jimenez-Gutierrez, LR and Hernandez-Lopez, J and Islas-Osuna, MA and Muhlia-Almazan, A},
title = {Three nucleus-encoded subunits of mitochondrial cytochrome c oxidase of the whiteleg shrimp Litopenaeus vannamei: cDNA characterization, phylogeny and mRNA expression during hypoxia and reoxygenation.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {166},
number = {1},
pages = {30-39},
doi = {10.1016/j.cbpb.2013.06.008},
pmid = {23831752},
issn = {1879-1107},
mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Cell Nucleus/enzymology ; DNA, Complementary/*genetics ; Electron Transport Complex IV/*genetics/metabolism ; Gene Expression ; Hypoxia/genetics/metabolism ; Mitochondria/*enzymology/genetics ; Oxygen/metabolism ; Penaeidae ; Phylogeny ; Protein Subunits/*genetics ; },
abstract = {The mitochondrial cytochrome c oxidase (COX) catalyzes the reduction of oxygen to water playing a key role in the respiratory chain and ATP synthesis. The nucleus-encoded COX subunits do not participate in catalysis, but some are known to play a role in the expression, assembly and activity of the enzyme. Since hypoxia continuously affects the shrimp environment, it is important to study COX to understand their ability to deal with low oxygen levels. The goal of this research was to characterize the complementary DNA (cDNA) sequences of three nucleus-encoded subunits -coxIV, coxVa, and coxVb- and to evaluate the shrimp COX response to hypoxia by measuring their gene expression. The cDNA sequence of coxIV consisted of 532bp, which encodes a 17.47kDa protein, while coxVa cDNA consisted of 460bp and coded a protein of 17.11kDa, and the coxVb coding sequence consisted of 364bp encoding a 13.74kDa protein. Shrimp subunits do not have isoforms, and they are not differentially expressed during hypoxia, as observed in mammals. Coordinated changes were detected in the mRNA amounts of nuclear and mitochondrial subnits; these changes, at the transcriptional level, are suggested to be controlled through transcriptional factors Sp1 and NRF2.},
}
@article {pmid23838143,
year = {2013},
author = {Seo, MY and Mekuchi, M and Teranishi, K and Kaneko, T},
title = {Expression of ion transporters in gill mitochondrion-rich cells in Japanese eel acclimated to a wide range of environmental salinity.},
journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology},
volume = {166},
number = {2},
pages = {323-332},
doi = {10.1016/j.cbpa.2013.07.004},
pmid = {23838143},
issn = {1531-4332},
mesh = {*Acclimatization ; Anguilla/*metabolism ; Animals ; Cloning, Molecular ; Fish Proteins/genetics/*metabolism ; Gene Expression ; Gene Expression Regulation ; Gills/*metabolism/ultrastructure ; Ion Transport ; Mitochondria/metabolism/ultrastructure ; Organ Specificity ; Osmoregulation ; Phylogeny ; Protein Subunits/metabolism ; RNA, Messenger/genetics/metabolism ; Salinity ; Salt Tolerance ; Sodium-Hydrogen Exchangers/genetics/metabolism ; Solute Carrier Family 12, Member 2/genetics/metabolism ; Vacuolar Proton-Translocating ATPases/genetics/metabolism ; },
abstract = {We examined morphological changes and molecular mechanisms of ion regulation in mitochondrion-rich (MR) cells of Japanese eel acclimated to different environmental salinities. Electron microscopic observations revealed that the apical membrane of MR cells appeared as a flat or slightly projecting disk with a mesh-like structure on its surface in eel acclimated to freshwater (FW). In seawater (SW)-acclimated eel, in contrast, the apical membrane of MR cells showed a slightly concave surface without a mesh-like structure. The mRNA expression of Na(+)/H(+) exchanger-3 (NHE3) in deionized FW and normal SW was higher than that in normal FW and 30%-diluted SW. Expression of Na(+)/K(+)/2Cl(-) cotransporter-1a (NKCC1a) became higher with increasing environmental salinity. Immunofluorescence staining showed that the apical NHE3 immunoreaction was stronger in deionized FW and normal SW than in the other groups. Basolateral NKCC1 immunoreaction was most intense in normal SW. These results indicate that apical NHE3 is involved in ion uptake in fish acclimated to hypotonic environments, and that basolateral NKCC1 is important for acclimation to hypertonic environments. The relatively high expression of NHE3 in SW further indicates a possible role of NHE3 in acid-base regulation in the gills in SW-acclimated fish.},
}
@article {pmid23839086,
year = {2013},
author = {Evangelou, VI and Bouga, M and Emmanouel, NG and Perdikis, DCh and Papadoulis, GT},
title = {Discrimination of two natural biocontrol agents in the Mediterranean region based on mitochondrial DNA sequencing data.},
journal = {Biochemical genetics},
volume = {51},
number = {11-12},
pages = {825-840},
doi = {10.1007/s10528-013-9610-0},
pmid = {23839086},
issn = {1573-4927},
mesh = {Animals ; Asteraceae ; *Biological Control Agents ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial ; Greece ; Haplotypes ; Heteroptera/*classification/genetics ; Male ; Mitochondria/genetics ; Phylogeny ; *Sequence Analysis, DNA ; Solanum ; Spain ; },
abstract = {Macrolophus pygmaeus and M. melanotoma (Hemiptera: Miridae) are biological control agents used in greenhouse crops, the former preferring plants of the Solanaceae family and the latter the aster Dittrichia viscosa. The discrimination of these species is of high significance for effective biological pest control, but identification based on morphological characters of the host plant is not always reliable. In this study, sequencing analysis of mitochondrial gene segments 12S rDNA and COI has been combined with crossing experiments and morphological observations to develop new markers for Macrolophus spp. discrimination and to provide new data on their genetic variability. This is the first comprehensive research in Greece on M. pygmaeus and M. melanotoma genetic variability based on sequencing data from 12S rDNA and COI gene segments. The relationship of this variability to host plant preference must be investigated in an agricultural ecosystem.},
}
@article {pmid23840326,
year = {2013},
author = {Teng, CY and Dang, Y and Danne, JC and Waller, RF and Green, BR},
title = {Mitochondrial Genes of Dinoflagellates Are Transcribed by a Nuclear-Encoded Single-Subunit RNA Polymerase.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e65387},
pmid = {23840326},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Bacteriophage T7/enzymology/genetics ; Cell Nucleus/genetics/metabolism ; Conserved Sequence ; DNA-Directed RNA Polymerases/*physiology ; Dinoflagellida/*genetics/ultrastructure ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Phylogeny ; Protein Subunits ; RNA, Nuclear/*physiology ; *Transcription, Genetic ; },
abstract = {Dinoflagellates are a large group of algae that contribute significantly to marine productivity and are essential photosynthetic symbionts of corals. Although these algae have fully-functioning mitochondria and chloroplasts, both their organelle genomes have been highly reduced and the genes fragmented and rearranged, with many aberrant transcripts. However, nothing is known about their RNA polymerases. We cloned and sequenced the gene for the nuclear-encoded mitochondrial polymerase (RpoTm) of the dinoflagellate Heterocapsa triquetra and showed that the protein presequence targeted a GFP construct into yeast mitochondria. The gene belongs to a small gene family, which includes a variety of 3'-truncated copies that may have originated by retroposition. The catalytic C-terminal domain of the protein shares nine conserved sequence blocks with other single-subunit polymerases and is predicted to have the same fold as the human enzyme. However, the N-terminal (promoter binding/transcription initiation) domain is not well-conserved. In conjunction with the degenerate nature of the mitochondrial genome, this suggests a requirement for novel accessory factors to ensure the accurate production of functional mRNAs.},
}
@article {pmid23840368,
year = {2013},
author = {Grindon, AJ and Davison, A},
title = {Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans.},
journal = {PloS one},
volume = {8},
number = {6},
pages = {e65792},
pmid = {23840368},
issn = {1932-6203},
mesh = {Animals ; DNA, Mitochondrial/*analysis ; Fossils ; France ; Human Migration ; Humans ; Ireland ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; Snails/*classification/genetics ; Spain ; },
abstract = {The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared "Lusitanian" history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.},
}
@article {pmid23859054,
year = {2015},
author = {Li, Q and Wei, SJ and Shi, M and Chen, XX},
title = {Complete mitochondrial genome of Neochauliodes bowringi (MacLachlan) (Megaloptera: Corydalidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {112-113},
doi = {10.3109/19401736.2013.803542},
pmid = {23859054},
issn = {1940-1744},
mesh = {Animals ; Codon, Initiator ; Codon, Terminator ; Gene Order ; Genes, Insect ; *Genome, Mitochondrial ; Insecta/*genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {We describe and analyze the complete mitochondrial genome of Neochauliodes bowringi (MacLachlan) (Megaloptera: Corydalidae). The length of the genome is 16,064 bp (GenBank accession No. JQ351950), the longest mitochondrial genome in the order Megaloptera already got, which includes 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNAs and an A + T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. All protein-coding genes start with ATN start codon except for the gene ND4, which uses GTG as start codon. Eight protein-coding genes use TAA as stop codon and others use incomplete stop codons "T" or "TA". The A + T-rich region is located between rrnS and trnI with a length of 1328 bp.},
}
@article {pmid23864032,
year = {2014},
author = {Tillander, V and Arvidsson Nordström, E and Reilly, J and Strozyk, M and Van Veldhoven, PP and Hunt, MC and Alexson, SE},
title = {Acyl-CoA thioesterase 9 (ACOT9) in mouse may provide a novel link between fatty acid and amino acid metabolism in mitochondria.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {71},
number = {5},
pages = {933-948},
pmid = {23864032},
issn = {1420-9071},
mesh = {Amino Acids/*metabolism ; Animals ; Base Sequence ; Blotting, Western ; Chromatography, High Pressure Liquid ; Chromosome Mapping ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Fatty Acids/*metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spectrophotometry ; Thiolester Hydrolases/*genetics/*metabolism ; },
abstract = {Acyl-CoA thioesterase (ACOT) activities are found in prokaryotes and in several compartments of eukaryotes where they hydrolyze a wide range of acyl-CoA substrates and thereby regulate intracellular acyl-CoA/CoA/fatty acid levels. ACOT9 is a mitochondrial ACOT with homologous genes found from bacteria to humans and in this study we have carried out an in-depth kinetic characterization of ACOT9 to determine its possible physiological function. ACOT9 showed unusual kinetic properties with activity peaks for short-, medium-, and saturated long-chain acyl-CoAs with highest V max with propionyl-CoA and (iso) butyryl-CoA while K cat/K m was highest with saturated long-chain acyl-CoAs. Further characterization of the short-chain acyl-CoA activity revealed that ACOT9 also hydrolyzes a number of short-chain acyl-CoAs and short-chain methyl-branched CoA esters that suggest a role for ACOT9 in regulation also of amino acid metabolism. In spite of markedly different K ms, ACOT9 can hydrolyze both short- and long-chain acyl-CoAs simultaneously, indicating that ACOT9 may provide a novel regulatory link between fatty acid and amino acid metabolism in mitochondria. Based on similar acyl-CoA chain-length specificities of recombinant ACOT9 and ACOT activity in mouse brown adipose tissue and kidney mitochondria, we conclude that ACOT9 is the major mitochondrial ACOT hydrolyzing saturated C2-C20-CoA in these tissues. Finally, ACOT9 activity is strongly regulated by NADH and CoA, suggesting that mitochondrial metabolic state regulates the function of ACOT9.},
}
@article {pmid23870133,
year = {2013},
author = {Soini, HK and Moilanen, JS and Vilmi-Kerälä, T and Finnilä, S and Majamaa, K},
title = {Mitochondrial DNA variant m.15218A &gt; G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus.},
journal = {BMC medical genetics},
volume = {14},
number = {},
pages = {73},
pmid = {23870133},
issn = {1471-2350},
mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; Diabetes Mellitus/*genetics ; Epilepsy/*genetics ; Female ; Finland ; Genetic Variation ; Hearing Loss, Sensorineural/*genetics ; Humans ; Male ; Mitochondria/*genetics ; Mitochondrial Diseases/genetics ; Pedigree ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus.<br><br>METHODS: The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced.<br><br>RESULTS: We found a common nonsynonymous variant m.15218A&#x2009;>&#x2009;G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A&#x2009;>&#x2009;G variant was present in five patients with epilepsy and in four out of 403 population controls (p&#x2009;=&#x2009;0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A&#x2009;>&#x2009;G is damaging in effect.<br><br>CONCLUSIONS: We suggest that the m.15218A&#x2009;>&#x2009;G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.},
}
@article {pmid23891721,
year = {2013},
author = {Shi, Z and Wang, ZJ and Xu, HL and Tian, Y and Li, X and Bao, JK and Sun, SR and Yue, BS},
title = {Modeling, docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.},
journal = {Computational biology and chemistry},
volume = {47},
number = {},
pages = {56-65},
doi = {10.1016/j.compbiolchem.2013.07.001},
pmid = {23891721},
issn = {1476-928X},
mesh = {Antigens, Plant/*chemistry/*metabolism ; Carrier Proteins/*chemistry/*metabolism ; *Molecular Docking Simulation ; *Molecular Dynamics Simulation ; Peganum/*chemistry ; Phylogeny ; Plant Proteins/*chemistry/*metabolism ; },
abstract = {Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid-protein interactions, indicating some future applications of ns-LTP-mediated transport.},
}
@article {pmid23899268,
year = {2014},
author = {Shi, SF and Li, M and Yan, S and Wang, M and Yang, CP and Lun, ZR and Brown, CL and Yang, TB},
title = {Phylogeography and demographic history of Gotocotyla sawara (Monogenea: Gotocotylidae) on Japanese Spanish mackerel (Scomberomorus niphonius) along the Coast of China.},
journal = {The Journal of parasitology},
volume = {100},
number = {1},
pages = {85-92},
doi = {10.1645/13-235.1},
pmid = {23899268},
issn = {1937-2345},
mesh = {Animals ; China/epidemiology ; DNA, Helminth/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Demography ; Electron Transport Complex IV/genetics ; Fish Diseases/epidemiology/*parasitology ; Genetic Variation ; Genetics, Population ; Gills/parasitology ; Haplotypes ; Ice Cover ; Mitochondria/enzymology ; Perciformes/*parasitology ; Phylogeny ; Phylogeography ; Platyhelminths/genetics/*isolation &amp; purification/physiology ; Polymerase Chain Reaction/veterinary ; Seawater ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; Trematode Infections/epidemiology/parasitology/*veterinary ; },
abstract = {Recent studies indicate that the northwestern Pacific Ocean is an ideal system in which to study and understand the roles of the Pleistocene sea-level fluctuations and ocean currents in shaping phylogeographic patterns of species, but most of these investigations have been concerned with vertebrates, and only a few have focused on invertebrates. In the present study, we examined the genetic population structure and historic demography of a platyhelminth species, Gotocotyla sawara (Monogenea, Gotocotylidae), a gill parasite of Japanese Spanish mackerel, Scomberomorus niphonius , along the coast of China. A fragment of the mitochondrial cytochrome oxidase I (COI) gene for 169 individuals and the internal transcribed spacers for 24 individuals were sequenced from specimens representing 8 populations of this parasite along the coast of China. High levels of COI haplotype diversity (0.9994) and nucleotide diversity (0.015805) were detected for G. sawara. Phylogenetic analysis revealed no phylogeographical pattern for G. sawara in the sample area. Analysis of molecular variance (AMOVA) revealed no significant differences at all hierarchical levels, and pairwise FST analysis demonstrated a high rate of gene flow of this parasite among different populations in coastal Chinese waters. Moreover, the exact test of differentiation supported the null hypothesis that G. sawara along the coast of China constitutes a panmictic population. Both neutrality tests and mismatch distribution revealed that G. sawara underwent population expansion in the late Pleistocene era. Recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium may account in part for the lack of genetic structure in the geographic areas considered in this study. Dispersal of parasite eggs and larvae along ocean currents, coupled with the long-distance migrations of host fishes, could also be responsible for genetic homogeneity of this parasite. It is also possible that other hosts of this monogean, such as the ridged-eye flounder, Pleruonichthys cornutus, may contribute to the genetic mixing of Gotocotyla sawara populations.},
}
@article {pmid23901913,
year = {2015},
author = {Han, M and Wang, CL and Shen, CN and Chen, IS},
title = {The complete mitochondrial genome of half-spined barbel Acrossocheilus hemispinus (Nichols) (Teleostei, Cyprinidae, Barbinae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {133-134},
doi = {10.3109/19401736.2013.815172},
pmid = {23901913},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {In this study, the complete mitogenome sequence of half-spined barbel Acrossocheilus hemispinus has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,590 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region (CR). CR of 940 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of A. hemispinus is 31.2% for A, 28.2% for C, 24.4% for T and 15.9 % for G, with a slight AT bias of 55.6%. The complete mitogenome may provide rather essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.},
}
@article {pmid23901915,
year = {2015},
author = {Shedko, SV and Miroshnichenko, IL and Nemkova, GA},
title = {Complete mitochondrial genome of the poorly known Amur sculpin Mesocottus haitej (Cottoidei: Cottidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {147-148},
doi = {10.3109/19401736.2013.819496},
pmid = {23901915},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genome sequence of Mesocottus haitej has been obtained by the next generation sequencing, which contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and non-coding control region with the total length of 16,527 bp. The gene content, arrangement, codon usage and base composition of M. haitej mitogenome have no unusual features that distinguish it from most other teleost fishes. According to the result of a pilot phylogenetic analysis, the freshwater Mesocottus is a sister lineage to the Cottus clade. The new mitogenomic data could provide useful information for the further studies on molecular systematics and conservation genetics of cottids.},
}
@article {pmid23901917,
year = {2015},
author = {Chen, IS and Han, M and Wang, CL and Shen, CN},
title = {The complete mitochondrial genome of rainbow barbel Acrossocheilus barbodon (Nichols and Pope) (Teleostei, Cyprinidae, Barbinae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {145-146},
doi = {10.3109/19401736.2013.819495},
pmid = {23901917},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {In this study, the complete mitogenome sequence of rainbow barbel Acrossocheilus barbodon has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,596 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region (CR). CR of 934 bp length is located between tRNAPro and tRNAPhe. The overall base composition of A. hemispinus is 31.5% for A, 28.2% for C, 24.4% for T and 15.9 % for G, with a higher AC content of 55.9%. The complete mitogenome may provide very essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.},
}
@article {pmid23901918,
year = {2015},
author = {Huang, SP and Shen, CN and Chen, IS},
title = {The complete mitochondrial genome of the Abe's mangrove goby Mugilogobius abei (Teleostei, Gobiidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {143-144},
doi = {10.3109/19401736.2013.819494},
pmid = {23901918},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {In this study, the complete mitochondrial genome of the Abe's mangrove goby Mugilogobius abei has been amplified. Mugilogobius abei is widely contributed species in Northeast to East Asia. The complete mitogenome is 16,483 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and 1 control region (CR). The overall base composition of M. abei is 27.7% for A, 27.0% for T, 28.6% for C, 16.7% for G, with higher AT content of 54.7%. This study will contribute for understanding the phylogenetic approach in genus Mugilogobius and related gobiid genera.},
}
@article {pmid23901920,
year = {2015},
author = {Wei, SJ and Wu, QL and Liu, W},
title = {Sequencing and characterization of the Monocellicampa pruni (Hymenoptera: Tenthredinidae) mitochondrial genome.},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {157-158},
doi = {10.3109/19401736.2013.819501},
pmid = {23901920},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Codon, Terminator ; Gene Order ; *Genome, Mitochondrial ; Hymenoptera/*genetics ; Insect Proteins/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial genome of the Monocellicampa pruni (Hymenoptera: Tenthredinidae) (GenBank accession No. JX566509) has been reported in this study. This is the first sequenced mitochondrial genome from the family Tenthredinidae of the order Hymenoptera. The sequenced region of this mitochondrial genome is 15,169 bp with an A + T content of 77.21%, including 13 protein-coding, 2 rRNA and 19 tRNA genes, and a partial region of the A + T-rich region. Three tRNA genes, i.e. trnI. trnQ and trnM, between the A + T-rich region and the nad2 gene were failed to sequence because of the present of PolyAT structure. The gene arrangement of the sequenced region was similar to the pupative ancestral arrangement of insects. There are two large non-coding regions located between trnC and trnY. trnF and nad5 with a length of 107 and 177 bp, respectively. All protein-coding genes start with ATN start codon. Eleven protein-coding genes stop with termination codon TAA, whereas one protein-coding gene uses incomplete stop codon TA and one uses T. All of the 22 tRNA genes have a typical cloverleaf structure except for the trnS1, in which, the D-stem pairings in the DHU arm are absent.},
}
@article {pmid23901921,
year = {2015},
author = {Huang, SP and Shen, CN and Chen, IS},
title = {The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {159-161},
doi = {10.3109/19401736.2013.819502},
pmid = {23901921},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {In this study, the complete mitochondrial genome of the fat-nose goby Pseudogobius javanicus has been amplified. P. javanicus is widely contributed species in Southeast to East Asia. The complete mitochondrial genome is 16,493 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of P. javanicus is 27.1% for A, 27.3% for T, 28.6% for C, 17.0% for G, with higher AT content of 54.4%. This study will contribute for understanding the phylogenetic approach in genus Pseudogobius.},
}
@article {pmid23916093,
year = {2013},
author = {Papah, MB and Kisia, SM and Ojoo, RO and Makanya, AN and Wood, CM and Kavembe, GD and Maina, JN and Johannsson, OE and Bergman, HL and Laurent, P and Chevalier, C and Bianchini, A and Bianchini, LF and Onyango, DW},
title = {Morphological evaluation of spermatogenesis in Lake Magadi tilapia (Alcolapia grahami): a fish living on the edge.},
journal = {Tissue &amp; cell},
volume = {45},
number = {6},
pages = {371-382},
doi = {10.1016/j.tice.2013.06.004},
pmid = {23916093},
issn = {1532-3072},
mesh = {Animals ; Humans ; Lakes ; Male ; *Meiosis ; Phylogeny ; Spermatids/ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; Testis/growth &amp; development ; *Tilapia ; },
abstract = {Spermatogenesis in Lake Magadi tilapia (Alcolapia grahami), a cichlid fish endemic to the highly alkaline and saline Lake Magadi in Kenya, was evaluated using light and transmission electron microscopy. Spermatogenesis, typified by its three major phases (spermatocytogenesis, meiosis and spermiogenesis), was demonstrated by the presence of maturational spermatogenic cells namely spermatogonia, spermatocytes, spermatids and spermatozoa. Primary spermatogonia, the largest of all the germ cells, underwent a series of mitotic divisions producing primary spermatocytes, which then entered two consecutive meiotic divisions to produce secondary spermatocytes and spermatids. Spermatids, in turn, passed through three structurally distinct developmental stages typical of type-I spermiogenesis to yield typical primitive anacrosomal spermatozoa of the externally fertilizing type (aquasperm). The spermatozoon of this fish exhibited a spheroidal head with the nucleus containing highly electron-dense chromatin globules, a midpiece containing ten ovoid mitochondria arranged in two rows and a flagellum formed by the typical 9 + 2 microtubule axoneme. In addition, the midpiece, with no cytoplasmic sheath, appeared to end blindly distally in a lobe-like pattern around the flagellum; a feature that was unique and considered adaptive for the spermatozoon of this species to the harsh external environment. These observations show that the testis of A. grahami often undergoes active spermatogenesis despite the harsh environmental conditions to which it is exposed on a daily basis within the lake. Further, the spermiogenic features and spermatozoal ultrastructure appear to be characteristic of Cichlidae and, therefore, may be of phylogenetic significance.},
}
@article {pmid23940100,
year = {2013},
author = {Smith, DR and Hua, J and Archibald, JM and Lee, RW},
title = {Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna.},
journal = {Genome biology and evolution},
volume = {5},
number = {9},
pages = {1661-1667},
pmid = {23940100},
issn = {1759-6653},
support = {//Canadian Institutes of Health Research/Canada ; },
mesh = {Chlorophyta/*genetics/physiology ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Genome, Plastid ; Inverted Repeat Sequences/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Photosynthesis ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made up entirely of palindromes, each containing 1-7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. The possible origins and consequences of this bizarre genomic architecture are discussed.},
}
@article {pmid23940792,
year = {2013},
author = {Hagen, CM and Aidt, FH and Hedley, PL and Jensen, MK and Havndrup, O and Kanters, JK and Moolman-Smook, JC and Larsen, SO and Bundgaard, H and Christiansen, M},
title = {Mitochondrial haplogroups modify the risk of developing hypertrophic cardiomyopathy in a Danish population.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e71904},
pmid = {23940792},
issn = {1932-6203},
mesh = {Adult ; Aged ; Cardiomyopathy, Hypertrophic/*epidemiology/*genetics ; DNA, Mitochondrial/*genetics ; Denmark/epidemiology ; Female ; Genetic Predisposition to Disease ; Genetics, Population ; *Haplotypes ; Humans ; Male ; Middle Aged ; Mitochondria/genetics ; Phylogeny ; Risk Factors ; },
abstract = {Hypertrophic cardiomyopathy (HCM) is a genetic disorder caused by mutations in genes coding for proteins involved in sarcomere function. The disease is associated with mitochondrial dysfunction. Evolutionarily developed variation in mitochondrial DNA (mtDNA), defining mtDNA haplogroups and haplogroup clusters, is associated with functional differences in mitochondrial function and susceptibility to various diseases, including ischemic cardiomyopathy. We hypothesized that mtDNA haplogroups, in particular H, J and K, might modify disease susceptibility to HCM. Mitochondrial DNA, isolated from blood, was sequenced and haplogroups identified in 91 probands with HCM. The association with HCM was ascertained using two Danish control populations. Haplogroup H was more prevalent in HCM patients, 60% versus 46% (p = 0.006) and 41% (p = 0.003), in the two control populations. Haplogroup J was less prevalent, 3% vs. 12.4% (p = 0.017) and 9.1%, (p = 0.06). Likewise, the UK haplogroup cluster was less prevalent in HCM, 11% vs. 22.1% (p = 0.02) and 22.8% (p = 0.04). These results indicate that haplogroup H constitutes a susceptibility factor and that haplogroup J and haplogroup cluster UK are protective factors in the development of HCM. Thus, constitutive differences in mitochondrial function may influence the occurrence and clinical presentation of HCM. This could explain some of the phenotypic variability in HCM. The fact that haplogroup H and J are also modifying factors in ischemic cardiomyopathy suggests that mtDNA haplotypes may be of significance in determining whether a physiological hypertrophy develops into myopathy. mtDNA haplotypes may have the potential of becoming significant biomarkers in cardiomyopathy.},
}
@article {pmid23954723,
year = {2013},
author = {Gao, D and Xu, Z and Zhang, X and Zhu, C and Wang, Y and Min, W},
title = {Cadmium triggers kidney cell apoptosis of purse red common carp (Cyprinus carpio) without caspase-8 activation.},
journal = {Developmental and comparative immunology},
volume = {41},
number = {4},
pages = {728-737},
doi = {10.1016/j.dci.2013.08.004},
pmid = {23954723},
issn = {1879-0089},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*drug effects ; Cadmium Compounds/*pharmacology ; Carps/anatomy &amp; histology/metabolism/*physiology ; Caspase 8/genetics/*metabolism ; China ; Cytoplasm/genetics/metabolism ; DNA, Complementary/genetics ; Enzyme Activation ; Epithelial Cells/cytology/drug effects/metabolism ; Kidney Tubules/cytology/*drug effects/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfates/*pharmacology ; Zebrafish ; },
abstract = {Caspase-8, the essential initiator caspase, is believed to play a pivotal role in death receptor-mediated apoptotic pathway. It also participates in mitochondria-mediated apoptosis via cleavage of proapoptotic Bid in mammals. However, its role in fish remains elusive in Cadmium-induced apoptotic pathway. In this study, we isolated the caspase-8 gene from common carp, one of the most important industrial aquatic animals in China using rapid amplification of cDNA ends (RACE). The deduced amino acid sequence of caspase-8 comprised 475 amino acids, which showed approximately 64.1% identity and 79.8% similarity to zebrafish (Danio rerio) caspase-8, possessed two conserved death effector domains, a large subunit and a small subunit. Phylogenetic analysis demonstrated that caspase-8 formed a clade with zebrafish caspase-8. In kidney, cadmium (Cd) exposure triggered apoptosis and increased caspase-3 and -9 activities, whereas it did not affect caspase-8 activity. Real-time quantitative PCR analysis revealed that caspase-8 transcriptional level was not significantly increased in kidney after exposure to Cd. Using Western blot analysis, no caspase-8 cleaved fragment was detected and no significant alteration of procaspase-8 level was found with the same Cd-treated condition. Moreover, the immunopositive staining was predominantly limited to the cytoplasm of renal tubular epithelial cells and no remarkable changes of immunoreactivities were observed using immunohistochemical detection after Cd treatment. The results reveal that Cd can trigger apoptosis, while it cannot activate caspase-8 in purse red common carp.},
}
@article {pmid23990946,
year = {2013},
author = {Qiu, D and Huang, L and Liu, S and Zhang, H and Lin, S},
title = {Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.},
journal = {PloS one},
volume = {8},
number = {8},
pages = {e71346},
pmid = {23990946},
issn = {1932-6203},
mesh = {Cell Nucleus/genetics ; Cell Separation ; China ; Classification ; Dinoflagellida/*classification/cytology/genetics ; Estuaries ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; },
abstract = {Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.},
}
@article {pmid23993419,
year = {2013},
author = {Bakhoum, AJ and Kacem, H and Neifar, L and Miquel, J},
title = {Ultrastructure of the spermatozoon of Centroderma spinosissima (Stossich, 1886) (Digenea: Mesometridae) and its phylogenetic potential.},
journal = {Tissue &amp; cell},
volume = {45},
number = {6},
pages = {428-433},
doi = {10.1016/j.tice.2013.07.006},
pmid = {23993419},
issn = {1532-3072},
mesh = {Animals ; Axoneme/*ultrastructure ; Cell Membrane/ultrastructure ; Cell Nucleus ; Male ; *Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; *Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/ultrastructure ; },
abstract = {The Mesometridae includes only five genera and eight species. The available data on the ultrastructure of sperm cells of mesometrid species referred to two species only, Elstia stossichianum and Wardula capitellata. The present study revealed the ultrastructure of the spermatozoon of a third genus and third species of Mesometridae, Centroderma spinosissima. The mature spermatozoon of C. spinosissima presents two axonemes with different lengths of the Ehlers' 9 + '1' trepaxonematan pattern, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, a lateral expansion, spine-like bodies, cytoplasmic ornamented buttons and granules of glycogen. The spermatozoon of C. spinosissima is similar to those of the previously studied mesometrids. However, some peculiarities such as the presence of two mitochondria, the disposition of the external ornamentation of the plasma membrane and the morphology of the posterior spermatozoon extremity, characterize the male gamete of C. spinosissima. Moreover, the presence of cytoplasmic ornamented buttons is a characteristic found only in the mature spermatozoon of mesometrids and it probably represents an autapomorphy for this family.},
}
@article {pmid24006867,
year = {2015},
author = {Wang, W and Guo, B and Li, J and Wang, H and Qi, P and Lv, Z and Wu, C},
title = {Complete mitochondrial genome of the spineless cuttlefish Sepiella inermis (Sepioidea, Sepiidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {151-152},
doi = {10.3109/19401736.2013.819498},
pmid = {24006867},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Decapodiformes/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {In this study, we determined the complete mitochondrial genome of the spineless cuttlefish Sepiella inermis. The genome was 16,191 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [both are control regions (CR)]. The composition and order of genes, for the mitogenome found in S. inermis were similar to most other invertebrates. The overall base composition of S. inermis is T 35.6%, C 16.4%, A 40.0% and G 8.0%, with a highly A + T bias of 75.6%. Two control regions contain both termination-associated sequences and conserved sequence blocks. Thus, mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Sepiidae.},
}
@article {pmid24009203,
year = {2013},
author = {Zhao, YE and Ma, JX and Hu, L and Wu, LP and De Rojas, M},
title = {Discrimination between Demodex folliculorum (Acari: Demodicidae) isolates from China and Spain based on mitochondrial cox1 sequences.},
journal = {Journal of Zhejiang University. Science. B},
volume = {14},
number = {9},
pages = {829-836},
pmid = {24009203},
issn = {1862-1783},
mesh = {Animals ; Base Sequence ; China ; Cloning, Molecular ; Cyclooxygenase 1/*genetics ; DNA, Mitochondrial/genetics ; Humans ; Mite Infestations/parasitology ; Mites/classification/*enzymology/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; Spain ; Species Specificity ; },
abstract = {For a long time, classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics. A new subspecies of Demodex folliculorum has been proposed, but not confirmed. Here, cox1 partial sequences of nine isolates of three Demodex species from two geographical sources (China and Spain) were studied to conduct molecular identification of D. folliculorum. Sequencing showed that the mitochondrial cox1 fragments of five D. folliculorum isolates from the facial skin of Chinese individuals were 429 bp long and that their sequence identity was 97.4%. The average sequence divergence was 1.24% among the five Chinese isolates, 0.94% between the two geographical isolate groups (China (5) and Spain (1)), and 2.15% between the two facial tissue sources (facial skin (6) and eyelids (1)). The genetic distance and rate of third-position nucleotide transition/transversion were 0.0125, 2.7 (3/1) among the five Chinese isolates, 0.0094, 3.1 (3/1) between the two geographical isolate groups, and 0.0217, 4.4 (3/1) between the two facial tissue sources. Phylogenetic trees showed that D. folliculorum from the two geographical isolate groups did not form sister clades, while those from different facial tissue sources did. According to the molecular characteristics, it appears that subspecies differentiation might not have occurred and that D. folliculorum isolates from the two geographical sources are of the same population. However, population differentiation might be occurring between isolates from facial skin and eyelids.},
}
@article {pmid24026678,
year = {2014},
author = {Bicker, A and Dietrich, D and Gleixner, E and Kristiansen, G and Gorr, TA and Hankeln, T},
title = {Extensive transcriptional complexity during hypoxia-regulated expression of the myoglobin gene in cancer.},
journal = {Human molecular genetics},
volume = {23},
number = {2},
pages = {479-490},
doi = {10.1093/hmg/ddt438},
pmid = {24026678},
issn = {1460-2083},
mesh = {Adenocarcinoma/genetics ; Alternative Splicing ; Animals ; Breast Neoplasms/*genetics/*metabolism ; *Cell Hypoxia ; Cell Line, Tumor ; Colorectal Neoplasms/genetics/metabolism ; Exons ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Mice ; Mitochondria/metabolism ; Myoglobin/*genetics/metabolism ; Phylogeny ; Promoter Regions, Genetic ; Transcriptome ; },
abstract = {Recently, the ectopic expression of myoglobin (MB) was reported in human epithelial cancer cell lines and breast tumor tissues, where MB expression increased with hypoxia. The better prognosis of MB-positive breast cancer patients suggested that the globin exerts a tumor-suppressive role, possibly by impairing mitochondrial activity in hypoxic breast carcinoma cells. To better understand MB gene regulation in cancer, we systematically investigated the architecture of the human MB gene, its transcripts and promoters. In silico analysis of transcriptome data from normal human tissues and cancer cell lines, followed by RACE-PCR verification, revealed seven novel exons in the MB gene region, most of which are untranslated exons located 5'-upstream of the coding DNA sequence (CDS). Sixteen novel alternatively spliced MB transcripts were detected, most of which predominantly occur in tumor tissue or cell lines. Quantitative RT-PCR analyses of MB expression in surgical breast cancer specimen confirmed the preferential usage of a hitherto unknown, tumor-associated MB promoter, which was functionally validated by luciferase reporter gene assays. In line with clinical observations of MB up-regulation in avascular breast tumors, the novel cancer-associated MB splice variants exhibited increased expression in tumor cells subjected to experimental hypoxia. The novel gene regulatory mechanisms unveiled in this study support the idea of a non-canonical role of MB during carcinogenesis.},
}
@article {pmid24045017,
year = {2013},
author = {Ng, S and Ivanova, A and Duncan, O and Law, SR and Van Aken, O and De Clercq, I and Wang, Y and Carrie, C and Xu, L and Kmiec, B and Walker, H and Van Breusegem, F and Whelan, J and Giraud, E},
title = {A membrane-bound NAC transcription factor, ANAC017, mediates mitochondrial retrograde signaling in Arabidopsis.},
journal = {The Plant cell},
volume = {25},
number = {9},
pages = {3450-3471},
pmid = {24045017},
issn = {1532-298X},
mesh = {Arabidopsis/cytology/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Binding Sites ; Cell Nucleus/metabolism ; Endoplasmic Reticulum/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Hydrogen Peroxide/pharmacology ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Oligonucleotide Array Sequence Analysis ; Oxidoreductases/genetics/metabolism ; Phenotype ; Phylogeny ; Plant Proteins/genetics/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins ; Seedlings/cytology/genetics/growth &amp; development/metabolism ; *Signal Transduction ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptome ; Alternative Oxidase ; },
abstract = {Plants require daily coordinated regulation of energy metabolism for optimal growth and survival and therefore need to integrate cellular responses with both mitochondrial and plastid retrograde signaling. Using a forward genetic screen to characterize regulators of alternative oxidase1a (rao) mutants, we identified RAO2/Arabidopsis NAC domain-containing protein17 (ANAC017) as a direct positive regulator of AOX1a. RAO2/ANAC017 is targeted to connections and junctions in the endoplasmic reticulum (ER) and F-actin via a C-terminal transmembrane (TM) domain. A consensus rhomboid protease cleavage site is present in ANAC017 just prior to the predicted TM domain. Furthermore, addition of the rhomboid protease inhibitor N-p-Tosyl-l-Phe chloromethyl abolishes the induction of AOX1a upon antimycin A treatment. Simultaneous fluorescent tagging of ANAC017 with N-terminal red fluorescent protein (RFP) and C-terminal green fluorescent protein (GFP) revealed that the N-terminal RFP domain migrated into the nucleus, while the C-terminal GFP tag remained in the ER. Genome-wide analysis of the transcriptional network regulated by RAO2/ANAC017 under stress treatment revealed that RAO2/ANAC017 function was necessary for >85% of the changes observed as a primary response to cytosolic hydrogen peroxide (H2O2), but only ~33% of transcriptional changes observed in response to antimycin A treatment. Plants with mutated rao2/anac017 were more stress sensitive, whereas a gain-of-function mutation resulted in plants that had lower cellular levels of H2O2 under untreated conditions.},
}
@article {pmid24055401,
year = {2014},
author = {Kowald, A and Dawson, M and Kirkwood, TB},
title = {Mitochondrial mutations and ageing: can mitochondrial deletion mutants accumulate via a size based replication advantage?.},
journal = {Journal of theoretical biology},
volume = {340},
number = {},
pages = {111-118},
doi = {10.1016/j.jtbi.2013.09.009},
pmid = {24055401},
issn = {1095-8541},
support = {MR/K006312/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Aging ; Animals ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Drift ; Humans ; Longevity ; Mice ; Mitochondria/genetics ; Models, Biological ; Mutation Rate ; Rats ; *Sequence Deletion ; Stochastic Processes ; Time Factors ; },
abstract = {The mitochondrial theory of ageing is one of the main contenders to explain the biochemical basis of the ageing process. An important line of support comes from the observation that mtDNA deletions accumulate over the life course in post-mitotic cells of many species. A single mutant expands clonally and finally replaces the wild-type population of a whole cell. One proposal to explain the driving force behind this accumulation states that the reduced size leads to a shorter replication time, which provides a selection advantage. However, this idea has been questioned on the grounds that the mitochondrial half-life is much longer than the replication time, so that the latter cannot be a rate limiting step. To clarify this question, we modelled this process mathematically and performed extensive deterministic and stochastic computer simulations to study the effects of replication time, mitochondrial half-life and deletion size. Our study shows that the shorter size does in principle provide a selection advantage, which can lead to an accumulation of the deletion mutant. However, this selection advantage diminishes the shorter is the replication time of wt mtDNA in relation to its half-life. Using generally accepted literature values, the resulting time frame for the accumulation of mutant mtDNAs is only compatible with the ageing process in very long lived species like humans, but could not reasonably explain ageing in short lived species like mice and rats.},
}
@article {pmid24058559,
year = {2013},
author = {Tanveer, A and Allen, SM and Jackson, KE and Charan, M and Ralph, SA and Habib, S},
title = {An FtsH protease is recruited to the mitochondrion of Plasmodium falciparum.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e74408},
pmid = {24058559},
issn = {1932-6203},
mesh = {Adenosine Triphosphate/pharmacology ; Animals ; Cytokinesis/drug effects ; Escherichia coli/metabolism ; Fluorescent Antibody Technique ; Membrane Proteins/metabolism ; Mitochondria/drug effects/*enzymology ; Parasites/cytology/drug effects/enzymology ; Peptide Hydrolases/chemistry/*metabolism ; Phylogeny ; Plasmodium falciparum/cytology/drug effects/*enzymology ; Protein Processing, Post-Translational/drug effects ; Protein Structure, Quaternary ; Protein Transport/drug effects ; Protozoan Proteins/chemistry/*metabolism ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Zinc/pharmacology ; },
abstract = {The two organelles, apicoplast and mitochondrion, of the malaria parasite Plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. Little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. We report the identification of an AAA+/FtsH protease homolog (PfFtsH1) that exhibits ATP- and Zn(2+)-dependent protease activity. PfFtsH1 undergoes processing, forms oligomeric assemblies, and is associated with the membrane fraction of the parasite cell. Generation of a transfectant parasite line with hemagglutinin-tagged PfFtsH1, and immunofluorescence assay with anti-PfFtsH1 Ab demonstrated that the protein localises to P. falciparum mitochondria. Phylogenetic analysis and the single transmembrane region identifiable in PfFtsH1 suggest that it is an i-AAA like inner mitochondrial membrane protein. Expression of PfFtsH1 in Escherichia coli converted a fraction of bacterial cells into division-defective filamentous forms implying a sequestering effect of the Plasmodium factor on the bacterial homolog, indicative of functional conservation with EcFtsH. These results identify a membrane-associated mitochondrial AAA+/FtsH protease as a candidate regulatory protein for organelle biogenesis in P. falciparum.},
}
@article {pmid24059529,
year = {2013},
author = {Angerer, H},
title = {The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins.},
journal = {Biochemical Society transactions},
volume = {41},
number = {5},
pages = {1335-1341},
doi = {10.1042/BST20130116},
pmid = {24059529},
issn = {1470-8752},
mesh = {Apoptosis Regulatory Proteins/chemistry/*genetics ; Bacteria/genetics ; Electron Transport Complex I/*genetics ; Eukaryota/genetics ; Humans ; Insulin Resistance/*genetics ; Mitochondria/*genetics/physiology ; Oxidative Phosphorylation ; Phylogeny ; Protein Interaction Maps ; },
abstract = {Mitochondrial LYRM (leucine/tyrosine/arginine motif) proteins are members of the Complex1_LYR-like superfamily. Individual LYRM proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V respectively, and they play particular roles in the essential Fe-S cluster biogenesis and in acetate metabolism. LYRM proteins have been implicated in mitochondrial dysfunction, e.g. in the context of insulin resistance. However, the functional significance of the common LYRM is still unknown. Analysis of protein-protein interaction screens suggests that LYRM proteins form protein complexes with phylogenetically ancient proteins of bacterial origin. Interestingly, the mitochondrial FAS (fatty acid synthesis) type II acyl-carrier protein ACPM associates with some of the LYRM protein-containing complexes. Eukaryotic LYRM proteins interfere with mitochondrial homoeostasis and might function as adaptor-like 'accessory factors'.},
}
@article {pmid24063717,
year = {2013},
author = {Langford S, SM and Kraitsek, S and Baskerville, B and Ho, SY and Gongora, J},
title = {Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens.},
journal = {BMC genetics},
volume = {14},
number = {},
pages = {91},
pmid = {24063717},
issn = {1471-2156},
mesh = {Animals ; Australia ; Chickens/classification/*genetics ; DNA, Mitochondrial/*chemistry/metabolism ; *Genetic Variation ; Genome ; Haplotypes ; Melanesia ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world.<br><br>RESULTS: Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam.<br><br>CONCLUSIONS: Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.},
}
@article {pmid24078157,
year = {2013},
author = {Wu, Y and Wu, Y and Wu, Y and Tang, H and Wu, H and Zhang, G and Wang, W},
title = {Screening of candidate proteins interacting with IE-2 of Bombyx mori nucleopolyhedrovirus.},
journal = {Molecular biology reports},
volume = {40},
number = {10},
pages = {5797-5804},
pmid = {24078157},
issn = {1573-4978},
mesh = {Amino Acid Sequence ; Animals ; Bombyx/*virology ; Cell Line ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Genes, Viral/genetics ; Mass Spectrometry ; Mitochondria/metabolism ; Molecular Sequence Data ; Multiprotein Complexes/isolation &amp; purification/metabolism ; Nucleopolyhedroviruses/*metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Viral Proteins/chemistry/*metabolism ; },
abstract = {IE-2 of Bombyx mori nucleopolyhedrovirus (BmNPV) has been shown to play important roles in baculovirus infection, which are involved in gene expression and viral replication. However, the mechanism remains unknown. In this paper, by TargetP software, four genes, i.e.-2, odv-e26, odv-e56 and BmNPV-gp101 (Ac-orf116) of BmNPV and Autographa californica multiple NPV (AcMNPV) were predicted to be located in mitochondria. By BLAST tool using BmNPV IE-2 protein sequence, 14 NPVs were found to have IE-2 homologues in GenBank, and most of them were predicted to be located in mitochondria, except for that of Antheraea pernyi NPV (AnpeNPV) and Anticarsia gemmatalis NPV (AngeNPV). To observe the subcellular localization of BmNPV IE-2, a recombinant virus overexpressed the IE-2 and eGFP fusion protein was constructed. In infected BmN cells, the fluorescence specifically enriched in the cellular mitochondria. This evidence was accordant with the prediction. Further, Pull-down assay was used to select protein candidates interacting with IE-2 in B. mori cells infected with BmNPV. Of several isolated protein components, sixteen candidates were identified by MALDI-TOF mass-spectrometry, eight baculoviral proteins (ALK-EXO, F protein, IAP-1, LEF-3, LEF-9, ODV-NC42, TLP, and VP39), and eight proteins from B. mori (Actin, ADP/ATP translocase, ATP synthase subunit beta, Beta-tubulin, DNA topoisomerase 2, Histone H4, Soluble guanylyl cyclae alpha-1 subunit, Transketolase). From the functional point of view, most of these proteins were generally divided into two groups, mitochondrial interaction proteins and viral DNA replication proteins. These results implied that the IE-2 had multiple functions involved in regulating viral gene expression, viral replication and also as a component of mitochondrial factors to regulate the cellular energy supply and apoptosis.},
}
@article {pmid24086244,
year = {2013},
author = {Leger, MM and Gawryluk, RM and Gray, MW and Roger, AJ},
title = {Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e69532},
pmid = {24086244},
issn = {1932-6203},
support = {U54 HG002051/HG/NHGRI NIH HHS/United States ; MOP-62809/CAPMC/CIHR/Canada ; MOP-4124/CAPMC/CIHR/Canada ; U01 HG02051/HG/NHGRI NIH HHS/United States ; },
mesh = {Acanthamoeba castellanii/enzymology/genetics/*metabolism ; Adenosine Triphosphate/*biosynthesis ; Amino Acid Sequence ; Anaerobiosis ; Electron Transport ; Enzymes/chemistry/metabolism ; Expressed Sequence Tags ; Genome, Protozoan ; Hydrogen/*metabolism ; Molecular Sequence Data ; Phylogeny ; Tandem Mass Spectrometry ; },
abstract = {Diverse, distantly-related eukaryotic lineages have adapted to low-oxygen environments, and possess mitochondrion-related organelles that have lost the capacity to generate adenosine triphosphate (ATP) through oxidative phosphorylation. A subset of these organelles, hydrogenosomes, has acquired a set of characteristic ATP generation enzymes commonly found in anaerobic bacteria. The recipient of these enzymes could not have survived prior to their acquisition had it not still possessed the electron transport chain present in the ancestral mitochondrion. In the divergence of modern hydrogenosomes from mitochondria, a transitional organelle must therefore have existed that possessed both an electron transport chain and an anaerobic ATP generation pathway. Here, we report a modern analog of this organelle in the habitually aerobic opportunistic pathogen, Acanthamoeba castellanii. This organism possesses a complete set of enzymes comprising a hydrogenosome-like ATP generation pathway, each of which is predicted to be targeted to mitochondria. We have experimentally confirmed the mitochondrial localizations of key components of this pathway using tandem mass spectrometry. This evidence is the first supported by localization and proteome data of a mitochondrion possessing both an electron transport chain and hydrogenosome-like energy metabolism enzymes. Our work provides insight into the first steps that might have occurred in the course of the emergence of modern hydrogenosomes.},
}
@article {pmid24096889,
year = {2013},
author = {Ubaidillah, M and Kim, KA and Kim, YH and Lee, IJ and Yun, BW and Kim, DH and Loake, GJ and Kim, KM},
title = {Identification of a drought-induced rice gene, OsSAP, that suppresses Bax-induced cell death in yeast.},
journal = {Molecular biology reports},
volume = {40},
number = {11},
pages = {6113-6121},
pmid = {24096889},
issn = {1573-4978},
support = {BB/H000984/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Apoptosis/genetics ; Base Sequence ; Biomass ; Cellular Senescence/genetics ; *Droughts ; Gene Expression ; Gene Expression Profiling ; *Genes, Plant ; Molecular Sequence Data ; Oryza/chemistry/*genetics ; Phylogeny ; Stress, Physiological/*genetics ; Water/chemistry ; Yeasts/*genetics/metabolism ; bcl-2-Associated X Protein/*genetics/metabolism ; },
abstract = {We identified rice genes that might be involved in drought stress tolerance by virtue of their anti-apoptotic activity. Potential anti-apoptosis related genes were identified by screening an Oryza sativa cDNA library derived from drought stressed tissues in a yeast functional assay. About 28 O. sativa cDNAs promoted yeast survival following engagement of Bax-induced apoptosis. An O. sativa cDNA encoding R12H780 was a highly conserved putative senescence-associated-protein (OsSAP). OsSAP was both highly and rapidly expressed in response to drought stress. Additionally, OsSAP was found to be localized to the mitochondria. Overall, OsSAP represents a new type of Bax suppressor related gene and endows multiple stress tolerance in yeast.},
}
@article {pmid24098763,
year = {2013},
author = {Hou, CC and Yang, WX},
title = {Acroframosome-dependent KIFC1 facilitates acrosome formation during spermatogenesis in the caridean shrimp Exopalaemon modestus.},
journal = {PloS one},
volume = {8},
number = {9},
pages = {e76065},
pmid = {24098763},
issn = {1932-6203},
mesh = {Acrosome/*physiology ; Animals ; Base Sequence ; Blotting, Western ; Cell Movement/physiology ; China ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Fluorescent Antibody Technique ; In Situ Hybridization ; Kinesins/genetics/*metabolism ; Male ; Microscopy, Electron, Transmission ; Microtubules/metabolism/*physiology ; Molecular Sequence Data ; Palaemonidae/genetics/*physiology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spermatogenesis/*physiology ; },
abstract = {BACKGROUND: Acrosome formation and nuclear shaping are the main events in spermatogenesis. During spermiogenesis in Exopalaemon modestus, a unique microtubular structure called the acroframosome (AFS) forms in spermatids. The AFS links to a temporary organelle called the lamellar complex (LCx) leading to the formation of an everted umbrella-shaped acrosome and a dish-shaped nucleus in the mature sperm. These morphological changes require complex cell motility in which the C-terminal kinesin motor protein called KIFC1 is involved. In this study, we demonstrate that KIFC1 moves along the AFS and plays an important role in acrosome formation and nuclear shaping during spermatogenesis in E. modestus.<br><br>We cloned a 3125 bp complete cDNA of kifc1 from the testis of E. modestus by PCR. The predicted secondary and tertiary structures of E. modestus KIFC1 contain three domains: a) the C-terminus, b) the stalk region, and the c) N-terminusl. Semi-quantitative RT-PCR detected the expression of kifc1 mRNA in different tissues of E. modestus. In situ hybridization demonstrated the temporal and spatial expression profile of kifc1 during spermiogenesis. Western blot identified the expression of KIFC1 in different tissues of E. modestus, including the testis. Immunofluorescence localized KIFC1, tubulin, GM130, and mitochondria in order to elucidate their role during spermiogenesis in E. modestus.<br><br>CONCLUSION/SIGNIFICANCE: Our results indicate that KIFC1 transports the Golgi complex, mitochondria, and other cellular components that results in acrosome formation and nuclear shaping in E. modestus. The KIFC1 transport function depends upon the microtubular structure called the acroframosome (AFS). This study describes some of the molecular mechanisms involved in the acrosome formation and nuclear shaping in E. modestus. In addition, this study may provide a model for studying the molecular mechanisms involved in spermatogenesis in other crustacean species and lead to a better understanding of the fertilization process in crustaceans.},
}
@article {pmid24102603,
year = {2015},
author = {Li, H and Gao, J and Cai, W},
title = {Complete mitochondrial genome of the assassin bug Oncocephalus breviscutum (Hemiptera: Reduviidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {674-675},
doi = {10.3109/19401736.2013.840602},
pmid = {24102603},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Reduviidae/*genetics ; },
abstract = {The mitochondrial genome of an assassin bug, Oncocephalus breviscutum Reuter, is a typical circular DNA molecule of 15,984 bp with 37 genes and a large control region. The gene order is identical to that of the putative ancestral arrangement of insects. Twelve protein-coding genes start with ATN codon and ND4L uses GTG. All of the 22 tRNAs, ranging from 61 to 70 bp, have the clover-leaf structure except for the dihydrouridine (DHU) arm of trnS2 forms a simple loop. The control region is 1345 bp in length and includes six tandem repeats of three 31-nt and three 145-nt units.},
}
@article {pmid24102605,
year = {2015},
author = {Chiang, TY and Chen, IS and Lin, HD and Hsiao, ST and Ju, YM},
title = {Complete mitochondrial genome of the amphidromous, red-tailed goby Sicyopterus lagocephalus (Pallas) (Teleostei, Gobiidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {670-671},
doi = {10.3109/19401736.2013.840600},
pmid = {24102605},
issn = {1940-1744},
mesh = {Animals ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In this article, the complete mitogenome of the amphidromous, red-tailed goby, Sicyopterus lagocephalus has been amplified and sequenced by long polymerase chain reaction. This mitochondrial genome consists of 16,500 bp, with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR), and its gene arrangement is identical to those of most vertebrates. The CR (841 bp) is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand is A, 28.9%; G, 16.4%; C, 28.3%; and T, 26.4%, with a slight AT bias of 55.3%. The complete mitogenomic data may provide more informative for phylogenetic approach for gobioid phylogeny especially for Sicydiine gobies.},
}
@article {pmid24102609,
year = {2015},
author = {Mohindra, V and Singh, RK and Kumar, R and Sah, RS and Lal, KK},
title = {Complete mitochondrial genome sequences of two endangered Indian catfish species, Clarias batrachus and Pangasius pangasius.},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {678-679},
doi = {10.3109/19401736.2013.840604},
pmid = {24102609},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Catfishes/*classification/*genetics ; Endangered Species ; Gene Order ; *Genome, Mitochondrial ; India ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {Complete mitogenome sequences for Clarias batrachus (magur) and Pangasius pangasius (family Claridae and Pangasiidae, respectively) were generated, which were 16,511 and 16,476 bp, respectively. Both the mitogenomes contained 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 1 non-coding (control) region. The order of the genes was identical to that observed in most other vertebrates. The genome resource of complete mitogenome sequence of Indian catfish species generated during this study would be useful in phylogenetic studies.},
}
@article {pmid24123495,
year = {2014},
author = {Castillo-Páez, A and Sosa-Nishizaki, O and Sandoval-Castillo, J and Galván-Magaña, F and Blanco-Parra, MD and Rocha-Olivares, A},
title = {Strong population structure and shallow mitochondrial phylogeny in the banded guitarfish, Zapteryx exasperata (Jordan y Gilbert, 1880), from the Northern Mexican Pacific.},
journal = {The Journal of heredity},
volume = {105},
number = {1},
pages = {91-100},
doi = {10.1093/jhered/est067},
pmid = {24123495},
issn = {1465-7333},
mesh = {Animals ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Gene Flow ; Genetic Variation ; Haplotypes ; Mexico ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Skates, Fish/*classification/*genetics ; },
abstract = {The northern Mexican Pacific (NMP), the Gulf of California (GC), and Baja California have been recognized as an ecological and evolutionarily dynamic region having experienced significant tectonic and climatic changes leading to the diversification of terrestrial and marine biotas. Zapteryx exasperata is a predominant ray caught in the artisanal fisheries of the NMP. Morphometric and reproductive differences between rays from the GC and the Pacific coast of Baja California (PCBC) regions suggest the presence of distinct populations. We investigate whether this distinction correlates with differences in genetic diversity and differentiation using sequences of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2) gene and the noncoding control region (CR) in 63 specimens. Contrary to our expectations, ND2 bore significantly more diversity (h = 0.76) than CR (h = 0.39). Geographic patterns of diversity of CR were opposite to those of ND2, with GC being significantly less (ND2) and more (CR) diverse than PCBC. The diversity of concatenated haplotypes was high (h = 0.84). Low nucleotide diversity suggests the recent coancestry of haplotypes. Marked genetic structure (Φst = 0.23, P < 0.0001) revealed the existence of reproductive isolation and limited matrilineal gene flow between GC and PCBC, which correlates with their phenotypic distinction. These results suggest the influence of factors such as female reproductive philopatry, and ecological or historical vicariant barriers to gene flow. Our results point to the existence of a distinct management unit of banded guitarfish in each region, and add to the increasing evidence attesting to the diversifying nature of this evolutionarily dynamic region.},
}
@article {pmid24153405,
year = {2013},
author = {Huang, Y and Chen, X and Liu, Y and Roth, C and Copeland, C and McFarlane, HE and Huang, S and Lipka, V and Wiermer, M and Li, X},
title = {Mitochondrial AtPAM16 is required for plant survival and the negative regulation of plant immunity.},
journal = {Nature communications},
volume = {4},
number = {},
pages = {2558},
doi = {10.1038/ncomms3558},
pmid = {24153405},
issn = {2041-1723},
mesh = {Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics/*immunology ; Gene Expression Regulation, Plant/*immunology ; Green Fluorescent Proteins ; High-Throughput Screening Assays ; Mitochondria/genetics/*immunology ; Mitochondrial Membrane Transport Proteins/classification/genetics/*immunology ; Mitochondrial Precursor Protein Import Complex Proteins ; Mutation ; Oomycetes/immunology ; Phylogeny ; Plant Diseases/genetics/immunology/microbiology ; Plant Immunity/*genetics ; Reactive Oxygen Species/metabolism ; Recombinant Fusion Proteins/genetics/immunology ; Saccharomyces cerevisiae Proteins/genetics/immunology ; Sequence Homology, Amino Acid ; Signal Transduction ; },
abstract = {Proteins containing nucleotide-binding and leucine-rich repeat domains (NB-LRRs) serve as immune receptors in plants and animals. Negative regulation of immunity mediated by NB-LRR proteins is crucial, as their overactivation often leads to autoimmunity. Here we describe a new mutant, snc1-enhancing (muse) forward genetic screen, targeting unknown negative regulators of NB-LRR-mediated resistance in Arabidopsis. From the screen, we identify MUSE5, which is renamed as AtPAM16 because it encodes the ortholog of yeast PAM16, part of the mitochondrial inner membrane protein import motor. Consistently, AtPAM16-GFP localizes to the mitochondrial inner membrane. AtPAM16L is a paralog of AtPAM16. Double mutant Atpam16-1 Atpam16l is lethal, indicating that AtPAM16 function is essential. Single mutant Atpam16 plants exhibit a smaller size and enhanced resistance against virulent pathogens. They also display elevated reactive oxygen species (ROS) accumulation. Therefore, AtPAM16 seems to be involved in importing a negative regulator of plant immunity into mitochondria, thus protecting plants from over-accumulation of ROS and preventing autoimmunity.},
}
@article {pmid24163630,
year = {2013},
author = {Wang, Z and Zhang, H and Yang, J and Chen, Y and Xu, X and Mao, X and Li, C},
title = {Phylogenetic, expression, and bioinformatic analysis of the ABC1 gene family in Populus trichocarpa.},
journal = {TheScientificWorldJournal},
volume = {2013},
number = {},
pages = {785070},
pmid = {24163630},
issn = {1537-744X},
mesh = {Computational Biology/*methods ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/classification/*genetics ; Populus/*chemistry ; },
abstract = {We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis.},
}
@article {pmid24183947,
year = {2013},
author = {Pohl, H and Dallai, R and Gottardo, M and Beutel, RG},
title = {The spermatozoon of Mengenilla moldrzyki (Strepsiptera, Mengenillidae): ultrastructure and phylogenetic considerations.},
journal = {Tissue &amp; cell},
volume = {45},
number = {6},
pages = {446-451},
doi = {10.1016/j.tice.2013.10.002},
pmid = {24183947},
issn = {1532-3072},
mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Insecta/*ultrastructure ; Male ; Mitochondria/ultrastructure ; *Phylogeny ; *Species Specificity ; Spermatozoa/*ultrastructure ; },
abstract = {Even though the spermatozoa of several strepsipteran species were described earlier, no data were available for the basal family Mengenillidae. Well-fixed material of the recently described Tunisian species Mengenilla moldrzyki was used for a detailed examination of the sperm ultrastructure. The total length is c. 30 μm. The head region contains a conical acrosome vesicle (0.3-0.35 μm) and an elongated nucleus (7.3 μm) with dense chromatin. Some granular material along with a uniformely dense centriole adjunct and two mitochondrial derivatives are visible at the posterior end of the nucleus. The material of the centriole adjunct does not extend along the flagellum and accessory bodies are absent. The mitochondrial derivatives are elongated structures crossed by a longitudinal crista but lacking parallel transverse cristae and paracrystalline material in the dense matrix. The mitochondrial derivatives gradually reduce their size and end at the most posterior tail region. The flagellar axoneme has a 9 + 9 + 2 pattern and originates beneath the nucleus. In the terminal tail region the axoneme gradually disintegrates. Despite the extreme specialization of the endoparasitc group, strepsipteran spermatozoa are mostly characterized by plesiomorphies. The pattern within the order is largely uniform, but Mengenilla displays several apomorphic features compared to the presumptive strepsipteran groundplan (e.g., absence of crystallizations and cristae in the mitochondrial derivatives). The subdivision of the intertubular material into two compartments with a dense beak-like structure adhering to the tubular wall supports a clade Coleopterida (= Strepsiptera + Coleoptera) + Neuropterida.},
}
@article {pmid24186265,
year = {2014},
author = {Gribbins, KM and Matchett, CL and DelBello, KA and Rheubert, J and Villagrán-SantaCruz, M and Granados-González, G and Hernández-Gallegos, O},
title = {The ultrastructure of spermatid development during spermiogenesis within the rosebelly lizard, Sceloporus variabilis (Reptilia, Squamata, Phrynosomatidae).},
journal = {Journal of morphology},
volume = {275},
number = {3},
pages = {258-268},
doi = {10.1002/jmor.20212},
pmid = {24186265},
issn = {1097-4687},
mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Chromatin/ultrastructure ; Golgi Apparatus/ultrastructure ; Lizards/*anatomy &amp; histology/physiology ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phylogeny ; Spermatids/*growth &amp; development/*ultrastructure ; *Spermatogenesis ; },
abstract = {Several recent studies have mapped out the characters of spermiogenesis within several species of squamates. Many of these data have shown both conserved and possibly apomorphic morphological traits that could be important in future phylogenetic analysis within Reptilia. There, however, has not been a recent study that compares spermiogenesis and its similarities or differences between two species of reptile that reside in the same genus. Thus, the present analysis details the changes to spermiogenesis in Sceloporus variabilis and then compares spermatid morphologies to that of Sceloporus bicanthalis. Many of the morphological changes that the spermatids undergo in these two species are similar or conserved, which is similar to what has been reported in other squamates. There are six main character differences that can be observed during the development of the spermatids between these two sceloporid lizards. They include the presence (S. variabilis) or absence (S. bicanthalis) of a mitochondrial/endoplasmic reticulum complex near the Golgi apparatus during acrosome development, a shallow (S. variabilis) or deep (S. bicanthalis) nuclear indentation that accommodates the acrosomal vesicle, filamentous (S. variabilis) or granular (S. bicanthalis) chromatin condensation, no spiraling (S. variabilis) or spiraling (S. bicanthalis) of chromatin during condensation, absence (S. variabilis) or presence (S. bicanthalis) of the longitudinal manchette microtubules, and the lack of (S. variabilis) or presence (S. bicanthalis) of nuclear lacunae. This is the first study that compares spermiogenic ultrastructural characters between species within the same genus. The significance of the six character differences between two distantly related species within Sceloporus is still unknown, but these data do suggest that spermiogenesis might be a good model to study the hypothesis that spermatid ontogeny is species specific.},
}
@article {pmid24189582,
year = {2014},
author = {Kamyingkird, K and Cao, S and Masatani, T and Moumouni, PF and Vudriko, P and Mousa, AA and Terkawi, MA and Nishikawa, Y and Igarashi, I and Xuan, X},
title = {Babesia bovis dihydroorotate dehydrogenase (BboDHODH) is a novel molecular target of drug for bovine babesiosis.},
journal = {The Journal of veterinary medical science},
volume = {76},
number = {3},
pages = {323-330},
pmid = {24189582},
issn = {1347-7439},
mesh = {Amino Acid Sequence ; Animals ; Babesia bovis/*enzymology ; Babesiosis/*drug therapy/metabolism ; Blotting, Western ; Cattle ; Cattle Diseases/*drug therapy/*parasitology ; Cloning, Molecular ; Computational Biology ; DNA Primers/genetics ; Dihydroorotate Dehydrogenase ; Drug Delivery Systems ; Drug Discovery ; Enzyme Inhibitors/*metabolism ; Escherichia coli ; Microscopy, Confocal ; Molecular Sequence Data ; Oxidoreductases Acting on CH-CH Group Donors/genetics/*metabolism ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; },
abstract = {The emergence of drug resistance and adverse side effects of current bovine babesiosis treatment suggest that the search of new drug targets and development of safer and effective compounds are required. This study focuses on dihydroorotate dehydrogenase (DHODH), the fourth enzyme of pyrimidine biosynthesis pathway as a potential drug target for bovine babesiosis. Recombinant Babesia bovis DHODH protein (rBboDHODH) was produced in Escherichia coli and used for characterization and measurement of enzymatic activity. Furthermore, the effects of DHODH inhibitors were evaluated in vitro. The recombinant B. bovis DHODH histidine fusion protein (rBboDHODH) had 42.4-kDa molecular weight and exhibited a specific activity of 475.7 ± 245 Unit/mg, a Km = 276.2 µM for L-dihydroorotate and a Km= 94.41 µM for decylubiquinone. A 44-kDa band of native BboDHODH was detected by Western blot analysis and found in parasites mitochondria using a confocal microscope. Among DHODH inhibitors, atovaquone (ATV) and leflunomide (LFN) significantly inhibited the activity of rBboDHODH as well as the growth of B. bovis in vitro. The half maximal inhibitory concentration (IC50) of ATV and LFN was 2.38 ± 0.53 nM and 52.41 ± 11.47 µM, respectively. These results suggest that BboDHODH might be a novel target for development of new drug for treatment of B. bovis infection.},
}
@article {pmid24194927,
year = {2013},
author = {Chen, X and Ghazanfar, B and Khan, AR and Hayat, S and Cheng, Z},
title = {Comparative analysis of putative orthologues of mitochondrial import motor subunit: Pam18 and Pam16 in plants.},
journal = {PloS one},
volume = {8},
number = {10},
pages = {e78400},
pmid = {24194927},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Arabidopsis Proteins/*genetics ; Cluster Analysis ; Computational Biology/methods ; Conserved Sequence/genetics ; Data Mining ; Microarray Analysis ; Mitochondrial Membrane Transport Proteins/*genetics ; Mitochondrial Precursor Protein Import Complex Proteins ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Plants/*genetics ; Sequence Alignment ; Sequence Homology ; Species Specificity ; },
abstract = {Pam18/Tim14 and Pam16/Tim16, highly conserved proteins among eukaryotes, are two essential subunits of protein import motors localized in the inner mitochondrial membrane. The heterodimer formed by Pam18 and Pam16 via their J-type domains serves a regulatory function in protein translocation. Here, we report that thirty-one Pam18 and twenty-six Pam16 putative orthologues in twelve plant species were identified and analyzed through bioinformatics strategy. Results data revealed that Pam18 and Pam16 were also highly conserved among plants including their J-type domains within the hydrophilic region. Key amino acid residues and an HPD motif of Pam18 were identical among the orthologues except OsPam18L5. N-myristoylation sites of Pam18 and casein kinase II phosphorylation sites of Pam 16 were more abundant, which might be important functional sites. Some Pam18 and Pam16 proteins contained a transmembrane region at the N-terminal region. Sub-cellular prediction results indicated that many orthologues localized at mitochondria. Gene expression analyses revealed that Pam18 and Pam16 in Arabidopsis might play roles in senescence and abiotic stress responses. Our detailed study provides a better understanding of Pam18 and Pam16 in plant kingdom.},
}
@article {pmid24203231,
year = {2014},
author = {Couturier, J and Wu, HC and Dhalleine, T and Pégeot, H and Sudre, D and Gualberto, JM and Jacquot, JP and Gaymard, F and Vignols, F and Rouhier, N},
title = {Monothiol glutaredoxin-BolA interactions: redox control of Arabidopsis thaliana BolA2 and SufE1.},
journal = {Molecular plant},
volume = {7},
number = {1},
pages = {187-205},
doi = {10.1093/mp/sst156},
pmid = {24203231},
issn = {1752-9867},
mesh = {Arabidopsis/cytology/enzymology/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Catalytic Domain ; Conserved Sequence ; DNA-Binding Proteins/chemistry/*metabolism ; Enzyme Activation ; Glutaredoxins/*metabolism ; Intracellular Space/metabolism ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Protein Binding ; Protein Transport ; Sulfurtransferases/*metabolism ; },
abstract = {A functional relationship between monothiol glutaredoxins and BolAs has been unraveled by genomic analyses and in several high-throughput studies. Phylogenetic analyses coupled to transient expression of green fluorescent protein (GFP) fusions indicated that, in addition to the sulfurtransferase SufE1, which contains a C-terminal BolA domain, three BolA isoforms exist in Arabidopsis thaliana, BolA1 being plastidial, BolA2 nucleo-cytoplasmic, and BolA4 dual-targeted to mitochondria and plastids. Binary yeast two-hybrid experiments demonstrated that all BolAs and SufE1, via its BolA domain, can interact with all monothiol glutaredoxins. Most interactions between protein couples of the same subcellular compartment have been confirmed by bimolecular fluorescence complementation. In vitro experiments indicated that monothiol glutaredoxins could regulate the redox state of BolA2 and SufE1, both proteins possessing a single conserved reactive cysteine. Indeed, a glutathionylated form of SufE1 lost its capacity to activate the cysteine desulfurase, Nfs2, but it is reactivated by plastidial glutaredoxins. Besides, a monomeric glutathionylated form and a dimeric disulfide-bridged form of BolA2 can be preferentially reduced by the nucleo-cytoplasmic GrxS17. These results indicate that the glutaredoxin-BolA interaction occurs in several subcellular compartments and suggest that a redox regulation mechanism, disconnected from their capacity to form iron-sulfur cluster-bridged heterodimers, may be physiologically relevant for BolA2 and SufE1.},
}
@article {pmid24216019,
year = {2014},
author = {Smith, DR and Arrigo, KR and Alderkamp, AC and Allen, AE},
title = {Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae.},
journal = {Molecular phylogenetics and evolution},
volume = {71},
number = {},
pages = {36-40},
doi = {10.1016/j.ympev.2013.10.018},
pmid = {24216019},
issn = {1095-9513},
mesh = {Cell Nucleus/*genetics ; Genome ; Haptophyta/classification/*genetics ; Mitochondria/*genetics ; Mutation Rate ; *Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; },
abstract = {We are just beginning to understand how mutation rates differ among mitochondrial, plastid, and nuclear genomes. In most seed plants the mitochondrial mutation rate is estimated to be lower than those of the plastid and nucleus, whereas in the red alga Porphyra the opposite is true, and in certain green algae all three genomes appear to have similar rates of mutation. Relative rate statistics of organelle vs nuclear genes, however, are lacking for lineages that acquired their plastids through secondary endosymbiosis, but recent organelle DNA analyses suggest that they may differ drastically from what is observed in lineages with primary plastids, such as green plants and red algae. Here, by measuring synonymous nucleotide substitutions, we approximate the relative mutation rates within the haptophyte genus Phaeocystis, which has a red-algal-derived, secondary plastid. Synonymous-site divergence data indicate that for Phaeocystis antarctica and P. globosa the mitochondrial mutation rate is 10 and 3 times that of the plastid and nucleus, respectively. This differs drastically from relative rate estimates for primary-plastid-bearing lineages and presents a much more dynamic view of organelle vs nuclear mutation rates across the eukaryotic domain.},
}
@article {pmid24216442,
year = {2013},
author = {Zhang, YK and Ding, XL and Zhang, KJ and Hong, XY},
title = {Wolbachia play an important role in affecting mtDNA variation of Tetranychus truncatus (Trombidiformes: Tetranychidae).},
journal = {Environmental entomology},
volume = {42},
number = {6},
pages = {1240-1245},
doi = {10.1603/EN13085},
pmid = {24216442},
issn = {1938-2936},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Haplotypes ; Phylogeny ; Tetranychidae/genetics/*microbiology ; Wolbachia/*genetics/physiology ; },
abstract = {The prevalence of the endosymbiont Wolbachia and its effects on mitochondria variation were analyzed in seven natural populations of Tetranychus truncatus Ehara (Trombidiformes: Tetranychidae) in current study. Five Wolbachia strains (wtru1, wtru5, wtru7, wtru8, and wtru12) were detected based on the surface protein of Wolbachia (wsp) sequence data and the multiple locus sequences typing data, suggesting that multiple separate invasions have occurred. Part of mitochondrial cytochrome oxidase subunit I gene was sequenced from infected individuals revealing 10 different haplotypes. As predicted, the haplotype and nucleotide diversity were lower in infected individuals than that in uninfected individuals. Furthermore, phylogenetic and analysis of molecular variance analyses revealed that the distribution of mtDNA haplotypes is not associated with geography. Rather, it is strongly concordant with infection status. These data support the hypothesis that Wolbachia infection can affect the genetic structure and diversity of the host mites.},
}
@article {pmid24221027,
year = {2014},
author = {Zhang, L and An, B and Backström, N and Liu, N},
title = {Phylogeography-based delimitation of subspecies boundaries in the common pheasant (Phasianus colchicus).},
journal = {Biochemical genetics},
volume = {52},
number = {1-2},
pages = {38-51},
doi = {10.1007/s10528-013-9626-5},
pmid = {24221027},
issn = {1573-4927},
mesh = {Animals ; China ; Galliformes/blood/*genetics ; Genetic Variation ; Mitochondria/genetics ; Mutation Rate ; Phylogeography ; Species Specificity ; },
abstract = {To test the validity of subspecies status within the common pheasant (Phasianus colchicus), we used genetic data to assess differences among five subspecies distributed across the Loess Plateau in central China. Samples were collected from 191 individuals representing subspecies P. c. strauchi, P. c. satscheuensis, P. c. kiangsuensis, P. c. suehschanensis, and P. c. edzinensis. Analysis of mitochondrial genetic variation suggested that there were no phylogenetically distinct subspecies clades, and we could not exclude that hybridization has occurred among subspecies. A potential explanation of the observed pattern is that an increase in common pheasant rearing farms may have led to enforcement of hybridization between different subspecies. Consistent with phenotypic data, our analysis suggests that a previously identified common pheasant subspecies (P. c. strauchi) represents an intermediate form between the subspecies P. c. satscheuensis and P. c. suehschanensis.},
}
@article {pmid24230915,
year = {2014},
author = {Gjerde, B},
title = {Sarcocystis species in red deer revisited: with a re-description of two known species as Sarcocystis elongata n. sp. and Sarcocystis truncata n. sp. based on mitochondrial cox1 sequences.},
journal = {Parasitology},
volume = {141},
number = {3},
pages = {441-452},
doi = {10.1017/S0031182013001819},
pmid = {24230915},
issn = {1469-8161},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Deer/*parasitology ; Electron Transport Complex IV/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/genetics ; Reindeer ; Sarcocystis/*classification/genetics/isolation &amp; purification ; Sarcocystosis/parasitology/*veterinary ; Sequence Analysis, DNA/veterinary ; Species Specificity ; },
abstract = {In a previous investigation, five Sarcocystis species were described from Norwegian red deer and believed to be conspecific with species occurring in either reindeer or moose based on sarcocyst morphology and nucleotide sequences of the nuclear ribosomal DNA unit. The aim of the present study was to characterize numerous isolates of these sarcocyst types at the mitochondrial cytochrome c oxidase subunit I gene (cox1) in order to corroborate or refute previous species designations of Sarcocystis in red deer. The Sarcocystis tarandi- and Sarcocystis rangiferi-like taxa in red deer and reindeer, respectively, were thoroughly compared by sequencing 14-27 isolates of each type. Sequence comparisons revealed four distinct sequence types, which by phylogenetic analyses were placed in four monophyletic groups according to host origin, and they were therefore considered to represent four separate species. The two taxa of this type in red deer were named Sarcocystis elongata and Sarcocystis truncata, respectively. Sequencing of many isolates of Sarcocystis hjorti and Sarcocystis ovalis from red deer and moose confirmed that these species occur in both hosts. A revised description of the two new species is given and the current knowledge concerning all six Sarcocystis species in red deer is reviewed.},
}
@article {pmid24231807,
year = {2013},
author = {Sancak, Y and Markhard, AL and Kitami, T and Kovács-Bogdán, E and Kamer, KJ and Udeshi, ND and Carr, SA and Chaudhuri, D and Clapham, DE and Li, AA and Calvo, SE and Goldberger, O and Mootha, VK},
title = {EMRE is an essential component of the mitochondrial calcium uniporter complex.},
journal = {Science (New York, N.Y.)},
volume = {342},
number = {6164},
pages = {1379-1382},
pmid = {24231807},
issn = {1095-9203},
support = {F32HL107021/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R24 DK080261/DK/NIDDK NIH HHS/United States ; P30 HD018655/HD/NICHD NIH HHS/United States ; F32 HL107021/HL/NHLBI NIH HHS/United States ; DK080261/DK/NIDDK NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Calcium Channels/chemistry/genetics/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; Cation Transport Proteins/genetics/*metabolism ; Cell Membrane/*metabolism ; EF Hand Motifs ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Proteomics ; },
abstract = {The mitochondrial uniporter is a highly selective calcium channel in the organelle's inner membrane. Its molecular components include the EF-hand-containing calcium-binding proteins mitochondrial calcium uptake 1 (MICU1) and MICU2 and the pore-forming subunit mitochondrial calcium uniporter (MCU). We sought to achieve a full molecular characterization of the uniporter holocomplex (uniplex). Quantitative mass spectrometry of affinity-purified uniplex recovered MICU1 and MICU2, MCU and its paralog MCUb, and essential MCU regulator (EMRE), a previously uncharacterized protein. EMRE is a 10-kilodalton, metazoan-specific protein with a single transmembrane domain. In its absence, uniporter channel activity was lost despite intact MCU expression and oligomerization. EMRE was required for the interaction of MCU with MICU1 and MICU2. Hence, EMRE is essential for in vivo uniporter current and additionally bridges the calcium-sensing role of MICU1 and MICU2 with the calcium-conducting role of MCU.},
}
@article {pmid24269344,
year = {2014},
author = {Jia, H and Sun, R and Shi, W and Yan, Y and Li, H and Guo, X and Xu, B},
title = {Characterization of a mitochondrial manganese superoxide dismutase gene from Apis cerana cerana and its role in oxidative stress.},
journal = {Journal of insect physiology},
volume = {60},
number = {},
pages = {68-79},
doi = {10.1016/j.jinsphys.2013.11.004},
pmid = {24269344},
issn = {1879-1611},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bees/enzymology/*genetics/radiation effects ; Gene Components ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Stress, Physiological ; Superoxide Dismutase/*genetics/isolation &amp; purification/metabolism ; Transcription Factors/metabolism ; },
abstract = {Mitochondrial manganese superoxide dismutase (mMnSOD) plays a vital role in the defense against reactive oxygen species (ROS) in eukaryotic mitochondria. In this study, we isolated and identified a mMnSOD gene from Apis cerana cerana, which we named AccSOD2. Several putative transcription factor-binding sites were identified within the 5'-flanking region of AccSOD2, which suggests that AccSOD2 may be involved in organismal development and/or environmental stress responses. Quantitative real-time PCR analysis showed that AccSOD2 is highly expressed in larva and pupae during different developmental stages. In addition, the expression of AccSOD2 could be induced by cold (4 °C), heat (42 °C), H2O2, ultraviolet light (UV), HgCl2, and pesticide treatment. Using a disc diffusion assay, we provide evidence that recombinant AccSOD2 protein can play a functional role in protecting cells from oxidative stress. Finally, the in vivo activities of AccSOD2 were measured under a variety of stressful conditions. Taken together, our results indicate that AccSOD2 plays an important role in cellular stress responses and anti-oxidative processes and that it may be of critical importance to honeybee survival.},
}
@article {pmid24289148,
year = {2015},
author = {Zheng, XH and Cao, DC and Lv, WH and Wu, J and Sun, XW},
title = {The complete mitochondrial genome sequence of Chinese lizard gudgeon (Saurogobio dabryi).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {708-709},
doi = {10.3109/19401736.2013.843085},
pmid = {24289148},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Lizards/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genome of Saurogobio dabryi is 16,604 bp in length with 55.88% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The termination-associated sequence and six conserved sequence blocks were also identified. Compared all protein-coding genes and whole genome sequence with four species, Saurogobio dabryi has higher similarity with Gobio gobio than others. The mitogenome sequence of Saurogobio dabryi would play an important role in population structure and conservation genetic studies.},
}
@article {pmid24303002,
year = {2013},
author = {Wilson, NG and Maschek, JA and Baker, BJ},
title = {A species flock driven by predation? Secondary metabolites support diversification of slugs in antarctica.},
journal = {PloS one},
volume = {8},
number = {11},
pages = {e80277},
pmid = {24303002},
issn = {1932-6203},
mesh = {Animals ; Antarctic Regions ; *Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/classification/genetics/*metabolism ; *Metabolome ; *Metabolomics/methods ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; *Predatory Behavior ; Selection, Genetic ; },
abstract = {Antarctica's rich marine animal biodiversity has been substantially influenced by a complex glacial history, but it is unclear why some taxa responded with diversification while others did not. Despite being considered a single endemic sea slug species in the Southern Ocean, mitochondrial DNA sequencing of Doris kerguelenensis (Bergh, 1884) revealed a multitude of highly divergent lineages. But because of the uniparental inheritance of mitochondria, it was unclear whether those lineages represented a radiation of cryptic species or simply stochastic sorting patterns of populations that rarely reach equilibrium. Here we demonstrate that the mitochondrial groups in D. kerguelenensis also correlate with nuclear DNA. Additionally, by extracting secondary metabolites from the same individuals we sequenced, we were also able to directly link the secondary metabolome to a mitochondrial lineage. These metabolites are not derived from the diet, but instead are synthesized de novo and implicated in an anti-predatory role. The strong linkage between these metabolites and the mitochondrial lineages strongly suggests that these lineages represent cryptic species in an adaptive radiation. Over millions of years, episodic glacial cycles reduced the distribution of a formerly widespread slug into a series of small vicariant refuges, vulnerable to genetic drift and predation pressure. The recognition of this marine invertebrate species flock implicates a strongly synergistic role for selection and allopatry driving speciation in this system.},
}
@article {pmid24312599,
year = {2013},
author = {Zhang, L and Liu, X and Liu, J and Zhang, Z},
title = {Characteristics and function of sulfur dioxygenase in Echiuran worm Urechis unicinctus.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e81885},
pmid = {24312599},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biocatalysis ; Cloning, Molecular ; DNA, Complementary/genetics ; Dioxygenases/*chemistry/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polychaeta/*enzymology ; Protein Refolding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; },
abstract = {BACKGROUND: Sulfide is a common toxin to animals and is abundant in coastal and aquatic sediments. Sulfur dioxygenase (SDO) is thought to be the key enzyme involved in sulfide oxidation in some organisms. The echiuran worm, Urechis unicinctus, inhabits coastal sediment and tolerates high concentrations of sulfide. The SDO is presumably important for sulfide tolerance in U. unicinctus.<br><br>RESULTS: The full-length cDNA of SDO from the echiuran worm U. unicinctus, proven to be located in the mitochondria, was cloned and the analysis of its sequence suggests that it belongs to the metallo-&#x3b2;-lactamase superfamily. The enzyme was produced using an E. coli expression system and the measured activity is approximately 0.80 U mg protein(-1). Furthermore, the expression of four sub-segments of the U. unicinctus SDO was accomplished leading to preliminary identification of functional domains of the enzyme. The identification of the conserved metal I (H113, H115, H169 and D188), metal II (D117, H118, H169 and H229) as well as the potential glutathione (GSH) (R197, Y231, M279 and I283) binding sites was determined by enzyme activity and GSH affinity measurements. The key residues responsible for SDO activity were identified by analysis of simultaneous mutations of residues D117 and H118 located close to the metal II binding site.<br><br>CONCLUSION: The recombinant SDO from U. unicinctus was produced, purified and characterized. The metal binding sites in the SDO were identified and Y231 recognized as the mostly important amino acid residue for GSH binding. Our results show that SDO is located in the mitochondria where it plays an important role in sulfide detoxification of U. unicinctus.},
}
@article {pmid24324722,
year = {2013},
author = {Hagino, K and Onuma, R and Kawachi, M and Horiguchi, T},
title = {Discovery of an endosymbiotic nitrogen-fixing cyanobacterium UCYN-A in Braarudosphaera bigelowii (Prymnesiophyceae).},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e81749},
pmid = {24324722},
issn = {1932-6203},
mesh = {Base Sequence ; Cyanobacteria/*physiology ; DNA, Ribosomal/genetics ; Haptophyta/genetics/*microbiology/ultrastructure ; Likelihood Functions ; Molecular Sequence Data ; *Nitrogen Fixation/genetics ; Phylogeny ; Spores/ultrastructure ; *Symbiosis/genetics ; },
abstract = {Braarudosphaera bigelowii (Prymnesiophyceae) is a coastal coccolithophore with a long fossil record, extending back to the late Cretaceous (ca. 100 Ma). A recent study revealed close phylogenetic relationships between B. bigelowii, Chrysochromulina parkeae (Prymnesiophyceae), and a prymnesiophyte that forms a symbiotic association with the nitrogen-fixing cyanobacterium UCYN-A. In order to further examine these relationships, we conducted transmission electron microscopic and molecular phylogenetic studies of B. bigelowii. TEM studies showed that, in addition to organelles, such as the nucleus, chloroplasts and mitochondria, B. bigelowii contains one or two spheroid bodies with internal lamellae. In the 18S rDNA tree of the Prymnesiophyceae, C. parkeae fell within the B. bigelowii clade, and was close to B. bigelowii Genotype III (99.89% similarity). Plastid 16S rDNA sequences obtained from B. bigelowii were close to the unidentified sequences from the oligotrophic SE Pacific Ocean (e.g. HM133411) (99.86% similarity). Bacterial16S rDNA sequences obtained from B. bigelowii were identical to the UCYN-A sequence AY621693 from Arabian Sea, and fell in the UCYN-A clade. From these results, we suggest that; 1) C. parkeae is the alternate life cycle stage of B. bigelowii sensu stricto or that of a sibling species of B. bigelowii, and 2) the spheroid body of B. bigelowii originated from endosymbiosis of the nitrogen-fixing cyanobacterium UCYN-A.},
}
@article {pmid24325672,
year = {2015},
author = {Mu, XD and Yang, YX and Liu, Y and Song, HM and Luo, JR and Hu, YC},
title = {Complete mitochondrial genome of northern spotted barramundi, Scleropages jardinii.},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {698-699},
doi = {10.3109/19401736.2013.843080},
pmid = {24325672},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Fishes/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We sequenced the complete mitogenome of northern spotted barramundi Scleropages jardinii, an ancestral bonytongue with economic and conservation value. The mitogenome is 16,670 bp in length with an A + T content of 52.9%, and contains 13 protein-coding genes, 2rRNAs, 22 tRNAs and a control region. The gene order and arrangement is similar to that of other Osteoglossidae species, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Osteoglossidae species.},
}
@article {pmid24328820,
year = {2015},
author = {Tian, SQ and Cui, P and Fang, SF and Liu, GH and Wang, CR and Zhu, XQ},
title = {The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {714-715},
doi = {10.3109/19401736.2013.843088},
pmid = {24328820},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Chickens/parasitology ; Coccidiosis/*parasitology/veterinary ; Eimeria/*genetics/isolation &amp; purification ; Genes, Protozoan ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Rabbits ; Sequence Analysis, DNA ; },
abstract = {In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis.},
}
@article {pmid24330701,
year = {2013},
author = {Bazzocchi, C and Mariconti, M and Sassera, D and Rinaldi, L and Martin, E and Cringoli, G and Urbanelli, S and Genchi, C and Bandi, C and Epis, S},
title = {Molecular and serological evidence for the circulation of the tick symbiont Midichloria (Rickettsiales: Midichloriaceae) in different mammalian species.},
journal = {Parasites &amp; vectors},
volume = {6},
number = {},
pages = {350},
pmid = {24330701},
issn = {1756-3305},
mesh = {Alphaproteobacteria/*genetics/*isolation &amp; purification ; Animals ; Gene Expression Regulation, Bacterial/*physiology ; Italy ; Ixodidae/*microbiology ; Mammals/blood/*microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; },
abstract = {BACKGROUND: The Midichloriaceae is a novel family of the order Rickettsiales, that encompasses intracellular bacteria associated with hard ticks (Ixodidae) and other arthropods. The most intensively investigated member of this family is Midichloria mitochondrii, a symbiotic bacterium of the sheep tick Ixodes ricinus, characterized by the capacity of multiplying inside the mitochondria. A recent study suggested that these bacteria might be inoculated into the human host during the tick bite. The purpose of this study was to determine the potential infectivity of Midichloria bacteria for non-human animals exposed to the risk of tick bite.<br><br>METHODS: Blood from horses, cattle, sheep and dogs exposed to the risk of tick bite was included in this study. DNAs were extracted, and amplified using 16S ribosomal RNA primers conserved in the Midichloria genus. Furthermore, sera from dogs exposed to the risk of tick bite were analyzed in order to evaluate the presence of antibodies against the recombinant flagellar protein (rFliD) from M. mitochondrii using an ELISA test.<br><br>RESULTS: Here we present two lines of evidence that support the possibility that bacteria from the genus Midichloria are inoculated into vertebrate hosts during a tick bite: (i) a direct evidence, i.e. the detection of circulating DNA from bacteria related with M. mitochondrii, in the blood of vertebrates exposed to tick parasitism; (ii) a further indirect evidence, i.e. the presence of antibodies against an antigen from M. mitochondrii in dogs exposed to the risk of tick bite. It is interesting to note that variability was detected in the Midichloria gene sequences recovered from positive animals, and that some of these sequences were identical to those generated from tick-associated Midichloria.<br><br>CONCLUSIONS: Based on the results, and on the overall information so far published on the genus Midichloria, we suggest that these bacteria are likely to represent a novel group of vector-borne agents, with the potential of infecting mammalian hosts. Whether inoculation of Midichloria bacteria could cause a true infection and pathological alteration in mammalian hosts is still to be determined. Surely, results emphasize the relevance of Midichloria bacteria in investigations on tick immunology and tick-bite markers.},
}
@article {pmid24349502,
year = {2013},
author = {Ferla, MP and Thrash, JC and Giovannoni, SJ and Patrick, WM},
title = {New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability.},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e83383},
pmid = {24349502},
issn = {1932-6203},
mesh = {Alphaproteobacteria/*genetics ; Genes, Bacterial/*genetics ; Genes, rRNA/*physiology ; Mitochondria/*genetics ; *Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Bacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes, as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of topologies and comparative results from Approximately Unbiased tests provide support for positioning the Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the Rickettsidae, and the Magnetococcidae.},
}
@article {pmid24357311,
year = {2013},
author = {Rice, DW and Alverson, AJ and Richardson, AO and Young, GJ and Sanchez-Puerta, MV and Munzinger, J and Barry, K and Boore, JL and Zhang, Y and dePamphilis, CW and Knox, EB and Palmer, JD},
title = {Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.},
journal = {Science (New York, N.Y.)},
volume = {342},
number = {6165},
pages = {1468-1473},
doi = {10.1126/science.1246275},
pmid = {24357311},
issn = {1095-9203},
support = {R01-GM-76012/GM/NIGMS NIH HHS/United States ; },
mesh = {Base Sequence ; Bryophyta/classification/genetics ; Chlorophyta/classification/genetics ; DNA, Mitochondrial/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Membrane Fusion ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Tracheophyta/classification/*genetics ; },
abstract = {We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.},
}
@article {pmid24360837,
year = {2014},
author = {Hoepfner, D and Helliwell, SB and Sadlish, H and Schuierer, S and Filipuzzi, I and Brachat, S and Bhullar, B and Plikat, U and Abraham, Y and Altorfer, M and Aust, T and Baeriswyl, L and Cerino, R and Chang, L and Estoppey, D and Eichenberger, J and Frederiksen, M and Hartmann, N and Hohendahl, A and Knapp, B and Krastel, P and Melin, N and Nigsch, F and Oakeley, EJ and Petitjean, V and Petersen, F and Riedl, R and Schmitt, EK and Staedtler, F and Studer, C and Tallarico, JA and Wetzel, S and Fishman, MC and Porter, JA and Movva, NR},
title = {High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions.},
journal = {Microbiological research},
volume = {169},
number = {2-3},
pages = {107-120},
doi = {10.1016/j.micres.2013.11.004},
pmid = {24360837},
issn = {1618-0623},
mesh = {Antifungal Agents/pharmacology ; Biosynthetic Pathways ; Drug Resistance, Fungal ; Gene Expression Regulation, Fungal ; High-Throughput Screening Assays ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/*chemistry/classification/drug effects/*genetics ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; },
abstract = {Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.},
}
@article {pmid24365595,
year = {2014},
author = {Hu, G and Zou, G and Liu, X and Liang, H and Li, Z and Hu, S},
title = {The carp-goldfish nucleocytoplasmic hybrid has mitochondria from the carp as the nuclear donor species.},
journal = {Gene},
volume = {536},
number = {2},
pages = {265-271},
doi = {10.1016/j.gene.2013.12.024},
pmid = {24365595},
issn = {1879-0038},
mesh = {Active Transport, Cell Nucleus/*genetics ; Animals ; Carps/*genetics ; Cell Nucleus/*genetics ; Cytoplasm/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Goldfish/*genetics ; Male ; Mitochondria/*genetics ; Oocytes ; Phylogeny ; },
abstract = {It is widely accepted that mitochondria and its DNA (mtDNA) exhibit strict maternal inheritance, with sperm contributing no or non-detectable mitochondria to the next generation. In fish, nuclear transfer (NT) through the combination of a donor nucleus and an enucleated oocyte can produce fertile nucleocytoplasmic hybrids (NCHs) even between different genera and subfamilies. One of the best studied fish NCHs is CyCa produced by transplanting the nuclei plus cytoplasm from the common carp (Cyprinus carpio var. wuyuanensis) into the oocytes of the wild goldfish (Carassius auratus), which has been propagated by self-mating for three generations. These NCH fish thus provide a unique model to study the origin of mitochondria. Here we report the complete mtDNA sequence of the CyCa hybrid and its parental species carp and goldfish as nuclear donor and cytoplasm host, respectively. Interestingly, the mtDNA of NCH fish CyCa is 99.69% identical to the nuclear donor species carp, and 89.25% identical to the oocyte host species goldfish. Furthermore, an amino acid sequence comparison of 13 mitochondrial proteins reveals that CyCa is 99.68% identical to the carp and 87.68% identical to the goldfish. On an mtDNA-based phylogenetic tree, CyCa is clustered with the carp but separated from the goldfish. A real-time PCR analysis revealed the presence of carp mtDNA but the absence of goldfish mtDNA. These results demonstrate--for the first time to our knowledge--that the mtDNA of a NCH such as CyCa fish may originate from its nuclear donor rather than its oocyte host.},
}
@article {pmid24376088,
year = {2014},
author = {Sharma, V and O'Halloran, DM},
title = {Recent structural and functional insights into the family of sodium calcium exchangers.},
journal = {Genesis (New York, N.Y. : 2000)},
volume = {52},
number = {2},
pages = {93-109},
doi = {10.1002/dvg.22735},
pmid = {24376088},
issn = {1526-968X},
mesh = {Animals ; Caenorhabditis elegans/chemistry/metabolism ; Calcium/*metabolism ; Calcium Signaling ; Gene Expression Regulation ; Humans ; Mitochondria/metabolism ; Models, Molecular ; *Multigene Family ; Phylogeny ; Sodium-Calcium Exchanger/*chemistry/genetics/*metabolism ; },
abstract = {Maintenance of calcium homeostasis is necessary for the development and survival of all animals. Calcium ions modulate excitability and bind effectors capable of initiating many processes such as muscular contraction and neurotransmission. However, excessive amounts of calcium in the cytosol or within intracellular calcium stores can trigger apoptotic pathways in cells that have been implicated in cardiac and neuronal pathologies. Accordingly, it is critical for cells to rapidly and effectively regulate calcium levels. The Na(+) /Ca(2+) exchangers (NCX), Na(+) /Ca(2+) /K(+) exchangers (NCKX), and Ca(2+) /Cation exchangers (CCX) are the three classes of sodium calcium antiporters found in animals. These exchanger proteins utilize an electrochemical gradient to extrude calcium. Although they have been studied for decades, much is still unknown about these proteins. In this review, we examine current knowledge about the structure, function, and physiology and also discuss their implication in various developmental disorders. Finally, we highlight recent data characterizing the family of sodium calcium exchangers in the model system, Caenorhabditis elegans, and propose that C. elegans may be an ideal model to complement other systems and help fill gaps in our knowledge of sodium calcium exchange biology.},
}
@article {pmid24389926,
year = {2014},
author = {Liu, H and Xin, Y and Xun, L},
title = {Distribution, diversity, and activities of sulfur dioxygenases in heterotrophic bacteria.},
journal = {Applied and environmental microbiology},
volume = {80},
number = {5},
pages = {1799-1806},
pmid = {24389926},
issn = {1098-5336},
mesh = {Cloning, Molecular ; Cluster Analysis ; Cyanobacteria/*enzymology/*genetics/metabolism ; Dioxygenases/*genetics/*metabolism ; Escherichia coli/genetics ; Gene Expression ; *Genetic Variation ; Heterotrophic Processes ; Iron/metabolism ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/*enzymology/*genetics/metabolism ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sulfur/metabolism ; },
abstract = {Sulfur oxidation by chemolithotrophic bacteria is well known; however, sulfur oxidation by heterotrophic bacteria is often ignored. Sulfur dioxygenases (SDOs) (EC 1.13.11.18) were originally found in the cell extracts of some chemolithotrophic bacteria as glutathione (GSH)-dependent sulfur dioxygenases. GSH spontaneously reacts with elemental sulfur to generate glutathione persulfide (GSSH), and SDOs oxidize GSSH to sulfite and GSH. However, SDOs have not been characterized for bacteria, including chemolithotrophs. The gene coding for human SDO (human ETHE1 [hETHE1]) in mitochondria was discovered because its mutations lead to a hereditary human disease, ethylmalonic encephalopathy. Using sequence analysis and activity assays, we discovered three subgroups of bacterial SDOs in the proteobacteria and cyanobacteria. Ten selected SDO genes were cloned and expressed in Escherichia coli, and the recombinant proteins were purified. The SDOs used Fe(2+) for catalysis and displayed considerable variations in specific activities. The wide distribution of SDO genes reveals the likely source of the hETHE1 gene and highlights the potential of sulfur oxidation by heterotrophic bacteria.},
}
@article {pmid24397757,
year = {2015},
author = {Wang, JF and Chen, MY and Chaw, SM and Morii, Y and Yoshimura, M and Sota, T and Lin, CP},
title = {Complete mitochondrial genome of an enigmatic dragonfly, Epiophlebia superstes (Odonata, Epiophlebiidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {718-719},
doi = {10.3109/19401736.2013.845756},
pmid = {24397757},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This study reported the 15,435 bp-long complete mitochondrial genome of the relict Epiophlebia superstes (Odonata, Epiophlebiidae), an enigmatic dragonfly of the paraphyletic 'Anisozygoptera' possessing characteristics similar to members of both extant odonate suborders, the Zygoptera and the Anisoptera. This mitogenome comprises the common set of 37 genes and an A + T-rich control region, and has a gene arrangement identical to those of all available odonates. The genome contains three non-coding inter-genic spacers (s1-s3), which occurs in all of other known odonates, but it lacks the inter-genic spacer s5 typically found in the Anisoptera. This result suggests that E. superstes possesses a mitogenmic organization more closely related to that of the Zygoptera than that of the Anizoptera.},
}
@article {pmid24397768,
year = {2015},
author = {Marín, A and Alfaro, R and Fujimoto, T and Arai, K},
title = {Mitochondrial genome of the Peruvian scallop Argopecten purpuratus (Bivalvia: Pectinidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {726-727},
doi = {10.3109/19401736.2013.845760},
pmid = {24397768},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Codon, Initiator ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Pectinidae/*genetics ; Peru ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial genome of the Peruvian scallop Argopecten purpuratus was determined. The length of the mitochondrial coding region is 15,608 bp. A typical bivalve mitochondrial composition was detected with 12 protein-coding genes, 2 ribosomal RNA genes and 21 transfer RNA genes, with the absence of the atp8 gene. Fifty percent of the protein-coding genes use typical ATG start codon, whereas five genes utilize ATA as their start codon. Only one gene was found to utilize TTG as its start codon. The A. purpuratus mitogenome shows a significant similarity to that of A. irradians irradians, in length as well as in gene composition.},
}
@article {pmid24410953,
year = {2014},
author = {Kaur, C and Mustafiz, A and Sarkar, AK and Ariyadasa, TU and Singla-Pareek, SL and Sopory, SK},
title = {Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium.},
journal = {Physiologia plantarum},
volume = {152},
number = {1},
pages = {1-16},
doi = {10.1111/ppl.12147},
pmid = {24410953},
issn = {1399-3054},
mesh = {Amino Acid Sequence ; Calcium/*metabolism ; Dioxygenases/*genetics/metabolism ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Light ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Onions/cytology/genetics/physiology ; Organ Specificity ; Oryza/drug effects/genetics/*physiology/radiation effects ; Phylogeny ; Plant Epidermis/drug effects/genetics/physiology/radiation effects ; Plant Growth Regulators/pharmacology ; Plant Proteins/genetics/metabolism ; Plant Roots/drug effects/genetics/physiology/radiation effects ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins ; Sequence Alignment ; *Stress, Physiological ; },
abstract = {ETHYLMALONIC ENCEPHALOPATHY PROTEIN 1 (ETHE1) encodes sulfur dioxygenase (SDO) activity regulating sulfide levels in living organisms. It is an essential gene and mutations in ETHE1 leads to ethylmalonic encephalopathy (EE) in humans and embryo lethality in Arabidopsis. At present, very little is known regarding the role of ETHE1 beyond the context of EE and almost nothing is known about factors affecting its regulation in plant systems. In this study, we have identified, cloned and characterized OsETHE1, a gene encoding ETHE1-like protein from Oryza sativa. ETHE1 proteins in general are most similar to glyoxalase II (GLYII) and hence OsETHE1 has been earlier annotated as OsGLYII1, a putative GLYII gene. Here we show that OsETHE1 lacks GLYII activity and is instead an ETHE1 homolog being localized in mitochondria like its human and Arabidopsis counterparts. We have isolated and analyzed 1618 bp OsETHE1 promoter (pOsETHE1) to examine the factors affecting OsETHE1 expression. For this, transcriptional promoter pOsETHE1: 5-bromo-5-chloro-3-indolyl-β-D-glucuronide (GUS) fusion construct was made and stably transformed into rice. GUS expression pattern of transgenic pOsETHE1:GUS plants reveal a high root-specific expression of OsETHE1. The pOsETHE1 activity was stimulated by Ca(II) and required light for induction. Moreover, pOsETHE1 activity was induced under various abiotic stresses such as heat, salinity and oxidative stress, suggesting a potential role of OsETHE1 in stress response.},
}
@article {pmid24415954,
year = {2014},
author = {Trier, CN and Hermansen, JS and Sætre, GP and Bailey, RI},
title = {Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species.},
journal = {PLoS genetics},
volume = {10},
number = {1},
pages = {e1004075},
pmid = {24415954},
issn = {1553-7404},
mesh = {Animals ; Cell Nucleus/genetics ; Chimera/*genetics ; Genome, Mitochondrial ; Genotype ; *Hybridization, Genetic ; Polymorphism, Single Nucleotide ; *Reproductive Isolation ; Sequence Analysis, DNA ; Sparrows/*genetics ; Species Specificity ; },
abstract = {Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows.},
}
@article {pmid24416271,
year = {2014},
author = {Thomas, RC and Willette, DA and Carpenter, KE and Santos, MD},
title = {Hidden diversity in sardines: genetic and morphological evidence for cryptic species in the goldstripe sardinella, Sardinella gibbosa (Bleeker, 1849).},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e84719},
pmid = {24416271},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/genetics ; Fishes/*anatomy &amp; histology/*genetics ; Genetic Markers/genetics ; *Genetic Variation ; Genotyping Techniques ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; },
abstract = {Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.},
}
@article {pmid24429285,
year = {2014},
author = {Hartmann, A and Hellmund, M and Lucius, R and Voelker, DR and Gupta, N},
title = {Phosphatidylethanolamine synthesis in the parasite mitochondrion is required for efficient growth but dispensable for survival of Toxoplasma gondii.},
journal = {The Journal of biological chemistry},
volume = {289},
number = {10},
pages = {6809-6824},
pmid = {24429285},
issn = {1083-351X},
mesh = {Amino Acid Sequence ; Animals ; Carboxy-Lyases/classification/genetics/*metabolism ; Cell Survival ; Cytidine Diphosphate/analogs &amp; derivatives/metabolism ; Diglycerides/metabolism ; Ethanolamines/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphatidylethanolamines/*biosynthesis ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Toxoplasma/genetics/*growth &amp; development/metabolism ; },
abstract = {Toxoplasma gondii is a highly prevalent obligate intracellular parasite of the phylum Apicomplexa, which also includes other parasites of clinical and/or veterinary importance, such as Plasmodium, Cryptosporidium, and Eimeria. Acute infection by Toxoplasma is hallmarked by rapid proliferation in its host cells and requires a significant synthesis of parasite membranes. Phosphatidylethanolamine (PtdEtn) is the second major phospholipid class in T. gondii. Here, we reveal that PtdEtn is produced in the parasite mitochondrion and parasitophorous vacuole by decarboxylation of phosphatidylserine (PtdSer) and in the endoplasmic reticulum by fusion of CDP-ethanolamine and diacylglycerol. PtdEtn in the mitochondrion is synthesized by a phosphatidylserine decarboxylase (TgPSD1mt) of the type I class. TgPSD1mt harbors a targeting peptide at its N terminus that is required for the mitochondrial localization but not for the catalytic activity. Ablation of TgPSD1mt expression caused up to 45% growth impairment in the parasite mutant. The PtdEtn content of the mutant was unaffected, however, suggesting the presence of compensatory mechanisms. Indeed, metabolic labeling revealed an increased usage of ethanolamine for PtdEtn synthesis by the mutant. Likewise, depletion of nutrients exacerbated the growth defect (∼56%), which was partially restored by ethanolamine. Besides, the survival and residual growth of the TgPSD1mt mutant in the nutrient-depleted medium also indicated additional routes of PtdEtn biogenesis, such as acquisition of host-derived lipid. Collectively, the work demonstrates a metabolic cooperativity between the parasite organelles, which ensures a sustained lipid synthesis, survival and growth of T. gondii in varying nutritional milieus.},
}
@article {pmid24430572,
year = {2014},
author = {Ji, Y and Liang, M and Zhang, J and Zhang, M and Zhu, J and Meng, X and Zhang, S and Gao, M and Zhao, F and Wei, QP and Jiang, P and Tong, Y and Liu, X and Qin Mo, J and Guan, MX},
title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the LHON-associated ND1 G3460A mutation in Chinese families.},
journal = {Journal of human genetics},
volume = {59},
number = {3},
pages = {134-140},
pmid = {24430572},
issn = {1435-232X},
mesh = {Amino Acid Substitution/genetics ; Asian People/genetics ; China ; Cohort Studies ; DNA Mutational Analysis ; DNA, Mitochondrial/genetics ; Diagnostic Techniques, Ophthalmological ; Family ; Female ; *Genetic Predisposition to Disease ; Genome, Mitochondrial/genetics ; Haplotypes/*genetics ; Humans ; Male ; Mitochondria/*genetics ; Mutation/*genetics ; Mutation, Missense/genetics ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/*enzymology/*genetics ; Phenotype ; Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {To investigate the pathophysiology of Leber's hereditary optic neuropathy (LHON), a cohort of 1164 Han Chinese subjects with LHON were screened for ND1 G3460A mutation. A total of 295 subjects from 16 Han Chinese families carrying the G3460A mutation underwent a clinical and genetic evaluation and molecular analysis of mitochondrial (mt)DNA. The incidence of G3460A mutation was 1.4% in this cohort of Chinese subjects with LHON. Twenty-seven (20 males/7 females) of 109 matrilineal relatives among 10 Chinese pedigrees carrying this mutation exhibited a wide range of severity and age-at-onset in visual impairment. Penetrances of optic neuropathy ranged from 7.1% to 50%, with the average of 24.5%. The age-at-onset of 27 affected matrilineal relatives varied from 10 to 40 years, with the average of 22 years. Molecular analysis identified the homoplasmic G3460A mutation and distinct sets of variants belonging to eight haplogroups. Haplogroup M with G3460A mutation was of higher frequency than those in controls. The penetrances of visual loss in families carrying mitochondrial DNA haplogroups A, B and M were higher than those in other families. Furthermore, haplogroup-specific variants tRNA(Ser(AGY)) A12223G, tRNA(Thr) G15927A and tRNA(Glu) A14693G may enhance the penetrance of visual loss in these families. The G3460A mutation occurred through recurrent origins and founder events in Chinese population. Mitochondrial modifiers may modulate the penetrance and expressivity of optic neuropathy among Chinese pedigrees carrying the G3460A mutation. Thus, our findings may provide new insights into the understanding of pathophysiology and valuable information on the management of LHON.},
}
@article {pmid24443224,
year = {2014},
author = {Abu-Bakar, SB and Razali, NM and Naggs, F and Wade, C and Mohd-Nor, SA and Aileen-Tan, SH},
title = {The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey.},
journal = {Molecular biology reports},
volume = {41},
number = {3},
pages = {1799-1805},
pmid = {24443224},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; *Genetic Variation ; Malaysia ; Mitochondria ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Snails/*genetics ; },
abstract = {A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.},
}
@article {pmid24447698,
year = {2014},
author = {Yuasa, T and Takahashi, O},
title = {Ultrastructural morphology of the reproductive swarmers of Sphaerozoum punctatum (Huxley) from the East China Sea.},
journal = {European journal of protistology},
volume = {50},
number = {2},
pages = {194-204},
doi = {10.1016/j.ejop.2013.12.001},
pmid = {24447698},
issn = {1618-0429},
mesh = {China ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Inclusion Bodies/chemistry ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Rhizaria/chemistry/classification/genetics/*ultrastructure ; Seawater/parasitology ; Spectrometry, X-Ray Emission ; },
abstract = {Reproductive swarmers of the polycystine radiolarian Sphaerozoum punctatum (Huxley) collected from the East China Sea were examined using light, scanning and transmission electron microscopy. The swarmer cells were about 8-10 μm in length with a pear-like shape and a conical end with two flagella. A nucleus, mitochondria, Golgi body, lipid droplets and, characteristically, a single, large, vacuole-bound SrSO4 crystal were present in the cytoplasm. Centering on the crystal inclusion, swarmers swam in a rapid rotational movement both clockwise and anticlockwise. Small subunit (SSU) rDNA sequences obtained for the reproductive swarmer cells from S. punctatum show a monophyletic group together with colonial spumellarians and grouped with S. punctatum from Bermuda in the clade. The morphological features and molecular phylogeny of the reproductive swarmers of S. punctatum show evidence of ancestral traits of radiolarians; acantharians and polycystines have a common ancestry. In addition, SrSO4 inclusion of the swarmer cell may be a form of ballast deposited by the swarmer to allow proper positioning in the water column. We hypothesize that radiolarian-affiliated sequences from SSU rDNA clone libraries of marine picoeukaryotes may be derived from the picoplanktonic cells of radiolarians; i.e., small flagellated life stages such as reproductive swarmers or gametes.},
}
@article {pmid24458826,
year = {2014},
author = {Shangguan, L and Wang, X and Leng, X and Liu, D and Ren, G and Tao, R and Zhang, C and Fang, J},
title = {Identification and bioinformatic analysis of signal responsive/calmodulin-binding transcription activators gene models in Vitis vinifera.},
journal = {Molecular biology reports},
volume = {41},
number = {5},
pages = {2937-2949},
pmid = {24458826},
issn = {1573-4978},
mesh = {Chromosome Mapping ; *Computational Biology/methods ; Databases, Nucleic Acid ; Gene Expression Profiling ; Intracellular Space/metabolism ; Models, Molecular ; Multigene Family ; Organ Specificity/genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Conformation ; Protein Transport ; Transcription Factors/chemistry/*genetics/metabolism ; Vitis/classification/*genetics/metabolism ; },
abstract = {In this study, 10 grapevine (Vitis vinifera) SR/CAMTA (Signal Responsive/Calmodulin-binding Transcription Activators) gene models were identified from three grapevine genome protein datasets. They belong to four gene groups: VvCAMTA1, VvCAMTA3, VvCAMTA4 and VvCAMTA5, which were located on chromosome 5, 7_random, 1 and 5, respectively. Alternative splicing could explain the multiple gene models in one gene group. Subcellular localization using the WoLF tool showed that most of the VvCAMTAs were located in the nucleus, except for VvCAMTA3.1, VvCAMTA3.2 and VvCAMTA5.2, which were located in the chloroplast, chloroplast and cytosol, respectively. Subcellular localization using TargetP showed that most of the VvCAMTAs were not located in the chloroplast, mitochondrion and secretory pathway in cells. VvCAMTA1.1 and VvCAMTA1.2 were located in the mitochondria. The digital gene expression profile showed that VvCAMTAs play important roles in Ca2+ signal transduction. The gene expression patterns of VvCAMTAs were different; for example, VvCAMTA1 was expressed mainly in the bud, while VvCAMTA3 was expressed mainly in fruit and inflorescence, with low expression in the bud. The results of this study make a substantial contribution to our knowledge concerning genes, genome annotation, and cell signal transduction in grapevine.},
}
@article {pmid24460157,
year = {2015},
author = {Chen, MY and Chaw, SM and Wang, JF and Villanueva, RJ and Nuñeza, OM and Lin, CP},
title = {Mitochondrial genome of a flashwing demoiselle, Vestalis melania from the Philippine Archipelago.},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {720-721},
doi = {10.3109/19401736.2013.845757},
pmid = {24460157},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Odonata/*genetics ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {This study determined the first complete mitochondrial genome of a demoiselle, Vestalis melania (Odonata, Zygoptera, Calopterygidae) using long-range PCR and a primer walking approach. This mitogenome is 16,685 bp long and contains the entire set of 37 genes and an A + T-rich control region typically found in insects. Presently, this mitogenome is the largest mitogenome of all available odonates, mainly because of its long A + T-rich region (2036 bp). The gene arrangement of the V. melania mitogenome is identical to that of other known odonates. The inter-genic spacer s5 shared by the Anisoptera is absent in V. melania, which supports the view that the absence of the s5 spacer is a synapomorphy of the Zygoptera.},
}
@article {pmid24460159,
year = {2015},
author = {Wu, X and Xie, Z and Yang, L and Yang, H and Yue, L and Hou, L and Zhang, Y and Shu, H},
title = {The complete mitochondrial genome of the duskytail grouper Epinephelus bleekeri (Serranidae: Epinephelinae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {722-723},
doi = {10.3109/19401736.2013.845758},
pmid = {24460159},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Bass/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genome of Epinephelus bleekeri was first presented in this study. It is 17,227 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The overall base composition of the H-strand is 26.32% A, 28.65% T, 28.72% G and 16.31% C. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. In particular, gene duplication is found on the tRNA-Asp gene, and five tandem repeat of this gene in E. bleekeri is different from most other vertebrates. The control region is rich in A + T (67.12%) and poor in G (14.00%), and tandem repeat sequences are observed in this non-coding region, indicating a useful marker for population genetic studies.},
}
@article {pmid24460168,
year = {2015},
author = {Chen, IS and Liao, CR and Shao, YT},
title = {The complete mitochondrial genome of Hainanese barbel steed Hemibarbus medius Yue (Teleostei: Cyprinidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {736-738},
doi = {10.3109/19401736.2013.845765},
pmid = {24460168},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {In this study, the complete mitogenome sequence of cyprinid fish, Hainanese barbel steed, Hemibarbus medius Yue (Teleostei: Cyprinidae) has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,614 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region (CR). CR of 933 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of Hemibarbus medius is 29.8% for A, 27.2% for C, 25.9% for T and 17.1% for G, with a slight AT bias of 55.7%. The complete mitogenome may provide rather essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.},
}
@article {pmid24460170,
year = {2015},
author = {Chen, X and Peng, Z and Cai, L and Xu, Y},
title = {Mitochondrial genome of the spot-tail shark Carcharhinus sorrah (Carcharhiniformes: Carcharhinidae).},
journal = {Mitochondrial DNA},
volume = {26},
number = {5},
pages = {734-735},
doi = {10.3109/19401736.2013.845764},
pmid = {24460170},
issn = {1940-1744},
mesh = {Animals ; Base Composition ; Endangered Species ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sharks/*genetics ; },
abstract = {In this article, we first presented the complete mitogenome of the spot-tail shark Carcharhinus sorrah, which is a medium-sized shark distributed in the tropical Indo-Pacific and is currently listed as "Near Threatened" on the International Union for Conservation of Nature (IUCN) Red List. The complete mitogenome of C. sorrah is 16,707 bp in length and contains typical 37 genes and one control region. The overall base composition is 31.4% A, 25.8% C, 13.2% G and 29.6% T. The control region is 1066 bp in length with the highest A + T content (66.8%) and lowest G content (13.2%).},
}
@article {pmid24465810,
year = {2014},
author = {Shamblin, BM and Bolten, AB and Abreu-Grobois, FA and Bjorndal, KA and Cardona, L and Carreras, C and Clusa, M and Monzón-Argüello, C and Nairn, CJ and Nielsen, JT and Nel, R and Soares, LS and Stewart, KR and Vilaça, ST and Türkozan, O and Yilmaz, C and Dutton, PH},
title = {Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.},
journal = {PloS one},
volume = {9},
number = {1},
pages = {e85956},
pmid = {24465810},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Indian Ocean ; Mediterranean Sea ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Turtles/*genetics ; },
abstract = {Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.},
}
@article {pmid24467909,
year = {2014},
author = {Poirier, P and Meloni, D and Nourrisson, C and Wawrzyniak, I and Viscogliosi, E and Livrelli, V and Delbac, F},
title = {Molecular subtyping of Blastocystis spp. using a new rDNA marker from the mitochondria-like organelle genome.},
journal = {Parasitology},
volume = {141},
number = {5},
pages = {670-681},
doi = {10.1017/S0031182013001996},
pmid = {24467909},
issn = {1469-8161},
mesh = {Animals ; Base Sequence ; Blastocystis/*classification/genetics/isolation &amp; purification ; Blastocystis Infections/*parasitology ; Coinfection ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genetic Markers/genetics ; Genome, Protozoan/*genetics ; Genotype ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Molecular Typing ; Organelles/genetics ; Phylogeny ; *Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Blastocystis spp. are common anaerobic intestinal protozoa found in both human and animals. They are characterized by a high genetic diversity with at least 17 subtypes (STs) that have been described on the basis of a 600 bp 'barcoding region' from the 18S rDNA gene. However, analysis of the recently sequenced genome of a Blastocystis ST7 isolate (strain B) revealed the presence of multiple variable copies of the 18S rDNA gene, with 17 completely assembled copies. Comparison of the barcoding region from these 17 copies allowed us to classify the 18S rDNA sequences into 6 clusters, each cluster containing identical sequences. Surprisingly, 4 of these clusters had the highest homology with 18S rDNA sequences from 2 other Blastocystis ST7 isolates referred as QQ98-4 and H. These results suggest that the 18S rDNA gene is not the marker of choice to discriminate between strains within STs. In the present study, we identified a single-copy subtyping rDNA marker in the genome of the mitochondria-like organelles (MLOs). Using a partial sequence of the MLO rDNA, we successfully subtyped 66 isolates from both human and animals belonging to Blastocystis ST1 to ST10. Our results also indicate that this mitochondrial marker could be useful to detect co-infections by different isolates of a same ST.},
}
@article {pmid24508098,
year = {2014},
author = {Guha, TK and Hausner, G},
title = {A homing endonuclease with a switch: characterization of a twintron encoded homing endonuclease.},
journal = {Fungal genetics and biology : FG &amp; B},
volume = {65},
number = {},
pages = {57-68},
doi = {10.1016/j.fgb.2014.01.004},
pmid = {24508098},
issn = {1096-0937},
mesh = {Chaetomium/*genetics/metabolism ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Endonucleases/*genetics/metabolism ; Genes, Fungal ; Introns ; Open Reading Frames ; Phylogeny ; RNA Splicing ; Ribosome Subunits, Small/*genetics ; },
abstract = {The small ribosomal subunit gene residing in the mitochondrial DNA of the thermophilic fungus Chaetomium thermophilum var. thermophilum La Touche DSM 1495 is interrupted by a twintron at position mS1247. The mS1247 twintron represents the first mixed twintron found in fungal mtDNA, composed of an external group I intron encoding a LAGLIDADG open reading frame that is interrupted by an internal group II intron. Splicing of the internal group II intron reconstitutes the open reading frame and thus facilitates the expression of the encoded homing endonuclease. The cleavage assays suggest that the twintron encodes an active homing endonuclease that could potentially mobilize the twintron to rns genes that have not yet been invaded by this mobile composite element.},
}
@article {pmid24515269,
year = {2014},
author = {Wu, B and Hao, W},
title = {Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.},
journal = {G3 (Bethesda, Md.)},
volume = {4},
number = {4},
pages = {605-612},
pmid = {24515269},
issn = {2160-1836},
mesh = {Deoxyribonucleases, Type II Site-Specific/genetics ; Exons ; Gene Conversion/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Mitochondrial ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Saccharomyces/classification/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Analysis, DNA ; },
abstract = {Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.},
}
@article {pmid24516391,
year = {2014},
author = {Itsara, LS and Kennedy, SR and Fox, EJ and Yu, S and Hewitt, JJ and Sanchez-Contreras, M and Cardozo-Pelaez, F and Pallanck, LJ},
title = {Oxidative stress is not a major contributor to somatic mitochondrial DNA mutations.},
journal = {PLoS genetics},
volume = {10},
number = {2},
pages = {e1003974},
pmid = {24516391},
issn = {1553-7404},
support = {F31 NS071857/NS/NINDS NIH HHS/United States ; R01 GM104990/GM/NIGMS NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; R01 GM086394/GM/NIGMS NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; },
mesh = {Aging/*genetics/pathology ; Animals ; DNA Glycosylases/genetics ; DNA Repair/genetics ; DNA, Mitochondrial/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster ; Humans ; Mitochondria/genetics/pathology ; Models, Animal ; Mutation/*genetics ; Mutation Rate ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Superoxide Dismutase/genetics ; Superoxide Dismutase 2 ; },
abstract = {The accumulation of somatic mitochondrial DNA (mtDNA) mutations is implicated in aging and common diseases of the elderly, including cancer and neurodegenerative disease. However, the mechanisms that influence the frequency of somatic mtDNA mutations are poorly understood. To develop a simple invertebrate model system to address this matter, we used the Random Mutation Capture (RMC) assay to characterize the age-dependent frequency and distribution of mtDNA mutations in the fruit fly Drosophila melanogaster. Because oxidative stress is a major suspect in the age-dependent accumulation of somatic mtDNA mutations, we also used the RMC assay to explore the influence of oxidative stress on the somatic mtDNA mutation frequency. We found that many of the features associated with mtDNA mutations in vertebrates are conserved in Drosophila, including a comparable somatic mtDNA mutation frequency (∼10(-5)), an increased frequency of mtDNA mutations with age, and a prevalence of transition mutations. Only a small fraction of the mtDNA mutations detected in young or old animals were G∶C to T∶A transversions, a signature of oxidative damage, and loss-of-function mutations in the mitochondrial superoxide dismutase, Sod2, had no detectable influence on the somatic mtDNA mutation frequency. Moreover, a loss-of-function mutation in Ogg1, which encodes a DNA repair enzyme that removes oxidatively damaged deoxyguanosine residues (8-hydroxy-2'-deoxyguanosine), did not significantly influence the somatic mtDNA mutation frequency of Sod2 mutants. Together, these findings indicate that oxidative stress is not a major cause of somatic mtDNA mutations. Our data instead suggests that somatic mtDNA mutations arise primarily from errors that occur during mtDNA replication. Further studies using Drosophila should aid in the identification of factors that influence the frequency of somatic mtDNA mutations.},
}
@article {pmid24532299,
year = {2014},
author = {Kitahara, R and Ikeda, Y and Shimura, H and Masuta, C and Ezawa, T},
title = {A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi.},
journal = {Archives of virology},
volume = {159},
number = {8},
pages = {2157-2160},
doi = {10.1007/s00705-014-1999-1},
pmid = {24532299},
issn = {1432-8798},
mesh = {Amino Acid Sequence ; Base Sequence ; Genome, Viral ; Glomeromycota/*virology ; Molecular Sequence Data ; Mycorrhizae/*virology ; Open Reading Frames ; Phylogeny ; RNA Viruses/chemistry/*classification/genetics/*isolation &amp; purification ; Sequence Alignment ; Viral Proteins/chemistry/genetics ; },
abstract = {Arbuscular mycorrhizal (AM) fungi that belong to the phylum Glomeromycota associate with most land plants and supply mineral nutrients to the host plants. One of the four viral segments found by deep-sequencing of dsRNA in the AM fungus Rhizophagus clarus strain RF1 showed similarity to mitoviruses and is characterized in this report. The genome segment is 2,895 nucleotides in length, and the largest ORF was predicted by applying either the mold mitochondrial or the universal genetic code. The ORF encodes a polypeptide of 820 amino acids with a molecular mass of 91.2 kDa and conserves the domain of the mitovirus RdRp superfamily. Accordingly, the dsRNA was designated as R. clarus mitovirus 1 strain RF1 (RcMV1-RF1). Mitoviruses are localized exclusively in mitochondria and thus generally employ the mold mitochondrial genetic code. The distinct codon usage of RcMV1-RF1, however, suggests that the virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. RcMV1-RF1 RdRp showed the highest similarity to the putative RdRp of a mitovirus-like ssRNA found in another AM fungus, followed by RdRp of a mitovirus in an ascomycotan ectomycorrhizal fungus. The three mitoviruses found in the three mycorrhizal fungi formed a deeply branching clade that is distinct from the two major clades in the genus Mitovirus.},
}
@article {pmid24535861,
year = {2014},
author = {Wang, YB and Guan, LL and Xu, YW and Shen, H and Wu, W},
title = {Cloning and sequence analysis of the safflower betaine aldehyde dehydrogenase gene.},
journal = {Genetics and molecular research : GMR},
volume = {13},
number = {1},
pages = {344-353},
doi = {10.4238/2014.January.21.2},
pmid = {24535861},
issn = {1676-5680},
mesh = {Amino Acid Sequence ; Base Sequence ; Betaine-Aldehyde Dehydrogenase/chemistry/*genetics/metabolism ; Carthamus tinctorius/chemistry/*enzymology/genetics ; Cloning, Molecular ; *Genes, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Structure, Tertiary ; Protein Transport ; },
abstract = {In response to salinity or drought stress, many plants accumulate glycine betaine, which is a regulator of osmosis. In plants, the last step in betaine synthesis is catalyzed by betaine aldehyde dehydrogenase (BADH), a nuclear-encoded chloroplastic enzyme. Based on the conserved oligo amino acid residues of the published BADH genes from other higher plant species, a cDNA sequence, designated CtBADH, was isolated from safflower (Carthamus tinctorius L.) using a polymerase chain reaction approach. The clones were 1.7 kb on average, and contained an open reading frame predicting a polypeptide of 503 amino acids with 84.5% identity to that of Helianthus annuus. The deduced amino acid sequence showed a decapeptide, Val-Thr-Leu-Geu-Leu-Gly-Gly-Lys-Ser-Pro and Cys, which is essential for proper functioning of BADH. Phylogenetic analysis indicated that CtBADH grouped with other dicotyledonous plant BADH genes, and subgrouped in the composite family. Prediction of secondary structure and subcellular localization suggested that the protein encoded by CtBADH contains 33 coils, 15 alpha helixes, and 21 beta strands, and most likely targets the chloroplast or mitochondria.},
}
@article {pmid24561571,
year = {2014},
author = {Perez, E and Lapaille, M and Degand, H and Cilibrasi, L and Villavicencio-Queijeiro, A and Morsomme, P and González-Halphen, D and Field, MC and Remacle, C and Baurain, D and Cardol, P},
title = {The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae.},
journal = {Mitochondrion},
volume = {19 Pt B},
number = {},
pages = {338-349},
doi = {10.1016/j.mito.2014.02.001},
pmid = {24561571},
issn = {1872-8278},
mesh = {Computational Biology ; *Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Euglena gracilis/*enzymology/*genetics ; Mitochondria/*enzymology/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; Trypanosomatina/*enzymology/*genetics ; },
abstract = {The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologues to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native- and SDS-PAGE both to confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa.},
}
@article {pmid24563201,
year = {2014},
author = {Li, F and Chung, T and Vierstra, RD},
title = {AUTOPHAGY-RELATED11 plays a critical role in general autophagy- and senescence-induced mitophagy in Arabidopsis.},
journal = {The Plant cell},
volume = {26},
number = {2},
pages = {788-807},
pmid = {24563201},
issn = {1532-298X},
mesh = {Amino Acid Sequence ; Arabidopsis/*cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; *Autophagy/genetics ; Autophagy-Related Proteins ; *Cellular Senescence/genetics ; Darkness ; Gene Expression Regulation, Plant ; Genes, Plant ; Genotype ; *Mitophagy/genetics ; Models, Biological ; Molecular Sequence Data ; Phenotype ; Phosphorylation ; Phylogeny ; Plant Leaves/cytology/growth &amp; development/metabolism ; Protein Binding ; Protein Subunits/metabolism ; Reverse Genetics ; Vacuoles/metabolism ; Vesicular Transport Proteins/chemistry/*metabolism ; },
abstract = {Autophagy-mediated turnover removes damaged organelles and unwanted cytoplasmic constituents and thus plays critical roles in cellular housekeeping and nutrient recycling. This "self eating" is tightly regulated by the AUTOPHAGY-RELATED1/13 (ATG1/13) kinase complex, which connects metabolic and environmental cues to the vacuolar delivery of autophagic vesicles. Here, we describe the Arabidopsis thaliana accessory proteins ATG11 and ATG101, which help link the ATG1/13 complex to autophagic membranes. ATG11 promotes vesicle delivery to the vacuole but is not essential for synthesizing the ATG12-ATG5 and ATG8-phosphatidylethanolamine adducts that are central to autophagic vesicle assembly. ATG11, ATG101, ATG1, and ATG13 colocalize with each other and with ATG8, with ATG1 tethered to ATG8 via a canonical ATG8-interacting motif. Also, the presence of ATG11 encourages starvation-induced phosphorylation of ATG1 and turnover of ATG1 and ATG13. Like other atg mutants, ATG11-deficient plants senesce prematurely and are hypersensitive to nitrogen and fixed-carbon limitations. Additionally, we discovered that the senescence-induced breakdown of mitochondria-resident proteins and mitochondrial vesicles occurs via an autophagic process requiring ATG11 and other ATG components. Together, our data indicate that ATG11 (and possibly ATG101) provides important scaffolds connecting the ATG1/13 complex to both general autophagy and selective mitophagy.},
}
@article {pmid24594978,
year = {2014},
author = {Reddy, PS and Kavi Kishor, PB and Seiler, C and Kuhlmann, M and Eschen-Lippold, L and Lee, J and Reddy, MK and Sreenivasulu, N},
title = {Unraveling regulation of the small heat shock proteins by the heat shock factor HvHsfB2c in barley: its implications in drought stress response and seed development.},
journal = {PloS one},
volume = {9},
number = {3},
pages = {e89125},
pmid = {24594978},
issn = {1932-6203},
mesh = {Computer Simulation ; DNA-Binding Proteins/metabolism ; *Droughts ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Heat Shock Transcription Factors ; Heat-Shock Proteins, Small/*genetics/metabolism ; Heat-Shock Response/genetics ; Hordeum/*genetics/growth &amp; development/metabolism ; Hot Temperature ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Development/genetics ; Plant Proteins/chemistry/genetics/*metabolism ; Promoter Regions, Genetic ; Protein Interaction Maps/genetics ; Seeds/*growth &amp; development/physiology ; *Stress, Physiological ; Structural Homology, Protein ; Transcription Factors/metabolism ; Transcription, Genetic ; },
abstract = {The rapid increase in heat shock proteins upon exposure to damaging stresses and during plant development related to desiccation events reveal their dual importance in plant development and stress tolerance. Genome-wide sequence survey identified 20 non-redundant small heat shock proteins (sHsp) and 22 heat shock factor (Hsf) genes in barley. While all three major classes (A, B, C) of Hsfs are localized in nucleus, the 20 sHsp gene family members are localized in different cell organelles like cytoplasm, mitochondria, plastid and peroxisomes. Hsf and sHsp members are differentially regulated during drought and at different seed developmental stages suggesting the importance of chaperone role under drought as well as seed development. In silico cis-regulatory motif analysis of Hsf promoters showed an enrichment with abscisic acid responsive cis-elements (ABRE), implying regulatory role of ABA in mediating transcriptional response of HvsHsf genes. Gene regulatory network analysis identified HvHsfB2c as potential central regulator of the seed-specific expression of several HvsHsps including 17.5CI sHsp. These results indicate that HvHsfB2c is co-expressed in the central hub of small Hsps and therefore it may be regulating the expression of several HvsHsp subclasses HvHsp16.88-CI, HvHsp17.5-CI and HvHsp17.7-CI. The in vivo relevance of binding specificity of HvHsfB2C transcription factor to HSE-element present in the promoter of HvSHP17.5-CI under heat stress exposure is confirmed by gel shift and LUC-reporter assays. Further, we isolated 477 bp cDNA from barley encoding a 17.5 sHsp polypeptide, which was predominantly upregulated under drought stress treatments and also preferentially expressed in developing seeds. Recombinant HvsHsp17.5-CI protein was expressed in E. coli and purified to homogeneity, which displayed in vitro chaperone activity. The predicted structural model of HvsHsp-17.5-CI protein suggests that the α-crystallin domain is evolutionarily highly conserved.},
}
@article {pmid24601779,
year = {2014},
author = {Yamada, M and Ishibashi, R and Toyoda, K and Kawamura, K and Komaru, A},
title = {Phylogeography of the brackish water clam Corbicula japonica around the Japanese archipelago inferred from mitochondrial COII gene sequences.},
journal = {Zoological science},
volume = {31},
number = {3},
pages = {168-179},
doi = {10.2108/zsj.31.168},
pmid = {24601779},
issn = {0289-0003},
mesh = {Animals ; Bivalvia/*genetics/*physiology ; Demography ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Japan ; Mitochondria/*enzymology ; Pacific Ocean ; Phylogeny ; Phylogeography ; },
abstract = {We investigated the phylogeography of the Asian brackish water clam, Corbicula japonica, to clarify its demographic history using partial mitochondrial COII gene sequences (990 bp) from 283 individuals collected from around the Japanese archipelago and adjacent areas. Phylogenetic analyses revealed the presence of two major groups within our samples: monophyletic Group I comprising Lineages A-E of C. japonica and paraphyletic Group II consisting of Corbicula sp. Lineages A-C were distributed in Japan and Sakhalin Island, and Lineages D, E, and Corbicula sp. were distributed in the Korean Peninsula. Nested clade analysis (NCA) revealed that Lineage A-the dominant lineage in Japan-consisted of Pacific and Japan Sea lineages, the latter comprising southern and northern Japan Sea groups. Genetic diversity indices of the southern group were higher than those of the northern group, suggesting historical range expansion in the Sea of Japan from southwest to northeast. Geographical distribution of these genetic groups appears to have been influenced by major ocean currents around the Japanese archipelago. Dominant haplotypes in the star-shaped haplotype network of Lineage A were distributed throughout the entire distribution range of each genetic group, implying rapid range expansion of this species. The results of mismatch distribution analysis and molecular clock estimation suggest that expansion of lineage A occurred during the late Middle or Late Pleistocene. In contrast, restricted or past gene flow suggested by NCA and the many unique haplotypes (110/123; 89.4%) present in Lineage A suggest that gene flow among extant populations is rather limited.},
}
@article {pmid24617472,
year = {2016},
author = {Yu, Y and Yi, W and Ma, Z and Yang, R and Shen, J},
title = {The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {284-285},
doi = {10.3109/19401736.2014.892079},
pmid = {24617472},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Cyprinidae/*genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; },
abstract = {The complete mitochondrial DNA (mtDNA) sequence of Rhodeus fangi is 16,733 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes and 2 non-coding regions. Base composition of the genome is A (28.54%), G (17.67%), C (27.03%) and T (26.76%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes. The complete mitogenome of the R. fangi can provide a basic data for phylogenetic relationship study and useful information for taxonomic identification of the R. smithii complex in genus Rhodeus.},
}
@article {pmid24617491,
year = {2016},
author = {Zhang, L and Jiang, J and Dong, Y and Qiu, J},
title = {Complete mitochondrial genome of a Pheretimoid earthworm Metaphire vulgaris (Oligochaeta: Megascolecidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {297-298},
doi = {10.3109/19401736.2014.892085},
pmid = {24617491},
issn = {2470-1408},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Oligochaeta/*genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {We have determined the mitochondrial genome of the first Pheretimoid earthworm, Metaphire vulgaris (Chen, 1930). This mitogenome is 15,061 bp in length containing 37 genes typical of other annelid. All genes are encoded by the same strand, ATP8 is not adjacent to ATP6, all 13 PCGs use ATG as a start codon. These features are consistent with first determined earthworm Lumbricus terrestris, but unusual among animal mtDNAs.},
}
@article {pmid24621222,
year = {2016},
author = {Li, M and Chen, Z and Chen, T and Xiong, D and Fan, J and Liang, P},
title = {Whole mitogenome of the Japanese scad Decapterus maruadsi (Perciformes: Carangidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {306-307},
doi = {10.3109/19401736.2014.892089},
pmid = {24621222},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; },
abstract = {The Japanese scad (Decapterus maruadsi) is one of the most commercially important fish species that is popularly harvested in tropical and temperate seas in South East Asian countries. In the present study, we obtained the whole mitochondrial genome sequence of D. maruadsi by overlapped polymerase chain reactions. The entire sequence was 16,541 bp in length, with a gene content (13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions: the control region and the light strand replication origin) and organization similar to most of the other vertebrates. Overall base composition of the genome was 27.5% of A, 30.2% of C, 25.5% of T and 16.8% of G, showing an obvious anti G bias commonly observed in teleosts. The sequence data of D. maruadsi could provide useful information for the studies on conservation genetics and molecular phylogenetics.},
}
@article {pmid24634485,
year = {2014},
author = {Sakamoto, W and Takami, T},
title = {Nucleases in higher plants and their possible involvement in DNA degradation during leaf senescence.},
journal = {Journal of experimental botany},
volume = {65},
number = {14},
pages = {3835-3843},
doi = {10.1093/jxb/eru091},
pmid = {24634485},
issn = {1460-2431},
mesh = {*DNA Fragmentation ; Deoxyribonucleases/*metabolism ; Phylogeny ; Plant Leaves/*metabolism ; Plants/*enzymology ; Subcellular Fractions/metabolism ; },
abstract = {During leaf senescence, macromolecules such as proteins and lipids are known to be degraded for redistribution into upper tissues. Similarly, nucleic acids appear to undergo fragmentation or degradation during senescence, but the physiological role of nucleic acid degradation, particularly of genomic DNA degradation, remains unclear. To date, more than a dozen of plant deoxyribonucleases have been reported, whereas it remains to be verified whether any of them degrade DNA during leaf senescence. This review summarizes current knowledge related to the plant nucleases that are induced developmentally or in a tissue-specific manner and are known to degrade DNA biochemically. Of these, several endonucleases (BFN1, CAN1, and CAN2) and an exonuclease (DPD1) in Arabidopsis seem to act in leaf senescence because they were shown to be inducible at the transcript level. This review specifically examines DPD1, which is dual-targeted to chloroplasts and mitochondria. Results show that, among the exonuclease family to which DPD1 belongs, DPD1 expression is extraordinary when estimated using a microarray database. DPD1 is the only example among the nucleases in which DNA degradation has been confirmed in vivo in pollen by mutant analysis. These data imply a significant role of organelle DNA degradation during leaf senescence and implicate DPD1 as a potential target for deciphering nucleotide salvage in plants.},
}
@article {pmid24711422,
year = {2014},
author = {Lang, BF and Jakubkova, M and Hegedusova, E and Daoud, R and Forget, L and Brejova, B and Vinar, T and Kosa, P and Fricova, D and Nebohacova, M and Griac, P and Tomaska, L and Burger, G and Nosek, J},
title = {Massive programmed translational jumping in mitochondria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {111},
number = {16},
pages = {5926-5931},
pmid = {24711422},
issn = {1091-6490},
support = {MOP-79309//Canadian Institutes of Health Research/Canada ; },
mesh = {Carbon/pharmacology ; DNA, Mitochondrial/metabolism ; Fermentation/drug effects/genetics ; Genes, Fungal/genetics ; Genes, Mitochondrial/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Open Reading Frames/genetics ; Phylogeny ; Protein Biosynthesis/*genetics ; RNA Processing, Post-Transcriptional/drug effects/genetics ; RNA, Messenger/genetics/metabolism ; Yeasts/drug effects/*genetics/growth &amp; development ; },
abstract = {Programmed translational bypassing is a process whereby ribosomes "ignore" a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational blockage at a "takeoff codon" immediately upstream of a stop codon followed by a hairpin, which causes peptidyl-tRNA dissociation and reassociation with a matching "landing triplet" 50 nt downstream, where translation resumes. Here, we report 81 translational bypassing elements (byps) in mitochondria of the yeast Magnusiomyces capitatus and demonstrate in three cases, by transcript analysis and proteomics, that byps are retained in mitochondrial mRNAs but not translated. Although mitochondrial byps resemble the bypass sequence in the T4 gene 60, they utilize unused codons instead of stops for translational blockage and have relaxed matching rules for takeoff/landing sites. We detected byp-like sequences also in mtDNAs of several Saccharomycetales, indicating that byps are mobile genetic elements. These byp-like sequences lack bypassing activity and are tolerated when inserted in-frame in variable protein regions. We hypothesize that byp-like elements have the potential to contribute to evolutionary diversification of proteins by adding new domains that allow exploration of new structures and functions.},
}
@article {pmid24726960,
year = {2014},
author = {Hu, L and Zhao, YE and Cheng, J and Ma, JX},
title = {Molecular identification of four phenotypes of human Demodex in China.},
journal = {Experimental parasitology},
volume = {142},
number = {},
pages = {38-42},
doi = {10.1016/j.exppara.2014.04.003},
pmid = {24726960},
issn = {1090-2449},
mesh = {Animals ; China ; Electron Transport Complex IV/genetics ; Humans ; Mites/anatomy &amp; histology/*classification/genetics ; Mitochondria/enzymology ; Phenotype ; Phylogeny ; },
abstract = {Traditional classification of Demodex mites by hosts and phenotypic characteristics is defective because of environmental influences. In this study, we proposed molecular identification of four phenotypes of two human Demodex species based on mitochondrial cox1 fragments for the first time. Mites collected from sufferers' facial skin were classified into four phenotypes: phenotype A-C with finger-like terminus, and phenotype D with cone-like terminus. The results of molecular data showed that cox1 sequences were all 429 bp. Divergences, genetic distances and transition/transversion ratios among the three phenotypes with finger-like terminus were 0.0-3.0%, 0.000-0.031, and 6/3-5/0, respectively, in line with intraspecific differences. However, those measures between the phenotype with cone-like terminus and phenotypes with finger-like terminus were 19.6-20.5%, 0.256-0.271, and 0.58 (31/53)-0.66 (35/53), respectively, reaching interspecific level. Phylogenetic trees also showed that the three phenotypes with finger-like terminus clustered as one clade, and the phenotype with cone-like terminus formed another one. Therefore, we conclude that mitochondrial cox1 sequence is a good marker for identification of two human Demodex species. Molecular data indicate no subspecies differentiation. Terminus is an effective character for species identification. Mites with finger-like terminus are Demodex folliculorum, and those with cone-like terminus are Demodex brevis.},
}
@article {pmid24766822,
year = {2014},
author = {Hornok, S and Kontschán, J and Kováts, D and Kovács, R and Angyal, D and Görföl, T and Polacsek, Z and Kalmár, Z and Mihalca, AD},
title = {Bat ticks revisited: Ixodes ariadnae sp. nov. and allopatric genotypes of I. vespertilionis in caves of Hungary.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {202},
pmid = {24766822},
issn = {1756-3305},
mesh = {Animals ; Caves ; Chiroptera/*parasitology ; Electron Transport Complex IV/genetics/metabolism ; Female ; *Genotype ; Hungary/epidemiology ; Ixodes/*classification/*genetics ; Larva/classification/genetics ; Male ; Mitochondria/enzymology ; Nymph/classification/genetics ; Phylogeny ; Seasons ; Tick Infestations/epidemiology/parasitology/*veterinary ; },
abstract = {BACKGROUND: In Europe two ixodid bat tick species, Ixodes vespertilionis and I. simplex were hitherto known to occur.<br><br>METHODS: Bat ticks were collected from cave walls and bats in Hungary. Their morphology and genotypes were compared with microscopy and conventional PCR (followed by sequencing), respectively.<br><br>RESULTS: A year-round activity of I. vespertilionis was observed. Molecular analysis of the cytochrome oxidase subunit I (COI) gene of twenty ticks from different caves showed that the occurrence of the most common genotype was associated with the caves close to each other. A few specimens of a morphologically different tick variant were also found and their COI analysis revealed only 86-88% sequence homology with I. simplex and I. vespertilionis, respectively.<br><br>CONCLUSIONS: The microenvironment of caves (well separated from each other) appears to support the existence of allopatric I. vespertilionis COI genotypes, most likely related to the distance between caves and to bat migration over-bridging certain caves. The name I. ariadnae sp. nov. is given to the new tick species described here for the first time.},
}
@article {pmid24779998,
year = {2014},
author = {Zaspel, JM and Scott, CH and Hill, SR and Ignell, R and Kononenko, VS and Weller, SJ},
title = {Geographic distribution, phylogeny, and genetic diversity of the fruit- and blood-feeding moth Calyptra thalictri Borkhausen (Insecta: Lepidoptera: Erebidae).},
journal = {The Journal of parasitology},
volume = {100},
number = {5},
pages = {583-591},
doi = {10.1645/13-484.1},
pmid = {24779998},
issn = {1937-2345},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biomarkers ; Climate ; DNA/chemistry/isolation &amp; purification ; *Genetic Variation ; Genetics, Population ; Geography ; Likelihood Functions ; Male ; Mitochondria/genetics ; Models, Biological ; Moths/classification/genetics/*physiology ; *Phylogeny ; Sequence Alignment ; },
abstract = {Facultative blood feeding on live animals or carrion is widespread within Lepidoptera. Male moths within the genus Calyptra are known to use their fruit-piercing mouthparts to occasionally feed on mammalian blood. The Palearctic species Calyptra thalictri is known to exhibit differential feeding behaviors that appear to be based on geographic location. This species is known to pierce fruit throughout its range but has recently been reported to also feed on human blood under experimental conditions in the Russian Far East. Here we document the distribution of this widespread species, reconstruct its evolutionary history, and calculate its genetic diversity for the first time. Recently collected samples are combined with museum specimens to model suitable environments for this taxon. Our findings suggest that while the blood-feeding populations are not monophyletic, there is geographical structure. Our analysis of macroclimate variables suggests that altitude and precipitation are the environmental variables most critical to habitat suitability in this lineage.},
}
@article {pmid24781019,
year = {2014},
author = {Mohanta, UK and Ichikawa-Seki, M and Shoriki, T and Katakura, K and Itagaki, T},
title = {Characteristics and molecular phylogeny of Fasciola flukes from Bangladesh, determined based on spermatogenesis and nuclear and mitochondrial DNA analyses.},
journal = {Parasitology research},
volume = {113},
number = {7},
pages = {2493-2501},
pmid = {24781019},
issn = {1432-1955},
mesh = {Animals ; Bangladesh ; Buffaloes/parasitology ; Cattle ; Cell Nucleus/chemistry ; DNA, Helminth/*genetics ; DNA, Intergenic/*genetics ; DNA, Mitochondrial/*genetics ; Fasciola hepatica/*classification/genetics ; Goats/parasitology ; Haplotypes ; Host Specificity ; Male ; Mitochondria/chemistry ; NADH Dehydrogenase/genetics ; *Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sheep/parasitology ; Spermatogenesis/*genetics ; },
abstract = {This study aimed to precisely discriminate Fasciola spp. based on DNA sequences of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 1 (nad1) gene. We collected 150 adult flukes from the bile ducts of cattle, buffaloes, sheep, and goats from six different regions of Bangladesh. Spermatogenic status was determined by analyzing stained seminal vesicles. The ITS1 types were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The nad1 haplotypes were identified based on PCR and direct sequencing and analyzed phylogenetically by comparing with nad1 haplotypes of Fasciola spp. from other Asian countries. Of the 127 aspermic flukes, 98 were identified as Fg type in ITS1, whereas 29 were identified as Fh/Fg type, indicating a combination of ITS1 sequences of Fasciola hepatica and Fasciola gigantica. All the 127 aspermic flukes showed Fsp-NDI-Bd11 in nad1 haplotype with nucleotide sequences identical to aspermic Fasciola sp. from Asian countries. Further, 20 spermic flukes were identified as F. gigantica based on their spermatogenic status and Fg type in ITS1. F. gigantica population was thought to be introduced into Bangladesh considerably earlier than the aspermic Fasciola sp. because 11 haplotypes with high haplotype diversity were detected from the F. gigantica population. However, three flukes from Bangladesh could not be precisely identified, because their spermatogenic status, ITS1 types, and nad1 haplotypes were ambiguous. Therefore, developing a robust method to distinguish aspermic Fasciola sp. from other Fasciola species is necessary in the future.},
}
@article {pmid24788869,
year = {2014},
author = {Kwan, JC and Tianero, MD and Donia, MS and Wyche, TP and Bugni, TS and Schmidt, EW},
title = {Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e95850},
pmid = {24788869},
issn = {1932-6203},
support = {R01 GM092009/GM/NIGMS NIH HHS/United States ; GM092009/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria/*metabolism ; Base Sequence ; Biological Products/*chemistry/metabolism ; Electron Transport Complex IV/genetics ; *Host-Pathogen Interactions ; Mitochondria/enzymology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Symbiosis ; Urochordata/*chemistry/genetics/metabolism/*microbiology ; },
abstract = {Natural products (secondary metabolites) found in marine invertebrates are often thought to be produced by resident symbiotic bacteria, and these products appear to play a major role in the symbiotic interaction of bacteria and their hosts. In these animals, there is extensive variation, both in chemistry and in the symbiotic bacteria that produce them. Here, we sought to answer the question of what factors underlie chemical variation in the ocean. As a model, we investigated the colonial tunicate Lissoclinum patella because of its rich and varied chemistry and its broad geographic range. We sequenced mitochondrial cytochrome c oxidase 1 (COXI) genes, and found that animals classified as L. patella fall into three phylogenetic groups that may encompass several cryptic species. The presence of individual natural products followed the phylogenetic relationship of the host animals, even though the compounds are produced by symbiotic bacteria that do not follow host phylogeny. In sum, we show that cryptic populations of animals underlie the observed chemical diversity, suggesting that the host controls selection for particular secondary metabolite pathways. These results imply novel approaches to obtain chemical diversity from the oceans, and also demonstrate that the diversity of marine natural products may be greatly impacted by cryptic local extinctions.},
}
@article {pmid24810173,
year = {2014},
author = {Ataya, FS and Al-Jafari, AA and Daoud, MS and Al-Hazzani, AA and Shehata, AI and Saeed, HM and Fouad, D},
title = {Genomics, phylogeny and in silico analysis of mitochondrial glutathione S-transferase-kappa from the camel Camelus dromedarius.},
journal = {Research in veterinary science},
volume = {97},
number = {1},
pages = {46-54},
doi = {10.1016/j.rvsc.2014.04.004},
pmid = {24810173},
issn = {1532-2661},
mesh = {Amino Acid Sequence ; Animals ; Camelus/*genetics ; Cattle ; Cloning, Molecular ; Computer Simulation ; DNA, Complementary/genetics ; Dogs ; Genomics ; Glutathione Transferase/analysis/*chemistry/*genetics ; Haplorhini ; Horses ; Humans ; Male ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Rats ; Swine ; },
abstract = {The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Peninsula. For most of its life, this species is exposed to both intrinsic and extrinsic genotoxic factors that cause gross DNA alterations in many organisms. GST enzymes constitute an important supergene family involved in protection against the deleterious effects of oxidative stress and xenobiotics. Cloning the camel mitochondrial GST kappa (GSTK) gene and comparing its structural similarities with different species may aid in understanding its evolutionary relics. We cloned the camel GSTK using RT-PCR. This yielded an open reading frame of 678 nucleotides, encoding a protein of 226 amino acid residues. In a comparative analysis, the cloned GSTK was used to screen orthologues from different organisms. Phylogenetic analysis demonstrated that the camel GSTK apparently evolved from an ancestral GSTK gene that predated the appearance of vertebrates, and it grouped with pig, cattle, dog, horse, human and monkey GSTKs. The calculated molecular weight of the translated ORF was 25.52 kDa and the isoelectric point was 8.4. The deduced cGSTK sequence exhibited high identity with many mammals, such as Bactrian camel (99.55%), pig, cattle and human (>74%), and lower identity with other unrelated organisms, such as frog (Xenopus tropicalis, 61%), chicken (Gallus gallus, 57%), salmon (Salmo salar, 49%), sponge (Amphimedon queenslandica, 46%), tick (Amblyomma maculatum, 45%) and roundworm (Caenorhabditis elegans, 33%). A 3D structure was built based on the crystal structure of the human and rat enzymes. The levels of cGSTK expression in five camel tissues were examined via real-time PCR. The highest level of cGSTK transcripts was found in the camel liver, followed by the testis, spleen, kidney and lung.},
}
@article {pmid24816719,
year = {2014},
author = {Dehghan Nayeri, F and Yarizade, K},
title = {Bioinformatics study of delta-12 fatty acid desaturase 2 (FAD2) gene in oilseeds.},
journal = {Molecular biology reports},
volume = {41},
number = {8},
pages = {5077-5087},
pmid = {24816719},
issn = {1573-4978},
mesh = {Amino Acid Sequence ; Computational Biology ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/biosynthesis ; Linoleic Acid/biosynthesis ; Molecular Sequence Data ; Oleic Acid/biosynthesis ; Phylogeny ; Plant Oils/analysis ; Plant Proteins/*genetics/metabolism ; Plants/classification/genetics ; Seeds/chemistry/*genetics ; },
abstract = {Fatty acid desaturases constitute a group of enzymes that introduce double bonds into the hydrocarbon chains of fatty acids to produce unsaturated fatty acids. In plants, seed-specific delta-12 fatty acid desaturase 2 (FAD2) is responsible for the high content of linoleic acid by inserting a double bond at the delta-12 (omega-6) position of oleic acid. In this study, sixteen FAD2 and FAD2-2 protein sequences from oilseeds were analyzed by computational tools including two databases of the NCBI and EXPASY and data management tools such as SignalP, TMHMM, Psort, ProtParam, TargetP, PLACE and PlantCARE. These services were used to predict the protein properties such as molecular mass, pI, signal peptide, transmembrane and conserved domains, secondary and spatial structures. The polypeptide sequences were aligned and a neighbour-joining tree was constructed using MEGA5.1 to elucidate phylogenetic relationships among FAD2 genes. Based on the phylogenetic analysis species with high similarity in FAD2 sequence grouped together. FAD2 proteins include highly conserved histidine-rich motifs (HECGHH, HRRHH and HV[A/C/T]HH) that are located by three to five transmembrane anchors. For further investigations Sesamum indicum FAD2 was selected and analyzed by bioinformatics tools. Analysis showed no N-terminal signal peptide for probable localization of FAD2 protein in cytoplasmic organelles such as chloroplast, mitochondria and Golgi. Instead the C-terminal signaling motif YNNKL, Y(K/N)NKF or YRNKI allows FAD2 protein to selectively bind to and embed in the endoplasmic reticulum. FAD2 promoter contains different cis-regulatory elements involve in the biotic and abiotic stresses response or control of gene expression specifically in seeds.},
}
@article {pmid24819950,
year = {2014},
author = {Wang, W and Scheffler, K and Esbensen, Y and Strand, JM and Stewart, JB and Bjørås, M and Eide, L},
title = {Addressing RNA integrity to determine the impact of mitochondrial DNA mutations on brain mitochondrial function with age.},
journal = {PloS one},
volume = {9},
number = {5},
pages = {e96940},
pmid = {24819950},
issn = {1932-6203},
mesh = {Aging/*genetics ; Animals ; Brain/*cytology/metabolism ; DNA, Mitochondrial/*genetics ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*genetics/*metabolism ; Mutagenesis ; *Mutation ; Mutation Rate ; RNA/*genetics ; RNA, Mitochondrial ; Transcription, Genetic/genetics ; },
abstract = {Mitochondrial DNA (mtDNA) mutations can result in mitochondrial dysfunction, but emerging experimental data question the fundamental role of mtDNA mutagenesis in age-associated mitochondrial impairment. The multicopy nature of mtDNA renders the impact of a given mtDNA mutation unpredictable. In this study, we compared mtDNA stability and mtRNA integrity during normal aging. Seven distinct sites in mouse brain mtDNA and corresponding mtRNA were analyzed. Accumulation of mtDNA mutations during aging was highly site-specific. The variation in mutation frequencies overrode the age-mediated increase by more than 100-fold and aging generally did not influence mtDNA mutagenesis. Errors introduced by mtRNA polymerase were also site-dependent and up to two hundred-fold more frequent than mtDNA mutations, and independent of mtDNA mutation frequency. We therefore conclude that mitochondrial transcription fidelity limits the impact of mtDNA mutations.},
}
@article {pmid24842572,
year = {2014},
author = {Li, CL and Wang, M and Ma, XY and Zhang, W},
title = {NRGA1, a putative mitochondrial pyruvate carrier, mediates ABA regulation of guard cell ion channels and drought stress responses in Arabidopsis.},
journal = {Molecular plant},
volume = {7},
number = {10},
pages = {1508-1521},
doi = {10.1093/mp/ssu061},
pmid = {24842572},
issn = {1752-9867},
mesh = {Abscisic Acid/*pharmacology ; Adaptation, Physiological/drug effects ; Amino Acid Sequence ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Arabidopsis/drug effects/genetics/*physiology ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Movement/drug effects ; *Droughts ; Genetic Complementation Test ; Ion Channel Gating/drug effects ; Membrane Transport Proteins/*metabolism ; Mitochondria/drug effects/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Proteins ; Models, Biological ; Molecular Sequence Data ; Monocarboxylic Acid Transporters ; Mutation/genetics ; Phylogeny ; Plant Stomata/*cytology ; Plants, Genetically Modified ; Potassium Channels/*metabolism ; Protein Transport/drug effects ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; Stress, Physiological/*drug effects ; Subcellular Fractions/drug effects/metabolism ; Transcription, Genetic/drug effects ; },
abstract = {Abscisic acid (ABA) regulates ion channel activity and stomatal movements in response to drought and other stresses. Here, we show that the Arabidopsis thaliana gene NRGA1 is a putative mitochondrial pyruvate carrier which negatively regulates ABA-induced guard cell signaling. NRGA1 transcript was abundant in the A. thaliana leaf and particularly in the guard cells, and its product was directed to the mitochondria. The heterologous co-expression of NRGA1 and AtMPC1 in yeast complemented a loss-of-function mitochondrial pyruvate carrier (MPC) mutant. The nrga1 loss-of-function mutant was very sensitive to the presence of ABA in the context of stomatal movements, and exhibited a heightened tolerance to drought stress. Disruption of NRGA1 gene resulted in increased ABA inhibition of inward K(+) currents and ABA activation of slow anion currents in guard cells. The nrga1/NRGA1 functional complementation lines restored the mutant's phenotypes. Furthermore, transgenic lines of constitutively overexpressing NRGA1 showed opposite stomatal responses, reduced drought tolerance, and ABA sensitivity of guard cell inward K(+) channel inhibition and anion channel activation. Our findings highlight a putative role for the mitochondrial pyruvate carrier in guard cell ABA signaling in response to drought.},
}
@article {pmid24850960,
year = {2014},
author = {Won, S and Park, BK and Kim, BJ and Kim, HW and Kang, JG and Park, TS and Seo, HY and Eun, Y and Kim, KG and Chae, JS},
title = {Molecular Identification of Haemadipsa rjukjuana (Hirudiniformes: Haemadipsidae) in Gageo Island, Korea.},
journal = {The Korean journal of parasitology},
volume = {52},
number = {2},
pages = {169-175},
pmid = {24850960},
issn = {1738-0006},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers/genetics ; Leeches/*classification/*genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Republic of Korea ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {There are 60 species of blood-feeding land leeches, 50 species belonging to the family Haemadipsidae and 10 species belonging to the family Xerobdellidae. Despite recent papers on the land leeches, their taxonomic identification is not fully understood, especially at a species level. In Korea, there have been no historical records of the terrestrial leeches, but recently an unrecorded blood-feeding land leech was discovered at Gageo-do (Island), Korea. Molecular analysis was used to identify the species of 29 leeches collected from Mt. Dock-Sil in Gageo-do. Conventional PCR was conducted using nuclear 18S rRNA and mitochondrial cytochrome c oxidase subunit 1 (CO1) genetic marker. The 18S rRNA sequences revealed that the leeches share 99.9% identity with Haemadipsa rjukjuana (inhabiting Taiwan), and the CO1 sequences revealed that the leeches are very close to H. rjukjuana (inhabiting Taiwan). The CO1 sequences were separated into 2 categories, 1 with 94.6% and the other with 94.3% similarity to the H. rjukjuana L00115A (inhabiting Taiwan). This new finding of the land leech is the first record in Korea. In addition, the north range of the distribution of the blood-feeding leech (Hirudiniformes: Haemadipisidae) should be reconsidered including Korea.},
}
@article {pmid24850965,
year = {2014},
author = {Song, SM and Yang, HW and Jung, MK and Heo, J and Cho, CM and Goo, YK and Hong, Y and Chung, DI},
title = {Two human cases of Diphyllobothrium nihonkaiense infection in Korea.},
journal = {The Korean journal of parasitology},
volume = {52},
number = {2},
pages = {197-199},
pmid = {24850965},
issn = {1738-0006},
mesh = {Adult ; Animals ; Anthelmintics/therapeutic use ; Base Sequence ; DNA, Helminth/*genetics ; Diphyllobothriasis/*diagnosis/drug therapy ; Diphyllobothrium/*genetics ; Electron Transport Complex IV/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/enzymology ; Phylogeny ; Praziquantel/therapeutic use ; Republic of Korea ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {Diphyllobothrium latum and Diphyllobothrium nihonkaiense are the 2 reported main causes of human diphyllobothriasis in the Republic of Korea. However, the differentiation of these 2 species based on morphologic features alone is difficult. The authors used nucleotide sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene to diagnose Diphyllobothrium spp. Two patients visited the emergency room at Kyungpook National University Hospital on 3 April and 12 April 2013, respectively, with fragments of parasites found while defecating. The parasites were identified as Diphyllobothrium spp. based on morphologic characteristics, and subsequent cox1 gene sequencing showed 99.9% similarity (1,478/1,480 bp) with D. nihonkaiense. Our findings support the hypothesis that D. nihonkaiense is a dominant species in Korea.},
}
@article {pmid24850967,
year = {2014},
author = {Zhong, X and Wang, N and Hu, D and Wang, J and Liu, T and Gu, X and Wang, S and Peng, X and Yang, G},
title = {Sequence analysis of cytb gene in Echinococcus granulosus from Western China.},
journal = {The Korean journal of parasitology},
volume = {52},
number = {2},
pages = {205-209},
pmid = {24850967},
issn = {1738-0006},
mesh = {Animals ; Animals, Domestic/parasitology ; Base Composition ; Base Sequence ; Cattle/*parasitology ; China ; Cytochromes b/*genetics ; DNA, Helminth/genetics ; Echinococcosis ; Echinococcus granulosus/classification/*genetics ; Genetic Variation ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*veterinary ; Sequence Alignment ; Sequence Analysis, DNA ; Sheep/*parasitology ; Tibet ; },
abstract = {Echinococcus granulosus is the causative agent of cystic echinococcosis with medical and veterinary importance in China. Our main objective was to discuss the genotypes and genetic diversity of E. granulosus present in domestic animals and humans in western China. A total of 45 hydatid cyst samples were collected from sheep, humans, and a yak and subjected to an analysis of the sequences of mitochondrial cytochrome b (cytb) gene. The amplified PCR product for all samples was a 1,068 bp band. The phylogenetic analysis showed that all 45 samples were identified as E. granulosus (genotype G1). Ten haplotypes were detected among the samples, with the main haplotype being H1. The haplotype diversity was 0.626, while the nucleotide diversity was 0.001. These results suggested that genetic diversity was low among our samples collected from the west of China based on cytb gene analysis. These findings may provide more information on molecular characteristics of E. granulosus from this Chinese region.},
}
@article {pmid24856215,
year = {2014},
author = {Stairs, CW and Eme, L and Brown, MW and Mutsaers, C and Susko, E and Dellaire, G and Soanes, DM and van der Giezen, M and Roger, AJ},
title = {A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.},
journal = {Current biology : CB},
volume = {24},
number = {11},
pages = {1176-1186},
doi = {10.1016/j.cub.2014.04.033},
pmid = {24856215},
issn = {1879-0445},
support = {MOP-82809//Canadian Institutes of Health Research/Canada ; MOP-84260//Canadian Institutes of Health Research/Canada ; },
mesh = {Anaerobiosis ; Eukaryota/*genetics/*metabolism ; Molecular Sequence Data ; Organelles/*metabolism ; Phylogeny ; *Proteome ; Saccharomyces cerevisiae/metabolism ; Sequence Analysis, RNA ; Sulfur/*metabolism ; },
abstract = {BACKGROUND: Many microbial eukaryotes have evolved anaerobic alternatives to mitochondria known as mitochondrion-related organelles (MROs). Yet, only a few of these have been experimentally investigated. Here we report an RNA-seq-based reconstruction of the MRO proteome of Pygsuia biforma, an anaerobic representative of an unexplored deep-branching eukaryotic lineage.<br><br>RESULTS: Pygsuia's MRO has a completely novel suite of functions, defying existing "function-based" organelle classifications. Most notable is the replacement of the mitochondrial iron-sulfur cluster machinery by an archaeal sulfur mobilization (SUF) system acquired via lateral gene transfer (LGT). Using immunolocalization in Pygsuia and heterologous expression in yeast, we show that the SUF system does indeed localize to the MRO. The Pygsuia MRO also possesses a unique assemblage of features, including: cardiolipin, phosphonolipid, amino acid, and fatty acid metabolism; a partial Kreb's cycle; a reduced respiratory chain; and a laterally acquired rhodoquinone (RQ) biosynthesis enzyme. The latter observation suggests that RQ is an electron carrier of a fumarate reductase-type complex II in this MRO.<br><br>CONCLUSIONS: The unique functional profile of this MRO underscores the tremendous plasticity of mitochondrial function within eukaryotes and showcases the role of LGT in forging metabolic mosaics of ancestral and newly acquired organellar pathways.},
}
@article {pmid24859646,
year = {2014},
author = {Yu, X and Wu, L and Xie, L and Yang, S and Charkraborty, T and Shi, H and Wang, D and Zhou, L},
title = {Characterization of two paralogous StAR genes in a teleost, Nile tilapia (Oreochromis niloticus).},
journal = {Molecular and cellular endocrinology},
volume = {392},
number = {1-2},
pages = {152-162},
doi = {10.1016/j.mce.2014.05.013},
pmid = {24859646},
issn = {1872-8057},
mesh = {Amino Acid Sequence ; Animals ; Chorionic Gonadotropin/administration &amp; dosage/pharmacology ; Cichlids/*genetics ; Female ; Gene Expression Profiling ; Humans ; Immunohistochemistry ; Injections ; Male ; Molecular Sequence Data ; Phosphoproteins/chemistry/*genetics/metabolism ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; *Sequence Homology, Nucleic Acid ; Synteny/genetics ; Steroidogenic Acute Regulatory Protein ; },
abstract = {Steroidogenic acute regulatory protein (StAR) transports cholesterol, the substrate for steroid synthesis, to the inner membranes of mitochondria. It is well known that estrogen is essential for female sex determination/differentiation in fish. However, no reports showed that the conventional StAR, which was supposed to be essential for estrogen production, was expressed in female gonads during the critical timing of sex determination/differentiation. In this study, two different StAR isoforms, named as StAR1 and StAR2, were characterized from the gonads of Nile tilapia (Oreochromis niloticus). Phylogenetic and synteny analysis revealed that two StAR genes existed in teleosts, Xenopus and chicken indicating that the duplication event occurred before the divergence of teleosts and tetrapods. Real-time PCR revealed that StAR1 was dominantly expressed in the testis, head kidney and kidney; while StAR2 was expressed exclusively in the gonads. In situ hybridization and immunohistochemistry demonstrated that StAR1 was expressed in the interrenal cells of the head kidney and Leydig cells of the testis; while StAR2 was expressed in the Leydig cells of the testis and the interstitial cells of the ovary. Ontogenic analysis demonstrated that StAR2 was expressed abundantly from 5 days after hatching (dah) in the somatic cells in XX gonads, whereas in XY gonads, both StARs could be detected from 30 dah until adulthood. Intraperitoneal injection of human chorionic gonadotropin experiments showed that expression of StAR1 and 2 was significantly elevated at 8h and persisted until 24h after injection in the testis. Taken together, our data suggested that StAR1 is likely to be required for cortisol production in the head kidney, and StAR2 is probably involved in estrogen production during early sex differentiation in XX gonads. In contrast, both StARs might be required for androgen production in testes. For the first time, our data demonstrated that two fish StARs might be involved in steroidogenesis in a tissue and developmental stage dependent manner.},
}
@article {pmid24865908,
year = {2016},
author = {Huo, JH and Wei, QP and Wan, MC and Liu, LX and Hu, LF and Zhou, QY and Xiong, LG and Yang, Q and Wu, YP},
title = {Population phylogenomic analysis and origin of mitochondrial DNA in Chinese domestic pig.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {892-895},
doi = {10.3109/19401736.2014.919492},
pmid = {24865908},
issn = {2470-1408},
mesh = {Animals ; Animals, Domestic/genetics ; Base Sequence ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Sus scrofa/classification/*genetics ; },
abstract = {The genetic diversity of eight domestic pigs was analyzed using a hypervariable fragment in the mitochondrial (mt) DNA control region; a portion of the hypervariable control region (515 bp) was sequenced from 153 samples. Haplotype diversity and nucleotide diversity in Yushan black pig populations were significantly higher than other populations (p < 0.01). A neighbor-joining tree was constructed from domestic pig mtDNA and five wild pigs. The results indicate that there are only small differences among individual pigs from different regions. Networks of the domestic pigs were constructed to better visualize the relationships between sequences. Each core haplotype was surrounded by a star-like pattern, consistent with recent population expansion.},
}
@article {pmid24880237,
year = {2014},
author = {Foitová, I and Civáňová, K and Baruš, V and Nurcahyo, W},
title = {Phylogenetic relationships between pinworms (Nematoda: Enterobiinae) parasitising the critically endangered orang-utan, according to the characterisation of molecular genomic and mitochondrial markers.},
journal = {Parasitology research},
volume = {113},
number = {7},
pages = {2455-2466},
pmid = {24880237},
issn = {1432-1955},
mesh = {Amino Acid Sequence ; Animals ; DNA, Intergenic/genetics ; Electron Transport Complex IV/genetics ; Enterobiasis/parasitology/*veterinary ; Enterobius/*classification/genetics ; Genetic Markers ; Genetic Speciation ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Pongo abelii/*parasitology ; Pongo pygmaeus/*parasitology ; },
abstract = {Pinworms (Nematoda: Enterobiinae) include 52 species parasitising primates throughout the world. In the present study, we performed the first ever molecular analysis to investigate the phylogenetic position of recently described pinworms parasitising the Sumatran orang-utan. The phylogenetic analysis of mitochondrial CO1 and chromosomal 18S rDNA and ITS1 regions could support the independent status of several Nematoda species. Our molecular data clearly suggest that Enterobius (Colobenterobius) buckleyi and Lemuricola (Protenterobius) pongoi together with Pongobius hugoti form separate clades among other studied species, which significantly supports the hypothesis of recently described new species parasitising the orang-utan (Pongo abelii and Pongo pygmaeus). The phylogenetic tree based on cytochrome oxidase 1 (CO1) gene variability showed possible close relationships between L. (Protenterobius) pongoi and P. hugoti; thus, we can assume that these species could have initially diverged in sympatry from a common ancestor.},
}
@article {pmid24891093,
year = {2014},
author = {Shi, Y and Zhao, Z and Hong, X and Chen, K and Zhu, X},
title = {Characterization and functional analysis of voltage-dependent anion channel 1 (VDAC1) from orange-spotted grouper (Epinephelus coioides).},
journal = {Journal of biochemical and molecular toxicology},
volume = {28},
number = {7},
pages = {292-301},
doi = {10.1002/jbt.21565},
pmid = {24891093},
issn = {1099-0461},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Cell Line ; China ; Fishes/*metabolism ; Gene Expression Regulation ; Molecular Sequence Data ; Phylogeny ; Subcellular Fractions/metabolism ; Transfection ; Voltage-Dependent Anion Channel 1/chemistry/genetics/*metabolism ; },
abstract = {The voltage-dependent anion channel (VDAC) is a highly conserved integral protein of mitochondria in different eukaryotic species. It forms a selective channel in the mitochondrial outer membrane that serves as the controlled pathway for small metabolites and ions. In this study, a VDAC gene, EcVDAC1, was isolated from orange-spotted grouper (Epinephelus coioides). The EcVDAC1 exhibits ubiquitous expression in various tissues of orange-spotted grouper and is upregulated in liver, gill, and spleen after stimulation with lipopolysaccharides (LPS). Subcellular localization analysis shows that the EcVDAC1 protein colocalized with the mitochondria. A caspase-3 assay demonstrates that overexpression of the EcVDAC1 induced apoptotic cell death in fathead minnow cells. The data presented in this study provide new information regarding the relationship between LPS and the EcVDAC1 gene, suggesting that the fish VDAC1 gene may play an important role in antibacterial immune response.},
}
@article {pmid24892429,
year = {2014},
author = {Rodrigues, AS and Silva, SE and Marabuto, E and Silva, DN and Wilson, MR and Thompson, V and Yurtsever, S and Halkka, A and Borges, PA and Quartau, JA and Paulo, OS and Seabra, SG},
title = {New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae).},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e98375},
pmid = {24892429},
issn = {1932-6203},
mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Demography ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes/genetics ; Hemiptera/*genetics ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; Population Growth ; Time Factors ; },
abstract = {Philaenus spumarius is a widespread insect species in the Holarctic region. Here, by focusing on the mtDNA gene COI but also using the COII and Cyt b genes and the nuclear gene EF-1α, we tried to explain how and when its current biogeographic pattern evolved by providing time estimates of the main demographic and evolutionary events and investigating its colonization patterns in and out of Eurasia. Evidence of recent divergence and expansion events at less than 0.5 Ma ago indicate that climate fluctuations in the Mid-Late Pleistocene were important in shaping the current phylogeographic pattern of the species. Data support a first split and differentiation of P. spumarius into two main mitochondrial lineages: the "western", in the Mediterranean region and the "eastern", in Anatolia/Caucasus. It also supports a following differentiation of the "western" lineage into two sub-lineages: the "western-Mediterranean", in Iberia and the "eastern-Mediterranean" in the Balkans. The recent pattern seems to result from postglacial range expansion from Iberia and Caucasus/Anatolia, thus not following one of the four common paradigms. Unexpected patterns of recent gene-flow events between Mediterranean peninsulas, a close relationship between Iberia and North Africa, as well as high levels of genetic diversity being maintained in northern Europe were found. The mitochondrial pattern does not exactly match to the nuclear pattern suggesting that the current biogeographic pattern of P. spumarius may be the result of both secondary admixture and incomplete lineage sorting. The hypothesis of recent colonization of North America from both western and northern Europe is corroborated by our data and probably resulted from accidental human translocations. A probable British origin for the populations of the Azores and New Zealand was revealed, however, for the Azores the distribution of populations in high altitude native forests is somewhat puzzling and may imply a natural colonization of the archipelago.},
}
@article {pmid24893877,
year = {2016},
author = {Zhang, D and Wang, L and Guo, H and Ma, Z and Jiang, S},
title = {The complete mitochondrial genome of snubnose pompano Trachinotus blochii (Teleostei, Carangidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {431-432},
doi = {10.3109/19401736.2014.898291},
pmid = {24893877},
issn = {2470-1408},
mesh = {Animals ; Conserved Sequence/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; TATA Box/genetics ; },
abstract = {The complete mitochondrial genome of Trachinotus blochii was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,558 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 29.21% for A, 15.74% for G, 26.49% for T, 28.56% for C, respectively, with a high A + T content (55.70%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The complete mitochondrial genome sequence of T. blochii can provide a basic data for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. blochii resource.},
}
@article {pmid24904012,
year = {2014},
author = {Christensen, AC},
title = {Genes and junk in plant mitochondria-repair mechanisms and selection.},
journal = {Genome biology and evolution},
volume = {6},
number = {6},
pages = {1448-1453},
pmid = {24904012},
issn = {1759-6653},
mesh = {*DNA Repair ; DNA, Plant/*genetics ; Fabaceae/*genetics ; *Genome, Mitochondrial ; Mutation Rate ; Phylogeny ; Selection, Genetic ; },
abstract = {Plant mitochondrial genomes have very low mutation rates. In contrast, they also rearrange and expand frequently. This is easily understood if DNA repair in genes is accomplished by accurate mechanisms, whereas less accurate mechanisms including nonhomologous end joining or break-induced replication are used in nongenes. An important question is how different mechanisms of repair predominate in coding and noncoding DNA, although one possible mechanism is transcription-coupled repair (TCR). This work tests the predictions of TCR and finds no support for it. Examination of the mutation spectra and rates in genes and junk reveals what DNA repair mechanisms are available to plant mitochondria, and what selective forces act on the repair products. A model is proposed that mismatches and other DNA damages are repaired by converting them into double-strand breaks (DSBs). These can then be repaired by any of the DSB repair mechanisms, both accurate and inaccurate. Natural selection will eliminate coding regions repaired by inaccurate mechanisms, accounting for the low mutation rates in genes, whereas mutations, rearrangements, and expansions generated by inaccurate repair in noncoding regions will persist. Support for this model includes the structure of the mitochondrial mutS homolog in plants, which is fused to a double-strand endonuclease. The model proposes that plant mitochondria do not distinguish a damaged or mismatched DNA strand from the undamaged strand, they simply cut both strands and perform homology-based DSB repair. This plant-specific strategy for protecting future generations from mitochondrial DNA damage has the side effect of genome expansions and rearrangements.},
}
@article {pmid24905695,
year = {2014},
author = {Won, EJ and Ra, K and Kim, KT and Lee, JS and Lee, YM},
title = {Three novel superoxide dismutase genes identified in the marine polychaete Perinereis nuntia and their differential responses to single and combined metal exposures.},
journal = {Ecotoxicology and environmental safety},
volume = {107},
number = {},
pages = {36-45},
doi = {10.1016/j.ecoenv.2014.03.026},
pmid = {24905695},
issn = {1090-2414},
mesh = {Amino Acid Sequence ; Animals ; Antioxidants/metabolism ; Base Sequence ; Biomarkers/metabolism ; Ecosystem ; *Environmental Monitoring ; *Heavy Metal Poisoning ; Metals/metabolism ; Metals, Heavy/analysis/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Poisoning/*metabolism ; Polychaeta/enzymology/*genetics ; RNA, Messenger/metabolism ; Superoxide Dismutase/*genetics/metabolism ; Water Pollution, Chemical/*analysis ; },
abstract = {To identify superoxide dismutase (SOD) genes and evaluate their usefulness as potential markers for monitoring metal toxicity in aquatic environment, we cloned, sequenced, and characterized 3 SOD genes (Cu/Zn-SOD1, Cu/Zn-SOD2, and Mn-SOD) from the marine polychaete Perinereis nuntia. The accumulated metal contents and expressions of 3 SOD genes were compared after exposure to single and combinations of heavy metals, As, Ni, and Pb. The deduced amino acid sequences of the 3 SODs had evolutionary conserved domains, such as metal binding sites, and signature sequences. The phylogenetic analysis revealed that Cu/Zn-SOD1, Cu/Zn-SOD2, and Mn-SOD were clustered with extracellular Cu/Zn-SOD, intracellular Cu/Zn-SOD and mitochondrial Mn-SOD, respectively, of other species. The accumulated contents of Ni and Pb increased significantly in a time - dependent manner after exposure to both single and combination of the metals. However, the concentration of As did not change significantly in the exposure test. The quantitative real-time polymerase chain reaction (PCR) array showed that the 3 SOD genes had differential expression patterns depending on the exposure condition. The expression of all SODs mRNAs was significantly elevated in response to Pb alone and in combination with As. The mRNA level of Cu/Zn-SOD1 was the highest after exposure to Pb alone, while that of Mn-SOD was remarkably enhanced after exposure to a combination of As and Pb. Exposure to Ni alone rapidly elevated the expression of Cu/Zn-SOD1 and Mn-SOD mRNA, which then gradually decreased. Exposure to As had no significant effect on the modulation of any of the SOD genes of P. nuntia. These results suggest that all SOD genes might play important roles in cellular protection as antioxidant enzymes against heavy metal toxicity via different modes of action in P. nuntia and might have the potential to act as indicators in an environment containing a mixture of metals.},
}
@article {pmid24918426,
year = {2014},
author = {Buj, I and Sanda, R and Marčić, Z and Caleta, M and Mrakovčić, M},
title = {Combining morphology and genetics in resolving taxonomy--a systematic revision of spined loaches (Genus Cobitis; Cypriniformes, Actinopterygii) in the Adriatic watershed.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e99833},
pmid = {24918426},
issn = {1932-6203},
mesh = {Animals ; Bosnia and Herzegovina ; Cypriniformes/*anatomy &amp; histology/*genetics ; DNA, Mitochondrial/genetics ; Fishes/*anatomy &amp; histology/*genetics ; Mitochondria/genetics ; Phylogeny ; Pigmentation/genetics ; Spine/anatomy &amp; histology ; },
abstract = {Taxonomic investigation of spined loaches from Dalmatia and Herzegovina was conducted on specimens from 14 localities. The results of the detailed morphological investigations were combined with genetic data (based on one mitochondrial and two nuclear genes) in order to resolve the taxonomic status of each Cobitis population. Among the investigated features of external morphology, the appearance of spots on the caudal fin base turned out to have the greatest diagnostic value. Furthermore, the number of branched fin rays enabled the discrimination of several species. No morphometric character alone could ensure determination of any Cobitis species. Nevertheless, groups of populations that are more similar in their body shapes correspond to mitochondrial phylogenetic lineages. Based on molecular genetic markers, Dalmatian and Herzegovinian spined loaches form independent lineages inside the Adriatic phylogenetic group. Mitochondrial DNA phylogenetic reconstruction revealed six monophyletic lineages, corresponding to six species distributed in the investigated area. The population distributed in Mostarsko blato karstic field in Bosnia and Herzegovina is described as a new species based on a unique combination of morphological characters: a single triangular Canestrini scale; usually 51/2 branched anal fin rays, 61/2 branched dorsal fin rays, 14 branched caudal fin rays; no spots in the surface pigmentation layer on the caudal fin base; scales on the body very small.},
}
@article {pmid24927653,
year = {2014},
author = {Polashock, J and Zelzion, E and Fajardo, D and Zalapa, J and Georgi, L and Bhattacharya, D and Vorsa, N},
title = {The American cranberry: first insights into the whole genome of a species adapted to bog habitat.},
journal = {BMC plant biology},
volume = {14},
number = {},
pages = {165},
pmid = {24927653},
issn = {1471-2229},
mesh = {Adaptation, Physiological/*genetics ; DNA Transposable Elements/genetics ; Disease Resistance/genetics ; Genetic Markers/genetics ; *Genome, Plant ; Inbreeding ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transcriptome/genetics ; Vaccinium macrocarpon/*genetics ; *Wetlands ; },
abstract = {BACKGROUND: The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.<br><br>RESULTS: The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50&#x2009;=&#x2009;4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).<br><br>CONCLUSIONS: Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.},
}
@article {pmid24939707,
year = {2014},
author = {Huu, NT and Yoshida, H and Umegawachi, T and Miyata, S and Yamaguchi, M},
title = {Structural characterization and subcellular localization of Drosophila organic solute carrier partner 1.},
journal = {BMC biochemistry},
volume = {15},
number = {},
pages = {11},
pmid = {24939707},
issn = {1471-2091},
mesh = {Animals ; Cell Membrane/*metabolism ; Dimerization ; Drosophila/genetics/*metabolism ; Drosophila Proteins/genetics/isolation &amp; purification/*metabolism ; Humans ; Larva ; Membrane Transport Proteins/genetics/isolation &amp; purification/*metabolism ; Molecular Structure ; Phylogeny ; Protein Transport ; Recombinant Proteins/genetics/*metabolism ; Sequence Alignment ; Transcriptome ; },
abstract = {BACKGROUND: Organic solute carrier partner 1 (OSCP1) is known to facilitate the transport of various organic solutes into cells and reported to play a role in cell growth and cell differentiation. Moreover, OSCP1 is known as a tumor suppressor gene that is frequently down-expressed in nasopharyngeal carcinomas and acute myeloid leukemia. However, the underlying mechanisms of action remain unclear and the subcellular localization of OSCP1 has yet to be determined in detail.<br><br>RESULTS: Drosophila contains a single orthologue of OSCP1 (dOSCP1) that shares 58% homology with its human counterpart. To study the expression pattern and subcellular localization of dOSCP1, we prepared a specific antibody. Subcellular localization analyses of dOSCP1 with these revealed localization in the plasma membrane, endoplasmic reticulum, Golgi apparatus and mitochondria, but no detection in cytosol. dOSCP1 signals were also detected in the nucleus, although at weaker intensity than in plasma membranes and subcellular organelles. In addition, native polyacrylamide gel electrophoresis analysis with and without &#x3b2;-mercaptoethanol treatment revealed that recombinant dOSCP1 forms dimers and trimers in solution. The dimer form of dOSCP1 could also be detected by Western immunoblot analyses in third instar larval extracts.<br><br>CONCLUSIONS: The data revealed that dOSCP1 localizes not only in the plasma membrane but also in the nucleus, ER, Golgi apparatus and mitochondria. It is therefore conceivable that this protein may interact with various partners or form multimeric complexes with other proteins to play multiple roles in cells, providing clues to understanding the functions of dOSCP1 during Drosophila development.},
}
@article {pmid24941043,
year = {2014},
author = {Low, VL and Adler, PH and Takaoka, H and Ya'cob, Z and Lim, PE and Tan, TK and Lim, YA and Chen, CD and Norma-Rashid, Y and Sofian-Azirun, M},
title = {Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka &amp; Davies along an elevational gradient in Malaysia.},
journal = {PloS one},
volume = {9},
number = {6},
pages = {e100512},
pmid = {24941043},
issn = {1932-6203},
mesh = {Altitude ; Amino Acid Sequence ; Animals ; DNA, Mitochondrial/*genetics ; Ecosystem ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Haplotypes ; Malaysia ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Protein Subunits/*genetics ; Simuliidae/classification/*genetics ; },
abstract = {The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected.},
}
@article {pmid24946232,
year = {2015},
author = {Abd El-Moneim, D and Contreras, R and Silva-Navas, J and Gallego, FJ and Figueiras, AM and Benito, C},
title = {On the consequences of aluminium stress in rye: repression of two mitochondrial malate dehydrogenase mRNAs.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {17},
number = {1},
pages = {123-133},
doi = {10.1111/plb.12219},
pmid = {24946232},
issn = {1438-8677},
mesh = {Aluminum/*metabolism ; Base Sequence ; Chromosome Mapping ; Lipid Peroxidation ; Malate Dehydrogenase/*genetics ; Malates/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/enzymology/genetics/physiology ; Plant Proteins/genetics ; Plant Roots/enzymology/genetics/physiology ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Secale/enzymology/genetics/*physiology ; Seedlings/enzymology/genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Plants have developed several external and internal aluminium (Al) tolerance mechanisms. The external mechanism best characterised is the exudation of organic acids induced by Al. Rye (Secale cereale L.), one of the most Al-tolerant cereal crops, secretes both citrate and malate from its roots in response to Al. However, the role of malate dehydrogenase (MDH) genes in Al-induced stress has not been studied in rye. We have isolated the ScMDH1 and ScMDH2 genes, encoding two different mitochondrial MDH isozymes, in three Al-tolerant rye cultivars (Ailés, Imperial and Petkus) and one sensitive inbred rye line (Riodeva). These genes, which have seven exons and six introns, were located on the 1R (ScMDH1) and 3RL (ScMDH2) chromosomes. Exon 1 of ScMDH1 and exon 7 of ScMDH2 were the most variable among the different ryes. The hypothetical proteins encoded by these genes were classified as putative mitochondrial MDH isoforms. The phylogenetic relationships obtained using both cDNA and protein sequences indicated that the ScMDH1 and ScMDH2 proteins are orthologous to mitochondrial MDH1 and MDH2 proteins of different Poaceae species. The expression studies of the ScMDH1 and ScMDH2 genes indicate that it is more intense in roots than in leaves. Moreover, the amount of their corresponding mRNAs in roots from plants treated and not treated with Al was higher in the tolerant cultivar Petkus than in the sensitive inbred line Riodeva. In addition, ScMDH1 and ScMDH2 mRNA levels decreased in response to Al stress (repressive behaviour) in the roots of both the tolerant Petkus and the sensitive line Riodeva.},
}
@article {pmid24947012,
year = {2014},
author = {Takahashi, S and Teranishi, M and Izumi, M and Takahashi, M and Takahashi, F and Hidema, J},
title = {Transport of rice cyclobutane pyrimidine dimer photolyase into mitochondria relies on a targeting sequence located in its C-terminal internal region.},
journal = {The Plant journal : for cell and molecular biology},
volume = {79},
number = {6},
pages = {951-963},
doi = {10.1111/tpj.12598},
pmid = {24947012},
issn = {1365-313X},
mesh = {Amino Acid Sequence ; Chloroplasts/ultrastructure ; DNA Damage ; Deoxyribodipyrimidine Photo-Lyase/chemistry/genetics/*metabolism ; Gene Expression ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Nuclear Localization Signals ; Oryza/*enzymology/genetics/radiation effects/ultrastructure ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Pyrimidine Dimers/metabolism ; Recombinant Fusion Proteins ; Sequence Alignment ; Sequence Deletion ; Ultraviolet Rays ; },
abstract = {The cyclobutane pyrimidine dimer (CPD), which represents a major type of DNA damage induced by ultraviolet-B (UVB) radiation, is a principal cause of UVB-induced growth inhibition in plants. CPD photolyase is the primary enzyme for repairing CPDs and is crucial for determining the sensitivity of Oryza sativa (rice) to UVB radiation. CPD photolyase is widely distributed among species ranging from eubacteria to eukaryotes, and is classified into class I or II based on its primary structure. We previously demonstrated that rice CPD photolyase (OsPHR), which belongs to class II and is encoded by a single-copy gene, is a unique nuclear/mitochondrial/chloroplast triple-targeting protein; however, the location and nature of the organellar targeting information contained within OsPHR are unknown. Here, the nuclear and mitochondrial targeting signal sequences of OsPHR were identified by systematic deletion analysis. The nuclear and mitochondrial targeting sequences are harbored within residues 487-489 and 391-401 in the C-terminal region of OsPHR (506 amino acid residues), respectively. The mitochondrial targeting signal represents a distinct topogenic sequence that differs structurally and functionally from classical N-terminal pre-sequences, and this region, in addition to its role in localization to the mitochondria, is essential for the proper functioning of the CPD photolyase. Furthermore, the mitochondrial targeting sequence, which is characteristic of class-II CPD photolyases, was acquired before the divergence of class-II CPD photolyases in eukaryotes. These results indicate that rice plants have evolved a CPD photolyase that functions in mitochondria to protect cells from the harmful effects of UVB radiation.},
}
@article {pmid24963773,
year = {2016},
author = {Dray, L and Neuhof, M and Diamant, A and Huchon, D},
title = {The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {1},
pages = {781-782},
doi = {10.3109/19401736.2014.928861},
pmid = {24963773},
issn = {2470-1408},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Open Reading Frames/genetics ; Phylogeny ; Sea Bream/*genetics ; },
abstract = {The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.},
}
@article {pmid24974962,
year = {2014},
author = {Walther, EL and Valkiūnas, G and González, AD and Matta, NE and Ricklefs, RE and Cornel, A and Sehgal, RN},
title = {Description, molecular characterization, and patterns of distribution of a widespread New World avian malaria parasite (Haemosporida: Plasmodiidae), Plasmodium (Novyella) homopolare sp. nov.},
journal = {Parasitology research},
volume = {113},
number = {9},
pages = {3319-3332},
pmid = {24974962},
issn = {1432-1955},
mesh = {Americas/epidemiology ; Animals ; Cytochromes b/genetics ; Malaria, Avian/epidemiology/*parasitology ; Mitochondria/genetics ; Parasitemia/parasitology ; Passeriformes/*parasitology ; Phylogeny ; Plasmodium/classification/*genetics/*isolation &amp; purification ; },
abstract = {Plasmodium (Novyella) homopolare, a newly described Plasmodium species, was found in a wide range of Passeriformes species in California, USA, and Colombia. This parasite infected more than 20% of the sampled bird community (N = 399) in California and was found in 3.6% of birds sampled (N = 493) in Colombia. Thus far, it has been confirmed in North and South America where it is present in numerous species of migratory and resident birds from six families. Based on 100% matches, or near-100% matches (i.e., ≤2-nucleotide difference), to DNA sequences previously deposited in GenBank, this parasite is likely also distributed in the Eastern USA, Central America, and the Caribbean. Here, we describe the blood stages of P. homopolare and its mtDNA cytochrome b sequence. P. homopolare belongs to the subgenus Novyella and can be readily distinguished from the majority of other Novyella species, primarily, by the strictly polar or subpolar position of meronts and advanced trophozoites in infected erythrocytes. We explore possible reasons why this widespread parasite has not been described in earlier studies. Natural malarial parasitemias are usually light and co-infections predominate, making the parasites difficult to detect and identify to species when relying exclusively on microscopic examination of blood films. The combined application of sequence data and digital microscopy techniques, such as those used in this study, provides identifying markers that will facilitate the diagnosis of this parasite in natural avian populations. We also address the evolutionary relationship of this parasite to other species of Plasmodium using phylogenetic reconstruction.},
}
@article {pmid24983244,
year = {2014},
author = {Thaler, AD and Plouviez, S and Saleu, W and Alei, F and Jacobson, A and Boyle, EA and Schultz, TF and Carlsson, J and Van Dover, CL},
title = {Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e101345},
pmid = {24983244},
issn = {1932-6203},
mesh = {Animals ; Anomura/*genetics ; Base Sequence ; Decapoda/*genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genetics, Population ; *Hydrothermal Vents ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Snails/genetics ; },
abstract = {Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates--the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis--that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.},
}
@article {pmid24985738,
year = {2015},
author = {Chettoor, AM and Yi, G and Gomez, E and Hueros, G and Meeley, RB and Becraft, PW},
title = {A putative plant organelle RNA recognition protein gene is essential for maize kernel development.},
journal = {Journal of integrative plant biology},
volume = {57},
number = {3},
pages = {236-246},
doi = {10.1111/jipb.12234},
pmid = {24985738},
issn = {1744-7909},
mesh = {Alleles ; Biomarkers/metabolism ; Endosperm/cytology/*embryology/metabolism ; Gene Expression Regulation, Plant ; *Genes, Plant ; Mitochondria/metabolism ; Mutagenesis, Insertional/genetics ; Mutation/genetics ; Organelles/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; Starch/deficiency/metabolism ; Nicotiana/genetics ; Zea mays/*embryology/*genetics ; },
abstract = {Basal endosperm transfer layer (BETL) cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6+gene function is required independently in both the embryo and endosperm. The emp6 mutant causes a notable effect on the differentiation of BETL cells; the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6-green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria. These results suggest that BETL cell differentiation might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.},
}
@article {pmid24999047,
year = {2014},
author = {Zhang, T and Jiang, Y and Dong, W},
title = {A novel monopartite dsRNA virus isolated from the phytopathogenic fungus Ustilaginoidea virens and ancestrally related to a mitochondria-associated dsRNA in the green alga Bryopsis.},
journal = {Virology},
volume = {462-463},
number = {},
pages = {227-235},
doi = {10.1016/j.virol.2014.06.003},
pmid = {24999047},
issn = {1096-0341},
mesh = {China ; Chlorophyta/genetics ; Cluster Analysis ; Genome, Viral ; Hypocreales/*virology ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Double-Stranded/*genetics ; RNA, Viral/*genetics ; Saccharomycetales/genetics ; Sequence Analysis, DNA ; Sequence Homology ; },
abstract = {In this study, we describe a novel mycovirus isolated from Ustilaginoidea virens, which was designated Ustilaginoidea virens nonsegmented virus 1 (UvNV-1). The sequence analysis revealed that UvNV-1 has two open reading frames (ORFs). ORF1 encodes an unknown protein, which is similar to the hypothetical protein BN7_5177 of Wickerhamomyces ciferrii. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp), which is most closely related to Bryopsis mitochondria-associated dsRNA (BDRM) and is likely expressed by a +1 ribosomal frameshift within the sequence CCC_UUU_CGA. The phylogenetic analysis of the RdRp of UvNV-1 showed that UvNV-1 represents a new virus taxon of mycoviruses with a partitivirus-like lineage that is classified into the family of picorna-like viruses. Based on northern hybridization, UvNV-1 was found to be common to U. virens from different geographic locations in China. The biological comparison of virus-free and infected fungal strains revealed that UvNV-1 is likely to be cryptic to its host.},
}
@article {pmid25005252,
year = {2014},
author = {Abe, KT and Mariguela, TC and Avelino, GS and Foresti, F and Oliveira, C},
title = {Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {152},
pmid = {25005252},
issn = {1471-2148},
mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; Characiformes/*classification/*genetics ; Fossils ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; South America ; },
abstract = {BACKGROUND: Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted.<br><br>RESULTS: In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae&#x2009;+&#x2009;Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 47 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted.<br><br>CONCLUSION: Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results point to a possible ancient invasion of Central America, dating about 20.3 &#xb1; 5.0 Ma (late Oligocene--early Miocene), to explain the occurrence of Brycon in Central America.},
}
@article {pmid25005355,
year = {2014},
author = {Bertrand, C and Janzen, DH and Hallwachs, W and Burns, JM and Gibson, JF and Shokralla, S and Hajibabaei, M},
title = {Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {153},
pmid = {25005355},
issn = {1471-2148},
mesh = {Animals ; Butterflies/*classification/*genetics/microbiology ; Cell Nucleus/genetics ; Costa Rica ; DNA, Ribosomal Spacer/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Wolbachia/genetics ; },
abstract = {BACKGROUND: Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexes within them. Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica.<br><br>RESULTS: Although no morphological traits appear to distinguish among the three, congruent nuclear and mitochondrial lineage patterns show that "Urbanus belli" in ACG is a complex of three sympatric species. A single strain of Wolbachia present in two of the three cryptic species indicates that Urbanus segnestami Burns (formerly Urbanus belliDHJ01), Urbanus bernikerni Burns (formerly Urbanus belliDHJ02), and Urbanus ehakernae Burns (formerly Urbanus belliDHJ03) may be biologically separated by Wolbachia, as well as by their genetics. Use of parallel sequencing through 454-pyrosequencing improved the utility of ITS2 as a phylogenetic marker and permitted examination of the intra- and interlineage relationships of ITS2 variants within the species complex. Interlineage, intralineage and intragenomic compensatory base pair changes were discovered in the secondary structure of ITS2.<br><br>CONCLUSION: These findings corroborate the existence of three cryptic species. Our confirmation of a novel cryptic species complex, initially suggested by DNA barcode lineages, argues for using a multi-marker approach coupled with next-generation sequencing for exploration of other suspected species complexes.},
}
@article {pmid25005920,
year = {2014},
author = {Candat, A and Paszkiewicz, G and Neveu, M and Gautier, R and Logan, DC and Avelange-Macherel, MH and Macherel, D},
title = {The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress.},
journal = {The Plant cell},
volume = {26},
number = {7},
pages = {3148-3166},
pmid = {25005920},
issn = {1532-298X},
mesh = {Amino Acid Motifs ; Arabidopsis/cytology/genetics/*physiology ; Arabidopsis Proteins/classification/genetics/metabolism ; Cell Membrane/metabolism ; Cold Temperature ; Computational Biology ; Desiccation ; Genes, Reporter ; Organelles/metabolism ; Phylogeny ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified ; Protein Transport ; Protoplasts ; Recombinant Fusion Proteins ; Seedlings/cytology/genetics/physiology ; Stress, Physiological ; },
abstract = {Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress.},
}
@article {pmid25010076,
year = {2016},
author = {Caragiulo, A and Dougherty, E and Soto, S and Rabinowitz, S and Amato, G},
title = {The complete mitochondrial genome structure of the jaguar (Panthera onca).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {914-915},
doi = {10.3109/19401736.2014.926483},
pmid = {25010076},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Central America ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Panthera/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; South America ; },
abstract = {The jaguar (Panthera onca) is the largest felid in the Western hemisphere, and the only member of the Panthera genus in the New World. The jaguar inhabits most countries within Central and South America, and is considered near threatened by the International Union for the Conservation of Nature. This study represents the first sequence of the entire jaguar mitogenome, which was the only Panthera mitogenome that had not been sequenced. The jaguar mitogenome is 17,049 bases and possesses the same molecular structure as other felid mitogenomes. Bayesian inference (BI) and maximum likelihood (ML) were used to determine the phylogenetic placement of the jaguar within the Panthera genus. Both BI and ML analyses revealed the jaguar to be sister to the tiger/leopard/snow leopard clade.},
}
@article {pmid25020128,
year = {2014},
author = {Barbosa, AJ and Sampaio, I and Schneider, H and Santos, S},
title = {Molecular phylogeny of weakfish species of the Stellifer group (Sciaenidae, Perciformes) of the western South Atlantic based on mitochondrial and nuclear data.},
journal = {PloS one},
volume = {9},
number = {7},
pages = {e102250},
pmid = {25020128},
issn = {1932-6203},
mesh = {Animals ; Atlantic Ocean ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Genetic Markers/genetics ; Mitochondria/*genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; },
abstract = {The phylogenetic relationships within the Stellifer group of weakfishes (Stellifer, Odontoscion, Ophioscion, and Bairdiella) were evaluated using 2723 base pairs comprising sequences of nuclear (rhodopsin, TMO-4C4, RAG-1) and mitochondrial (16S rRNA and COI) markers obtained from specimens of nine species. Our results indicate a close relationship between Bairdiella and Odontoscion, and also that the genus Stellifer is not monophyletic, but rather that it consists of two distinct lineages, one clade containing S. microps/S. naso/S. brasiliensis and the other, S. rastrifer/S. stellifer/Stellifer sp. B, which is closer to Ophioscion than the former clade. The O. punctatissimus populations from the northern and southern Brazilian coast were also highly divergent in both nuclear (0.8% for rhodopsin and 0.9% for RAG-1) and mitochondrial sequences (2.2% for 16S rRNA and 7.3% for COI), which we conclude is consistent with the presence of two distinct species. The morphological similarities of the members of the Stellifer group is reinforced by the molecular data from both the present study and previous analyses, which have questioned the taxonomic status of the Stellifer group. If, on the one hand, the group is in fact composed of four genera (Stellifer, Ophioscion, Odontoscion, and Bairdiella), one of the two Stellifer clades should be reclassified as a new genus. However, if the close relationship and the reduced genetic divergence found within the group is confirmed in a more extensive study, including representatives of additional taxa, this, together with the morphological evidence, would support downgrading the whole group to a single genus. Obviously, these contradictory findings reinforce the need for a more systematic taxonomic revision of the Stellifer group as a whole.},
}
@article {pmid25040194,
year = {2014},
author = {Watson, PM and Sorrell, SC and Brown, MW},
title = {Ptolemeba n. gen., a novel genus of hartmannellid amoebae (Tubulinea, Amoebozoa); with an emphasis on the taxonomy of Saccamoeba.},
journal = {The Journal of eukaryotic microbiology},
volume = {61},
number = {6},
pages = {611-619},
doi = {10.1111/jeu.12139},
pmid = {25040194},
issn = {1550-7408},
mesh = {DNA, Ribosomal/genetics ; Lobosea/*classification/genetics/ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Hartmannellid amoebae are an unnatural assemblage of amoeboid organisms that are morphologically difficult to discern from one another. In molecular phylogenetic trees of the nuclear-encoded small subunit rDNA, they occupy at least five lineages within Tubulinea, a well-supported clade in Amoebozoa. The polyphyletic nature of the hartmannellids has led to many taxonomic problems, in particular paraphyletic genera. Recent taxonomic revisions have alleviated some of the problems. However, the genus Saccamoeba is paraphyletic and is still in need of revision as it currently occupies two distinct lineages. Here, we report a new clade on the tree of Tubulinea, which we infer represents a novel genus that we name Ptolemeba n. gen. This genus subsumes a clade of hartmannellid amoebae that were previously considered in the genus Saccamoeba, but whose mitochondrial morphology is distinct from Saccamoeba. In accordance with previous research, we formalize the clade as distinct from Saccamoeba. Transmission electron microscopy of our isolates illustrate that both molecularly discrete species can be further differentiated by their unique mitochondrial cristal morphology.},
}
@article {pmid25045044,
year = {2014},
author = {Dolce, V and Cappello, AR and Capobianco, L},
title = {Mitochondrial tricarboxylate and dicarboxylate-tricarboxylate carriers: from animals to plants.},
journal = {IUBMB life},
volume = {66},
number = {7},
pages = {462-471},
doi = {10.1002/iub.1290},
pmid = {25045044},
issn = {1521-6551},
mesh = {Animals ; Base Sequence ; Carrier Proteins/*physiology ; Dicarboxylic Acid Transporters/*physiology ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/physiology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Promoter Regions, Genetic ; },
abstract = {The citrate carrier (CiC), characteristic of animals, and the dicarboxylate-tricarboxylate carrier (DTC), characteristic of plants and protozoa, belong to the mitochondrial carrier protein family whose members are responsible for the exchange of metabolites, cofactors, and nucleotides between the cytoplasm and the mitochondrial matrix. Most of the functional data on these transporters are obtained from the studies performed with the protein purified from rat, eel yeast, and maize mitochondria or recombinant proteins from different sources incorporated into phospholipid vesicles (liposomes). The functional data indicate that CiC is responsible for the efflux of acetyl-CoA from the mitochondria to the cytosol in the form of citrate, the primer for fatty acid, cholesterol synthesis, and histone acetylation. Like the CiC, the citrate exported by DTC from the mitochondria to the cytosol in exchange for oxaloacetate can be cleaved by citrate lyase to acetyl-CoA and oxaloacetate and used for fatty acid elongation and isoprenoid synthesis. In addition to its role in fatty acid synthesis, CiC is involved in other processes such as gluconeogenesis, insulin secretion, inflammation, and cancer progression, whereas DTC is involved in the production of glycerate, nitrogen assimilation, ripening of fruits, ATP synthesis, and sustaining of respiratory flux in fruit cells. This review provides an assessment of the current understanding of CiC and DTC structural and biochemical characteristics, underlying the structure-function relationship of these carriers. Furthermore, a phylogenetic relationship between CiC and DTC is proposed.},
}
@article {pmid25090399,
year = {2016},
author = {Zhang, Z and Sun, T and Kang, C and Liu, Y and Liu, S and Yue, B and Zeng, T},
title = {The complete mitochondrial genome of lesser long-tailed Hamster Cricetulus longicaudatus (Milne-Edwards, 1867) and phylogenetic implications.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1303-1304},
doi = {10.3109/19401736.2014.945567},
pmid = {25090399},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Bayes Theorem ; Cricetinae ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents' mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.},
}
@article {pmid25103433,
year = {2016},
author = {Ren, Q and Qian, C and Yuan, J and Li, X and Yang, J and Wang, P and Jiang, L and Zhang, Q and Wang, Y and Kan, X},
title = {Complete mitochondrial genome of the Black-capped Bulbul, Pycnonotus melanicterus (Passeriformes: Pycnonotidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1378-1380},
doi = {10.3109/19401736.2014.947589},
pmid = {25103433},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; },
abstract = {The first complete maternally-inherited mitochondrial genome of Pycnonotus melanicterus has been sequenced and annotated in this study. The mitogenome is 17,011 bp in size with an A+T content of 55.15%, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (srRNA and lrRNA) genes, and 2 extensive heteroplasmic control regions. Genome organization and gene arrangements of P. melanicterus are similar to those of other bulbuls. All 13 PCGs initiated with ATG as the start codon, while terminated by seven types of stop codons. All tRNA genes sequences have the potential to fold into typical cloverleaf secondary structures. Gene overlapping was observed in the P. melanicterus mitogenome. Moreover, our results of phylogenetic analysis well support the monophyly of Pycnonotidae as previously studies.},
}
@article {pmid25103434,
year = {2016},
author = {Liao, F and Zeng, G and Yuan, X and Li, S and Wang, C and Liang, Z},
title = {Complete mitochodrial genome of Elopichthys bambusa (Cypriniformes, Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1387-1388},
doi = {10.3109/19401736.2014.947593},
pmid = {25103434},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/chemistry ; },
abstract = {The complete mitochondrial genome of Elopichthys bambusa was determined in this study. The gene composition, arrangement and transcriptional orientation in E. bambusa mitogenome were identical to most vertebrates. Two start codon patterns (ATG and GTG) and three stop codon patterns (TAG, TAA and T) were found in protein-coding genes. Only the tRNA-Ser2 could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. Sequences alignment results suggest that the complete mitogenome of E. bambusa is an efficient tool to check species identification by comparing different gene sequences.},
}
@article {pmid25103437,
year = {2016},
author = {Su, YB and Kong, SC and Wang, LX and Chen, L and Fang, R},
title = {Complete mitochondrial genome of Philometra carassii (Nematoda: Philometridae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1397-1398},
doi = {10.3109/19401736.2014.947598},
pmid = {25103437},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; Genome, Helminth ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Nematoda/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genome of Philometra carassii is 14,378 bp in size, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 rRNA genes (12S and 16S), as well as one non-coding region (NCR, the control region), but lacks an atp8 gene. The genome organization, nucleotide composition and codon usage do not differ significantly from other nematodes. The complete mitogenome sequence information of P. carassii can provides useful data for further studies on phylogenetics, stock evaluation and conservation genetics.},
}
@article {pmid25112327,
year = {2014},
author = {Thompson, FC and Skevington, JH},
title = {Afrotropical flower flies (Diptera: Syrphidae). A new genus and species from Kenya, with a review of the melanostomine group of genera.},
journal = {Zootaxa},
volume = {3847},
number = {1},
pages = {97-114},
doi = {10.11646/zootaxa.3847.1.5},
pmid = {25112327},
issn = {1175-5334},
mesh = {Animals ; Diptera/*anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Kenya ; Male ; Mitochondria/enzymology/genetics ; Phylogeny ; Species Specificity ; Uganda ; },
abstract = {A new genus and species of flower flies (Diptera: Syrphidae: Syrphinae: Syrphini) are described from central Africa (Kenya &amp; Uganda), Afrostoma quadripunctatum. A key to the Afrotropical genera of the subfamily Syrphinae is given. A review of the melanostomine [Bacchini] genera and subgenera is provided along with a key to them. Phylogenetic placement of Afrostoma is included based on mitochondrial cytochrome c oxidase subunit I (COI) data.},
}
@article {pmid25121834,
year = {2016},
author = {Oh, JS and Ahn, do H and Lee, J and Choi, J and Chi, YM and Park, H},
title = {Complete mitochondrial genome of the Antarctic bullhead notothen, Notothenia coriiceps (Perciformes, Nototheniidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1407-1408},
doi = {10.3109/19401736.2014.947603},
pmid = {25121834},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete sequence of the mitochondrial genome of Notothenia coriiceps was obtained by genome assembly. The complete sequence was determined to be 18,347 base pairs in length and to contain 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. Of the thirteen protein-coding genes, two genes (cox1 and atp6) had GTG start codons, and six genes (nad2, cox2, cox3, nad3, nad4, and cytb) had incomplete stop codons that require the post-transcriptional addition of A bases. The base composition of the mitogenome was 26.3% A, 27.6% T, 17.5% G, and 28.5% C.},
}
@article {pmid25121835,
year = {2016},
author = {Del Río-Portilla, MA and Vargas-Peralta, CE and Farfán, C and Barriga-Sosa, Ide L and García-De-León, FJ},
title = {The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1381-1382},
doi = {10.3109/19401736.2014.947590},
pmid = {25121835},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cichlids/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {The mitogenome of the tenguayaca, Petenia splendida (GenBank accession number KJ914664) has a total length of 16,518 bp, and the arrangement consist of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Gene order was equal to the mitogenomes of other new world cichlids.},
}
@article {pmid25122658,
year = {2015},
author = {López Del Amo, V and Seco-Cervera, M and García-Giménez, JL and Whitworth, AJ and Pallardó, FV and Galindo, MI},
title = {Mitochondrial defects and neuromuscular degeneration caused by altered expression of Drosophila Gdap1: implications for the Charcot-Marie-Tooth neuropathy.},
journal = {Human molecular genetics},
volume = {24},
number = {1},
pages = {21-36},
doi = {10.1093/hmg/ddu416},
pmid = {25122658},
issn = {1460-2083},
mesh = {Animals ; Charcot-Marie-Tooth Disease ; Disease Models, Animal ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster/*metabolism ; F-Box Proteins/*genetics/*metabolism ; Gene Expression Regulation ; Humans ; Mitochondria/*physiology ; Mitochondrial Size ; Nerve Tissue Proteins/metabolism ; Neuromuscular Diseases/*etiology/pathology ; Phylogeny ; Retina/metabolism ; },
abstract = {One of the genes involved in Charcot-Marie-Tooth (CMT) disease, an inherited peripheral neuropathy, is GDAP1. In this work, we show that there is a true ortholog of this gene in Drosophila, which we have named Gdap1. By up- and down-regulation of Gdap1 in a tissue-specific manner, we show that altering its levels of expression produces changes in mitochondrial size, morphology and distribution, and neuronal and muscular degeneration. Interestingly, muscular degeneration is tissue-autonomous and not dependent on innervation. Metabolic analyses of our experimental genotypes suggest that alterations in oxidative stress are not a primary cause of the neuromuscular degeneration but a long-term consequence of the underlying mitochondrial dysfunction. Our results contribute to a better understanding of the role of mitochondria in CMT disease and pave the way to generate clinically relevant disease models to study the relationship between mitochondrial dynamics and peripheral neurodegeneration.},
}
@article {pmid25132566,
year = {2014},
author = {Zhao, YE and Cheng, J and Hu, L and Ma, JX},
title = {Molecular identification and phylogenetic study of Demodex caprae.},
journal = {Parasitology research},
volume = {113},
number = {10},
pages = {3601-3608},
pmid = {25132566},
issn = {1432-1955},
mesh = {Animals ; Base Sequence ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Dogs ; Female ; Mite Infestations/parasitology/*veterinary ; Mites/*classification/genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Ovum ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.},
}
@article {pmid25133695,
year = {2016},
author = {Wang, X and Zhang, Y and Zhang, H and Meng, T and Lin, Q},
title = {Complete mitochondrial genome sequence of the longsnout seahorse Hippocampus reidi (Ginsburg, 1933; Gasterosteiformes: Syngnathidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1401-1402},
doi = {10.3109/19401736.2014.947600},
pmid = {25133695},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Smegmamorpha/*genetics ; },
abstract = {The complete mitochondrial genome sequence of the longsnout seahorse Hippocampus reidi was fisrt determined in this article. The total length of H. reidi mitogenome is 16,529 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The gene order and composition of H. reidi were similar to those of most other vertebrates. The overall base composition of H. reidi is 32.47% A, 29.41% T, 14.75% G and 23.37% C, with a slight A + T rich feature (61.88%).},
}
@article {pmid25133698,
year = {2016},
author = {Tao, W and Zhao, H},
title = {The complete mitogenome of Gnathopogon polytaenia (Cypriniformes; Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1307-1308},
doi = {10.3109/19401736.2014.945569},
pmid = {25133698},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome was sequenced from one of the endemic freshewater gudgeons (Gnathopogon polytaenia) in China. The mitochondrial genome sequence was 16,594 bp in size, and the gene order and contents were identical with the congeneric species G. strigatus and G. elongatus. Six genes (COII, ATP6, COIII, ND3, ND4, Cytb) had an incomplete stop codon. Base composition of the genome is A (29.1%), T (26.9%), C (25.9%) and G (18.1%) with an A + T rich feature (56%) as that of other vertebrate mitochondrial genomes.},
}
@article {pmid25143035,
year = {2014},
author = {Silva, G and Lima, FP and Martel, P and Castilho, R},
title = {Thermal adaptation and clinal mitochondrial DNA variation of European anchovy.},
journal = {Proceedings. Biological sciences},
volume = {281},
number = {1792},
pages = {},
pmid = {25143035},
issn = {1471-2954},
mesh = {*Adaptation, Biological ; Animals ; Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Environment ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Genetics, Population ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; *Temperature ; },
abstract = {Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.},
}
@article {pmid25151510,
year = {2015},
author = {Grimm, C and Böhl, L and Osiewacz, HD},
title = {Overexpression of Pa_1_10620 encoding a mitochondrial Podospora anserina protein with homology to superoxide dismutases and ribosomal proteins leads to lifespan extension.},
journal = {Current genetics},
volume = {61},
number = {1},
pages = {73-86},
pmid = {25151510},
issn = {1432-0983},
mesh = {Amino Acid Sequence ; Cloning, Molecular ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Genes, Lethal ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Podospora/classification/*genetics/*metabolism ; Protein Transport ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Superoxide Dismutase/chemistry/*genetics/metabolism ; Transcription, Genetic ; },
abstract = {In biological systems, reactive oxygen species (ROS) represent 'double edged swords': as signaling molecules they are essential for proper development, as reactive agents they cause molecular damage and adverse effects like degeneration and aging. A well-coordinated control of ROS is therefore of key importance. Superoxide dismutases (SODs) are enzymes active in the detoxification of superoxide. The number of isoforms of these proteins varies among species. Here we report the characterization of the putative protein encoded by Pa_1_10620 that has been previously annotated to code for a mitochondrial ribosomal protein but shares also sequence domains with SODs. We report that the gene is transcribed in P. anserina cultures of all ages and that the encoded protein localizes to mitochondria. In strains overexpressing Pa_1_10620 in a genetic background in which PaSod3, the mitochondrial MnSOD of P. anserina, is deleted, no SOD activity could be identified in isolated mitochondria. However, overexpression of the gene leads to lifespan extension suggesting a pro-survival function of the protein in P. anserina.},
}
@article {pmid25162155,
year = {2016},
author = {Chen, Q and Wang, K and Tan, YL and Xing, LX},
title = {The complete mitochondrial genome of the subterranean termite, Reticulitermes chinensis Snyder (Isoptera: Rhinotermitidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1428-1429},
doi = {10.3109/19401736.2014.953077},
pmid = {25162155},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {We have determined the complete mitochondrial genome of Reticulitermes chinensis Snyder. The total length of the R. chinensis is 15,925 bp with 65.27% A + T content. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes and an A + T-rich control region. All the protein-coding genes used ATN as start codon. But the stop codons were TAA, TAG, and an incomplete termination codon (T) abutting an adjacent tRNA gene. The A + T-rich control region was 1125 bp in length with 67.02% A + T content.},
}
@article {pmid25162381,
year = {2016},
author = {Xue, Y and Chen, HJ and Li, Y and Tang, M and Chen, HJ and Ye, Q and Li, Y},
title = {Mitochondrial genome of the sucking disc gudgeon, Discogobio yunnanensis (Teleostei, Cypriniformes).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1451-1452},
doi = {10.3109/19401736.2014.953088},
pmid = {25162381},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genome of Discogobio yunnanensis was determined using the polymerase chain reaction and directly sequenced with the primer walking method. The whole mitogenome was 16,602 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It had the typical circular molecule structure of vertebrate's mitogenome. The whole base composition was estimated to be 32.10% A, 26.79% T, 25.95% C, 15.16% G with AT bias of 58.89%. The complete mitogenome of D. yunnanensis provides the fundamental data for conservation genetics study on this freshwater fish species.},
}
@article {pmid25162454,
year = {2016},
author = {Liang, R and Zhou, M and Gu, N},
title = {Complete mitochondrial genome of the yellow-banded sweetlips Plectorhinchus lineatus (Perciformes: Haemulidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1466-1467},
doi = {10.3109/19401736.2014.953095},
pmid = {25162454},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genome of yellow-banded sweetlips Plectorhinchus lineatus was determined in this study. The genome was 16,548 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one non-coding control region. The overall base composition was estimated to be A, 28.2%; T, 24.8%; C, 30.7% and G, 16.2% with AT bias of 53.0%. All protein-coding genes used ATG as a start codon except for COI, which started with GTG. Six protein-coding genes ended with termination codon TAA, one ended with AGG, the remaining genes had incomplete stop codons TA or T. The genomic composition, organization, and gene order of P. lineatus was similar to most of vertebrates.},
}
@article {pmid25162469,
year = {2016},
author = {E, G and Na, RS and Zhao, YJ and Gao, HJ and An, TW and Huang, YF},
title = {Complete mitochondrial genome of the a rare subspecies of genus Bos, Tianzhu white yak from Tibetan area in China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1443-1444},
doi = {10.3109/19401736.2014.953084},
pmid = {25162469},
issn = {2470-1408},
mesh = {Animals ; Animals, Domestic/classification/genetics ; Base Composition ; Cattle/classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tibet ; },
abstract = {The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.},
}
@article {pmid25162495,
year = {2016},
author = {Hengjiu, T and Jianwei, J and Shi, Y and Zhiming, Z and Laghari, MY and Narejo, NT and Lashari, P},
title = {Complete mitochondrial genome of Eagle Owl (Bubo bubo, Strigiformes; Strigidae) from China.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1455-1456},
doi = {10.3109/19401736.2014.953090},
pmid = {25162495},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Strigiformes/*genetics ; },
abstract = {In the present study, the complete mitochondrial genome sequence of Bubo bubo using PCR amplification, sequencing and assembling has been obtained for the first time. The total length of the mitochondrial genome was 16,250 bp, with the base composition of 29.88% A, 34.16% C, 14.35% G, and 21.58% T. It contained 37 genes (2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes) and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Bubo bubo provides an important data set for further investigation on the phylogenetic relationships within Strigiformes.},
}
@article {pmid25162588,
year = {2016},
author = {Hu, XD and Gao, LZ},
title = {The complete mitochondrial genome of eastern lowland gorilla, Gorilla beringei graueri, and comparative mitochondrial genomics of Gorilla species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1484-1485},
doi = {10.3109/19401736.2014.953103},
pmid = {25162588},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genetic Variation ; Genome Size ; *Genome, Mitochondrial ; Gorilla gorilla/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {In this study, we determined the complete mitochondrial (mt) genome of eastern lowland gorilla, Gorilla beringei graueri for the first time. The total genome was 16,416 bp in length. It contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop region). The base composition was A (30.88%), G (13.10%), C (30.89%) and T (25.13%), indicating that the percentage of A+T (56.01%) was higher than G+C (43.99%). Comparisons with the other publicly available Gorilla mitogenome showed the conservation of gene order and base compositions but a bunch of nucleotide diversity. This complete mitochondrial genome sequence will provide valuable genetic information for further studies on conservation genetics of eastern lowland gorilla.},
}
@article {pmid25162745,
year = {2016},
author = {Chen, DS and Jin, PY and Hong, XY},
title = {The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1480-1481},
doi = {10.3109/19401736.2014.953101},
pmid = {25162745},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tetranychidae/*genetics ; },
abstract = {The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae) is a typical circular DNA with length of 13,089 bp (GenBank accession number: KM111296). The genome contains all 13 protein-coding genes (PCGs), an A + T-rich region, two rRNA genes and 22 tRNA genes. The A + T content of the mitochondrial genome is 84.5%. The AT-skew is positive (0.032) while the GC-skew is negative (-0.058). The gene arrangement is conserved in T. urticae, Panonychus citri and P. ulmi which are in the same family (Tetranychidae). The A + T-rich region is only 43 bp in length with high A + T content (97.7%). All the PCGs start with typical ATD codons. Eight PCGs have complete TAA stop codons, while five PCGs have an incomplete stop codon (T).},
}
@article {pmid25162765,
year = {2016},
author = {Li, Y and Tang, M and Xue, Y and Chen, HJ and Ye, Q and Li, Y},
title = {Complete mitochondrial genome of the Chinese balitorine loach, Metahomaloptera omeiensis (Teleostei, Cypriniformes).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1449-1450},
doi = {10.3109/19401736.2014.953087},
pmid = {25162765},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The Metahomaloptera omeiensis is the only one species within the genus, Metahomaloptera. The complete mitochondrial genome of M. omeiensis was sequenced, which was 16,558 bp in length, including 13 protein-coding genes, 7 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 29.44% A, 25.44% T, 28.28% C and 16.84% G with AT bias of 54.88%. The complete mitogenome of M. omeiensis provides the basis for genetic resources and phylogenetic analyses on this freshwater fish species.},
}
@article {pmid25162799,
year = {2016},
author = {Liu, F and Pang, S and Chen, W},
title = {Complete mitochondrial genome of the brown alga Sargassum hemiphyllum (Sargassaceae, Phaeophyceae): comparative analyses.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1468-1470},
doi = {10.3109/19401736.2014.953096},
pmid = {25162799},
issn = {2470-1408},
mesh = {Base Composition ; DNA, Intergenic ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sargassum/classification/*genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Sargassum hemiphyllum (Turner) C. Agardh is a common low intertidal brown alga in the northwestern Pacific, and two varieties (var. chinense and var. hemiphyllum) of this alga have been determined based on morphological and molecular data. In this study, we present the complete mitochondrial genome of S. hemiphyllum var. chinense. The circular-mapping S. hemiphyllum mitogenome of 34,686 bp has an overall A+T content of 63.43%, and contains 65 densely packed genes. The total intergenic spacer regions are 1597 bp, constituting 4.60% of the mitogenome. The gene content and genome organization of S. hemiphyllum are identical to that of other reported Sargassum species. The identity comparison of overall mitogenome sequences and phylogenomic analyses indicate that S. hemiphyllum has a closer evolutionary relationship with Sargassum muticum than other Sargassum species analyzed. The present mitogenomic data provide a powerful tool for definition of varieties and studies of population structure in S. hemiphyllum.},
}
@article {pmid25163032,
year = {2016},
author = {Li, X and Wang, Y and Su, S and Yang, D},
title = {The complete mitochondrial genomes of Musca domestica and Scathophaga stercoraria (Diptera: Muscoidea: Muscidae and Scathophagidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1435-1436},
doi = {10.3109/19401736.2014.953080},
pmid = {25163032},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Houseflies/*genetics ; Mitochondria/*genetics ; Muscidae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete mitochondrial genomes of Musca domestica (Muscidae) and Scathophaga stercoraria (Scathophagidae) are circular molecules of 16,108 bp and 16,223 bp in length, respectively. The first complete mitochondrial genome of Scathophagidae is reported here. Both genomes contain all 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a large control region, with conserved arrangement pattern reported in all cyclorrhaphan flies. All PCGs start with standard ATN codons except for the CO1 which starts with TCG in both species. All PCGs terminate with the common stop codons TAA or TAG, except for the CO2 and ND5 in both species and ND4 in S. stercoraria which end with a single T.},
}
@article {pmid25183231,
year = {2014},
author = {Arockiaraj, J and Palanisamy, R and Bhatt, P and Kumaresan, V and Gnanam, AJ and Pasupuleti, M and Kasi, M},
title = {A novel murrel Channa striatus mitochondrial manganese superoxide dismutase: gene silencing, SOD activity, superoxide anion production and expression.},
journal = {Fish physiology and biochemistry},
volume = {40},
number = {6},
pages = {1937-1955},
pmid = {25183231},
issn = {1573-5168},
mesh = {Aeromonas hydrophila ; Amino Acid Sequence ; Animals ; Aphanomyces ; Base Sequence ; Cells, Cultured ; Computational Biology ; Fishes/*metabolism ; Gene Expression Regulation, Enzymologic/*physiology ; *Gene Silencing ; Gram-Negative Bacterial Infections/metabolism/veterinary ; Infections/metabolism/veterinary ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Species Specificity ; Superoxide Dismutase/genetics/*metabolism ; Superoxides/*metabolism ; },
abstract = {We have reported the molecular characterization including gene silencing, superoxide activity, superoxide anion production, gene expression and molecular characterization of a mitochondrial manganese superoxide dismutase (mMnSOD) from striped murrel Channa striatus (named as CsmMnSOD). The CsmMnSOD polypeptide contains 225 amino acids with a molecular weight of 25 kDa and a theoretical isoelectric point of 8.3. In the N-terminal region, CsmMnSOD carries a mitochondrial targeting sequence and a superoxide dismutases (SOD) Fe domain (28-109), and in C-terminal region, it carries another SOD Fe domain (114-220). The CsmMnSOD protein sequence shared significant similarity with its homolog of MnSOD from rock bream Oplegnathus fasciatus (96%). The phylogenetic analysis showed that the CsmMnSOD fell in the clade of fish mMnSOD group. The monomeric structure of CsmMnSOD possesses 9 α-helices (52.4%), 3 β-sheets (8.8%) and 38.8% random coils. The highest gene expression was noticed in liver, and its expression was inducted with fungal (Aphanomyces invadans) and bacterial (Aeromonas hydrophila) infections. The gene silencing results show that the fish that received dsRNA exhibited significant (P < 0.05) changes in expression when compared to their non-injected and fish physiological saline-injected controls. The SOD activity shows that the activity increases with the spread of infection and decreases once the molecule controls the pathogen. The capacity of superoxide anion production was determined by calculating the granular blood cell count during infection in murrel. It shows that the infection influenced the superoxide radical production which plays a major role in killing the pathogens. Overall, this study indicated the defense potentiality of CsmMnSOD; however, further research is necessary to explore its capability at protein level.},
}
@article {pmid25184569,
year = {2014},
author = {Harrison, E and Trexler, JC and Collins, TM and Vazquez-Domínguez, E and Razo-Mendivil, U and Matamoros, WA and Barrientos, C},
title = {Genetic evidence for multiple sources of the non-native fish Cichlasoma urophthalmus (Günther; Mayan Cichlids) in southern Florida.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e104173},
pmid = {25184569},
issn = {1932-6203},
mesh = {Animal Distribution ; Animals ; Cell Nucleus/genetics ; Cichlids/classification/*genetics ; Cytochromes b/genetics ; Ecosystem ; Female ; Florida ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; *Hybridization, Genetic ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; South America ; },
abstract = {The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, where all individuals were fixed for the mitochondrial haplotype found in the introduced population, and a more diverse but also relatively small number of individuals from Belize. The Florida cytochrome b haplotype appears to be absent from Belize (0 out of 136 fish screened from Belize had this haplotype). Genetic structure within the Florida population was minimal, indicating a panmictic population, while Mexican and Central American samples displayed more genetic subdivision. Individuals from the Upper Yucatán Peninsula and the Petén region of Guatemala were more genetically similar to each other than to fish from nearby sites and movement of Mayan Cichlids between these regions occurred thousands of generations ago, suggestive of pre-Columbian human transportation of Mayan Cichlids through this region. Mayan Cichlids present a rare example of cytonuclear disequilibrium and reduced genetic diversity in the introduced population that persists more than 30 years (at least 7-8 generations) after introduction. We suggest that hybridization occurred in ornamental fish farms in Florida and may contribute their establishment in the novel habitat. Hybridization prior to release may contribute to other successful invasions.},
}
@article {pmid25185698,
year = {2016},
author = {Deng, PJ and Wang, WM and Huang, XC and Wu, XP and Xie, GL and Ouyang, S},
title = {The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1441-1442},
doi = {10.3109/19401736.2014.953083},
pmid = {25185698},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Rearrangement ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Snails/*genetics ; },
abstract = {Mastigeulota kiangsinensis is an endemic and widespread land snail in China. The complete mitochondrial genome of M. kiangsinensis was first determined using long PCR reactions and primer walking method (accession number KM083123). The genome has a length of 14,029 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 29.48%, T 37.92%, C 14.38% and G 18.22%. Gene order of M. kiangsinensis is identical to Euhadra herklotsi, but gene rearrangements are found compared with other mitochondrial genomes described in Stylommatophora. tRNA(Thr) is located in COIII, which has not been found in other helicoids so far. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analysis in land snails and Molluscs at large.},
}
@article {pmid25186141,
year = {2016},
author = {Wang, B and Wang, S and Hu, M and Wang, F},
title = {Complete mitochondrial genome of Rhodeus lighti (Cypriniformes: Cyprinidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1497-1498},
doi = {10.3109/19401736.2014.953109},
pmid = {25186141},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {In this study, the complete mitochondrial genome (mitogenome) sequence of Rhodeus lighti (Cypriniformes: Cyprinidae) was determined by long PCR and primer walking methods. The complete mitochondrial genome is 16,677 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a displacement loop (D-loop). The overall base composition of the genome is A (28.87%), T (27.22%), C (26.53%) and G (17.38%). The mitogenome of R. lighti displayed novel gene order arrangement compared with published Rhodeus sinensis to date. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Acheilognathinae.},
}
@article {pmid25187350,
year = {2016},
author = {Véliz, D and Vega-Retter, C and Quezada-Romegialli, C},
title = {Next generation sequencing yields the complete mitochondrial genome of the Endangered Chilean silverside Basilichthys microlepidotus (Jenyns, 1841) (Teleostei, Atherinopsidae), validated with RNA-seq.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1505-1506},
doi = {10.3109/19401736.2014.953113},
pmid = {25187350},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Endangered Species ; Fishes/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/*methods ; },
abstract = {The complete sequence of the mitochondrial genome for the Chilean silverside Basilichthys microlepidotus is reported for the first time. The entire mitochondrial genome was 16,544 bp in length (GenBank accession no. KM245937); gene composition and arrangement was conformed to that reported for most fishes and contained the typical structure of 2 rRNAs, 13 protein-coding genes, 22 tRNAs and a non-coding region. The assembled mitogenome was validated against sequences of COI and Control Region previously sequenced in our lab, functional genes from RNA-Seq data for the same species and the mitogenome of two other atherinopsid species available in Genbank.},
}
@article {pmid25187425,
year = {2016},
author = {Zhou, A and Chen, J and Xie, S and Chen, Y and Zou, J},
title = {The complete mitochondrial genome of Ophicephalus argus kimurai (Perciformes: Channidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {2},
pages = {1419-1420},
doi = {10.3109/19401736.2014.953073},
pmid = {25187425},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; },
abstract = {The complete sequence of the mitochondrial genome of Ophicephalus argus kimurai was determined in this study. The genome was 16,558 bp in length. As in other vertebrates, it consisted of 22 transfer RNA (tRNA) genes, 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 1 noncoding control region. The overall base composition was estimated to be A, 27.2%; T, 24.2%; C, 31.6% and G, 17% with AT bias of 51.4%. The genomic composition, organization, and gene order of O. argus kimurai was similar to that obtained in most vertebrates. These results may provide the basis for the study of genetic structure as well as resource conservation and protection of O. argus kimurai.},
}
@article {pmid25211091,
year = {2016},
author = {Yan, J and Liao, H and Zhu, Z and Xie, K and Guo, Y and Cai, J},
title = {The complete mitochondria genome of Parasarcophaga similis (Diptera: Sarcophagidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {1642-1643},
doi = {10.3109/19401736.2014.958708},
pmid = {25211091},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sarcophagidae/classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genome of Parasarcophaga similis collected from China was determined using PCR reactions. The mitogenome was 15,158 bp in length with a total A + T content of 76.4%, consisting of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and a control region. The gene contents of the mitogenome were identical to those observed in other insects. The overall base compositions of A, G, C and T were 39.54%, 9.43%, 14.20% and 36.83%, respectively. This paper aimed to improve and perfect dipteran mitochondrial genomes and provided the first complete mitochondrial genome of Parasarcophaga similis for entomologists as a potential tool for application of phylogenetic analysis and forensic entomology.},
}
@article {pmid25232829,
year = {2014},
author = {Greaves, LC and Nooteboom, M and Elson, JL and Tuppen, HA and Taylor, GA and Commane, DM and Arasaradnam, RP and Khrapko, K and Taylor, RW and Kirkwood, TB and Mathers, JC and Turnbull, DM},
title = {Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing.},
journal = {PLoS genetics},
volume = {10},
number = {9},
pages = {e1004620},
pmid = {25232829},
issn = {1553-7404},
support = {096919Z/11/Z/WT_/Wellcome Trust/United Kingdom ; G0601943/MRC_/Medical Research Council/United Kingdom ; G0700718/MRC_/Medical Research Council/United Kingdom ; 096919/WT_/Wellcome Trust/United Kingdom ; R01 AG019787/AG/NIA NIH HHS/United States ; BB/C008200/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R01AG19787/AG/NIA NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aging/*genetics ; Cytochromes c/genetics/metabolism ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestinal Mucosa/metabolism ; Middle Aged ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation Rate ; *Point Mutation ; Sensitivity and Specificity ; Young Adult ; },
abstract = {Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. However the dynamics of this process and when these mtDNA mutations occur initially are poorly understood. Using human colorectal epithelium as an exemplar tissue with a well-defined stem cell population, we analysed samples from 207 healthy participants aged 17-78 years using a combination of techniques (Random Mutation Capture, Next Generation Sequencing and mitochondrial enzyme histochemistry), and show that: 1) non-pathogenic mtDNA mutations are present from early embryogenesis or may be transmitted through the germline, whereas pathogenic mtDNA mutations are detected in the somatic cells, providing evidence for purifying selection in humans, 2) pathogenic mtDNA mutations are present from early adulthood (<20 years of age), at both low levels and as clonal expansions, 3) low level mtDNA mutation frequency does not change significantly with age, suggesting that mtDNA mutation rate does not increase significantly with age, and 4) clonally expanded mtDNA mutations increase dramatically with age. These data confirm that clonal expansion of mtDNA mutations, some of which are generated very early in life, is the major driving force behind the mitochondrial dysfunction associated with ageing of the human colorectal epithelium.},
}
@article {pmid25239514,
year = {2014},
author = {Tripathi, V and Tripathi, P},
title = {Molecular phylogenetics and comparative modeling of MnSOD, an enzyme involved during environmental stress conditions in Oryza sativa.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {6},
number = {4},
pages = {251-258},
doi = {10.1007/s12539-011-0050-4},
pmid = {25239514},
issn = {1867-1462},
mesh = {Amino Acid Sequence ; Antioxidants/chemistry ; Catalysis ; Catalytic Domain/genetics ; Magnoliopsida ; Manganese/*chemistry ; Mitochondria/enzymology ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Oryza/*enzymology/*genetics ; Oxidative Stress/*genetics ; Peroxisomes/enzymology ; *Phylogeny ; Plant Proteins/chemistry/genetics ; Sequence Homology ; Structure-Activity Relationship ; Superoxide Dismutase/*chemistry/*genetics ; },
abstract = {Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn (III) at the active site. The three dimensional structure of MnSOD of Oryza sativa is not yet available in protein data bank so we have predicted the structure model of O. sativa MnSOD using homology modeling. The predicted model can further be explored for identification of ligand binding sites which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated that the phylogenetic analysis of O. sativa MnSOD protein with distinct dicot and monocot plant species. The MnSOD protein of O. sativa has shown similarity with both monocot and as well as dicot plant species.},
}
@article {pmid25249225,
year = {2015},
author = {Meriam, T and Wafa, T and Khawla, T and Tarek, H and Abdeljelil, G and Mhamed, E},
title = {Genetic diversity and population structure of Sepia officinalis from the Tunisian cost revealed by mitochondrial COI sequences.},
journal = {Molecular biology reports},
volume = {42},
number = {1},
pages = {77-86},
pmid = {25249225},
issn = {1573-4978},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sepia/*genetics ; Tunisia ; },
abstract = {Population substructure of Sepia officinalis sampled along the Tunisian coastline was studied. We have scored the genetic variation of the mitochondrial gene cytochrome oxidase 1. A total of 20 specimens from four sampling sites were analysed and revealed 12 different haplotypes. Haplotype diversity showed a decreasing north to south gradient which may be explained by the hydrogeography of the study area. The overall estimate of genetic divergence (FST) revealed significant genetic differentiation between the pair-wise population comparisons supported by the AMOVA analysis which reveals significant genetic divergence. Finally, populations showed an excess of rare haplotypes. The mismatch distribution and several population genetic statistics indicate that the excess of rare variants is due to a recent expansion for Djerba and Kelibia populations. For Rades and Bizerte populations a constant population size was detected. These findings are important for fisheries management to preserve this marine resource for long-term utilization.},
}
@article {pmid25251765,
year = {2014},
author = {Rocha, AV and Rivera, LO and Martinez, J and Prestes, NP and Caparroz, R},
title = {Biogeography of speciation of two sister species of neotropical amazona (Aves, Psittaciformes) based on mitochondrial sequence data.},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108096},
pmid = {25251765},
issn = {1932-6203},
mesh = {Animals ; Argentina ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Parrots/*genetics ; Phylogeny ; },
abstract = {Coalescent theory provides powerful models for population genetic inference and is now increasingly important in estimates of divergence times and speciation research. We use molecular data and methods based on coalescent theory to investigate whether genetic evidence supports the hypothesis of A. pretrei and A. tucumana as separate species and whether genetic data allow us to assess which allopatric model seems to better explain the diversification process in these taxa. We sampled 13 A. tucumana from two provinces in northern Argentina and 28 A. pretrei from nine localities of Rio Grande do Sul, Brazil. A 491 bp segment of the mitochondrial gene cytochrome c oxidase I was evaluated using the haplotype network and phylogenetic methods. The divergence time and other demographic quantities were estimated using the isolation and migration model based on coalescent theory. The network and phylogenetic reconstructions showed similar results, supporting reciprocal monophyly for these two taxa. The divergence time of lineage separation was estimated to be approximately 1.3 million years ago, which corresponds to the lower Pleistocene. Our results enforce the current taxonomic status for these two Amazon species. They also support that A. pretrei and A. tucumana diverged with little or no gene flow approximately 1.3 million years ago, most likely after the establishment of a small population in the Southern Yungas forest by dispersion of a few founders from the A. pretrei ancestral population. This process may have been favored by habitat corridors formed in hot and humid periods of the Quaternary. Considering that these two species are considered threatened, the results were evaluated for their implications for the conservation of these two species.},
}
@article {pmid25251766,
year = {2014},
author = {Lozano-Jaramillo, M and Rico-Guevara, A and Cadena, CD},
title = {Genetic differentiation, niche divergence, and the origin and maintenance of the disjunct distribution in the Blossomcrown Anthocephala floriceps (Trochilidae).},
journal = {PloS one},
volume = {9},
number = {9},
pages = {e108345},
pmid = {25251766},
issn = {1932-6203},
mesh = {Adaptation, Biological ; Animals ; Birds/*classification/*genetics ; Cell Nucleus/genetics ; Colombia ; DNA/*analysis ; *Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Selection, Genetic ; Sequence Analysis, DNA ; },
abstract = {Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7-2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.},
}
@article {pmid25259854,
year = {2014},
author = {Singh, K and Zouhar, M and Mazakova, J and Rysanek, P},
title = {Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: a causal agent of Blackleg disease in Oilseed Rape (Brassica napus).},
journal = {Omics : a journal of integrative biology},
volume = {18},
number = {10},
pages = {645-657},
pmid = {25259854},
issn = {1557-8100},
mesh = {Amino Acid Sequence ; Ascomycota/*genetics ; Brassica napus/*microbiology ; Conserved Sequence ; Fungal Proteins/*genetics ; Gene Ontology ; Genome, Fungal ; Immunophilins/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Protein Structure, Tertiary ; Transcriptome ; },
abstract = {Abstract Phoma stem canker (blackleg) is a disease of world-wide importance on oilseed rape (Brassica napus) and can cause serious losses for crops globally. The disease is caused by dothideomycetous fungus, Leptosphaeria maculans, which is highly virulent/aggressive. Cyclophilins (CYPs) and FK506-binding proteins (FKBPs) are ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) family. They are collectively referred to as immunophilins (IMMs). In the present study, IMM genes, CYP and FKBP in haploid strain v23.1.3 of L. maculans genome, were identified and classified. Twelve CYPs and five FKBPs were determined in total. Domain architecture analysis revealed the presence of a conserved cyclophilin-like domain (CLD) in the case of CYPs and FKBP_C in the case of FKBPs. Interestingly, IMMs in L. maculans also subgrouped into single domain (SD) and multidomain (MD) proteins. They were primarily found to be localized in cytoplasm, nuclei, and mitochondria. Homologous and orthologous gene pairs were also determined by comparison with the model organism Saccharomyces cerevisiae. Remarkably, IMMs of L. maculans contain shorter introns in comparison to exons. Moreover, CYPs, in contrast with FKBPs, contain few exons. However, two CYPs were determined as being intronless. The expression profile of IMMs in both mycelium and infected primary leaves of B. napus demonstrated their potential role during infection. Secondary structure analysis revealed the presence of atypical eight β strands and two α helices fold architecture. Gene ontology analysis of IMMs predicted their significant role in protein folding and PPIase activity. Taken together, our findings for the first time present new prospects of this highly conserved gene family in phytopathogenic fungus.},
}
@article {pmid25260044,
year = {2015},
author = {Kim, BM and Lee, JW and Seo, JS and Shin, KH and Rhee, JS and Lee, JS},
title = {Modulated expression and enzymatic activity of the monogonont rotifer Brachionus koreanus Cu/Zn- and Mn-superoxide dismutase (SOD) in response to environmental biocides.},
journal = {Chemosphere},
volume = {120},
number = {},
pages = {470-478},
doi = {10.1016/j.chemosphere.2014.08.042},
pmid = {25260044},
issn = {1879-1298},
mesh = {Animals ; Disinfectants/*toxicity ; Gene Expression Regulation, Enzymologic/drug effects ; Helminth Proteins/genetics/*metabolism ; Mitochondria/enzymology ; Oxidative Stress/genetics ; Phylogeny ; Rotifera/*drug effects/enzymology ; Superoxide Dismutase/genetics/*metabolism ; Water Pollutants, Chemical/*toxicity ; },
abstract = {Superoxide dismutases (SODs) are important antioxidant enzymes whose expression levels are often used as biomarkers for oxidative stress. To investigate the biomarker potential of the monogonont rotifer Brachionus koreanus SOD genes, the full-length Cu/Zn-SOD (Bk-Cu/Zn-SOD) and Mn-SOD (Bk-Mn-SOD) genes were cloned from genomic DNA and characterized. All amino acid residues involved in the formation of tertiary structure and metal binding in Bk-Cu/Zn-SOD and Bk-Mn-SOD were highly conserved across species. Phylogenetic analysis revealed that Bk-Mn-SOD, in particular, was closely clustered with mitochondrial Mn-SOD. Transcript analysis after exposure to six different biocides (alachlor, chlorpyrifos, dimethoate, endosulfan, lindane, and molinate) revealed that the transcriptional level of Bk-Cu/Zn-SOD was significantly increased in a dose-dependent manner. In contrast, the level of Bk-Mn-SOD transcript was significantly increased compared with control cells in response to chlorpyrifos, endosulfan, and molinate at their no observed effect concentrations (NOECs). However, exposure to alachlor, chlorpyrifos, and molinate significantly reduced the enzymatic activity of total SOD protein, while a decreased pattern was observed in all biocide treatments. Taken together, these results indicate that exposure to waterborne environmental biocides induces the transcription of Bk-Cu/Zn-SOD and Bk-Mn-SOD, but inhibits the enzymatic activity of Bk-SODs. These results contribute to our understanding of the modes of action of oxidative stress-mediating biocides on rotifer.},
}
@article {pmid25302405,
year = {2015},
author = {Greiner, S and Sobanski, J and Bock, R},
title = {Why are most organelle genomes transmitted maternally?.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {37},
number = {1},
pages = {80-94},
pmid = {25302405},
issn = {1521-1878},
mesh = {Animals ; Female ; *Genome ; Humans ; Inheritance Patterns/*genetics ; Models, Genetic ; Organelles/*genetics ; Phylogeny ; Selection, Genetic ; },
abstract = {Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.},
}
@article {pmid25329274,
year = {2016},
author = {Joseph, S and Poriya, P and Kundu, R},
title = {Probing the phylogenetic relationships of a few newly recorded intertidal zoanthids of Gujarat coast (India) with mtDNA COI sequences.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3858-3864},
doi = {10.3109/19401736.2014.971239},
pmid = {25329274},
issn = {2470-1408},
mesh = {Animals ; Anthozoa/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation/*genetics ; Geography ; India ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The present study reports the phylogenetic relationship of six zoanthid species belonging to three genera, Isaurus, Palythoa, and Zoanthus identified using systematic computational analysis of mtDNA gene sequences. All six species are first recorded from the coasts of Kathiawar Peninsula, India. Genus: Isaurus is represented by Isaurus tuberculatus, genus Zoanthus is represented by Zoanthus kuroshio and Zoanthus sansibaricus, while genus Palythoa is represented by Palythoa tuberculosa, P. sp. JVK-2006 and Palythoa heliodiscus. Results of the present study revealed that among the various species observed along the coastline, a minimum of 99% sequence divergence and a maximum of 96% sequence divergence were seen. An interspecific divergence of 1-4% and negligible intraspecific divergence was observed. These results not only highlighted the efficiency of the COI gene region in species identification but also demonstrated the genetic variability of zoanthids along the Saurashtra coastline of the west coast of India.},
}
@article {pmid25333882,
year = {2014},
author = {Song, H and Moulton, MJ and Whiting, MF},
title = {Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta).},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110508},
pmid = {25333882},
issn = {1932-6203},
mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/chemistry/classification/*metabolism ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Molecular Sequence Data ; Orthoptera/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.},
}
@article {pmid25340523,
year = {2014},
author = {Smart, HC and Mast, FD and Chilije, MF and Tavassoli, M and Dacks, JB and Zaremberg, V},
title = {Phylogenetic analysis of glycerol 3-phosphate acyltransferases in opisthokonts reveals unexpected ancestral complexity and novel modern biosynthetic components.},
journal = {PloS one},
volume = {9},
number = {10},
pages = {e110684},
pmid = {25340523},
issn = {1932-6203},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Biocatalysis ; Endoplasmic Reticulum/enzymology ; Eukaryota/*enzymology ; Fungi/enzymology ; Gene Duplication ; Glycerol-3-Phosphate O-Acyltransferase/chemistry/*metabolism ; Glycolipids/*biosynthesis ; Humans ; Intracellular Space/metabolism ; Isoenzymes/metabolism ; Mitochondria/enzymology ; Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT), have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of 'fungal' orthologs in the basal taxa of the holozoa and 'animal' orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.},
}
@article {pmid25342463,
year = {2015},
author = {Binkienė, R and Kornienko, SA and Tkach, VV},
title = {Soricinia genovi n. sp. from Neomys fodiens in Bulgaria, with redescription of Soricinia globosa (Baer, 1931) (Cyclophyllidea: Hymenolepididae).},
journal = {Parasitology research},
volume = {114},
number = {1},
pages = {209-218},
pmid = {25342463},
issn = {1432-1955},
mesh = {Animals ; Bulgaria/epidemiology ; Cestoda/*anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Cestode Infections/epidemiology/parasitology/*veterinary ; DNA, Ribosomal/genetics ; Female ; Mitochondria/genetics ; Phylogeny ; *Shrews ; },
abstract = {Examination of specimens collected from water shrews Neomys fodiens in the Rhodope Mountains, Bulgaria, revealed a new species of Soricinia. Soricinia genovi n. sp., is described and the syntype of Soricinia globosa (the only other Soricinia species known from Neomys) is redescribed. The new species differs from S. globosa in the number of proglottids, relative length of the cirrus-sac, number of eggs in gravid proglottids, absence of vaginal sphincter and other characters. Among Soricinia, parasitic in shrews of the genus Sorex, the new species is most similar to Soricinia quarta. Soricinia genovi can be distinguished from S. quarta by the length of the cirrus-sac, larger testes and ovary, position of vitellarium and armament of cirrus. Comparison of nuclear ribosomal 28S DNA sequences and mitochondrial nad1 sequences clearly distinguishes S. genovi sp. n. from S. quarta, Soricinia bargusinica and Soricinia infirma. The levels of interspecific sequence divergence among Soricinia species exceed those reported for some other hymenolepidids of mammals. Phylogenetic analysis places S. quarta and S. genovi sp. n. as the closest taxa which is in agreement with morphological evidence. Our data suggest that the specimens of Soricinia from the Altai Mountains that were morphologically closest to S. infirma represent a new species. Pairwise sequence comparisons and phylogenetic analysis also indicate that "S. infirma" group may constitute a genus separate from the remaining Soricinia.},
}
@article {pmid25359314,
year = {2014},
author = {Harl, J and Páll-Gergely, B and Kirchner, S and Sattmann, H and Duda, M and Kruckenhauser, L and Haring, E},
title = {Phylogeography of the land snail genus Orcula (Orculidae, Stylommatophora) with emphasis on the Eastern Alpine taxa: speciation, hybridization and morphological variation.},
journal = {BMC evolutionary biology},
volume = {14},
number = {},
pages = {223},
pmid = {25359314},
issn = {1471-2148},
mesh = {Animals ; Biodiversity ; *Genetic Speciation ; Hybridization, Genetic ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Snails/*classification/*genetics ; },
abstract = {BACKGROUND: The Central and Southern European mountain ranges represent important biodiversity hotspots and show high levels of endemism. In the land snail genus Orcula Held, 1837 nine species are distributed in the Alps and a few taxa inhabit the Carpathians, the Dinarids and the Western Black Sea region. In order to elucidate the general patterns of temporal and geographic diversification, mitochondrial and nuclear markers were analyzed in all 13 Orcula species. We particularly aimed to clarify whether the Alpine taxa represent a monophyletic group and if the local species diversity is rather the result of isolation in geographically separated Pleistocene glacial refuges or earlier Tertiary and Quaternary palaeogeographic events. In order to test if patterns of molecular genetic and morphological differentiation were congruent and/or if hybridization had occurred, shell morphometric investigations were performed on the Orcula species endemic to the Alps.<br><br>RESULTS: The phylogenetic trees resulting from the analyses of both the mitochondrial (COI, 12S and 16S) and the nuclear (H4/H3) data sets revealed three main groups, which correspond to the three subgenera Orcula, Illyriobanatica and Hausdorfia. The reconstruction of the historic geographic ranges suggested that the genus originated in the Dinarides during the Middle Miocene and first colonized the Alps during the Late Miocene, giving rise to the most diverse subgenus Orcula. Within the latter subgenus (including all Alpine endemics) almost all species were differentiated by both molecular genetic markers and by shell morphometrics, except O. gularis and O. pseudodolium.<br><br>CONCLUSIONS: The present study confirms the importance of the Alps as biodiversity hotspot and origin center of land snail diversity. The species diversity in the subgenus Orcula was likely promoted by Miocene to Pliocene palaeogeographic events and the insular distribution of preferred limestone areas. In some cases, speciation events could be linked to the divergence of populations in glacial refuges during the Pleistocene. Sporadic contact between geographically separated and reproductively not yet isolated populations led to intermixture of haplogroups within species and even hybridization and mitochondrial capture between species.},
}
@article {pmid25368074,
year = {2014},
author = {Hao, JJ and Hao, JS and Sun, XY and Zhang, LL and Yang, Q},
title = {The complete mitochondrial genomes of the Fenton's wood white, Leptidea morsei, and the lemon emigrant, Catopsilia pomona.},
journal = {Journal of insect science (Online)},
volume = {14},
number = {},
pages = {130},
pmid = {25368074},
issn = {1536-2442},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; Butterflies/*classification/*genetics ; Codon ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; *Genome, Insect ; *Genome, Mitochondrial ; Insect Proteins/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial genomes of Leptidea morsei Fenton (Lepidoptera: Pieridae: Dis-morphiinae) and Catopsilia pomona (F.) (Lepidoptera: Pieridae: Coliadinae) were determined to be 15,122 and 15,142 bp in length, respectively, with that of L. morsei being the smallest among all known butterflies. Both mitogenomes contained 37 genes and an A+T-rich region, with the gene order identical to those of other butterflies, except for the presence of a tRNA-like insertion, tRNA(Leu) (UUR), in C. pomona. The nucleotide compositions of both genomes were higher in A and T (80.2% for L. morsei and 81.3% for C. pomona) than C and G; the A+T bias had a significant effect on the codon usage and the amino acid composition. The protein-coding genes utilized the standard mitochondrial start codon ATN, except the COI gene using CGA as the initiation codon, as reported in other butterflies. The intergenic spacer sequence between the tRNA(Ser) (UCN) and ND1 genes contained the ATACTAA motif. The A+T-rich region harbored a poly-T stretch and a conserved ATAGA motif located at the end of the region. In addition, there was a triplicated 23 bp repeat and a microsatellite-like (TA)9(AT)3 element in the A+T-rich region of the L. morsei mitogenome, while in C. pomona, there was a duplicated 24 bp repeat element and a microsatellite-like (TA)9 element. The phylogenetic trees of the main butterfly lineages (Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Lycaenidae, and Riodinidae) were reconstructed with maximum likelihood and Bayesian inference methods based on the 13 concatenated nucleotide sequences of protein-coding genes, and both trees showed that the Pieridae family is sister to Lycaenidae. Although this result contradicts the traditional morphologically based views, it agrees with other recent studies based on mitochondrial genomic data.},
}
@article {pmid25389773,
year = {2014},
author = {Vahtera, V and Edgecombe, GD},
title = {First molecular data and the phylogenetic position of the millipede-like centipede Edentistoma octosulcatum Tömösváry, 1882 (Chilopoda: Scolopendromorpha: Scolopendridae).},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e112461},
pmid = {25389773},
issn = {1932-6203},
mesh = {Animals ; Arthropods/anatomy &amp; histology/*classification/genetics ; Carnivory/physiology ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genetic Speciation ; Malaysia ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; },
abstract = {Edentistoma octosulcatum Tömösváry, 1882, is a rare, superficially millipede-like centipede known only from Borneo and the Philippines. It is unique within the order Scolopendromorpha for its slow gait, robust tergites, and highly modified gizzard and mandible morphology. Not much is known about the biology of the species but it has been speculated to be arboreal with a possibly vegetarian diet. Until now its phylogenetic position within the subfamily Otostigminae has been based only on morphological characters, being variably ranked as a monotypic tribe (Arrhabdotini) or classified with the Southeast Asian genus Sterropristes Attems, 1934. The first molecular data for E. octosulcatum sourced from a newly collected specimen from Sarawak were analysed with and without morphology. Parsimony analysis of 122 morphological characters together with two nuclear and two mitochondrial loci resolves Edentistoma as sister group to three Indo-Australian species of Rhysida, this clade in turn grouping with Ethmostigmus, whereas maximum likelihood and parsimony analyses of the molecular data on their own ally Edentistoma with species of Otostigmus. A position of Edentistoma within Otostigmini (rather than being its sister group as predicted by the Arrhabdotini hypothesis) is consistently retrieved under different analytical conditions, but support values within the subfamily remain low for most nodes. The species exhibits strong pushing behaviour, suggestive of burrowing habits. Evidence against a suggested vegetarian diet is provided by observation of E. octosulcatum feeding on millipedes in the genus Trachelomegalus.},
}
@article {pmid25390889,
year = {2014},
author = {Dejong, CA and Wilson, JY},
title = {The Cytochrome P450 superfamily complement (CYPome) in the annelid Capitella teleta.},
journal = {PloS one},
volume = {9},
number = {11},
pages = {e107728},
pmid = {25390889},
issn = {1932-6203},
mesh = {Amino Acid Motifs ; Animals ; Annelida/*genetics ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; Mitochondria/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Steroids/chemistry ; Sterol 14-Demethylase/chemistry ; Transcription, Genetic ; Xenobiotics/chemistry ; },
abstract = {The Cytochrome P450 super family (CYP) is responsible for a wide range of functions in metazoans, having roles in both exogenous and endogenous substrate metabolism. Annelids are known to metabolize polycyclic aromatic hydrocarbons (PAHs) and produce estrogen. CYPs are postulated to be key enzymes in these processes in annelids. In this study, the CYP complement (CYPome) of the annelid Capitella teleta has been robustly identified and annotated with the genome assembly available. Phylogenetic analyses were performed to understand the evolutionary relationships between CYPs in C. teleta and other species. Predictions of which CYPs are potentially involved in both PAH metabolism and steroidogensis were made based on phylogeny. Annotation of 84 full length and 12 partial CYP sequences predicted a total of 96 functional CYPs in C. teleta. A further 13 CYP fragments were found but these may be pseudogenes. The C. teleta CYPome contained 24 novel CYP families and seven novel CYP subfamilies within existing families. A phylogenetic analysis identified that the C. teleta sequences were found in 9 of the 11 metazoan CYP clans. Two CYPs, CYP3071A1 and CYP3072A1, did not cluster with any metazoan CYP clans. We found xenobiotic response elements (XREs) upstream of C. teleta CYPs related to vertebrate CYP1 (CYP3060A1, CYP3061A1) and from families with reported transcriptional upregulation in response to PAH exposure (CYP4, CYP331). C. teleta had a CYP51A1 with ∼65% identity to vertebrate CYP51A1 sequences and has been predicted to have lanosterol 14 α-demethylase activity. CYP376A1, CYP3068A1, CYP3069A1, and CYP3070A1 were the most appropriate candidates for steroidogenesis genes based on their phylogeny and warrant further analyses, though no specific aromatase (estrogen synthesis) candidates were found. Presence of XREs upstream of C. teleta CYPs may indicate a functional aryl hydrocarbon receptor in C. teleta and candidate CYPs for studies of PAH metabolism.},
}
@article {pmid25393008,
year = {2014},
author = {Vasconcellos, Rde S and Mariotini-Moura, C and Gomes, RS and Serafim, TD and Firmino, Rde C and Silva E Bastos, M and Castro, FF and Oliveira, CM and Borges-Pereira, L and de Souza, AC and de Souza, RF and Gómez, GA and Pinheiro, Ada C and Maciel, TE and Silva-Júnior, A and Bressan, GC and Almeida, MR and Baqui, MM and Afonso, LC and Fietto, JL},
title = {Leishmania infantum ecto-nucleoside triphosphate diphosphohydrolase-2 is an apyrase involved in macrophage infection and expressed in infected dogs.},
journal = {PLoS neglected tropical diseases},
volume = {8},
number = {11},
pages = {e3309},
pmid = {25393008},
issn = {1935-2735},
mesh = {Amino Acid Sequence ; Animals ; Apyrase/chemistry/genetics/*metabolism ; Cell Line ; Dogs ; Female ; Leishmania infantum/chemistry/cytology/*enzymology/metabolism ; Leishmaniasis, Visceral/*parasitology ; Lymph Nodes/parasitology ; Macrophages/*parasitology ; Mice ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/genetics/*metabolism ; Rabbits ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; },
abstract = {BACKGROUND: Visceral leishmaniasis is an important tropical disease, and Leishmania infantum chagasi (synonym of Leishmania infantum) is the main pathogenic agent of visceral leishmaniasis in the New World. Recently, ecto-nucleoside triphosphate diphosphohydrolases (E-NTPDases) were identified as enablers of infection and virulence factors in many pathogens. Two putative E-NTPDases (∼70 kDa and ∼45 kDa) have been found in the L. infantum genome. Here, we studied the ∼45 kDa E-NTPDase from L. infantum chagasi to describe its natural occurrence, biochemical characteristics and influence on macrophage infection.<br><br>We used live L. infantum chagasi to demonstrate its natural ecto-nucleotidase activity. We then isolated, cloned and expressed recombinant rLicNTPDase-2 in bacterial system. The recombinant rLicNTPDase-2 hydrolyzed a wide variety of triphosphate and diphosphate nucleotides (GTP> GDP &#x200a;=&#x200a; UDP> ADP> UTP &#x200a;=&#x200a; ATP) in the presence of calcium or magnesium. In addition, rLicNTPDase-2 showed stable activity over a pH range of 6.0 to 9.0 and was partially inhibited by ARL67156 and suramin. Microscopic analyses revealed the presence of this protein on cell surfaces, vesicles, flagellae, flagellar pockets, kinetoplasts, mitochondria and nuclei. The blockade of E-NTPDases using antibodies and competition led to lower levels of parasite adhesion and infection of macrophages. Furthermore, immunohistochemistry showed the expression of E-NTPDases in amastigotes in the lymph nodes of naturally infected dogs from an area of endemic visceral leishmaniasis.<br><br>CONCLUSIONS/SIGNIFICANCE: In this work, we cloned, expressed and characterized the NTPDase-2 from L. infantum chagasi and demonstrated that it functions as a genuine enzyme from the E-NTPDase/CD39 family. We showed that E-NTPDases are present on the surface of promastigotes and in other intracellular locations. We showed, for the first time, the broad expression of LicNTPDases in naturally infected dogs. Additionally, the blockade of NTPDases led to lower levels of in vitro adhesion and infection, suggesting that these proteins are possible targets for rational drug design.},
}
@article {pmid25394323,
year = {2014},
author = {Bakhoum, AJ and Quilichini, Y and Miquel, J and Feliu, C and Bâ, CT and Marchand, B},
title = {Collyricloides massanae (Digenea, Collyriclidae): spermatozoon ultrastructure and phylogenetic importance.},
journal = {Parasite (Paris, France)},
volume = {21},
number = {},
pages = {59},
pmid = {25394323},
issn = {1776-1042},
support = {U17 CE002013/CE/NCIPC CDC HHS/United States ; },
mesh = {Animals ; Axoneme/ultrastructure ; France ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Murinae/parasitology ; Phylogeny ; Rodent Diseases/parasitology ; Spermatozoa/*ultrastructure ; Trematoda/classification/*cytology ; Trematode Infections/parasitology/veterinary ; },
abstract = {The spermatological characteristics of Collyricloides massanae (Digenea: Collyriclidae), a parasite of Apodemus sylvaticus caught in France, were studied by means of transmission electron microscopy. The mature sperm of C. massanae presents two axonemes of different lengths with the 9 + "1" pattern of the Trepaxonemata, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, one mitochondrion, a nucleus and granules of glycogen. An analysis of spermatological organisation emphasised some differences between the mature spermatozoon of C. massanae and those reported in the Gorgoderoidea species studied to date, specially belonging to the families Dicrocoeliidae, Paragonimidae and Troglotrematidae. The ultrastructural criteria described in C. massanae such as the morphology of both anterior and posterior spermatozoon extremities, the association "external ornamentation+cortical microtubules", the type 2 of external ornamentation and the spine-like bodies would allow us to bring closer the Collyriclidae to Microphalloidea. However, further ultrastructural and molecular studies are needed particularly in the unexplored taxa in order to fully resolve the phylogenetic position of the Collyriclidae.},
}
@article {pmid25415967,
year = {2015},
author = {Barreto, FS and Pereira, RJ and Burton, RS},
title = {Hybrid dysfunction and physiological compensation in gene expression.},
journal = {Molecular biology and evolution},
volume = {32},
number = {3},
pages = {613-622},
doi = {10.1093/molbev/msu321},
pmid = {25415967},
issn = {1537-1719},
mesh = {Animals ; Copepoda/genetics ; Female ; Gene Expression/*genetics ; Genetic Fitness/*genetics ; *Genetic Speciation ; Hybridization, Genetic/*genetics ; Male ; Mitochondria/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA ; },
abstract = {The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes exhibiting transgressive expression (i.e., higher or lower levels compared with both parental taxa), and these were mostly in the direction of downregulation. However, as most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids at F2 or later generations show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome is transgressively expressed in F3+ interpopulation hybrids of T. californicus, and nearly 80% of these genes are overexpressed rather than underexpressed; remarkably, none of these genes are among those showing divergent expression between parentals, nor is magnitude of transgressive gene expression in hybrids dependent on levels of protein sequence divergence. Moreover, many genes with transgressive expression are components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses.},
}
@article {pmid25423506,
year = {2016},
author = {Gong, X and Zhu, W and Bao, B},
title = {Complete mitochondrial DNA sequence of the Eastern keelback mullet Liza affinis.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2178-2179},
doi = {10.3109/19401736.2014.982614},
pmid = {25423506},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Smegmamorpha/*genetics ; Whole Genome Sequencing/methods ; },
abstract = {Eastern keelback mullet (Liza affinis) inhabits inlet waters and estuaries of rivers. In this paper, we initially determined the complete mitochondrial genome of Liza affinis. The entire mtDNA sequence is 16,831 bp in length, including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 putative control region. Its order and numbers of genes are similar to most bony fishes.},
}
@article {pmid25423509,
year = {2016},
author = {Li, M and Li, Y and Chen, Z},
title = {Description of the mitochondrial genome of yellowtail scad Atule mate (Perciformes: Carangidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2186-2187},
doi = {10.3109/19401736.2014.982618},
pmid = {25423509},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {The yellowtail scad Atule mate is an economic fish species distributed throughout the tropical and subtropical oceans of the Indo-Pacific region. In the present study, we assembled the complete mitochondrial genome of A. mate from contiguous, overlapping segments amplified by PCR. The mitogenome sequence was 16,565 bp in length, consisting of 37 typical animal mitochondrial genes and 1 control region, same with the typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand was 28.4% for A, 27.6% for T, 16.3% for G, and 27.7% for C. Phylogenetic analyses using the protein-coding gene sequences reveal that genus Atule was most closely related to Alepes.},
}
@article {pmid25423515,
year = {2016},
author = {Shen, KN and Chen, CH and Hsiao, CD},
title = {Next generation sequencing yields the complete mitochondrial genome of the Hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2192-2193},
doi = {10.3109/19401736.2014.982621},
pmid = {25423515},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Smegmamorpha/*genetics ; Whole Genome Sequencing/methods ; },
abstract = {In this study, the complete mitogenome sequence of hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae) has been sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,829 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 1057 bp length is located between tRNA-Pro and tRNA-Phe. The overall base composition of P. labiosus is 28.0% for A, 29.3% for C, 15.5% for G and 27.2% for T. The complete mitogenome may provide essential and important DNA molecular data for further population, phylogenetic and evolutionary analysis for Mugilidae.},
}
@article {pmid25423518,
year = {2016},
author = {Guo, Y and Bai, Q and Yan, T and Wang, Z and Liu, C},
title = {Mitogenomes of genus Pristipomoides, Lutjanus and Pterocaesio confirm Caesionidae nests in Lutjanidae.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2198-2199},
doi = {10.3109/19401736.2014.982624},
pmid = {25423518},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {In this study, the complete mitochondrial genome of Goldbanded jobfish (Perciformes: Lutjanidae: Etelinae: Pristipomoides multidens) was sequenced using long-PCR amplification (Accession No.: KF430626). The mitochondrial genome is highly homologous to those of other teleosts. Consensus tree based on phylogeny analysis of nucleotide sequences using the protein-coding regions combined sequences (apart from ND6) in 11 species supports the fact that Pristipomoides multidens of Etelinae and the cluster of Subfamily Lutjaninae remain the sister relationship, consistent with the traditional taxonomy, while the fusiliers (Pterocaesio tile) of family Caesionidae nested within the genus Lutjanus of family Lutjanidae and showed more closely relationship with the non-reddish snappers cluster including L. russellii and L. argentimaculatus. Conclusively, this mitogenomic phylogeny indicates that the Caesionidae is a synonym of family Lutjanidae. Given the morphologic and feeding diversity, we hypothesize that the variation of feeding systems of genus Lutjanus may drive the speciation of snappers and fusiliers.},
}
@article {pmid25423519,
year = {2016},
author = {Landínez-García, RM and Alzate, JF and Márquez, EJ},
title = {Mitochondrial genome of the Neotropical detritivore fish Curimata mivartii Steindachner 1878 (Characiformes, Curimatidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2196-2197},
doi = {10.3109/19401736.2014.982623},
pmid = {25423519},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Characiformes/*genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {Curimata mivartii is a detritivorous species Neotropical, which is of great importance to local fisheries and riverine ecosystems. In this work, the mitochondrial genome of C. mivartii was completely sequenced using a combination of 454 FLX(+) platform and Sanger/capillary sequencing. The mitogenome is 16,705 bp in length, encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and exhibit perfect synteny with others Characiformes.},
}
@article {pmid25423520,
year = {2016},
author = {Landínez-García, RM and Alzate, JF and Márquez, EJ},
title = {Mitochondrial genome of the Neotropical trans-Andean fish Ichthyoelephas longirostris, Steindachner 1879 (Characiformes, Prochilodontidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2194-2195},
doi = {10.3109/19401736.2014.982622},
pmid = {25423520},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Characiformes/*genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {Ichthyoelephas longirostris is a trans-Andean migratory species belonging to Prochilodontidae family. In this work, the mitochondrial genome of I. longirostris was sequenced by Illumina technology. The 16,840 bp mitogenome encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and present a conserved synteny with others species of the Order Characiformes.},
}
@article {pmid25427806,
year = {2016},
author = {Lin, HY and Chang, CH and Ho, HC and Shao, KT},
title = {The complete mitochondrial genome of Wanieso lizardfish Saurida wanieso Shindo &amp; Yamada, 1972 (Aulopiformes: Synodontidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2190-2191},
doi = {10.3109/19401736.2014.982620},
pmid = {25427806},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {The complete mitochondrial genome of the Wanieso lizardfish (Saurida wanieso) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,552 base pairs including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region as other Saurida spp. and bony fish. Base composition of the genome is A (25.7%), T (25.2%), C (31.5%), and G (17.6%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes.},
}
@article {pmid25431826,
year = {2015},
author = {Zhou, CL and Turdy, R and Halik, M},
title = {Genetic differentiation between red deer from different sample sites on the Tianshan Mountains (Cervus elaphus), China.},
journal = {Mitochondrial DNA},
volume = {26},
number = {1},
pages = {101-111},
doi = {10.3109/19401736.2014.984165},
pmid = {25431826},
issn = {1940-1744},
mesh = {Animals ; China ; Cytochromes b/genetics ; Deer/classification/*genetics ; Genes, Mitochondrial ; *Genetic Variation ; Geography ; Haplotypes ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; },
abstract = {About 273 individuals were identified from 471 fecal samples from six different red deer populations in China. The genetic structure showed that the red deer from the western and eastern Tianshan Mountains was different. A total number of 12 haplotypes were defined by 97 variable sites by the control region (CR), and 10 haplotypes were defined by 34 variable sites by cytochrome b. There was no haplotype sharing between red deer populations from western and eastern Tianshan Mountains by the CR and the cytochrome b. The red deer populations from west were clade with wapiti from North American and red deer from Siberia, while red deer populations from east were clade with red deer from Crimea in Pleistocene rather than west at present. The result of NETWORK also showed that red deer populations from western and eastern Tianshan Mountains were different. The haplotype and the Fst value between western and eastern Tianshan red deer were significantly different. The AMOVA analysis showed that 97.34% and 1.14% of the total genetic variability were found within populations and among populations within groups, respectively, by microsatellite. AMOVA for mitochondria showed that most of the variance was explained among-group. The Fst, pairwise distance, and phylogenetic relationship result showed that red deer between western and eastern Tianshan were more different than some of the red deer from North-Asia, South-Asia, East-Asia, and wapiti. All data from this study do support that the genetic characteristics of red deer between western and eastern Tianshan Mountains by microsatellite, control region, and cytochrome b were different.},
}
@article {pmid25433563,
year = {2014},
author = {Borsa, P and Sembiring, A and Fauvelot, C and Chen, WJ},
title = {Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.).},
journal = {Comptes rendus biologies},
volume = {337},
number = {12},
pages = {709-716},
doi = {10.1016/j.crvi.2014.09.001},
pmid = {25433563},
issn = {1768-3238},
mesh = {Animals ; Base Sequence ; Coral Reefs ; DNA, Mitochondrial/genetics ; Indian Ocean ; Mitochondria/genetics ; Molecular Sequence Data ; Pacific Ocean ; Perciformes/classification/*physiology ; Phylogeny ; Pigmentation/genetics ; Species Specificity ; },
abstract = {Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus.},
}
@article {pmid25435547,
year = {2015},
author = {Murcha, MW and Narsai, R and Devenish, J and Kubiszewski-Jakubiak, S and Whelan, J},
title = {MPIC: a mitochondrial protein import components database for plant and non-plant species.},
journal = {Plant &amp; cell physiology},
volume = {56},
number = {1},
pages = {e10},
doi = {10.1093/pcp/pcu186},
pmid = {25435547},
issn = {1471-9053},
mesh = {Base Sequence ; *Databases, Factual ; Fungi/*genetics ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Annotation ; Phaeophyceae/*genetics ; Phylogeny ; Plants/*genetics ; Protein Transport ; Rhodophyta/*genetics ; },
abstract = {In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and divergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.},
}
@article {pmid25460232,
year = {2014},
author = {Shiratori, T and Yokoyama, A and Ishida, K},
title = {Phylogeny, ultrastructure, and flagellar apparatus of a new Marimonad flagellate Abollifer globosa sp. nov. (Imbricatea, Cercozoa).},
journal = {Protist},
volume = {165},
number = {6},
pages = {808-824},
doi = {10.1016/j.protis.2014.10.003},
pmid = {25460232},
issn = {1618-0941},
mesh = {Cercozoa/*classification/genetics/*ultrastructure ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Flagella/ultrastructure ; Microscopy, Electron, Transmission ; *Phylogeny ; Phylogeography ; Seawater ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {Abollifer is a little-known genus of marine heterotrophic flagellates with no ultrastructural and molecular information, and its taxonomic position remains uncertain. In this study, we report a new species of Abollifer, Abollifer globosa sp. nov., isolated from a seawater sample collected at Tokyo Bay. To reveal the taxonomic position and morphological characteristics of A. globosa, we performed light and electron microscopic observations and a phylogenetic analysis using small subunit ribosomal DNA sequences. A. globosa cells were 29.5 μm in length and 22.4 μm in width, oval or ovoid in shape with an apical projection. Two unequal flagella emerged from a deep subapical flagellar pit. The rim of the flagellar pit except for the ventral side was swollen. Electron microscopic observations showed that A. globosa possessed mitochondria with tubular cristae, a Golgi apparatus, microbodies, extrusomes, and many endosymbiotic bacteria. Basal bodies were arranged in parallel. The flagellar apparatus of A. globosa showed affinity with common gliding cercozoan flagellates. Our phylogenetic tree showed that A. globosa branched as the sister position of order Marimonadida (Imbricatea, Cercozoa). On the basis of the morphological and molecular phylogenetic analysis, we conclude that A. globosa is a new member of the order Marimonadida.},
}
@article {pmid25463290,
year = {2015},
author = {Li, T and Wang, Y and Gao, Y and Li, Q},
title = {Identification and characterisation of the anti-oxidative stress properties of the lamprey prohibitin 2 gene.},
journal = {Fish &amp; shellfish immunology},
volume = {42},
number = {2},
pages = {447-456},
doi = {10.1016/j.fsi.2014.11.016},
pmid = {25463290},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; DNA, Complementary/genetics/metabolism ; Female ; Fish Proteins/*genetics/metabolism ; Gene Expression Regulation/*drug effects ; Hydrogen Peroxide/pharmacology ; Lampreys/*genetics/*immunology/metabolism ; Male ; Molecular Sequence Data ; Organ Specificity ; Oxidative Stress/*drug effects ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction/veterinary ; Repressor Proteins/*genetics/metabolism ; Sequence Alignment/veterinary ; },
abstract = {The highly conserved protein prohibitin 2 (PHB2) has been implicated as a cell-surface receptor in the regulation of proliferation, apoptosis, transcription, and mitochondrial protein folding. In the present study, we identified a Lampetra morii homologue of PHB2, Lm-PHB2, showing greater than 61.8% sequence identity with its homologues. Phylogenetic analysis indicated that the position of Lm-PHB2 is consistent with lamprey phylogeny. Expression of the Lm-PHB2 protein was nearly equivalent in the heart, liver, kidneys, intestines, and muscles of normal lampreys. However, the Lm-PHB2 protein was down-regulated in the myocardia of lampreys challenged for 5 days with adriamycin (Adr), followed by a significant up-regulation 10 days after treatment. In vitro, recombinant Lm-PHB2 (rLm-PHB2) protein could significantly enhance the H2O2-induced oxidative stress tolerance in Chang liver (CHL) cells. Further mechanism studies indicated that the nucleus-to-mitochondria translocation of Lm-PHB2 was closely involved in the oxidative stress protection. Our results suggests that the strategies to modulate Lm-PHB2 levels may constitute a novel therapeutic approach for myocardial injury and liver inflammatory diseases, conditions in which oxidative stress plays a critical role in tissue injury and inflammation.},
}
@article {pmid25463302,
year = {2015},
author = {Xiang, Z and Qu, F and Wang, F and Xiao, S and Jun, L and Zhang, Y and Yu, Z},
title = {ChBax/Bak as key regulators of the mitochondrial apoptotic pathway: cloned and characterized in Crassostrea hongkongensis.},
journal = {Fish &amp; shellfish immunology},
volume = {42},
number = {2},
pages = {225-232},
doi = {10.1016/j.fsi.2014.11.013},
pmid = {25463302},
issn = {1095-9947},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*genetics ; Base Sequence ; Cloning, Molecular ; Crassostrea/*genetics/metabolism ; DNA, Complementary/genetics/metabolism ; Genes, Reporter ; HEK293 Cells ; Hemocytes/metabolism ; Humans ; Mitochondria/physiology ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Tumor Suppressor Protein p53/genetics/metabolism ; bcl-2 Homologous Antagonist-Killer Protein/*genetics/metabolism ; bcl-2-Associated X Protein/*genetics/metabolism ; },
abstract = {Apoptosis has been primarily investigated in mammals, and little is known about apoptosis in mollusks. The proteins Bax and Bak play critical roles in the mitochondrial apoptosis pathway and in determining cell fate. In this study, ChBax and ChBak, homologs of the well-known Bax and Bak proteins, were identified from the oyster Crassostrea hongkongensis. The ChBax/Bak proteins consist of 207/232 amino acids with the typical domains found in BCL-2 family members. ChBax and ChBak mRNA expression were detected in all 8 of the selected oyster tissues and at the different stages of development. Fluorescence microscopy revealed that the full-length proteins of ChBax/Bak were located in the cytoplasm and mitochondrial outer membrane, of HEK293T cells, respectively. Furthermore, both of the genes' expression levels were found to increase in the hemocytes of oysters challenged with pathogens. The over-expression of ChBax or ChBak activates the p53-Luc reporter gene in HEK293T cells in a dose-dependent manner. These results indicate that ChBax and ChBak may play important roles in the mitochondrial apoptotic pathway in oysters.},
}
@article {pmid25470288,
year = {2014},
author = {Wang, J and Peng, LY and You, CP and Li, QL and Wen, M and Liu, SJ and Hong, YH},
title = {Minifish mtDNA has abundance of repeat sequences and inefficient replication in vitro.},
journal = {Current molecular medicine},
volume = {14},
number = {10},
pages = {1299-1307},
doi = {10.2174/1566524014666141202163927},
pmid = {25470288},
issn = {1875-5666},
mesh = {Animals ; Base Sequence ; China ; Cypriniformes/classification/*genetics ; DNA Replication ; DNA, Mitochondrial/chemistry/*genetics ; *Genes, Mitochondrial ; Genome Size ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Tandem Repeat Sequences ; Wetlands ; },
abstract = {Paedocypris is a newly described minifish genus endemic to Southeast Asia. Besides a tiny adult size of ~8 mm in length, minifish feature fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode, truncated development and one of the smallest known genomes. A complete sequence is absent for the minifish mitochondrial DNA (mtDNA). Here we report the complete mtDNA sequence and its unusual feature in the minifish P. progenetica (Pp). We show that the Pp mtDNA is a circular molecule of 17,382 bp in length and has the same number of similarly oriented genes as in other vertebrates. Specifically, it comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 D-loop. Surprisingly, the D-loop is elusive for amplification by standard PCR conditions. The D-loop possesses a 28-bp dinucleotide TA repeat and more intriguingly, up to 25 copies of a 34-bp tandem repeat sequence. These tandem repeats predict the formation of paired regions. Hence, besides a generally conserved mtDNA with other vertebrates, the Pp mtDNA features an unusual D-loop and compromised DNA replication in vitro.},
}
@article {pmid25470289,
year = {2014},
author = {Chen, D and Li, Y and Li, H and Wang, K and Du, S and Chu, W and Zhang, J},
title = {The genetic diversity of sinipercid fishes based on complete mitochondrial DNA of six sinipercid fishes from different drainages in China.},
journal = {Current molecular medicine},
volume = {14},
number = {10},
pages = {1279-1285},
doi = {10.2174/1566524014666141202162058},
pmid = {25470289},
issn = {1875-5666},
mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mutation Rate ; Perciformes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Sinipercids are a group of freshwater perciform fish endemic in East Asia with the majority of species recorded in China. In the present study, we analyzed the organizations of complete mitogenomes of the six sinipercid fish populations from the Yangtze River and the Pearl River systems in China. The proportion of G was relatively low just at 16.2%-16.5% among the fish populations analyzed. The similarity and divergence analysis showed that the populations from different drainages have more sequence similarities than those from different species in the same drainages. The rate of point mutation was 0.39% and a total of 422 variable sites were identified in the 12 protein-coding genes (excluding the ND6) among the four S. scherzeri populations. The analysis of evolutionary relationship showed that the four S. scherzeri populations can be divided into two groups of Yangtze River system and the Pearl River. Overall the data provide significant information for the genetic and evolutionary status of sinipercids upon adapting to different environments, and for genetic conservation and selective breeding of these fish species in fishery and aquaculture.},
}
@article {pmid25471440,
year = {2016},
author = {Zhang, C and Fu, X and Zhu, Z and Xie, K and Guo, Y},
title = {The complete mitochondrial genome sequence of Helicophagella melanura (Diptera: Sarcophagidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3905-3906},
doi = {10.3109/19401736.2014.987258},
pmid = {25471440},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Diptera/classification/*genetics ; *Genome, Mitochondrial ; Insect Proteins/chemistry/genetics/metabolism ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/chemistry/genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial genome of Helicophagella melanura, a representative of the Sarcophagidae family, was completely sequenced for the first time. The genome is a double-stranded circular molecule of 15,190 bp length, including the 37 genes and 1 non-coding AT-rich region. The gene contents of the mtDNA were identical to those observed in the ancestral arthropod. The total base composition of Helicophagella melanura mitochondrial genome is 39.42% for A, 36.22% for T, 14.71% for C and 9.65% for G and in the order A > T > C > G. The mitochondrial genome data of Helicophagella melanura is useful markers for species discrimination in forensic entomology and for phylogenetic analysis.},
}
@article {pmid25471441,
year = {2016},
author = {Dietrich, C and Brune, A},
title = {The complete mitogenomes of six higher termite species reconstructed from metagenomic datasets (Cornitermes sp., Cubitermes ugandensis, Microcerotermes parvus, Nasutitermes corniger, Neocapritermes taracua, and Termes hospes).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3903-3904},
doi = {10.3109/19401736.2014.987257},
pmid = {25471441},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Gastrointestinal Tract/metabolism ; *Genome, Mitochondrial ; Isoptera/classification/*genetics ; Likelihood Functions ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {We reconstructed the complete mitochondrial genomes of six higher termite species from metagenomic datasets of their isolated hindgut compartments. The sequencing reads were retrieved and assembled with the mitochondrial-baiting and iterative-mapping algorithm (MITObim), which yielded closed mitogenomes without additional finishing efforts (average coverage ranging from 2300- to 17,000-fold). The genomes ranged from 16.1 to 17.6 kbp in size and had G+C contents between 32 and 35 mol%; each contained the same 37 genes present also in the mitochondria of other termite species. Our study substantially increases the number of termite mitogenomes available for phylogenetic studies and offers a facile strategy for identifying host species in metagenomic studies of their associated microbiota.},
}
@article {pmid25482773,
year = {2014},
author = {Wang, M and Ma, X and Shen, J and Li, C and Zhang, W},
title = {The ongoing story: the mitochondria pyruvate carrier 1 in plant stress response in Arabidopsis.},
journal = {Plant signaling &amp; behavior},
volume = {9},
number = {10},
pages = {e973810},
pmid = {25482773},
issn = {1559-2324},
mesh = {Anion Transport Proteins ; Arabidopsis/genetics/*physiology ; Arabidopsis Proteins ; Gene Expression Regulation, Plant ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Monocarboxylic Acid Transporters ; Phylogeny ; Protein Interaction Mapping ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; *Stress, Physiological ; Subcellular Fractions/metabolism ; },
abstract = {Abscisic acid (ABA) is an important regulator of guard cell ion channels and stomatal movements in response to drought stress. Pyruvate is the final product of glycolysis in the cytosol, and could be transported by mitochondrial pyruvate carriers (MPCs) into mitochondrion for consequent cellular substance and energy metabolism. We recently characterized the first putative mitochondrial pyruvate carrier, NRGA1, in planta, and found that this small protein is involved in the negative regulation of drought and ABA induced guard cell signaling in Arabidopsis thaliana. The findings revealed a probable link between mitochondrial pyruvate transport and guard cell signaling. It has also been shown that NRGA1 protein product was directed to the mitochondria, and co-expression of MPC1 and NRGA1 functionally complement the absence of a native pyruvate transport protein in yeast. Here, we further demonstrated that MPC1 showed similar sub-cellular localization pattern to NRGA1. Quantitative RT-PCR analysis showed that the transcription of both NRGA1 and MPC1 were induced by pyruvate or ABA, and pyruvate strengthened the ABA induced transcription of these 2 genes. The similarity in subcellular localization and gene expression to ABA strongly suggests that MPC1 may associate with NRGA1 for mitochondrial pyruvate transport and is involved in ABA mediated stomatal movements in Arabidopsis.},
}
@article {pmid25482898,
year = {2015},
author = {Smith, KF and Abbott, CL and Saito, Y and Fidler, AE},
title = {Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum.},
journal = {Marine genomics},
volume = {19},
number = {},
pages = {75-83},
doi = {10.1016/j.margen.2014.11.007},
pmid = {25482898},
issn = {1876-7478},
mesh = {Adaptation, Biological/*genetics ; Animal Distribution ; Animals ; Base Sequence ; Computational Biology ; DNA Primers/genetics ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Species Specificity ; Urochordata/*genetics ; },
abstract = {The mitochondria are the main source of cellular energy production and have an important role in development, fertility, and thermal limitations. Adaptive mitochondrial DNA mutations have the potential to be of great importance in determining aspects of the life history of an organism. Phylogenetic analyses of the globally invasive marine ascidian Didemnum vexillum using the mitochondrial cytochrome c oxidase 1 (COX1) coding region, revealed two distinct clades. Representatives of one clade (denoted by 'B') are geographically restricted to D. vexillum's native region (north-west Pacific Ocean, including Japan), whereas members of the other clade (denoted by 'A') have been introduced and become invasive in temperate coastal areas around the world. Persistence of clade B's restricted distribution may reflect it being inherently less invasive than clade A. To investigate this we sought to determine if the two clades differ significantly in other mitochondrial genes of functional significance, specifically, alterations in amino acids encoded in mitochondrial enzyme subunits. Differences in functional mitochondrial genes could indicate an increased ability for clade A colonies to tolerate a wider range of environmental temperature. Full mitochondrial genomic sequences from D. vexillum clades A and B were obtained and they predict significant sequence differences in genes encoding for enzymes involved in oxidative phosphorylation. Diversity levels were relatively high and showed divergence across almost all genes, with p-distance values between the two clades indicating recent divergence. Both clades showed an excess of rare variants, which is consistent with balancing selection or a recent population expansion. Results presented here will inform future research focusing on examining the functional properties of the corresponding mitochondrial respiration enzymes, of A and B clade enzymes. By comparing closely related taxa that have differing distributions it is possible to identify genes and phenotypes suited to particular environments. The examination of mitochondrial genotypes, and associated enzyme functioning, across populations may aid in our understanding of thermal tolerance and environmental adaptation.},
}
@article {pmid25484173,
year = {2016},
author = {Liang, R and Wang, C and Zou, Q and Zhou, A and Zhou, M},
title = {Molecular phylogenetic relationships of some common sweetlips (Haemulidae: Plectorhynchinae) and the synonyms controversy of two Plectorhinchus species.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2209-2214},
doi = {10.3109/19401736.2014.982628},
pmid = {25484173},
issn = {2470-1408},
mesh = {Animals ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Mitochondria/genetics ; Perciformes/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Molecular phylogenetic topologies from 40 individuals of 17 sweetlips were constructed based on the mitochondrial cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) genes. All phylogenetic results strongly revealed the division of the sweetlips into three morphological distinct groups. Group I: sweetlips with colorful patterns, Group II and Group III: species with uniformly dark patterns. The relationships of those morphologically confused Plectorhinchus species were well-resolved in the phylogenetic results. We also confirmed that the genus Diagramma was placed inside the colorful Plectorhinchus groups, suggesting close relationship of Diagramma within Plectorhinchus. Additionally, we found that two species, P. orientalis and P. vittatus, which were traditionally considered as synonyms for oriental sweetlips, which were suggested to be two distinct species. Sequence divergence also revealed a great genetic variation between P. orientalis and P. vittatus (6.0% in Cyt b and 7.4% in COI), which was largely greater than the species diagnosis divergence value (2%) suggested by Hebert et al. This new finding suggested P. orientalis and P. vittatus might be two distinct species and should not be placed as synonyms.},
}
@article {pmid25484174,
year = {2016},
author = {Chen, H and Huang, H and Li, J and Zhao, Y and Deng, S and Li, G and Huang, H and Zhu, C},
title = {Characterization of the complete mitochondrial genome of Seriolella porosa (Perciformes: Centrolophidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {3},
pages = {2203-2204},
doi = {10.3109/19401736.2014.982626},
pmid = {25484174},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; },
abstract = {We have presented the complete mitochondrial genome of the Seriolella porosa in this study. The mitochondrial genome is 16,814 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Seriolella porosa mitochondrial genome was similar to those of most vertebrates. The nucleotide compositions of the light strand in descending order is 29.75% of T, 29.39% of G, 24.84% of A and 16.02% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all the other mitochondrial genes are encoded on the heavy strand.},
}
@article {pmid25489773,
year = {2016},
author = {Du, LN and Shi, FL and Liu, ZJ and Zhou, QH},
title = {Complete mitochondrial genome of the crested black macaque (Macaca nigra).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {3888-3889},
doi = {10.3109/19401736.2014.987248},
pmid = {25489773},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Mitochondrial/chemistry/genetics ; Genome, Mitochondrial/*genetics ; Macaca/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; },
abstract = {The complete mitochondrial sequence of the crested black macaque (Macaca nigra) has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,564 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 D-loop control region. The base composition of mtDNA genome is 31.76% A, 25.27% T, 30.17% C, and 12.80% G, with an AT content of 57.03%. The arrangement of genes in M. nigra is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. nigra presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.},
}
@article {pmid25498759,
year = {2014},
author = {Chan, A and Chiang, LP and Hapuarachchi, HC and Tan, CH and Pang, SC and Lee, R and Lee, KS and Ng, LC and Lam-Phua, SG},
title = {DNA barcoding: complementing morphological identification of mosquito species in Singapore.},
journal = {Parasites &amp; vectors},
volume = {7},
number = {},
pages = {569},
pmid = {25498759},
issn = {1756-3305},
mesh = {Animal Distribution ; Animals ; Culicidae/classification/*genetics/physiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Mitochondria/enzymology ; Phylogeny ; Singapore ; },
abstract = {BACKGROUND: Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore.<br><br>METHODS: We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity.<br><br>RESULTS: The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases.<br><br>CONCLUSIONS: Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.},
}
@article {pmid25499696,
year = {2015},
author = {Sun, S and Kong, L and Yu, H and Li, Q},
title = {The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species.},
journal = {Gene},
volume = {557},
number = {1},
pages = {61-70},
doi = {10.1016/j.gene.2014.12.011},
pmid = {25499696},
issn = {1879-0038},
mesh = {Animals ; Arcidae/*genetics ; Base Composition ; Base Sequence ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Tandem Repeat Sequences/genetics ; },
abstract = {To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).},
}
@article {pmid25502045,
year = {2014},
author = {Hu, J and Jiang, ZL and Nardi, F and Liu, YY and Luo, XR and Li, HX and Zhang, ZK},
title = {Members of Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species and the status of two invasive alien species in the Yunnan Province (China).},
journal = {Journal of insect science (Online)},
volume = {14},
number = {},
pages = {},
pmid = {25502045},
issn = {1536-2442},
mesh = {Animals ; Base Sequence ; Bayes Theorem ; China ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Hemiptera/*classification/genetics ; Introduced Species ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeography ; Polymerase Chain Reaction ; },
abstract = {Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex that includes some of the most significant pests of agriculture and horticulture worldwide. To understand the diversity and distribution of B. tabaci cryptic species in Yunnan, a famous biodiversity hotspot in China, a large-scale sampling was conducted from year 2010 to 2013 in 10 prefectures. Mitochondrial cytochrome oxidase I gene sequences were used to identify different cryptic species. Phylogenetic analyses were performed using Bayesian methods to assess the position of a new B. tabaci cryptic species in the context of the B. tabaci diversity in Asia. The survey indicates at least eight B. tabaci cryptic species are present in Yunnan, two invasive (MEAM1 and MED) and six indigenous (China 2, China3, China 4, Asia I, Asia II 1, and Asia II 6), MEAM1, MED, and Asia I being the three predominant cryptic species in Yunnan. Compared with MEAM1, MED has a wider distribution. Based on molecular data, a new cryptic species, here named China 4, was identified that appears to be related to China 1, China 2, and China 3. Future efforts should focus on the interactions between predominant B. tabaci cryptic species and begomoviruses and on the development of effective control strategies.},
}
@article {pmid25510528,
year = {2015},
author = {Tsuchiya, M and Toyofuku, T and Uematsu, K and Brüchert, V and Collen, J and Yamamoto, H and Kitazato, H},
title = {Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera).},
journal = {The Journal of eukaryotic microbiology},
volume = {62},
number = {4},
pages = {454-469},
doi = {10.1111/jeu.12200},
pmid = {25510528},
issn = {1550-7408},
mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Bacteria/*cytology/*genetics/isolation &amp; purification/metabolism ; Carbon/metabolism ; Cell Membrane/microbiology ; Cytoplasm/microbiology ; Deltaproteobacteria/*cytology/*genetics/isolation &amp; purification ; Foraminifera/*microbiology ; Geologic Sediments/microbiology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; },
abstract = {The benthic foraminifer Virgulinella fragilis Grindell and Collen 1976 has multiple putative symbioses with both bacterial and kleptoplast endobionts, possibly aiding its survival in environments from dysoxia (5-45 μmol-O2 /L) to microxia (0-5 μmol-O2 /L) and in the dark. To clarify the origin and function of V. fragilis endobionts, we used genetic analyses and transmission electron microscope observations. Virgulinella fragilis retained δ-proteobacteria concentrated at its cell periphery just beneath the cell membranes. Unlike another foraminifer Stainforthia spp., which retains many bacterial species, V. fragilis has a less variable bacterial community. This suggests that V. fragilis maintains a specific intracellular bacterial flora. Unlike the endobiotic bacteria, V. fragilis klepto-plasts originated from various diatom species and are found in the interior cytoplasm. We found evidence of both retention and digestion of kleptoplasts, and of fragmentation of the kleptoplastid outer membrane that likely facilitates transport of kleptoplastid products to the host. Accumulations of mitochondria were observed encircling endobiotic bacteria. It is likely that the bacteria use host organic material for carbon oxidation. The mitochondria may use oxygen available around the δ-proteobacteria and synthesize adenosine triphosphate, perhaps for sulfide oxidation.},
}
@article {pmid25544518,
year = {2014},
author = {Ito, M and Watanabe, K and Maeto, K},
title = {Revision of the genus Arotes Gravenhorst (Hymenoptera: Ichneumonidae: Acaenitinae) from Japan.},
journal = {Zootaxa},
volume = {3893},
number = {2},
pages = {196-208},
doi = {10.11646/zootaxa.3893.2.2},
pmid = {25544518},
issn = {1175-5334},
mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Islands ; Japan ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Wasps/anatomy &amp; histology/*classification/genetics/growth &amp; development ; },
abstract = {Three Japanese species of the genus Arotes Gravenhorst, 1829 are revised. A new species, A. japonicus Ito &amp; Watanabe, sp. nov., is described from the four main islands of Japan. This species can easily be distinguished from congeneric species by the black body without yellow markings and the entirely black hind tibia. Arotes sugiharai Uchida, 1934 is newly recorded from the islands of Kyushu and Tsushima, and the males of this species are described for the first time. The synonymy of A. moiwanus (Matsumura, 1912) and its color variant alboannulatus Uchida, 1928 are confirmed by DNA sequence analysis of the mitochondrial COI gene. The key to the world's species of Arotes proposed by Castillo et al. (2011) is updated and a key to the Japanese species is provided.},
}
@article {pmid25557487,
year = {2015},
author = {Škodová-Sveráková, I and Verner, Z and Skalický, T and Votýpka, J and Horváth, A and Lukeš, J},
title = {Lineage-specific activities of a multipotent mitochondrion of trypanosomatid flagellates.},
journal = {Molecular microbiology},
volume = {96},
number = {1},
pages = {55-67},
doi = {10.1111/mmi.12920},
pmid = {25557487},
issn = {1365-2958},
mesh = {Electron Transport/genetics/*physiology ; Leishmania/genetics/metabolism ; Mitochondria/genetics/*physiology ; Oxidative Phosphorylation ; Phylogeny ; Trypanosoma brucei brucei/genetics/metabolism ; Trypanosomatina/genetics/*metabolism ; },
abstract = {Trypanosomatids are a very diverse group composed of monoxenous and dixenous parasites belonging to the excavate class Kinetoplastea. Here we studied the respiration of five monoxenous species (Blechomonas ayalai, Herpetomonas muscarum, H. samuelpessoai, Leptomonas pyrrhocoris and Sergeia podlipaevi) introduced into culture, each representing a novel yet globally distributed and/or species-rich clade, and compare them with well-studied flagellates Trypanosoma brucei, Phytomonas serpens, Crithidia fasciculata and Leishmania tarentolae. Differences in structure and activities of respiratory chain complexes, respiration and other biochemical parameters recorded under laboratory conditions reveal their substantial diversity, likely a reflection of different host environments. Phylogenetic relationships of the analysed trypanosomatids do not correlate with their biochemical parameters, with the differences within clades by far exceeding those among clades. As the S. podlipaevi canonical respiratory chain complexes have very low activities, we believe that its mitochondrion is utilised for purposes other than oxidative phosphorylation. Hence, the single reticulated mitochondrion of diverse trypanosomatids seems to retain multipotency, with the capacity to activate its individual components based on the host environment.},
}
@article {pmid25564461,
year = {2015},
author = {Bongaerts, P and Frade, PR and Hay, KB and Englebert, N and Latijnhouwers, KR and Bak, RP and Vermeij, MJ and Hoegh-Guldberg, O},
title = {Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {7652},
pmid = {25564461},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/classification/*genetics/growth &amp; development ; Caribbean Region ; Coral Reefs ; Ecosystem ; Genetic Variation ; Genotype ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/chemistry/genetics/metabolism ; Symbiosis/genetics ; Temperature ; },
abstract = {The composition, ecology and environmental conditions of mesophotic coral ecosystems near the lower limits of their bathymetric distributions remain poorly understood. Here we provide the first in-depth assessment of a lower mesophotic coral community (60-100 m) in the Southern Caribbean through visual submersible surveys, genotyping of coral host-endosymbiont assemblages, temperature monitoring and a growth experiment. The lower mesophotic zone harbored a specialized coral community consisting of predominantly Agaricia grahamae, Agaricia undata and a "deep-water" lineage of Madracis pharensis, with large colonies of these species observed close to their lower distribution limit of ~90 m depth. All three species associated with "deep-specialist" photosynthetic endosymbionts (Symbiodinium). Fragments of A. grahamae exhibited growth rates at 60 m similar to those observed for shallow Agaricia colonies (~2-3 cm yr(-1)), but showed bleaching and (partial) mortality when transplanted to 100 m. We propose that the strong reduction of temperature over depth (Δ5°C from 40 to 100 m depth) may play an important contributing role in determining lower depth limits of mesophotic coral communities in this region. Rather than a marginal extension of the reef slope, the lower mesophotic represents a specialized community, and as such warrants specific consideration from science and management.},
}
@article {pmid25592231,
year = {2015},
author = {Pervaiz, T and Sun, X and Zhang, Y and Tao, R and Zhang, J and Fang, J},
title = {Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium).},
journal = {BMC plant biology},
volume = {15},
number = {},
pages = {4},
pmid = {25592231},
issn = {1471-2229},
mesh = {Alleles ; Base Sequence ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genotype ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Prunus/*genetics ; Prunus avium/genetics ; Prunus domestica/genetics ; Prunus persica/genetics ; Sequence Alignment ; },
abstract = {BACKGROUND: The nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium.<br><br>RESULTS: We investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths.<br><br>CONCLUSIONS: These results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.},
}
@article {pmid25592976,
year = {2015},
author = {Goldberg, J and Bresseel, J and Constant, J and Kneubühler, B and Leubner, F and Michalik, P and Bradler, S},
title = {Extreme convergence in egg-laying strategy across insect orders.},
journal = {Scientific reports},
volume = {5},
number = {},
pages = {7825},
pmid = {25592976},
issn = {2045-2322},
mesh = {Animals ; Coleoptera/classification/growth &amp; development ; Female ; Histones/genetics ; Insecta/classification/growth &amp; development/*physiology ; Mantodea/classification/growth &amp; development ; Mitochondria/genetics ; Ovum/growth &amp; development/metabolism ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Tomography, X-Ray Computed ; },
abstract = {The eggs of stick and leaf insects (Phasmatodea) bear strong resemblance to plant seeds and are commonly dispersed by females dropping them to the litter. Here we report a novel egg-deposition mode for Phasmatodea performed by an undescribed Vietnamese species of the enigmatic subfamily Korinninae that produces a complex egg case (ootheca), containing numerous eggs in a highly ordered arrangement. This novel egg-deposition mode is most reminiscent of egg cases produced by members of unrelated insect orders, e.g. by praying mantises (Mantodea) and tortoise beetles (Coleoptera: Cassidinae). Ootheca production constitutes a striking convergence and major transition in reproductive strategy among stick insects, viz. a shift from dispersal of individual eggs to elaborate egg concentration. Adaptive advantages of ootheca formation on arboreal substrate are likely related to protection against parasitoids and desiccation and to allocation of specific host plants. Our phylogenetic analysis of nuclear (28S, H3) and mitochondrial (COI, COII) genes recovered Korinninae as a subordinate taxon among the species-rich Necrosciinae with Asceles as sister taxon, thus suggesting that placement of single eggs on leaves by host plant specialists might be the evolutionary precursor of ootheca formation within stick insects.},
}
@article {pmid25598369,
year = {2014},
author = {Yu, X and He, Z and Xiang, H and Zheng, J and Nan, B and Zheng, B and Gao, J and Huang, S and Guan, M and Chen, B},
title = {[Function study of non-syndromic deafness associated mitochondrial 12S rRNA A839G mutation].},
journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery},
volume = {49},
number = {11},
pages = {908-915},
pmid = {25598369},
issn = {1673-0860},
mesh = {Aminoglycosides ; Cell Line ; DNA, Mitochondrial ; Deafness/*genetics ; Galactose ; Hearing Tests ; Mitochondria ; Mutation ; Pedigree ; Phylogeny ; RNA, Ribosomal/*genetics ; },
abstract = {OBJECTIVE: To investigate the correlation between nonsyndromic deafness and mitochondrial 12s rRNA A839G mutation.<br><br>METHODS: According to the clinical manifestations of mitochondrial DNA sequencing and analysis to find and determine family containing mitochondrial 12s rRNA A839G mutation. Harvested its family members blood and transferred their lymphocytes into lymphoblastoid cell lines, followed by cells cultured, cell doubling experiment, susceptibility testing, cellular oxygen consumption rate experiment, ROS and mitochondrial membrane potential experimental tests were progressed to explore the correlation between the A839G mutation and nonsyndromic deafness.<br><br>RESULTS: The mitochondrial 12s rRNA A839G mutation pedigrees were determined through the full sequence detections of the Mitochondrial DNA, further phylogenetic analysis showed that 839 point conservative index (CI) up to 78.6%; in RPMI-galactose medium containing A839G gene mutant cell line, the doubling time was significantly longer than the control group, and the difference was significant (P = 0.033). The effect to cell lines containing the A839G mutation of aminoglycoside drugs was not obvious. When compared with the control group, cell lines containing the A839G mutation significantly reduced cellular oxygen consumption rate(P = 0.033); compared with the control group, the ROS levels of cell lines containing the A839G mutation appeared more substantial elevated with significan difference (P < 0.01). The mitochondrial membrane potential of cells of experimental group was significantly reduced than the control group.<br><br>CONCLUSION: The present study proved that the mitochondria 12s rRNA A839G mutations affect the function of the mitochondrial respiratory chain at the cell level, which might reduce the growth rate of the mutant cell lines, result in hearing.},
}
@article {pmid25600501,
year = {2015},
author = {Seligmann, H},
title = {Phylogeny of genetic codes and punctuation codes within genetic codes.},
journal = {Bio Systems},
volume = {129},
number = {},
pages = {36-43},
doi = {10.1016/j.biosystems.2015.01.003},
pmid = {25600501},
issn = {1872-8324},
mesh = {Amino Acids ; Animals ; Bacteria/genetics ; *Codon, Initiator ; *Codon, Terminator ; Frameshifting, Ribosomal ; *Genetic Code ; Humans ; *Mitochondria ; *Phylogeny ; Principal Component Analysis ; RNA, Transfer ; },
abstract = {Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.},
}
@article {pmid25608518,
year = {2015},
author = {Walpole, TB and Palmer, DN and Jiang, H and Ding, S and Fearnley, IM and Walker, JE},
title = {Conservation of complete trimethylation of lysine-43 in the rotor ring of c-subunits of metazoan adenosine triphosphate (ATP) synthases.},
journal = {Molecular &amp; cellular proteomics : MCP},
volume = {14},
number = {4},
pages = {828-840},
pmid = {25608518},
issn = {1535-9484},
support = {MC_U105663148/MRC_/Medical Research Council/United Kingdom ; MC_U105663150/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; *Conserved Sequence ; Humans ; Invertebrates/metabolism ; Lysine/*metabolism ; Methylation ; Molecular Sequence Data ; Molecular Weight ; Peptides/metabolism ; Phylogeny ; Protein Processing, Post-Translational ; Protein Subunits/chemistry/isolation &amp; purification/*metabolism ; Proton-Translocating ATPases/chemistry/*metabolism ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry ; },
abstract = {The rotors of ATP synthases turn about 100 times every second. One essential component of the rotor is a ring of hydrophobic c-subunits in the membrane domain of the enzyme. The rotation of these c-rings is driven by a transmembrane proton-motive force, and they turn against a surface provided by another membrane protein, known as subunit a. Together, the rotating c-ring and the static subunit a provide a pathway for protons through the membrane in which the c-ring and subunit a are embedded. Vertebrate and invertebrate c-subunits are well conserved. In the structure of the bovine F1-ATPase-c-ring subcomplex, the 75 amino acid c-subunit is folded into two transmembrane α-helices linked by a short loop. Each bovine rotor-ring consists of eight c-subunits with the N- and C-terminal α-helices forming concentric inner and outer rings, with the loop regions exposed to the phospholipid head-group region on the matrix side of the inner membrane. Lysine-43 is in the loop region and its ε-amino group is completely trimethylated. The role of this modification is unknown. If the trimethylated lysine-43 plays some important role in the functioning, assembly or degradation of the c-ring, it would be expected to persist throughout vertebrates and possibly invertebrates also. Therefore, we have carried out a proteomic analysis of c-subunits across representative species from different classes of vertebrates and from invertebrate phyla. In the twenty-nine metazoan species that have been examined, the complete methylation of lysine-43 is conserved, and it is likely to be conserved throughout the more than two million extant metazoan species. In unicellular eukaryotes and prokaryotes, when the lysine is conserved it is unmethylated, and the stoichiometries of c-subunits vary from 9-15. One possible role for the trimethylated residue is to provide a site for the specific binding of cardiolipin, an essential component of ATP synthases in mitochondria.},
}
@article {pmid25624149,
year = {2015},
author = {Jung, KH and Kim, SR and Giong, HK and Nguyen, MX and Koh, HJ and An, G},
title = {Genome-wide identification and functional analysis of genes expressed ubiquitously in rice.},
journal = {Molecular plant},
volume = {8},
number = {2},
pages = {276-289},
doi = {10.1016/j.molp.2014.10.013},
pmid = {25624149},
issn = {1752-9867},
mesh = {*Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Oryza/classification/*genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Seedlings/genetics/metabolism ; },
abstract = {Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.},
}
@article {pmid25629468,
year = {2016},
author = {Wu, YP and Xie, JF and He, QS and Xie, JL},
title = {The complete mitochondrial genome sequence of Colossoma macropomum (Characiformes: Serrasalmidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4080-4081},
doi = {10.3109/19401736.2014.1003853},
pmid = {25629468},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; Characiformes/*genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; South America ; Whole Genome Sequencing/methods ; },
abstract = {Colossoma macropomum (Cuvier, 1816) is the largest characin of South America. This species and its congeners mainly feed on zooplankton, insects, snails and decaying plants. In this paper, we sequenced and annotated the complete mitogenome of C. macropomum. The total length is 16,703 bp, and it typically consist of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNA, a light-strand replication origin (OL) and a large control region (D-loop). The overall base composition is 29.9%, 24.6%, 29.5% and 15.9% for A, T, C and G, respectively, with a slight bias on AT content (54.6%). All protein-coding genes share the start codon ATG, except for COI, which begins with GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 use AGA and COI, Cytb use an incomplete stop codon T. This information could provide useful molecular data and contribute to further phylogenetic studies of Characiformes and Serrasalmidae.},
}
@article {pmid25630736,
year = {2016},
author = {Zhang, Y and Xie, Z and Deng, X and Xie, Z and Liu, J and Xie, L and Luo, S and Huang, L and Huang, J and Zeng, T and Wang, S},
title = {Mitochondrial genome of the Luchuan pig (Sus scrofa).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4139-4141},
doi = {10.3109/19401736.2014.1003881},
pmid = {25630736},
issn = {2470-1408},
mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Sus scrofa ; Swine/*genetics ; },
abstract = {The complete mitochondrial genome sequence of the Luchuan pig was measured by PCR-based methods, primer-walking sequencing, and fragment cloning. The entire mitochondrial genome of the Luchuan pig was identified as a circular molecule consisting of 16,730 bp (GenBank accession number: KP126954). The contents of A, T, C, and G in the mitochondrial genome were found to be 34.65%, 25.80%, 26.19%, and 13.36%, respectively. The complete mitochondrial genome of the Luchuan pig contains a typical structure, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region (D-loop region). This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Sus scrofa domestic mitochondrial genomes.},
}
@article {pmid25655327,
year = {2015},
author = {Zhou, W and Zhou, J and Lv, Y and Qu, Y and Chi, M and Li, J and Feng, H},
title = {Identification and characterization of MAVS from black carp Mylopharyngodon piceus.},
journal = {Fish &amp; shellfish immunology},
volume = {43},
number = {2},
pages = {460-468},
doi = {10.1016/j.fsi.2015.01.016},
pmid = {25655327},
issn = {1095-9947},
mesh = {Adaptor Proteins, Signal Transducing/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Cyprinidae ; Fish Diseases/genetics/*immunology/virology ; Fish Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation ; *Immunity, Innate ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reoviridae/physiology ; Reoviridae Infections/genetics/immunology/veterinary/virology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/genetics/immunology/veterinary/virology ; },
abstract = {MAVS (mitochondria antiviral signaling protein) plays an important role in the host cellular innate immune response against microbial pathogens. In this study, MAVS has been cloned and characterized from black carp (Mylopharyngodon piceus). The full-length cDNA of black carp MAVS (bcMAVS) consists of 2352 nucleotides and the predicted bcMAVS protein contains 579 amino acids. Structural analysis showed that bcMAVS is composed of functional domains including an N-terminal CARD, a central proline-rich domain, a putative TRAF2-binding motif and a C-terminal TM domain, which is similar to mammalian MAVS. bcMAVS is constitutively transcribed in all the selected tissues including gill, kidney, heart, intestine, liver, muscle, skin and spleen; bcMAVS mRNA level in intestine, liver, muscle increased but decreased in spleen right after GCRV or SVCV infection. Multiple bands of bcMAVS were detected in western blot when it was expressed in tissue culture, which is similar to mammalian MAVS. Immunofluorescence assay determined that bcMAVS is a mitochondria protein and luciferase reporter assay demonstrated that bcMAVS could induce zebrafish IFN and EPC IFN expression in tissue culture. Data generated in this manuscript has built a solid foundation for further elucidating the function of bcMAVS in the innate immune system of black carp.},
}
@article {pmid25675712,
year = {2015},
author = {Shashank, PR and Ojha, R and Venkatesan, T and Jalali, SK and Bhanu, KR},
title = {Molecular characterization of brinjal shoot and fruit borer, Leucinodes orbonalis (Guenée) (Lepidoptera: Crambidae) based on mitochondrial marker cytochrome oxidase I and their phylogenetic relationship.},
journal = {Indian journal of experimental biology},
volume = {53},
number = {1},
pages = {51-55},
pmid = {25675712},
issn = {0019-5189},
mesh = {Animals ; Biomarkers ; DNA Primers ; Electron Transport Complex IV/*genetics ; Lepidoptera/enzymology/*genetics ; Mitochondria/*enzymology ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {Shoot and fruit borer, Leucinodes orbonalis is an important insect pest infesting brinjal or eggplant in India. Molecular characterization of nine different populations belonging to various brinjal growing regions was done using Cytochorome C Oxidase I (COI) gene. Nucleotide analysis of genetic diversity and phylogenetic analysis of the COI indicate that the L. orbonalis from different geographical regions are homogenous. The results showed less nucleotide diversity (π = 0.007895) and overall mean distance (0.008 ± 0.003). Topologies of neighbour-joining (NJ) trees indicate all the populations belong to single major clade. Therefore, it is inferred that there was no significant molecular diversity within L. orbonalis of different geographical locations of India with respect to COI.},
}
@article {pmid25701603,
year = {2015},
author = {Randhawa, R and Sehgal, M and Singh, TR and Duseja, A and Changotra, H},
title = {Unc-51 like kinase 1 (ULK1) in silico analysis for biomarker identification: a vital component of autophagy.},
journal = {Gene},
volume = {562},
number = {1},
pages = {40-49},
doi = {10.1016/j.gene.2015.02.056},
pmid = {25701603},
issn = {1879-0038},
mesh = {Amino Acid Sequence ; Animals ; Autophagy/*genetics ; Autophagy-Related Protein-1 Homolog ; Biomarkers/metabolism ; Computer Simulation ; Humans ; Intracellular Signaling Peptides and Proteins/chemistry/*genetics/metabolism ; Lipoylation ; Mammals/genetics ; Molecular Sequence Data ; Peptide Mapping ; Phosphorylation ; Phylogeny ; Protein Binding ; Protein Interaction Mapping ; Protein Isoforms/chemistry/genetics/metabolism ; *Protein Processing, Post-Translational ; Protein Serine-Threonine Kinases/chemistry/*genetics/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Transcription Factors/*genetics/metabolism ; Transcription, Genetic ; Xenopus/genetics ; },
abstract = {Autophagy is a degradation pathway involving lysosomal machinery for degradation of damaged organelles like the endoplasmic reticulum and mitochondria into their building blocks to maintain homeostasis within the cell. ULK1, a serine/threonine kinase, is conserved across species, from yeasts to mammals, and plays a central role in autophagy pathway. It receives signals from upstream modulators such as TIP60, mTOR and AMPK and relays them to its downstream substrates like Ambra1 and ZIP kinase. The activity of this complex is regulated through protein-protein interactions and post-translational modifications. Applying in silico analysis we identified (i) conserved patterns of ULK1 that showed its evolutionary relationship between the species which were closely related in a family compared to others. (ii) A total of 23 TFBS distributed throughout ULK1 and nuclear factor (erythroid-derived) 2 (NFE2) is of utmost significance because of its high importance rate. NEF2 has already been shown experimentally to play a role in the autophagy pathway. Most of these were of zinc coordinating class and we suggest that this information could be utilized to modulate this pathway by modifying interactions of these TFs with ULK1. (iii) CATTT haplotype was prominently found with frequency 0.774 in the studied population and nsSNPs which could have harmful effect on ULK1 protein and these could further be tested. (iv) A total of 83 phosphorylation sites were identified; 26 are already known and 57 are new that include one at tyrosine residue which could further be studied for its involvement in ULK1 regulation and hence autophagy. Furthermore, 4 palmitoylation sites at positions 426, 927, 1003 and 1049 were also found which could further be studied for protein-protein interactions as well as in trafficking.},
}
@article {pmid25702753,
year = {2015},
author = {Kaya, A and Lobanov, AV and Gladyshev, VN},
title = {Evidence that mutation accumulation does not cause aging in Saccharomyces cerevisiae.},
journal = {Aging cell},
volume = {14},
number = {3},
pages = {366-371},
pmid = {25702753},
issn = {1474-9726},
support = {R37 GM065204/GM/NIGMS NIH HHS/United States ; AG038004/AG/NIA NIH HHS/United States ; GM065204/GM/NIGMS NIH HHS/United States ; },
mesh = {DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Mutation/*genetics ; *Mutation Accumulation ; Mutation Rate ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; },
abstract = {The concept that mutations cause aging phenotypes could not be directly tested previously due to inability to identify age-related mutations in somatic cells and determine their impact on organismal aging. Here, we subjected Saccharomyces cerevisiae to multiple rounds of replicative aging and assessed de novo mutations in daughters of mothers of different age. Mutations did increase with age, but their low numbers, < 1 per lifespan, excluded their causal role in aging. Structural genome changes also had no role. A mutant lacking thiol peroxidases had the mutation rate well above that of wild-type cells, but this did not correspond to the aging pattern, as old wild-type cells with few or no mutations were dying, whereas young mutant cells with many more mutations continued dividing. In addition, wild-type cells lost mitochondrial DNA during aging, whereas shorter-lived mutant cells preserved it, excluding a causal role of mitochondrial mutations in aging. Thus, DNA mutations do not cause aging in yeast. These findings may apply to other damage types, suggesting a causal role of cumulative damage, as opposed to individual damage types, in organismal aging.},
}
@article {pmid25714339,
year = {2015},
author = {Nojima, Y and Ito, K and Ono, H and Nakazato, T and Bono, H and Yokoyama, T and Sato, R and Suetsugu, Y and Nakamura, Y and Yamamoto, K and Satoh, J and Tabunoki, H and Fugo, H},
title = {Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori.},
journal = {PloS one},
volume = {10},
number = {2},
pages = {e0116007},
pmid = {25714339},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Bombyx/drug effects/genetics/*metabolism ; Cell Line ; Cloning, Molecular ; DNA, Complementary/genetics ; Fat Body/*metabolism ; Gene Expression Regulation ; Insecticides/pharmacology ; Isosorbide Dinitrate/pharmacology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reactive Oxygen Species/metabolism ; Rotenone/pharmacology ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Superoxide Dismutase/genetics/*metabolism ; Superoxide Dismutase-1 ; Superoxide Dismutase 2 ; },
abstract = {One way that aerobic biological systems counteract the generation of reactive oxygen species (ROS) is with superoxide dismutase proteins SOD1 and SOD2 that metabolize superoxide radicals to molecular oxygen and hydrogen peroxide or scavenge oxygen radicals produced by the extensive oxidation-reduction and electron-transport reactions that occur in mitochondria. We characterized SOD1 and SOD2 of Bombyx mori isolated from the fat body of larvae. Immunological analysis demonstrated the presence of BmSOD1 and BmSOD2 in the silk gland, midgut, fat body, Malpighian tubules, testis and ovary from larvae to adults. We found that BmSOD2 had a unique expression pattern in the fat body through the fifth instar larval developmental stage. The anti-oxidative functions of BmSOD1 and BmSOD2 were assessed by exposing larvae to insecticide rotenone or vasodilator isosorbide dinitrate, which is an ROS generator in BmN4 cells; however, exposure to these compounds had no effect on the expression levels of either BmSOD protein. Next, we investigated the physiological role of BmSOD1 and BmSOD2 under environmental oxidative stress, applied through whole-body UV irradiation and assayed using quantitative RT-PCR, immunoblotting and microarray analysis. The mRNA expression level of both BmSOD1 and BmSOD2 was markedly increased but protein expression level was increased only slightly. To examine the differences in mRNA and protein level due to UV irradiation intensity, we performed microarray analysis. Gene set enrichment analysis revealed that genes in the insulin signaling pathway and PPAR signaling pathway were significantly up-regulated after 6 and 12 hours of UV irradiation. Taken together, the activities of BmSOD1 and BmSOD2 may be related to the response to UV irradiation stress in B. mori. These results suggest that BmSOD1 and BmSOD2 modulate environmental oxidative stress in the cell and have a specific role in fat body of B. mori during pupation.},
}
@article {pmid25724193,
year = {2015},
author = {Tang, WG and Song, P and Cao, ZY and Wang, P and Zhu, GP},
title = {A unique homodimeric NAD[+]-linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {29},
number = {6},
pages = {2462-2472},
doi = {10.1096/fj.14-257014},
pmid = {25724193},
issn = {1530-6860},
mesh = {Algal Proteins/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites/genetics ; Blotting, Western ; Chlorophyta/*enzymology/genetics ; Circular Dichroism ; Isocitrate Dehydrogenase/*chemistry/classification/metabolism ; Isocitrates/metabolism ; Kinetics ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Molecular Weight ; Mutation ; NAD/*chemistry/metabolism ; NADP/chemistry/metabolism ; Phylogeny ; Protein Binding ; *Protein Multimerization ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {In eukaryotes, NAD(+)-dependent isocitrate dehydrogenase (IDH) is strictly mitochondrial and is a key enzyme in the Krebs cycle. To date, all known NAD(+)-specific IDHs (NAD-IDHs) in the mitochondria are believed to be heteromeric in solution. Here, a unique homodimeric NAD-IDH from Ostreococcus tauri (OtIDH), the smallest autotrophic picoeukaryote, was unveiled. Active OtIDH has a molecular weight of ∼93 kDa with each subunit of 46.7 kDa. In the presence of Mn(2+) and Mg(2+), OtIDH displayed 42-fold and 51-fold preference for NAD(+) over NADP(+), respectively. Interestingly, OtIDH exhibited a sigmoidal kinetic behavior in response to isocitrate unlike other homodimeric homologs, and a remarkably high affinity for isocitrate (S0.5 < 10 μM) unlike other hetero-oligomeric homologs. Furthermore, its coenzyme specificity can be completely converted from NAD(+) (ancient trait) to NADP(+) (adaptive trait) by rational mutagenesis based on the evolutionary trace. Mutants D344R and D344R/M345H displayed a 15-fold and 72-fold preference for NADP(+) over NAD(+), respectively, indicating that D344 and M345 are the determinants of NAD(+) specificity. These findings also suggest that OtIDH may be an ancestral form of type II IDHs (all reported members are NADP(+)-linked enzymes) and may have evolved into NADP(+)-dependent IDH for adaptation to the increased demand of NADPH under carbon starvation.},
}
@article {pmid25748711,
year = {2015},
author = {Bai, X and Kim, TI and Lee, JY and Dai, F and Hong, SJ},
title = {Identification and molecular characterization of Parkin in Clonorchis sinensis.},
journal = {The Korean journal of parasitology},
volume = {53},
number = {1},
pages = {65-75},
pmid = {25748711},
issn = {1738-0006},
mesh = {Amino Acid Sequence ; Animals ; Clonorchis sinensis/*enzymology ; Cluster Analysis ; Conserved Sequence ; DNA, Complementary/genetics ; Energy Metabolism ; Gene Expression Profiling ; Mitochondria/metabolism ; Models, Molecular ; Molecular Weight ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Ubiquitin-Protein Ligases/chemistry/*genetics/*metabolism ; },
abstract = {Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to Zn(2+) were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis.},
}
@article {pmid25760948,
year = {2015},
author = {Hadas, L and Hermon, D and Boldo, A and Arieli, G and Gafny, R and King, R and Bar-Gal, GK},
title = {Wild gazelles of the southern Levant: genetic profiling defines new conservation priorities.},
journal = {PloS one},
volume = {10},
number = {3},
pages = {e0116401},
pmid = {25760948},
issn = {1932-6203},
mesh = {Animals ; Antelopes/*classification/*genetics ; Cell Nucleus/genetics ; Conservation of Natural Resources ; DNA/*genetics ; Gene Flow ; Genetic Variation ; Israel ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; },
abstract = {The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.},
}
@article {pmid25788442,
year = {2016},
author = {Pandey, N and Rajagopal, R},
title = {Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH.},
journal = {Insect science},
volume = {23},
number = {5},
pages = {704-711},
doi = {10.1111/1744-7917.12220},
pmid = {25788442},
issn = {1744-7917},
mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/*genetics ; Hemiptera/genetics/*microbiology ; In Situ Hybridization, Fluorescence ; India ; Mitochondria/genetics ; Phylogeny ; Polyalthia/parasitology ; RNA, Ribosomal, 16S/*genetics ; Symbiosis ; },
abstract = {Dialeurolonga malleswaramensis Sundararaj (Hemiptera: Aleyrodidae) is a phytophagous sap sucking insect. It infests Polyalthia longifolia, an important avenue tree of India, effective in alleviating noise pollution and having immense medicinal importance. Samples of this insect were collected from Polyalthia longifolia. The cytochrome c oxidase subunit I gene (mtCO1) helped in the molecular characterization of the insect. This study reports the bacterial diversity in D. malleswaramensis adults by high throughput 16S rDNA amplicon pyrosequencing. The major genera identified were Portiera and Arsenophonus. Other bacterial genera detected were uncultured alpha proteobacterium, Sphingopyxis and Methylobacterium. We also employed fluorescence in situ hybridization (FISH) in whole mount samples to confirm the presence of dominant endosymbionts Portiera and Arsenophonus to the bacteriocyte of D. malleswaramensis. This study concludes that combining techniques like 16S rDNA amplicon pyrosequencing and FISH reveal both dominant and rare bacteria. The data also predict the evolutionary position of this pest with respect to other whitefly species using a mitochondrial marker.},
}
@article {pmid25788489,
year = {2015},
author = {Jacobsen, MW and Pujolar, JM and Hansen, MM},
title = {Relationship between amino acid changes in mitochondrial ATP6 and life-history variation in anguillid eels.},
journal = {Biology letters},
volume = {11},
number = {3},
pages = {},
pmid = {25788489},
issn = {1744-957X},
mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Anguilla/genetics/*physiology ; Animal Migration/*physiology ; Animals ; DNA, Mitochondrial/genetics ; Genotype ; Larva/*physiology ; Life Cycle Stages ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*metabolism ; Phenotype ; Phylogeny ; Reproduction/physiology ; },
abstract = {Mitochondrial genes are part of the oxidative phosphorylation pathway and important for energy production. Although evidence for positive selection at the mitochondrial level exists, few studies have investigated the link between amino acid changes and phenotype. Here we test the hypothesis that differences in two life-history related traits, migratory distance between spawning and foraging areas and larval phase duration, are associated with divergent selection within the mitochondrial ATP6 gene in anguillid eels. We compare amino acid changes among 18 species with the sequence of the putative ancestral species, believed to have shown short migratory distance and larval phase duration. We find positive correlations between both life-history related traits and (i) the number of amino acid changes and (ii) the strength of the combined physico-chemical and structural changes at positions previously identified as candidates for positive selection. This supports a link between genotype and phenotype driven by positive selection at ATP6.},
}
@article {pmid25806583,
year = {2016},
author = {Hofman, S and Pabijan, M and Osikowski, A and Litvinchuk, SN and Szymura, JM},
title = {Phylogenetic relationships among four new complete mitogenome sequences of Pelophylax (Amphibia: Anura) from the Balkans and Cyprus.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3434-3437},
doi = {10.3109/19401736.2015.1025266},
pmid = {25806583},
issn = {2470-1408},
mesh = {Animals ; Anura/genetics ; Balkan Peninsula ; Base Composition ; Cyprus ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We present the full-length mitogenome sequences of four European water frog species: Pelophylax cypriensis, P. epeiroticus, P. kurtmuelleri and P. shqipericus. The mtDNA size varied from 17,363 to 17,895 bp, and its organization with the LPTF tRNA gene cluster preceding the 12 S rRNA gene displayed the typical Neobatrachian arrangement. Maximum likelihood and Bayesian inference revealed a well-resolved mtDNA phylogeny of seven European Pelophylax species. The uncorrected p-distance for among Pelophylax mitogenomes was 9.6 (range 0.01-0.13). Most divergent was the P. shqipericus mitogenome, clustering with the "P. lessonae" group, in contrast to the other three new Pelophylax mitogenomes related to the "P. bedriagae/ridibundus" lineage. The new mitogenomes resolve ambiguities of the phylogenetic placement of P. cretensis and P. epeiroticus.},
}
@article {pmid25854186,
year = {2015},
author = {Breitenbach, M and Weber, M and Rinnerthaler, M and Karl, T and Breitenbach-Koller, L},
title = {Oxidative stress in fungi: its function in signal transduction, interaction with plant hosts, and lignocellulose degradation.},
journal = {Biomolecules},
volume = {5},
number = {2},
pages = {318-342},
pmid = {25854186},
issn = {2218-273X},
support = {P 26713/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Amino Acid Sequence ; Fungi/enzymology/genetics/*metabolism/pathogenicity ; Lignin/*metabolism ; Molecular Sequence Data ; *Oxidative Stress ; Oxidoreductases/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; *Signal Transduction ; Virulence/genetics ; },
abstract = {In this review article, we want to present an overview of oxidative stress in fungal cells in relation to signal transduction, interaction of fungi with plant hosts, and lignocellulose degradation. We will discuss external oxidative stress which may occur through the interaction with other microorganisms or plant hosts as well as internally generated oxidative stress, which can for instance originate from NADPH oxidases or "leaky" mitochondria and may be modulated by the peroxiredoxin system or by protein disulfide isomerases thus contributing to redox signaling. Analyzing redox signaling in fungi with the tools of molecular genetics is presently only in its beginning. However, it is already clear that redox signaling in fungal cells often is linked to cell differentiation (like the formation of perithecia), virulence (in plant pathogens), hyphal growth and the successful passage through the stationary phase.},
}
@article {pmid25861990,
year = {2015},
author = {Antonenkov, VD and Isomursu, A and Mennerich, D and Vapola, MH and Weiher, H and Kietzmann, T and Hiltunen, JK},
title = {The Human Mitochondrial DNA Depletion Syndrome Gene MPV17 Encodes a Non-selective Channel That Modulates Membrane Potential.},
journal = {The Journal of biological chemistry},
volume = {290},
number = {22},
pages = {13840-13861},
pmid = {25861990},
issn = {1083-351X},
mesh = {Amino Acid Sequence ; Animals ; Autophagy ; Circular Dichroism ; DNA Damage ; DNA, Mitochondrial/*genetics ; Fibroblasts/metabolism ; Fluoresceins/chemistry ; Genotype ; Homeostasis ; Humans ; Hydrogen-Ion Concentration ; Mass Spectrometry ; *Membrane Potential, Mitochondrial ; Membrane Proteins/*genetics ; Mice ; Mice, Transgenic ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phosphorylation ; Phylogeny ; Pichia/metabolism ; Reactive Oxygen Species/metabolism ; },
abstract = {The human MPV17-related mitochondrial DNA depletion syndrome is an inherited autosomal recessive disease caused by mutations in the inner mitochondrial membrane protein MPV17. Although more than 30 MPV17 gene mutations were shown to be associated with mitochondrial DNA depletion syndrome, the function of MPV17 is still unknown. Mice deficient in Mpv17 show signs of premature aging. In the present study, we used electrophysiological measurements with recombinant MPV17 to reveal that this protein forms a non-selective channel with a pore diameter of 1.8 nm and located the channel's selectivity filter. The channel was weakly cation-selective and showed several subconductance states. Voltage-dependent gating of the channel was regulated by redox conditions and pH and was affected also in mutants mimicking a phosphorylated state. Likewise, the mitochondrial membrane potential (Δψm) and the cellular production of reactive oxygen species were higher in embryonic fibroblasts from Mpv17(-/-) mice. However, despite the elevated Δψm, the Mpv17-deficient mitochondria showed signs of accelerated fission. Together, these observations uncover the role of MPV17 as a Δψm-modulating channel that apparently contributes to mitochondrial homeostasis under different conditions.},
}
@article {pmid25877339,
year = {2015},
author = {Catalano, SR and Whittington, ID and Donnellan, SC and Bertozzi, T and Gillanders, BM},
title = {First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation.},
journal = {Parasitology},
volume = {142},
number = {8},
pages = {1066-1079},
doi = {10.1017/S0031182015000384},
pmid = {25877339},
issn = {1469-8161},
mesh = {Animals ; Base Sequence ; Cephalopoda/*parasitology ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Invertebrates/*classification/enzymology/genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Untranslated/genetics ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; Species Specificity ; },
abstract = {Dicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I-III) of the cytochrome c oxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochrome c oxidase subunit I (COI) minicircle molecule, containing the COI gene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence in COI nucleotide sequences between dicyemid species was high (average net divergence = 31.6%) while within species diversity was lower (average net divergence = 0.2%). The NCR and putative 5' section of the COI gene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5' COI section = 61.1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.},
}
@article {pmid25880387,
year = {2015},
author = {Nguyen, DT and Spooner-Hart, RN and Riegler, M},
title = {Polyploidy versus endosymbionts in obligately thelytokous thrips.},
journal = {BMC evolutionary biology},
volume = {15},
number = {},
pages = {23},
pmid = {25880387},
issn = {1471-2148},
mesh = {Animals ; Cell Nucleus/genetics ; Female ; Genetic Variation ; Male ; Mitochondria/genetics ; *Parthenogenesis ; Phylogeny ; Polymerase Chain Reaction ; *Polyploidy ; Symbiosis ; Thysanoptera/classification/*genetics/*microbiology/physiology ; Wolbachia/genetics/*isolation &amp; purification ; },
abstract = {BACKGROUND: Thelytoky, the parthenogenetic development of females, has independently evolved in several insect orders yet the study of its mechanisms has so far mostly focussed on haplodiploid Hymenoptera, while alternative mechanisms of thelytoky such as polyploidy are far less understood. In haplodiploid insects, thelytoky can be encoded in their genomes, or induced by maternally inherited bacteria such as Wolbachia or Cardinium. Microbially facilitated thelytoky usually results in complete homozygosity due to gamete duplication and can be reverted into arrhenotoky, the parthenogenetic development of males, through treatment with antibiotics. In contrast, genetically encoded thelytoky cannot be removed and may result in conservation of heterozygosity due to gamete fusion. We have probed the obligate thelytoky of the greenhouse thrips, Heliothrips haemorrhoidalis (Bouché), a significant cosmopolitan pest and a model species of thelytoky in the haplodiploid insect order Thysanoptera. Earlier studies suggested terminal fusion as a mechanism for thelytoky in this species, while another study reported presence of Wolbachia; later it was speculated that Wolbachia plays a role in this thrips' thelytokous reproduction.<br><br>RESULTS: By using PCR and sequence analysis, we demonstrated that global population samples of H. haemorrhoidalis were not infected with Wolbachia, Cardinium or any other known bacterial reproductive manipulators. Antibiotic treatment of this thrips did also not result in male production. Some individuals carried two different alleles in two nuclear loci, histone 3 and elongation factor 1 alpha, suggesting heterozygosity. However, the majority of individuals had three different alleles suggesting that they were polyploid. Genetic diversity across both nuclear loci was low in all populations, and absent from mitochondrial cytochrome oxidase I, indicating that this species had experienced genetic bottlenecks, perhaps due to its invasion biology or a switch to thelytoky.<br><br>CONCLUSIONS: Geographically broad sampling and experimental manipulation revealed low genetic diversity, absence of Wolbachia but presence of three different alleles of nuclear loci in most analysed individuals of obligately thelytokous H. haemorrhoidalis. This suggests that polyploidy may be involved in the thelytokous reproduction of this thrips species, and polyploidy may be a contributing factor in the reproduction of Thysanoptera and other haplodiploid insect orders.},
}
@article {pmid25885076,
year = {2015},
author = {Fanciulli, PP and Mercati, D and Machida, R and Dallai, R},
title = {Spermiogenesis and sperm ultrastructure of Machilontus sp (Insecta: Archaeognatha) with phylogenetic consideration.},
journal = {Micron (Oxford, England : 1993)},
volume = {73},
number = {},
pages = {47-53},
doi = {10.1016/j.micron.2015.03.011},
pmid = {25885076},
issn = {1878-4291},
mesh = {Acrosome/ultrastructure ; Animals ; Axoneme ; Cell Nucleus/ultrastructure ; Insecta/*physiology/*ultrastructure ; Male ; Microscopy, Electron, Transmission/methods ; Microtubules/ultrastructure ; Phylogeny ; Species Specificity ; Sperm Tail/ultrastructure ; Spermatids/ultrastructure ; Spermatogenesis ; Spermatozoa/*ultrastructure ; },
abstract = {The sperm structure of the jumping bristletail Machilontus sp has been described. The species shares several sperm characteristics with other genera of the same order Archaeognatha. During late spermiogenesis the spermatid bends at half of its length with the two limbs closely apposed within the same plasma membrane. The sperm has a helicoidal bi-layered acrosome with a filamentous perforatorium and a long nucleus. The elongated flagellum consists of an axoneme with 9 accessory microtubules external to the 9+2, two rows of conventional mitochondria and two accessory bodies. The accessory bodies are located lateral to the axoneme and are probably responsible for the shifting of the accessory tubules in two opposite groups of 5 and 4 tubules, respectively. These sperm characteristics represent common traits of all Archaeognatha.},
}
@article {pmid25902514,
year = {2015},
author = {Gornik, SG and Febrimarsa, and Cassin, AM and MacRae, JI and Ramaprasad, A and Rchiad, Z and McConville, MJ and Bacic, A and McFadden, GI and Pain, A and Waller, RF},
title = {Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {18},
pages = {5767-5772},
pmid = {25902514},
issn = {1091-6490},
mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Oxidoreductases/metabolism ; Animals ; Cell Nucleus/metabolism ; Crustacea ; Cytosol/metabolism ; Dinoflagellida/genetics/*physiology ; Fatty Acid Synthases/metabolism ; Fatty Acids/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Parasites ; Photosynthesis ; Phylogeny ; Plasmodium ; Plastids/*genetics ; RNA/metabolism ; Symbiosis/*genetics ; Transcriptome ; },
abstract = {Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes--notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium--highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite's host. Hematodinium sp. thus represents a further dimension of endosymbiosis--life after the organelle.},
}
@article {pmid25909565,
year = {2015},
author = {Loader, SP and Lawson, LP and Portik, DM and Menegon, M},
title = {Three new species of spiny throated reed frogs (Anura: Hyperoliidae) from evergreen forests of Tanzania.},
journal = {BMC research notes},
volume = {8},
number = {},
pages = {167},
pmid = {25909565},
issn = {1756-0500},
mesh = {Altitude ; Animals ; Anura/*physiology ; Bayes Theorem ; Ecosystem ; Female ; *Forests ; Genetic Variation ; Male ; Mitochondria/metabolism ; Nucleotides/genetics ; Phylogeny ; Species Specificity ; Tanzania ; },
abstract = {BACKGROUND: The East African spiny-throated reed frog complex (Hyperolius spinigularis, H. tanneri, and H. minutissimus) is comprised of morphologically similar species with highly fragmented populations across the Eastern Afromontane Region. Recent genetic evidence has supported the distinctiveness of populations suggesting a number of cryptic species. We analyse newly collected morphological data and evaluate the taxonomic distinctiveness of populations.<br><br>RESULTS: We find three new distinct species on the basis of morphological and molecular evidence. The primary morphological traits distinguishing species within the Hyperolius spinigularis complex include the proportions and degree of spinosity of the gular flap in males and snout-urostyle length in females. Other features allow the three species to be distinguished from each other (genetics). We refine the understanding of H. minutissimus which can be found in both forest and grassland habitats of the Udzungwa Mountains, and provide more details on the call of this species. Further details on ecology are noted for all species where known.<br><br>CONCLUSIONS: Three new species are described and we narrow the definition and distribution of Hyperolius spinigularis and H. minutissimus in East Africa. The spiny-throated reed frogs have highly restricted distributions across the fragmented mountains of the Eastern Afromontane region. Given the newly defined and substantially narrower distributions of these spiny-throated reed frog species, conservation concerns are outlined.},
}
@article {pmid25916611,
year = {2015},
author = {Zhang, T and Li, W and Chen, H and Yu, H},
title = {Full genome sequence of a putative novel mitovirus isolated from Rhizoctonia cerealis.},
journal = {Archives of virology},
volume = {160},
number = {7},
pages = {1815-1818},
doi = {10.1007/s00705-015-2431-1},
pmid = {25916611},
issn = {1432-8798},
mesh = {Base Sequence ; *Genome, Viral ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA Viruses/classification/*genetics/*isolation &amp; purification ; Rhizoctonia/*virology ; Viral Proteins/genetics ; },
abstract = {A putative novel mitovirus was found in isolate R1084 of the fungus Rhizoctonia cerealis, the causal agent of sharp eyespot of wheat in China. The full genome sequence of the virus was determined and analyzed. The complete cDNA sequence is 3149 nucleotides long with 59.7% A+T content. Using either the fungal mitochondrial or universal genetic code, the viral genome was found to contain a single large open reading frame that is predicted to encode a protein of 812 amino acids with an RNA-dependent RNA polymerase (RdRp) domain that is conserved in the mitovirus RdRp superfamily. The amino acid sequence of the RdRp domain is only 50% identical to the corresponding domain in Sclerotinia sclerotiorum mitovirus 11, and therefore, this virus is proposed to be a novel mitovirus, designated as Rhizoctonia cerealis mitovirus 1-R1084 (RcMV1-R1084). The distinct codon usage of RcMV1-R1084 hints that this virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. This is the first report of a full-length genomic sequence of a putative mitovirus in R. cerealis.},
}
@article {pmid25917582,
year = {2015},
author = {Yeşilöz, H and Yıldırım, A},
title = {[The Molecular Classification Of Blackfly (Diptera: Simuliidae) Species Which Pose a Problem in Nevşehir Part of Central Kızılırmak Basin].},
journal = {Turkiye parazitolojii dergisi},
volume = {39},
number = {1},
pages = {33-40},
doi = {10.5152/tpd.2015.3778},
pmid = {25917582},
issn = {2146-3077},
mesh = {Animals ; DNA/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; DNA, Ribosomal Spacer/chemistry ; Electron Transport Complex IV/genetics ; Larva/anatomy &amp; histology/genetics ; Mitochondria/enzymology ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Simuliidae/anatomy &amp; histology/*classification/genetics ; Turkey ; },
abstract = {OBJECTIVE: This study was carried out to determine the molecular characterization of simuliid species which cause a problem in the part of Kızılırmak passes from Ürgüp and Gülşehir districts of Nevşehir.<br><br>METHODS: Between May and September 2011, totally 150 simuliid larvae were sampled. Morphological identifications of the collected larvae specimens were done before the molecular analyses. Genomic DNA extractions were utilized on 7 larvae specimens which were selected from morphologically identified samples and the sequence and phylogenetic analyses were performed after the amplification of the partial mitochondrial cytochrome oxidase subunit 1 (mt-COI) and ribosomal complete internal transcript spacer 2 and partial 28S (ITS-2/28S) gene regions.<br><br>RESULTS: Eighty-five, 46 and 19 out of 150 morphologically examined specimens were identified as Simulium (S.) Wilhelmia sp., S. Wilhelmia lineatum and S. Wilhelmia balcanicum, respectively. Among the amplified samples with respect to mt-COI and ITS-2/28S gene regions, sequence analyses were performed on 3 and 2 isolates from S. Wilhelmia sp. and both S. lineatum and S. balcanicum. The isolates were found to be clustered together depending on the species for both gene regions phylogenetically and the sequence heterogeneity was found to be higher in S. lineatum. When comparing with the other species under the Wilhelmia subgenus, S. lineatum and S. balcanicum were determined to be more close to each other.<br><br>CONCLUSION: Scientific data on the molecular characterization and phylogeny of blackfly species under the S. Wilhelima subgenus which pose a problem in the Central K&#x131;z&#x131;l&#x131;rmak Basin were provided with this study.},
}
@article {pmid25936970,
year = {2015},
author = {Hayashi, K and Ichikawa-Seki, M and Mohanta, UK and Singh, TS and Shoriki, T and Sugiyama, H and Itagaki, T},
title = {Molecular phylogenetic analysis of Fasciola flukes from eastern India.},
journal = {Parasitology international},
volume = {64},
number = {5},
pages = {334-338},
doi = {10.1016/j.parint.2015.04.004},
pmid = {25936970},
issn = {1873-0329},
mesh = {Animals ; Buffaloes/parasitology ; Cattle ; Cattle Diseases/epidemiology/parasitology ; Fasciola/*genetics ; Fascioliasis/genetics/*veterinary ; Haplotypes ; India/epidemiology ; Mitochondria/enzymology ; NADH Dehydrogenase/genetics/metabolism ; Phylogeny ; },
abstract = {Fasciola flukes from eastern India were characterized on the basis of spermatogenesis status and nuclear ITS1. Both Fasciola gigantica and aspermic Fasciola flukes were detected in Imphal, Kohima, and Gantoku districts. The sequences of mitochondrial nad1 were analyzed to infer their phylogenetical relationship with neighboring countries. The haplotypes of aspermic Fasciola flukes were identical or showed a single nucleotide substitution compared to those from populations in the neighboring countries, corroborating the previous reports that categorized them in the same lineage. However, the prevalence of aspermic Fasciola flukes in eastern India was lower than those in the neighboring countries, suggesting that they have not dispersed throughout eastern India. In contrast, F. gigantica was predominant and well diversified, and the species was thought to be distributed in the area for a longer time than the aspermic Fasciola flukes. Fasciola gigantica populations from eastern India were categorized into two distinct haplogroups A and B. The level of their genetic diversity suggests that populations belonging to haplogroup A have dispersed from the west side of the Indian subcontinent to eastern India with the artificial movement of domestic cattle, Bos indicus, whereas populations belonging to haplogroup B might have spread from Myanmar to eastern India with domestic buffaloes, Bubalus bubalis.},
}
@article {pmid25945801,
year = {2015},
author = {Roncalli, V and Cieslak, MC and Passamaneck, Y and Christie, AE and Lenz, PH},
title = {Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus--Contributors to Cellular Detoxification.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0123322},
pmid = {25945801},
issn = {1932-6203},
mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/chemistry/*genetics/metabolism ; Crustacea/enzymology/*genetics ; Cytoplasm/enzymology ; *Genetic Variation ; Glutathione Transferase/chemistry/*genetics/metabolism ; Isoenzymes/genetics/metabolism ; Microsomes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Transcriptome ; },
abstract = {Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.},
}
@article {pmid25962482,
year = {2016},
author = {Liu, G and Tan, X and Shi, F and Liu, Z},
title = {Complete mitochondrial genome of the Macaca mulatta brevicaudus.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3432-3433},
doi = {10.3109/19401736.2015.1022735},
pmid = {25962482},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Macaca mulatta/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial sequence of the Macaca mulatta brevicaudus has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,561 bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop control region. The base composition of the mtDNA genome is 31.77% A, 25.14% T, 30.33% C, and 12.76% G, with an AT content of 56.90%. The arrangement of genes in M. m. brevicaudus is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. m. brevicaudus presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.},
}
@article {pmid25962484,
year = {2016},
author = {Cai, Y and Zhang, L and Wang, Y and Liu, Q and Shui, Q and Yue, B and Zhang, Z and Li, J},
title = {Identification of deer species (Cervidae, Cetartiodactyla) in China using mitochondrial cytochrome c oxidase subunit I (mtDNA COI).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {6},
pages = {4240-4243},
doi = {10.3109/19401736.2014.1003919},
pmid = {25962484},
issn = {2470-1408},
mesh = {Animals ; China ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {In China, many deer species are threatened and their wild populations are decreasing. In this study, a segment of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify Cervidae species. COI sequences of 30 individuals from nine species were determined. Together with 148 sequences from BOLD and Genbank, a total of 178 sequences from 21 species of the family Cervidae were analyzed. The results showed that all species had unique COI sequences, and there was no barcode sharing among them. The mean K2P distances within species, genus, and family were 1.3%, 3.4%, and 8.9%, respectively. The neighbor-joining (NJ) tree was in most cases concordant with modern deer classification. Three species showed maximum intraspecific divergences higher than their minimum interspecific divergences. However, all species could be discriminated by their diagnostic characters in BLOG analysis. The present study confirmed that COI barcodes can effectively distinguish Cervidae species in China.},
}
@article {pmid25977472,
year = {2015},
author = {Signorovitch, A and Hur, J and Gladyshev, E and Meselson, M},
title = {Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.},
journal = {Genetics},
volume = {200},
number = {2},
pages = {581-590},
pmid = {25977472},
issn = {1943-2631},
mesh = {*Alleles ; Animals ; Gene Order ; Genes, Mitochondrial ; Genetic Loci ; Meiosis ; Mitochondria/*genetics ; Phylogeny ; Rotifera/classification/*genetics ; *Sexual Behavior ; },
abstract = {Rotifers of Class Bdelloidea are common freshwater invertebrates of ancient origin whose apparent asexuality has posed a challenge to the view that sexual reproduction is essential for long-term evolutionary success in eukaryotes and to hypotheses for the advantage of sex. The possibility nevertheless exists that bdelloids reproduce sexually under unknown or inadequately investigated conditions. Although certain methods of population genetics offer definitive means for detecting infrequent or atypical sex, they have not previously been applied to bdelloid rotifers. We conducted such a test with bdelloids belonging to a mitochondrial clade of Macrotrachela quadricornifera. This revealed a striking pattern of allele sharing consistent with sexual reproduction and with meiosis of an atypical sort, in which segregation occurs without requiring homologous chromosome pairs.},
}
@article {pmid25979672,
year = {2015},
author = {Xu, H and Zhang, DL and Yu, DH and Lv, CH and Luo, HY and Wang, ZY},
title = {Molecular cloning and expression analysis of scd1 gene from large yellow croaker Larimichthys crocea under cold stress.},
journal = {Gene},
volume = {568},
number = {1},
pages = {100-108},
doi = {10.1016/j.gene.2015.05.027},
pmid = {25979672},
issn = {1879-0038},
mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cold-Shock Response ; Fish Proteins/*genetics/metabolism ; Gene Expression Profiling ; Molecular Sequence Data ; Organ Specificity ; Perciformes/*genetics/metabolism ; Phylogeny ; Stearoyl-CoA Desaturase/*genetics/metabolism ; Transcriptome ; },
abstract = {Desaturation of fatty acids is an important adaptation mechanism to maintain membrane fluidity under cold stress. To comprehend the mechanism of adaptation to low temperatures in fish, we investigated stearoyl-CoA desaturase 1 (SCD1) endocrine expression in the process of cold acclimation from 15°C to 7°C in Larimichthys crocea. The cDNA and genomic sequences of scd1 were cloned and characterized and named as Lcscd1. The cDNA encoded an iron-containing protein of 337 amino acids with functional motifs. The full-length genome sequence of Lcscd1 was composed of 2556 nucleotides, including five exons and four introns. Tissue expression profiles by qPCR and western blot analysis revealed that Lcscd1 was highly expressed in the liver, followed by the brain. The expression of Lcscd1 mRNA in the liver was firstly down-regulated from 15°C to 11°C, and then up-regulated until the first day of 7°C, followed by a decline until the last day. In the brain, the expression showed no significant change from 15°C to 9°C, but then significantly increased until the last day of 7°C. SCD1 protein expression in the liver decreased from 15°C to the first day of 7°C, and then gradually recovered to the starting level. In the brain, SCD1 protein expression maintained rising trends in the whole process. Immunoelectron microscopic analysis showed that SCD1 was localized in fat granules, mitochondria and granular endoplasmic reticulum of hepatic cells, but only in mitochondria of encephalic cells. The results above suggested that SCD1 expression was responsive to both cold and starvation stresses in the liver, but only to cold stress in the brain. In conclusion, these findings suggested that SCD1 may be involved in fish adaptation to cold stress.},
}
@article {pmid25992976,
year = {2015},
author = {Niemi, M and Bläuer, A and Iso-Touru, T and Harjula, J and Nyström Edmark, V and Rannamäe, E and Lõugas, L and Sajantila, A and Lidén, K and Taavitsainen, JP},
title = {Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.},
journal = {PloS one},
volume = {10},
number = {5},
pages = {e0123821},
pmid = {25992976},
issn = {1932-6203},
mesh = {Animals ; Animals, Domestic/genetics ; Baltic States ; Base Sequence ; Bone and Bones/cytology ; Breeding ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Radiometric Dating ; Sequence Analysis, DNA/veterinary ; Y Chromosome/*genetics ; },
abstract = {BACKGROUND: Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies.<br><br>RESULTS: Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples).<br><br>CONCLUSIONS: The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.},
}
@article {pmid26016880,
year = {2016},
author = {Rider, SD},
title = {The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (Coleoptera, Tenebrionidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2447-2449},
doi = {10.3109/19401736.2015.1033692},
pmid = {26016880},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Coleoptera/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; },
abstract = {The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (LeConte, 1851) was sequenced using paired-end technology to an average depth of 42,111× and assembled using De Bruijn graph-based methods. The genome is 15,828 bp in length and conforms to the basal arthropod mitochondrial gene composition with the same gene orders and orientations as other darkling beetle mitochondria. This arrangement includes a control region, 22 tRNA genes, 2 rRNA genes and 13 protein-coding genes. The main coding strand is probably replicated as the lagging strand (GC skew of -0.36 and AT skew of +0.19). Phylogenomics analyses are consistent with taxonomic classifications and indicate that Tenebrio molitor is the closest relative that has a completely sequenced mitochondrial genome available for analysis. This is the first fully assembled mitogenome sequence for a darkling beetle in the subfamily Pimeliinae and will be useful for population studies on members of this ecologically important group of beetles.},
}
@article {pmid26032732,
year = {2015},
author = {Zaidi, A and Singh, KP and Anwar, S and Suman, SS and Equbal, A and Singh, K and Dikhit, MR and Bimal, S and Pandey, K and Das, P and Ali, V},
title = {Interaction of frataxin, an iron binding protein, with IscU of Fe-S clusters biogenesis pathway and its upregulation in AmpB resistant Leishmania donovani.},
journal = {Biochimie},
volume = {115},
number = {},
pages = {120-135},
doi = {10.1016/j.biochi.2015.05.016},
pmid = {26032732},
issn = {1638-6183},
mesh = {Amino Acid Sequence ; Amphotericin B/*pharmacology ; Animals ; Binding Sites ; Carbon-Sulfur Lyases/metabolism ; Cloning, Molecular ; *Drug Resistance ; Female ; Humans ; Iron/metabolism ; Iron-Binding Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Iron-Sulfur Proteins/*biosynthesis/*metabolism ; Leishmania donovani/drug effects/*metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Conformation ; Protein Transport ; Protozoan Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Analysis ; *Up-Regulation ; Frataxin ; },
abstract = {Leishmania donovani is a unicellular protozoon parasite that causes visceral leishmaniasis (VL), which is a fatal disease if left untreated. Certain Fe-S proteins of the TCA cycle and respiratory chain have been found in the Leishmania parasite but the precise mechanisms for their biogenesis and the maturation of Fe-S clusters remains unknown. Fe-S clusters are ubiquitous cofactors of proteins that perform critical cellular functions. The clusters are biosynthesized by the mitochondrial Iron-Sulphur Cluster (ISC) machinery with core protein components that include the catalytic cysteine desulphurase IscS, the scaffold proteins IscU and IscA, and frataxin as an iron carrier/donor. However, no information regarding frataxin, its regulation, or its role in drug resistance is available for the Leishmania parasite. In this study, we characterized Ld-frataxin to investigate its role in the ISC machinery of L. donovani. We expressed and purified the recombinant Ld-frataxin protein and observed its interaction with Ld-IscU by co-purification and pull-down assay. Furthermore, we observed that the cysteine desulphurase activity of the purified Ld-IscS protein was stimulated in the presence of Ld-frataxin and Ld-IscU, particularly in the presence of iron; neither Ld-frataxin nor Ld-IscU alone had significant effects on Ld-IscS activity. Interestingly, RT-PCR and western blotting showed that Ld-frataxin is upregulated in AmpB-resistant isolates compared to sensitive strains, which may support higher Fe-S protein activity in AmpB-resistant L. donovani. Additionally, Ld-frataxin was localized in the mitochondria, as revealed by digitonin fractionation and indirect immunofluorescence. Thus, our results suggest the role of Ld-frataxin as an iron binding/carrier protein for Fe-S cluster biogenesis that physically interacts with other core components of the ISC machinery within the mitochondria.},
}
@article {pmid26051128,
year = {2015},
author = {Gjerde, B and Hilali, M and Mawgood, SA},
title = {Molecular characterisation of three regions of the nuclear ribosomal DNA unit and the mitochondrial cox1 gene of Sarcocystis fusiformis from water buffaloes (Bubalus bubalis) in Egypt.},
journal = {Parasitology research},
volume = {114},
number = {9},
pages = {3401-3413},
pmid = {26051128},
issn = {1432-1955},
mesh = {Animals ; *Buffaloes ; Cyclooxygenase 1/genetics/*metabolism ; DNA, Ribosomal/genetics ; Egypt/epidemiology ; Gene Expression Regulation, Enzymologic ; Genes, Mitochondrial ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 28S/genetics/metabolism ; Sarcocystis/*enzymology/genetics/isolation &amp; purification/metabolism ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sequence Analysis, DNA ; },
abstract = {A total of 33 macroscopically visible (3-11 × 1-5 mm) sarcocysts of Sarcocystis fusiformis were excised from the oesophagus of 12 freshly slaughtered water buffalos in Giza, Egypt. Genomic DNA was extracted from the sarcocysts, and all isolates were characterised at the mitochondrial cytochrome c oxidase subunit I (cox1) gene through PCR amplification and direct sequencing, whereas a few selected isolates were characterised at the 18S and 28S ribosomal (r) RNA genes and the internal transcribed spacer 1 (ITS1) region of the nuclear rDNA unit following cloning. Among the 33 cox1 sequences (1,038-bp long), there was a total of 13 haplotypes, differing from each other by one to seven substitutions and sharing an identity of 99.3-99.9 %. In comparison, the sequence identity was 98.8-99.0 % among eight complete 18S rRNA gene sequences (1,873-1,879-bp long), 98.1-100 % among 28 complete ITS1 sequences (853-864-bp long) and 97.4-99.6 % among five partial 28S rRNA gene sequences (1,607-1,622 bp). At the three nuclear loci, the intraspecific (and intra-isolate) sequence variation was due to both substitutions and indels, which necessitated cloning of the PCR products before sequencing. Some additional clones of the 18S and 28S rRNA genes were highly divergent from the more typical clones, but the true nature of these aberrant clones could not be determined. Sequence comparisons and phylogenetic analyses based on either 18S rRNA gene or cox1 nucleotide sequences, placed S. fusiformis closest to Sarcocystis cafferi from the African buffalo, but only the analyses based on cox1 data separated the two taxa clearly from each other and showed that they were separate species (monophyletic clusters and 93 % sequence identity at cox1 versus interleaved sequences and 98.7-99.1 % sequence identity at the 18S rRNA gene). Two cats experimentally infected with sarcocysts of S. fusiformis started shedding small numbers of sporocysts 8-10 days post-infection (dpi) and were euthanized 15 dpi. Sporocysts isolated from the intestinal mucosa of both cats were identified molecularly as belonging to S. fusiformis through PCR amplification and sequencing of the partial cox1. The two sporocyst-derived cox1 sequences were identical with the most common sarcocyst-derived cox1 haplotype.},
}
@article {pmid26105995,
year = {2015},
author = {Zhang, H and Luo, M and Day, RC and Talbot, MJ and Ivanova, A and Ashton, AR and Chaudhury, AM and Macknight, RC and Hrmova, M and Koltunow, AM},
title = {Developmentally regulated HEART STOPPER, a mitochondrially targeted L18 ribosomal protein gene, is required for cell division, differentiation, and seed development in Arabidopsis.},
journal = {Journal of experimental botany},
volume = {66},
number = {19},
pages = {5867-5880},
pmid = {26105995},
issn = {1460-2431},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/chemistry/*genetics/metabolism ; Cell Differentiation ; Cell Division ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Mutation ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Alignment ; },
abstract = {Evidence is presented for the role of a mitochondrial ribosomal (mitoribosomal) L18 protein in cell division, differentiation, and seed development after the characterization of a recessive mutant, heart stopper (hes). The hes mutant produced uncellularized endosperm and embryos arrested at the late globular stage. The mutant embryos differentiated partially on rescue medium with some forming callus. HES (At1g08845) encodes a mitochondrially targeted member of a highly diverged L18 ribosomal protein family. The substitution of a conserved amino residue in the hes mutant potentially perturbs mitoribosomal function via altered binding of 5S rRNA and/or influences the stability of the 50S ribosomal subunit, affecting mRNA binding and translation. Consistent with this, marker genes for mitochondrial dysfunction were up-regulated in the mutant. The slow growth of the endosperm and embryo indicates a defect in cell cycle progression, which is evidenced by the down-regulation of cell cycle genes. The down-regulation of other genes such as EMBRYO DEFECTIVE genes links the mitochondria to the regulation of many aspects of seed development. HES expression is developmentally regulated, being preferentially expressed in tissues with active cell division and differentiation, including developing embryos and the root tips. The divergence of the L18 family, the tissue type restricted expression of HES, and the failure of other L18 members to complement the hes phenotype suggest that the L18 proteins are involved in modulating development. This is likely via heterogeneous mitoribosomes containing different L18 members, which may result in differential mitochondrial functions in response to different physiological situations during development.},
}
@article {pmid26107900,
year = {2015},
author = {Gong, L and Shi, W and Si, LZ and Wang, ZM and Kong, XY},
title = {[The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles].},
journal = {Molekuliarnaia biologiia},
volume = {49},
number = {3},
pages = {461-471},
doi = {10.7868/S0026898415030064},
pmid = {26107900},
issn = {0026-8984},
mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; Flatfishes/classification/*genetics ; *Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; *Locus Control Region ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Tandem Repeat Sequences ; },
abstract = {The complete mitogenome of the peacock sole Pardachirus pavoninus (Lacepède, 1802) was determined. The total length is 16 536 bp, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes, as well as one control region (CR). The L-strand replication origin (OL), which is typically located in the WANCY cluster, is lost in P. pavoninus. The gene arrangement is identical to that in most teleosts. Comparison of the CR sequences among 13 soles reveals that a 211-bp fragment at the 5'-end of the CR is lost in the P. pavoninus mitogenome, responsible for its short sequence with a length of 872 bp. All typical conservative blocks (TAS, CSB-F, E, D, C, B, A, CSB-1, 2, 3) are identified. Seven out of 13 soles contain tandem repeats in the CR and the possible mechanisms of their formation are discussed. These results may provide the consensus sequences of the conserved units in the sole CR as well as molecular data for phylogenetic studies on Soleidae and Pleuronectiformes.},
}
@article {pmid26119842,
year = {2016},
author = {Chen, K and Sun, L and Zong, L and Wu, X and Zhan, Y and Dong, C and Cao, H and Tang, H and Jiang, H},
title = {GJB2 and mitochondrial 12S rRNA susceptibility mutations in sudden deafness.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {273},
number = {6},
pages = {1393-1398},
pmid = {26119842},
issn = {1434-4726},
mesh = {Adult ; Case-Control Studies ; Connexin 26 ; Connexins/*genetics ; DNA Mutational Analysis/methods ; Deafness/genetics ; Female ; Gene Frequency ; Genes, Mitochondrial ; *Genetic Predisposition to Disease ; Hearing Loss, Sudden/*genetics ; Heterozygote ; Homozygote ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Phylogeny ; Polymorphism, Genetic ; *RNA, Ribosomal ; },
abstract = {Genetic susceptibility may play an important role in the pathogenesis of sudden deafness. However, the specific genes involved are largely unknown. We sought to explore the frequency of GJB2 and mitochondrial 12S rRNA susceptibility mutations in patients with sudden deafness. Between September 2011 and May 2012, 62 consecutive patients with sudden deafness were seen. In 50 of these, no etiological factors for sudden deafness were found. We detected GJB2 and mitochondrial 12S rRNA variants by direct sequencing in these 50 patients and in 53-aged matched controls with normal hearing. In addition, we undertook functional analyses of the mitochondrial mutations which we detected, applying structural and phylogenetic analysis. GJB2 sequencing identified six mutations, including three pathogenic mutations (c.235delC, c.299-300delAT, c.109G>A) and three polymorphisms, in the study participants, giving an allele frequency of 15.0 %. A homozygous c.109G>A mutation was detected in two participants. A total of 16 variants in mitochondrial 12S rRNA gene were identified in the participants. No significant differences were found in GJB2 heterozygosity or in mitochondrial 12S rRNA variants between patients with sudden deafness and in controls. Our results suggest that the homozygous GJB2 c.109G>A mutation may be a cause of sudden deafness involving both ears. This finding should increase awareness of the likely role of genetic factors in the etiology of sudden deafness in general.},
}
@article {pmid26121931,
year = {2016},
author = {Mishra, RC and Grover, A},
title = {ClpB/Hsp100 proteins and heat stress tolerance in plants.},
journal = {Critical reviews in biotechnology},
volume = {36},
number = {5},
pages = {862-874},
doi = {10.3109/07388551.2015.1051942},
pmid = {26121931},
issn = {1549-7801},
mesh = {Endopeptidase Clp/*genetics ; Global Warming ; Heat-Shock Proteins/*genetics ; Molecular Chaperones ; Mutation ; Phylogeny ; Plants, Genetically Modified/*genetics ; Stress, Physiological/genetics ; Thermotolerance/*genetics ; },
abstract = {High-temperature stress can disrupt cellular proteostasis, resulting in the accumulation of insoluble protein aggregates. For survival under stressful conditions, it is important for cells to maintain a pool of native soluble proteins by preventing and/or dissociating these aggregates. Chaperones such as GroEL/GroES (Hsp60/Hsp10) and DnaK/DnaJ/GrpE (Hsp70/Hsp40/nucleotide exchange factor) help cells minimize protein aggregation. Protein disaggregation is accomplished by chaperones belonging to the Caseinolytic Protease (Clp) family of proteins. ClpB/Hsp100 proteins are strikingly ubiquitous and are found in bacteria, yeast and multi-cellular plants. The expression of these proteins is regulated by heat stress (HS) and developmental cues. Bacteria and yeast contain one and two forms of ClpB proteins, respectively. Plants possess multiple forms of these proteins that are localized to different cellular compartments (i.e. cytoplasm/nucleus, chloroplast or mitochondria). Overwhelming evidence suggests that ClpB/Hsp100 proteins play decisive roles in cell adaptation to HS. Mutant bacteria and yeast cells lacking active ClpB/Hsp100 proteins are critically sensitive to high-temperature stress. Likewise, Arabidopsis, maize and rice mutants lacking cytoplasmic ClpB proteins are very sensitive to heat. In this study, we present the structural and functional attributes of plant ClpB forms.},
}
@article {pmid26122344,
year = {2016},
author = {Hwang, JY and Jin, GD and Park, J and Kim, H and Lee, CK and Kwak, W and Nam, BH and An, CM and Park, JY and Park, KH and Huh, CS and Kim, EB},
title = {Complete genome sequence and SNPs of Raja pulchra (Rajiformes, Rajidae) mitochondria.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {4},
pages = {2975-2977},
doi = {10.3109/19401736.2015.1060467},
pmid = {26122344},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Whole Genome Sequencing ; },
abstract = {Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.},
}
@article {pmid26134044,
year = {2015},
author = {Li, W and Wen, C and Li, W and Wang, H and Guan, X and Zhang, W and Ye, W and Lu, J},
title = {The tRNA(Gly) T10003C mutation in mitochondrial haplogroup M11b in a Chinese family with diabetes decreases the steady-state level of tRNA(Gly), increases aberrant reactive oxygen species production, and reduces mitochondrial membrane potential.},
journal = {Molecular and cellular biochemistry},
volume = {408},
number = {1-2},
pages = {171-179},
pmid = {26134044},
issn = {1573-4919},
mesh = {Aged ; Asian People/ethnology/*genetics ; China/ethnology ; Diabetes Mellitus, Type 2/ethnology/*genetics ; Female ; Genetic Predisposition to Disease ; Genome, Mitochondrial ; Haplotypes ; Humans ; Male ; Membrane Potential, Mitochondrial ; Middle Aged ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; *Mutation ; Oxygen Consumption ; Pedigree ; Phylogeny ; RNA, Transfer, Gly/*genetics ; Reactive Oxygen Species/metabolism ; },
abstract = {Mitochondrial diabetes originates mainly from mutations located in maternally transmitted, mitochondrial tRNA-coding genes. In a genetic screening program of type 2 diabetes conducted with a Chinese Han population, we found one family with suggestive maternally transmitted diabetes. The proband's mitochondrial genome was analyzed using DNA sequencing. Total 42 known nucleoside changes and 1 novel variant were identified, and the entire mitochondrial DNA sequence was assigned to haplogroup M11b. Phylogenetic analysis showed that a homoplasmic mutation, 10003T>C transition, occurred at the highly conserved site in the gene encoding tRNA(Gly). Using a transmitochondrial cybrid cell line harboring this mutation, we observed that the steady-state level of tRNA(Gly) significantly affected and the amount of tRNA(Gly) decreased by 97%, production of reactive oxygen species was enhanced, and mitochondrial membrane potential, mtDNA copy number and cellular oxygen consumption rate were remarkably decreased compared with wild-type cybrid cells. The homoplasmic 10003T>C mutation in the mitochondrial tRNA(Gly) gene suggested to be as a pathogenesis-related mutation which might contribute to the maternal inherited diabetes in the Han Chinese family.},
}
@article {pmid26135515,
year = {2015},
author = {Zhou, G and Song, Z and Yin, Y and Jiang, W and Wang, Z},
title = {Involvement of an alternative oxidase in the regulation of hyphal growth and microsclerotial formation in Nomuraea rileyi CQNr01.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {31},
number = {9},
pages = {1343-1352},
pmid = {26135515},
issn = {1573-0972},
mesh = {Cloning, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Hyphae/enzymology/genetics/*growth &amp; development ; Hypocreales/enzymology/genetics/*growth &amp; development ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; },
abstract = {Mitochondria of Nomuraea rileyi contain an alternative oxidase (Aox), which reduces oxygen to water by accepting electrons directly from ubiquinol. Furthermore, through a transcriptional analysis, we found that an alternative oxidase (Nraox) was up-regulated during microsclerotial formation. To study the function of NrAox, Nraox was cloned from N. rileyi CQNr01. The full-length cDNA was 1266 bp with an open reading frame of 1068 bp encoding 355 amino acids. A phylogenetic analysis revealed that the NrAox of N. rileyi was closely related to Metarhizium acridum Aox. The relative expression level of the Nraox was up-regulated during microsclerotial (MS) initiation. A salicylhydroxamic acid, a specific alternative oxidase inhibitor, application to the culture media severely decreased MS yields, changed the hyphae morphology and slowed the H2O2 removal. Nraox silencing caused mycelial deformations, reduced the MS yields by 97.3 % and increased MS size compared with those of the control. MS virulence was decreased to 26.2 % after Nraox was silenced. However, the Nraox-silenced strain was sensitive to environmental stress, and the growth rate was reduced under stress conditions. The results obtained suggested that Nraox is required for MS differentiation by regulating the intracellular H2O2 concentration and hypha growth. Additionally, Nraox had a great impact on the virulence of N. rileyi.},
}
@article {pmid26139575,
year = {2015},
author = {Xu, J and Zhang, L and Yang, DL and Li, Q and He, Z},
title = {Thymidine kinases share a conserved function for nucleotide salvage and play an essential role in Arabidopsis thaliana growth and development.},
journal = {The New phytologist},
volume = {208},
number = {4},
pages = {1089-1103},
doi = {10.1111/nph.13530},
pmid = {26139575},
issn = {1469-8137},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cytosol/metabolism ; Escherichia coli ; *Genes, Plant ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Nucleotides/*metabolism ; Oryza/genetics ; *Phylogeny ; Plant Development/*genetics ; Pyrimidine Nucleosides/metabolism ; Sequence Alignment ; Thymidine Kinase/*genetics/metabolism ; },
abstract = {Thymidine kinases (TKs) are important components in the nucleotide salvage pathway. However, knowledge about plant TKs is quite limited. In this study, the molecular function of TKs in Arabidopsis thaliana was investigated. Two TKs were identified and named AtTK1 and AtTK2. Expression of both genes was ubiquitous, but AtTK1 was strongly expressed in high-proliferation tissues. AtTK1 was localized to the cytosol, whereas AtTK2 was localized to the mitochondria. Mutant analysis indicated that the two genes function coordinately to sustain normal plant development. Enzymatic assays showed that the two TK proteins shared similar catalytic specificity for pyrimidine nucleosides. They were able to complement an Escherichia coli strain lacking TK activity. 5'-Fluorodeoxyuridine (FdU) resistance and 5-ethynyl 2'-deoxyuridine (EdU) incorporation assays confirmed their activity in vivo. Furthermore, the tk mutant phenotype could be alleviated by nucleotide feeding, establishing that the biosynthesis of pyrimidine nucleotides was disrupted by the TK deficiency. Finally, both human and rice (Oryza sativa) TKs were able to rescue the tk mutants, demonstrating the functional conservation of TKs across organisms. Taken together, our findings clarify the specialized function of two TKs in A. thaliana and establish that the salvage pathway mediated by the kinases is essential for plant growth and development.},
}
@article {pmid26142878,
year = {2016},
author = {Juhász, Z and Fehér, T and Németh, E and Pamjav, H},
title = {mtDNA analysis of 174 Eurasian populations using a new iterative rank correlation method.},
journal = {Molecular genetics and genomics : MGG},
volume = {291},
number = {1},
pages = {493-509},
pmid = {26142878},
issn = {1617-4623},
mesh = {DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; },
abstract = {In this study, we analyse 27-dimensional mtDNA haplogroup distributions of 174 Eurasian, North-African and American populations, including numerous ancient data as well. The main contribution of this work was the description of the haplogroup distribution of recent and ancient populations as compounds of certain hypothetic ancient core populations immediately or indirectly determining the migration processes in Eurasia for a long time. To identify these core populations, we developed a new iterative algorithm determining clusters of the 27 mtDNA haplogroups studied having strong rank correlation among each other within a definite subset of the populations. Based on this study, the current Eurasian populations can be considered as compounds of three early core populations regarding to maternal lineages. We wanted to show that a simultaneous analysis of ancient and recent data using a new iterative rank correlation algorithm and the weighted SOC learning technique may reveal the most important and deterministic migration processes in the past. This technique allowed us to determine geographically, historically and linguistically well-interpretable clusters of our dataset having a very specific, hardly classifiable structure. The method was validated using a 2-dimensional stepping stone model.},
}
@article {pmid26147677,
year = {2015},
author = {Nakajima, Y and Shinzato, C and Satoh, N and Mitarai, S},
title = {Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0130176},
pmid = {26147677},
issn = {1932-6203},
mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Drift ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Mutation/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA/methods ; Sympatry/*genetics ; },
abstract = {The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.},
}
@article {pmid26153738,
year = {2016},
author = {Park, CE and Park, GS and Kwak, Y and Hong, SJ and Khan, AR and Jung, BK and Park, YJ and Kim, JG and Park, HC and Shin, JH},
title = {Complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3442-3443},
doi = {10.3109/19401736.2015.1063133},
pmid = {26153738},
issn = {2470-1408},
mesh = {Animals ; Anseriformes/*genetics ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae) was revealed in this study. Total 16 739 base pairs (bp) of this mitogenome encoded genes for 13 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a D-loop (control region). The 12S rRNA and 16S rRNA genes are located between tRNA-Phe and tRNA-Leu (UUR) and segmentalized by the tRNA-Val. D-loop is located between tRNA-Glu and tRNA-Phe. The overall base composition of C. olor is G + C: 47.8%, A + T: 52.2%, apparently with a slight AT bias. Following the phylogenetic analysis, the C. olor was closed to Anser cygnoides.},
}
@article {pmid26153741,
year = {2016},
author = {Tsunashima, T and Yamada, R and Abe, K and Noguchi, S and Itoi, S and Nakai, S and Takai, N and Sugita, H},
title = {Phylogenetic position of Scombropidae within teleostei: the complete mitochondrial genome of the gnomefish, Scombrops gilberti.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3446-3448},
doi = {10.3109/19401736.2015.1063135},
pmid = {26153741},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Fishes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of the Japanese gnomefish, Scombrops gilberti, was determined using a PCR-based method. The total length of mitochondrial DNA (mtDNA) is 16 518 bp, which includes 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The mitochondrial gene arrangement of S. gilberti was found to be identical to that of other scombropid and indeed, other teleosts as well. Maximum likelihood analysis revealed that Scombropidae forms a sister group to Pempheriformes.},
}
@article {pmid26162048,
year = {2016},
author = {Wu, Z and Wang, D and Hu, J and Wang, Q},
title = {Complete mitochondrial genome of the Scorpaenopsis cirrhosa (Scorpaeniformes: Scorpaenidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3449-3450},
doi = {10.3109/19401736.2015.1063136},
pmid = {26162048},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of the Scorpaenopsis cirrhosa has been sequenced. The mitochondrial genome is 16 966 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The gene order and composition of S. cirrhosa mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.91%), G (17.71%), C (28.02%), and T (26.35%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, S. cirrhosa, a stonefish and four rockfishes from the same order (Scorpaeniformes) clustered into one branch.},
}
@article {pmid26181210,
year = {2016},
author = {Park, CE and Park, GS and Kwak, Y and Hong, SJ and Khan, AR and Jung, BK and Park, YJ and Kim, MC and Kim, KH and Park, HC and Lee, IJ and Shin, JH},
title = {Complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3493-3495},
doi = {10.3109/19401736.2015.1066364},
pmid = {26181210},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perches/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {In this study, we sequenced the complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae). The mitogenome, consisting of 16 495 base pairs (bp), encoded 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of C. herzi is G + C: 46.3%, A + T: 53.7%, apparently with a slight AT bias. Phylogenetic analysis showed that the C. herzi was closed to Coreoperca kawamebari.},
}
@article {pmid26186304,
year = {2016},
author = {Chhakchhuak, L and De Mandal, S and Gurusubramanian, G and Nachimuthu, SK},
title = {The near complete mitochondrial genome of the Giant honey bee, Apis dorsata (Hymenoptera: Apidae: Apinae) and its phylogenetic status.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3483-3484},
doi = {10.3109/19401736.2015.1066359},
pmid = {26186304},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Bees/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {In this report, we sequenced and characterized the near complete mitochondrial genome of Apis dorsata collected from Mizoram, India. For sequencing of the complete mitochondrial genome, Illumina NextSeq500 platform was used. The near complete mitochondrial genome was assembled to be 15 076 bplong and contains the same gene order as the other honey bees. The assembly contains 13 protein coding genes, 21 transfer RNA, 2 ribosomal RNA and a partial control (A + T-rich) region estimated to be 75 bp. This is the first near complete sequenced mitochondrial genome from the giant honeybee A. dorsata which will benefit future genomics studies for understanding the phylogenetic relationship within the bee family.},
}
@article {pmid26186306,
year = {2016},
author = {Lu, WJ and Hu, WG and Wang, GP},
title = {Complete mitochondrial genome of Pseudoperonospora cubensis.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3487-3488},
doi = {10.3109/19401736.2015.1066361},
pmid = {26186306},
issn = {2470-1408},
mesh = {Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Oomycetes/*genetics ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Pseudoperonospora cubensis is a species of water mould known for causing downy mildew on cucurbits. 454 GS FLX Titanium sequencing data was used to obtain its complete mitochondrial genome (38 553 bp). The mitogenome contains 60 genes, including two ribosomal RNA, 25 transfer RNA, 15 ribosomal proteins, five open reading frames (ORFs). The rps3 and rpl16 overlapped each other by 14 bp. The gene order and composition of P. cubensis was similar to that of most other oomycetes, and its GC content was 22.4%. It is the first report of the complete mitochondrial genome in the genus Pseudoperonospora. Phylogeny analysis indicates that P. cubensis has a close genetic relationship with genus Phytophthora.},
}
@article {pmid26195214,
year = {2016},
author = {Ning, Y and Liu, H and Jiang, G and Ma, J},
title = {Phylogenetic relationship of Eurasian lynx (Lynx lynx) revealed by complete mitochondrial genome.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3477-3478},
doi = {10.3109/19401736.2015.1066356},
pmid = {26195214},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Lynx/classification/*genetics ; Mitochondria/*genetics ; Muscles/chemistry ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The Eurasian lynx (Lynx lynx) is an Endangered species in northeast China. We first obtained muscle sample, extracted the sample DNA and sequenced the whole mtDNA genome of lynx from northeast China. We reconstructed the phylogenetic tree of Eurasian lynx and 10 other most closely related Felidae species. This lynx's complete mitogenome is 17 054bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The phylogenetic tree confirmed previous research results.},
}
@article {pmid26195217,
year = {2016},
author = {Ding, M and Wu, J and Qian, L and Pan, T and Zhang, B},
title = {Complete mitochondrial genome of Lycodon flavozonatum and implications for Colubridae taxonomy.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3473-3474},
doi = {10.3109/19401736.2015.1066354},
pmid = {26195217},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Colubridae/*classification/genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Lycodon flavozonatum, a species of Colubcridae family, is mainly inhabited in hilly region of forest in South China, India, Myanmar, and Vietnam. In this study, the complete mtDNA of L. flavozonatum is 17 172 bp long, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA (12S and 16S rRNA), and two control regions and a stem-loop region. Most of these genes are encoded in the H-strand; only ND6, stem-loop and other nine tRNA genes are on the L-strand. The phylogenetic tree among the 14 Serpentiformes species was divided into three major clade; Lycodon makes up the first clade, which showed a sister relationship to the second clade, Elaphe; Hypsiglena forms the third clade and is sister to Lycodon and Elaphe. And the species of L. flavozonatum which we studied belongs to the first clade.},
}
@article {pmid26196835,
year = {2015},
author = {Kosakyan, A and Mulot, M and Mitchell, EA and Lara, E},
title = {Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae).},
journal = {European journal of protistology},
volume = {51},
number = {4},
pages = {311-320},
doi = {10.1016/j.ejop.2015.06.005},
pmid = {26196835},
issn = {1618-0429},
mesh = {Amoebozoa/*classification/*genetics ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/genetics ; Phylogeny ; Soil/parasitology ; },
abstract = {Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.},
}
@article {pmid26202992,
year = {2015},
author = {Okamura, T and Kondo, R},
title = {Suigetsumonas clinomigrationis gen. et sp. nov., a Novel Facultative Anaerobic Nanoflagellate Isolated from the Meromictic Lake Suigetsu, Japan.},
journal = {Protist},
volume = {166},
number = {4},
pages = {409-421},
doi = {10.1016/j.protis.2015.06.003},
pmid = {26202992},
issn = {1618-0941},
mesh = {Japan ; Lakes/parasitology ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Stramenopiles/*classification/genetics/isolation &amp; purification/ultrastructure ; },
abstract = {A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov.},
}
@article {pmid26205690,
year = {2015},
author = {Nagataki, M and Tantrawatpan, C and Agatsuma, T and Sugiura, T and Duenngai, K and Sithithaworn, P and Andrews, RH and Petney, TN and Saijuntha, W},
title = {Mitochondrial DNA sequences of 37 collar-spined echinostomes (Digenea: Echinostomatidae) in Thailand and Lao PDR reveals presence of two species: Echinostoma revolutum and E. miyagawai.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {35},
number = {},
pages = {56-62},
doi = {10.1016/j.meegid.2015.07.022},
pmid = {26205690},
issn = {1567-7257},
mesh = {Animals ; DNA, Helminth/analysis ; DNA, Mitochondrial/*analysis ; Ducks/*parasitology ; Echinostoma/*classification/*genetics ; Electron Transport Complex IV/analysis ; Genetic Variation ; Haplotypes ; Laos ; Mitochondria/*genetics ; NADH Dehydrogenase/analysis ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; Thailand ; },
abstract = {The "37 collar-spined" or "revolutum" group of echinostomes is recognized as a species complex. The identification of members of this complex by morphological taxonomic characters is difficult and confusing, and hence, molecular analyses are a useful alternative method for molecular systematic studies. The current study examined the genetic diversity of those 37 collar-spined echinostomes which are recognized morphologically as Echinostoma revolutum in Thailand and Lao PDR using the cytochrome c oxidase subunit 1 (CO1) and the NADH dehydrogenase subunit 1 (ND1) sequences. On the basis of molecular investigations, at least two species of 37 collar-spined echinostomes exist in Southeast Asia, namely E. revolutum and Echinostoma miyagawai. The specimens examined in this study, coming from ducks in Thailand and Lao PDR, were compared to isolates from America, Europe and Australia for which DNA sequences are available in public databases. Haplotype analysis detected 6 and 26 haplotypes when comparing the CO1 sequences of E. revolutum and E. miyagawai, respectively, from different geographical isolates from Thailand and Lao PDR. The phylogenetic trees, ND1 haplotype network and genetic differentiation (ɸST) analyses showed that E. revolutum were genetically different on a continental scale, i.e. Eurasian and American lineages.},
}
@article {pmid26218308,
year = {2016},
author = {Wang, HL and Zhang, Z and Bing, XL and Liu, YQ and Liu, SS and Wang, XW},
title = {A complete mitochondrial DNA genome derived from a Chinese population of the Bemisia afer species complex (Hemiptera: Aleyrodidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3500-3501},
doi = {10.3109/19401736.2015.1066367},
pmid = {26218308},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Hemiptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We report here the sequence of a complete mitochondrial genome (mitogenome) of a population of Bemisia afer species complex, which was collected from Abutilonaviecnnae gaerner at LinYi, Shan Dong province of China (hereafter B. afer_China_Ag) (GenBank accession number: KR819174). The mitogenome of B. afer_China_Ag is 15 300 bp and contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 2 control regions. The content and arrangement of mitochondrial genes of B. afer_China_Ag exhibit remarkable differences from the mitogenome of a B. afer population collected from African cassava (KF734668). Phylogenetic analyses based on 13 protein-coding genes support the close relationship of the two sequenced B. afer mitogenomes and confirm the species status of our specimen.},
}
@article {pmid26226163,
year = {2015},
author = {Atray, I and Bentur, JS and Nair, S},
title = {The Asian Rice Gall Midge (Orseolia oryzae) Mitogenome Has Evolved Novel Gene Boundaries and Tandem Repeats That Distinguish Its Biotypes.},
journal = {PloS one},
volume = {10},
number = {7},
pages = {e0134625},
pmid = {26226163},
issn = {1932-6203},
mesh = {Animals ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Diptera/*genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Tandem Repeat Sequences/*drug effects ; },
abstract = {The complete mitochondrial genome of the Asian rice gall midge, Orseolia oryzae (Diptera; Cecidomyiidae) was sequenced, annotated and analysed in the present study. The circular genome is 15,286 bp with 13 protein-coding genes, 22 tRNAs and 2 ribosomal RNA genes, and a 578 bp non-coding control region. All protein coding genes used conventional start codons and terminated with a complete stop codon. The genome presented many unusual features: (1) rearrangement in the order of tRNAs as well as protein coding genes; (2) truncation and unusual secondary structures of tRNAs; (3) presence of two different repeat elements in separate non-coding regions; (4) presence of one pseudo-tRNA gene; (5) inversion of the rRNA genes; (6) higher percentage of non-coding regions when compared with other insect mitogenomes. Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed. Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome. This led to the identification of genetic markers capable of differentiating rice gall midge biotypes and the two Orseolia species investigated.},
}
@article {pmid26226593,
year = {2016},
author = {Yao, J and Zhao, X and Li, Y and Li, L and Yan, S},
title = {The complete sequence of mitochondrial genome of Siberian accentor (Prunella montanella).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3440-3441},
doi = {10.3109/19401736.2015.1063132},
pmid = {26226593},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The Siberian accentor, Prunella montanella (Passeriformes, Prunellidae), is a small passerine bird. In this study, the complete mitochondrial genome sequence of Siberian accentor was determined. It has a total length of 16 832 bp, and contains 13 protein coding genes, 22 tRNA genes, two ribosome RNA genes, and one control region. The nucleotide composition is 30.1% for A, 31.0% for C, 15.0% for G and 23.9% for T, respectively. The overall GC content is lower than AT. The phylogenetic tree of Siberian accentor and 10 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of Siberian accentors.},
}
@article {pmid26240360,
year = {2015},
author = {Bauer, D and Merz, DR and Pelz, B and Theisen, KE and Yacyshyn, G and Mokranjac, D and Dima, RI and Rief, M and Žoldák, G},
title = {Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {112},
number = {33},
pages = {10389-10394},
pmid = {26240360},
issn = {1091-6490},
mesh = {Actins/chemistry ; Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Computer Simulation ; Elasticity ; Escherichia coli Proteins/*chemistry ; HSP70 Heat-Shock Proteins/*chemistry ; Lasers ; Mitochondria/metabolism ; Models, Molecular ; Molecular Chaperones ; Molecular Sequence Data ; Nucleotides/*chemistry ; Phylogeny ; Protein Binding ; Protein Denaturation ; Protein Folding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry ; Signal Transduction ; },
abstract = {The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.},
}
@article {pmid26242721,
year = {2016},
author = {Li, YX and Wang, XG and Ou, J and Yao, FJ and Yang, Y and Wei, ZM},
title = {The complete mitochondrial genome of Coptotermes testaceus (Isoptera: Rhinotermitidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3466-3468},
doi = {10.3109/19401736.2015.1066351},
pmid = {26242721},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete circular mitochondrial genome (mitogenome) of Coptotermes testaceus is 15 752bp in size, containing 37 typical genes and one non-coding AT-rich region. The AT content of the AT-rich region is 68.3%. All protein coding genes (PCGs) start with standard ATN initiation codons and end with complete termination codons TAA or TAG except for cox2, atp8, and nad5 genes using an incomplete stop codon T. tRNA genes are predicted with a characteristic cloverleaf secondary structure except for trnS1(()(AGN)()), whose dihydrouridine (DHU) arm is replaced by a simple loop. The size of the large and small ribosomal RNA genes are 1315 and 818 bp, respectively. Phylogenetic analysis found that (i) the C. testaceus clade formed the sister group with another clade containing Coptotermes lacteus and Coptotermes formosanus; and (ii) Coptotermes lacteus had a close relationship with Coptotermes clade, but with lower credibility than other clades, the bootstrap value was 97%.},
}
@article {pmid26244691,
year = {2016},
author = {Liu, C and Wu, X and Shen, HD},
title = {Complete mitochondrial genome of Vaginulus alte and Homoiodoris japonica.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3454-3457},
doi = {10.3109/19401736.2015.1066345},
pmid = {26244691},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gastropoda/classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome sequence of Vaginulus alte and Homoiodoris japonica are described first in the article. The mitogenomes (14 772 bp and 14 601 bp) contain 22 tRNA genes, two ribosomal RNA genes, and 13 protein-coding genes, and one putative control region (CR). CR is not well characterized due to the lack of discrete conserved sequence blocks. This characteristic is similar with CRs of other invertebrate mitochondrial genomes, which is the typical bivalvia mitochondrial gene composition.},
}
@article {pmid26248000,
year = {2016},
author = {Hwang, JY and Han, GG and Park, JY and Kim, EM and An, CM and Kang, JH and Choi, YJ and Kim, EB},
title = {Complete sequence and polymorphisms of female Ruditapes philippinarum (Mollusca: Bivalvia) mitochondria genome.},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3462-3463},
doi = {10.3109/19401736.2015.1066348},
pmid = {26248000},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Bivalvia/*genetics ; DNA, Ribosomal/genetics ; Female ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {Mitogenome of female Ruditapes philippinarum organism was sequenced, and genomic variation and phylogeny were examined in this study. Length of the mitogenome was 22 089 bp showing 94.28% of sequence identity with previously reported sequence. Total 707 single nucleotide polymorphisms, SNPs, were detected and 50 residues were non-synonymous SNPs among the 202 SNPs in protein-coding genes. Deleted genomic fragments with of 265 bp and 322 bp were observed in non-coding regions, ND2 to ND4L and ND4L to tRNA(Ile), respectively. Phylogenic analysis confirmed that used organisms were female R. philippinarum, and the species has closer evolutionary distance with genus Paphia rather than genus Meretrix. Our finding will be help to set an insight for population and evolutionary genomics of Veneroida clams as well as application to marine industry.},
}
@article {pmid26248187,
year = {2015},
author = {Burgess, TI},
title = {Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species.},
journal = {PloS one},
volume = {10},
number = {8},
pages = {e0134225},
pmid = {26248187},
issn = {1932-6203},
mesh = {Bayes Theorem ; Cell Cycle Proteins/classification/genetics/metabolism ; Genome ; HSP90 Heat-Shock Proteins/genetics/metabolism ; Haplotypes ; *Hybridization, Genetic ; Mitochondria/classification/genetics ; NADH Dehydrogenase/classification/genetics/metabolism ; Phylogeny ; Phytophthora/*genetics ; Polymorphism, Single Nucleotide ; Tubulin/genetics/metabolism ; },
abstract = {Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones.},
}
@article {pmid26256644,
year = {2015},
author = {Mokodongan, DF and Yamahira, K},
title = {Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae.},
journal = {Molecular phylogenetics and evolution},
volume = {93},
number = {},
pages = {150-160},
doi = {10.1016/j.ympev.2015.07.024},
pmid = {26256644},
issn = {1095-9513},
mesh = {Animals ; Biodiversity ; Fishes/*genetics ; Genetic Speciation ; Indonesia ; Lakes ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Although the family Adrianichthyidae is broadly distributed throughout East and Southeast Asia, 19 endemic species, over half of the family, are distributed in Sulawesi, which is an island in Wallacea. However, it remains unclear how this Adrianichthyidae biodiversity hotspot was shaped. In this study, we reconstructed molecular phylogenies for the Sulawesi adrianichthyids and estimated the divergence times of major lineages to infer the detailed history of their origin and subsequent intra-island diversification. The mitochondrial and nuclear phylogenies revealed that Sulawesi adrianichthyids are monophyletic, which indicates that they diverged from a single common ancestor. Species in the earliest branching lineages are currently distributed in the central and southeastern parts of the island, indicating that the common ancestor colonized Sula Spur, which is a large promontory that projects from the Australian continental margin, from Asia by oversea dispersal c.a. 20Mya. The first diversification event on Sulawesi, the split of the genus Adrianichthys, occurred c.a. 16Mya, and resulted in the nesting of Adrianichthys within Oryzias. Strong geographic structure was evident in the phylogeny; many species in the lineages branching off early are riverine and widely distributed in the southeastern and southwestern arms of Sulawesi, which suggests that oversea dispersal between tectonic subdivisions of this island during the late Miocene (7-5Mya) contributed to the distributions and diversification of the early branching lineages. In contrast, most species in the lineages branched off later are endemic to a single tectonic lake or lake system in the central Sulawesi, suggesting that habitat fragmentation due to the Pliocene collisions (c.a. 4Mya) among the tectonic subdivisions was the primary factor for diversification of the late branching, lacustrine lineages. Adrianichthys and some Oryzias in a certain late branching lineage are sympatric in Lake Poso, which indicates multiple colonizations of these distinct lineages into this tectonic lake. Thus, the diversification of Sulawesi adrianichthyids largely reflects the complex geological history of this island.},
}
@article {pmid26258504,
year = {2016},
author = {Li, W and Tian, S and Zhu, J and Wu, F and Wang, K and Dai, X},
title = {Characterization of the complete mitochondrial genome of Sickle pomfret Taractichthys steindachneri (Perciformes: Bramidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3481-3482},
doi = {10.3109/19401736.2015.1066358},
pmid = {26258504},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitogenome sequence of Taractichthys steindachneri was sequenced and analyzed in this study. The complete mitogenome of T. steindachneri is 16 723 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding region, a rep region and a control region (D-loop). This study will be useful for studying on the molecular systematic, taxonomic status and conservation genetics.},
}
@article {pmid26258507,
year = {2016},
author = {Wang, Q and Wu, Z and Sun, D and Luo, J},
title = {The complete mitochondrial genome of the Ephippus orbis (Perciformes: Ephippidae).},
journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis},
volume = {27},
number = {5},
pages = {3444-3445},
doi = {10.3109/19401736.2015.1063134},
pmid = {26258507},
issn = {2470-1408},
mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {The complete mitochondrial genome of the Ephippus orbis has been sequenced. The mitochondrial genome is 16 670 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of E. orbis mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.17%), G (16.41%), C (31.46%), and T (24.96%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Seen from the phylogenetic tree (Figure 1), E. orbis, Platax teira, and Platax orbicularis from the same family (Ephippidae) clustered into one branch and were significantly divergent from the other families of closely related fish species.},
}
@article {pmid116847,
year = {1979},
author = {Scovassi, AI and Wicker, R and Bertazzoni, U},
title = {A phylogenetic study on vertebrate mitochondrial DNA polymerase.},
journal = {European journal of biochemistry},
volume = {100},
number = {2},
pages = {491-496},
doi = {10.1111/j.1432-1033.1979.tb04193.x},
pmid = {116847},
issn = {0014-2956},
mesh = {Animals ; Cell Line ; Chick Embryo ; DNA, Mitochondrial/*biosynthesis ; DNA-Directed DNA Polymerase/*analysis ; Female ; Haplorhini ; Liver/enzymology ; Mice ; Mitochondria/*enzymology ; Oocytes/enzymology ; *Phylogeny ; Species Specificity ; Trout ; Turtles ; Xenopus ; },
abstract = {We have started a phylogenetic survey for the mitochondrial DNA polymerase and present in this study the results obtained for all the different classes for the vertebrates. The operating conditions include the purification of mitochondria, the analysis of the DNA polymerase activity in the extract and the determination of the sedimentation coefficient on sucrose gradients. The utilization of digitonin for removing the external membrane of the organelle and contaminating proteins has been generalized since this detergent shows no effect on the activities of either DNA polymerases alpha or gamma. The results obtained for the mitochondria of different classes of vertebrates show that the activity responding to the specific assay of DNA polymerase gamma tended invariably to increase during purification while that of DNA polymerase alpha tended to decrease. Furthermore in almost all the cases the gamma-polymerase represented the only DNA polymerase activity found in the mitochondria after digitonin treatment. The analysis of the sedimentation patterns of the mitochondrial DNA polymerase strongly suggests the presence of a single type of DNA polymerase showing the typical properties of the gamma-polymerase. It is concluded that the vertebrate mitochondria contain a well-defined and unique form of DNA polymerase which corresponds to the DNA polymerase gamma.},
}
@article {pmid221822,
year = {1979},
author = {Ambler, RP and Daniel, M and Hermoso, J and Meyer, TE and Bartsch, RG and Kamen, MD},
title = {Cytochrome c2 sequence variation among the recognised species of purple nonsulphur photosynthetic bacteria.},
journal = {Nature},
volume = {278},
number = {5705},
pages = {659-660},
doi = {10.1038/278659a0},
pmid = {221822},
issn = {0028-0836},
mesh = {Amino Acid Sequence ; Bacteria/*genetics ; *Cytochrome c Group/genetics ; Mitochondria/analysis ; Phylogeny ; Species Specificity ; },
}
@article {pmid293756,
year = {1979},
author = {Avise, JC and Giblin-Davidson, C and Laerm, J and Patton, JC and Lansman, RA},
title = {Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {76},
number = {12},
pages = {6694-6698},
pmid = {293756},
issn = {0027-8424},
mesh = {Albumins/genetics ; Animals ; Base Sequence ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Environment ; Gene Frequency ; Heterozygote ; Isoenzymes/genetics ; Phosphogluconate Dehydrogenase/genetics ; Phylogeny ; Rodentia/*genetics ; },
abstract = {Restriction endonuclease assay of mitochondria DNA (mtDNA) and standard starch-gel electrophoresis of proteins encoded by nuclear genes have been used to analyze phylogenetic relatedness among a large number of pocket gophers (Geomys pinetis) collected throughout the range of the species. The restriction analysis clearly distinguishes two populations within the species, an eastern and a western form, which differ by at least 3% in mtDNA sequence. Qualitative comparisons of the restriction phenotypes can also be used to identify mtDNA "clones" within each form. The mtDNA clones interconnect in a phylogenetic network which represents an estimate of matriarchal phylogeny for G. pinetis. Although the protein electrophoretic data also differentiate the eastern and western forms, the data are of limited usefulness in establishing relationships among more local subpopulations. The comparison between these two data sets suggests that restriction analysis of mtDNA is probably unequalled by other techniques currently available for determining phylogenetic relationships among conspecific organisms.},
}
@article {pmid656565,
year = {1978},
author = {Powell, MJ},
title = {Phylogenetic implications of the microbody-lipid globule complex in zoosporic fungi.},
journal = {Bio Systems},
volume = {10},
number = {1-2},
pages = {167-180},
doi = {10.1016/0303-2647(78)90038-2},
pmid = {656565},
issn = {0303-2647},
mesh = {Fungi/classification/*ultrastructure ; *Lipids ; Microbodies/physiology/*ultrastructure ; Organoids/*ultrastructure ; *Phylogeny ; Species Specificity ; Spores, Fungal/ultrastructure ; },
abstract = {Chytridiomycetous fungal zoospores contain a unique and intricate association of organelles, the 'microbody-lipid globule complex' (MLC). The spatial arrangement of organelles in the MLC appears important in the utilization of lipid globules for energy, but in addition, the structural association of organelles in the MLC reveals phylogenetic trends within this diverse group of organisms. Variations in the structure of the MLC correlate well with current phylogenetic concepts of aquatic fungi, yet suggest new relationships among these posteriorly uniflagellate zoospores. Based upon the organization of organelles in the MLC, 4 basic patterns of MLCs can be recognized, and these correspond to the 4 orders of Chytridiomycetes. The MLC in its simplest form consists of a microbody appressed to the edge of a lipid globule. In more highly organized MLCs, mitochondria subtend the microbody and a cisterna surmounts one side of the lipid globule. The organization and structure is still more complex in other MLCs where ER is elaborated into a tubular network of membranes or where small microbodies or mitochondria fuse into 'giant' organelles. The structural organization of the MLC provides an additional criterion by which the phylogeny of awuatic fungi can be evaluated.},
}
@article {pmid941681,
year = {1976},
author = {Varakis, JN and ZuRhein, GM},
title = {Experimental pineocytoma of the Syrian hamster induced by a human papovavirus (JC). A light and electron microscopic study.},
journal = {Acta neuropathologica},
volume = {35},
number = {3},
pages = {243-264},
pmid = {941681},
issn = {0001-6322},
mesh = {Animals ; Cell Differentiation ; Cricetinae ; Female ; Mesocricetus ; Microtubules/ultrastructure ; Neoplasms, Experimental ; Organoids/ultrastructure ; *Papillomaviridae ; Photoreceptor Cells/ultrastructure ; Phylogeny ; Pineal Gland/ultrastructure ; Pinealoma/microbiology/*pathology ; *Polyomaviridae ; },
abstract = {The gross, light and electron microscopic features of a pineocytoma of the Syrian hamster (mesocricetus auratus) which had been induced by a human oncogenic virus (JC papovavirus) have been defined. For comparison, adult hamster pineal tissue was studied, and the literature was consulted in regard to other pineal parenchymal tumors, and to pineal cell differentiation during ontogeny and phylogeny. Many differentiated tumor cells contained organelles, such as vesicle-crowned lamellae (synaptic ribbons) and microtubular sheaves, as consistent with adult hamster pineocytes. Some cells showed rudimentary photoreceptor-like differentiation as consistent with fetal hamster pineocytes and with cells seen in the pineal systems of some lower vertebrate species. Such tumor cells had lumen-directed specialized cytoplasmic extensions which, by their richness in mitochondria and presence of centrioles and striated rootlets, resembled inner segments. Extending 9+0 cilia were accompanied by occasional lamellar whorls. Oncogenesis seems to have simulated different stages of hamster pineal ontogeny. This observation would support the theory that the secretory mammalian pineocyte derived phylogenetically from the true photoreceptor cell of the pineal system of fishes and amphibians. The possible influences of host and of virus in the accomplishment of tumor morphology were discussed. This tumor differed considerably in pattern and cell detail from the only other pineocytoma studied previously by electron microscopy. It is the first experimentally induced pineocytoma.},
}
@article {pmid1107820,
year = {1976},
author = {Baccetti, B and Afzelius, BA},
title = {The biology of the sperm cell.},
journal = {Monographs in developmental biology},
volume = {},
number = {10},
pages = {1-254},
pmid = {1107820},
issn = {0077-0825},
mesh = {Acrosome/ultrastructure ; Animals ; Cell Membrane/ultrastructure ; Cell Nucleus/ultrastructure ; Chromosomes/ultrastructure ; Environment ; Fertilization ; Flagella/ultrastructure ; Glycoproteins ; Humans ; Invertebrates ; Male ; Mammals ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phylogeny ; Polysaccharides ; Sperm Capacitation ; Sperm Motility ; Sperm Tail/ultrastructure ; Spermatozoa/*physiology/ultrastructure ; },
}
@article {pmid1145607,
year = {1975},
author = {Rieger, RM and Rieger, GE},
title = {Fine structure of the pharyngeal bulb in Trilobodrilus and its phylogenetic significance within archiannelida.},
journal = {Tissue &amp; cell},
volume = {7},
number = {2},
pages = {267-279},
doi = {10.1016/0040-8166(75)90005-1},
pmid = {1145607},
issn = {0040-8166},
mesh = {Animals ; Annelida/classification/*ultrastructure ; Cell Nucleus/ultrastructure ; Membranes/ultrastructure ; Mitochondria, Muscle/ultrastructure ; Models, Structural ; Muscle Contraction ; Muscles ; Myofibrils/ultrastructure ; Pharynx/ultrastructure ; Phylogeny ; Sarcoplasmic Reticulum/ultrastructure ; },
abstract = {Transmission electron microscopical studies of the pharyngeal bulb in the archiannelid Trilobodrilus sp. proved the presence of two opposing myofilament systems in the plate muscle cells forming this bulb. These muscles are obliquely striated. The significance as well as the origin of this specialized plate-muscle cells in the pharyngeal bulb of archiannelids is discussed in the light of their controversial phylogenetic and systematic position. In addition a hypothesis is suggested to explain the origin of the special arrangement of two opposing systems of myofilaments in one single muscle cell.},
}
@article {pmid1203955,
year = {1975},
author = {Lamer, HI and Chavin, W},
title = {Ultrastructure of the integumental melanophores of the coelacanth, Latimeria chalumnae.},
journal = {Cell and tissue research},
volume = {163},
number = {3},
pages = {383-394},
pmid = {1203955},
issn = {0302-766X},
mesh = {Animals ; Chromatophores/*ultrastructure ; Fishes/*anatomy &amp; histology ; Melanocytes/ultrastructure ; Melanophores/*ultrastructure ; Microtubules/ultrastructure ; Organoids/ultrastructure ; Phylogeny ; Skin Pigmentation ; },
abstract = {The integumental melanophores of Latimeria chalumnae were studied by light and electron microscopy. The epidermal melanophore located in the mid-epidermis consists of a round perikaryon with long slender dendrites extending into epidermal cells and intercellular spaces. The dermal melanophores occur in the loose dermal matrix underlying a relatively thick layer of collagen fibers. The dermal melanophores are usually flattened and their dendrites lie parallel to the collagen layer. Both epidermal and dermal melanophores contain oval, electron-opaque melanosomes, large mitochondria, agranular vacuoles of endoplasmic reticulum and microtubules. Microfilaments and RNP particles are less conspicuous. While the peripheral cytoplasm of both dermal and epidermal melanophores is filled with a large number of melanosomes, the perinuclear cytoplasm of many dermal melanophores is occupied by premelanosomes in various stages of differentiation, and that of the epidermal melanophore contains numerous large vacuoles. Despite the scarcity of epidermal melanophores, the epidermal melanin unit is present in the form of melanosome complexes. In addition, the melanophores of Latimeria possess the basic characteristics common to other vertebrates, but they more closely resemble those of lungfish and other aquatic vertebrates.},
}
@article {pmid1234809,
year = {1975},
author = {Pác, L},
title = {Ultrastructure of the joint receptors of the tortoise (Testudo graeca. Emys orbicularis).},
journal = {Zeitschrift fur mikroskopisch-anatomische Forschung},
volume = {89},
number = {6},
pages = {1068-1078},
pmid = {1234809},
issn = {0044-3107},
mesh = {Animals ; Extremities ; Joints/*innervation ; Mechanoreceptors/*ultrastructure ; Phylogeny ; Turtles/*anatomy &amp; histology ; },
abstract = {The ultrastructure of the spray-like ramified encapsulated corpuscles with the primitive inner core from the joint capsules of the large limb joints of the tortoise (Testudo graeca and Emys orbicularis) was examined. Each of the branches of the receptor consists of three components. Through the middle of the receptor branche runs the nerve terminal, containing in the receptor matrix numerous mitochondria, tiny light vesicles and neurofilaments and neurotubules running in the axial way. The nerve terminal gives off on some places among the inner core cells tiny finger-like processes. The axon is surrounded by the inner core cells and their irregular plasmatic processes. Among the inner core cells and their irregular plasmatic processes there is a labyrinth of spaces, connected centrally with the periaxonal space and with the boundary space on the periphery. The inner core cells are covered on the surface, turning to the boundary space by the basal membrane. The inner core has a very primitive structure, it still lacks the typical lamellar structure. The capsule of the receptor is formed by flat cells, which surround the inner core in 1--3 layers. Between the capsule of the receptor and the inner core is the boundary space, containihg sporadical collagenous fibrils. The structure of the spray-like ramified encapsulated corpuscles with the primitive inner core from the joint capsules of the tortoise is analogous to the simple lamellar receptors from the skin of some reptiles (Von Düring 1973, 1974). The primitive structure of the inner core of the joint receptors in the tortoise reminds of the structure of the inner core of the developing simple (paciniform) corpuscles (Poláĉek and Halata 1970) and Pacinian corpuscles (Malinovský 1974). The observed nerve endings represent a primitive, early stage in phylogeny development of the lamellar mechanoreceptors.},
}
@article {pmid1378037,
year = {1992},
author = {Ruttkay, H and Solignac, M and Sperlich, D},
title = {Nuclear and mitochondrial ribosomal RNA variability in the obscura group of Drosophila.},
journal = {Genetica},
volume = {85},
number = {2},
pages = {131-138},
pmid = {1378037},
issn = {0016-6707},
mesh = {Animals ; Base Sequence ; Cell Nucleus/*metabolism ; Drosophila/*genetics ; *Genetic Variation ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 28S/*genetics ; Sequence Alignment ; Species Specificity ; },
abstract = {Parts of 28S (nuclear) and 12S (mitochondrial) ribosomal RNA of Palearctic, Nearctic and African species of the obscura group have been sequenced by the direct method of sequencing. Rates of nucleotide substitutions in both molecules were compared. The nucleotide divergence is higher in the mitochondrial rRNA. Average distances of species taken in pairwise were compared to results obtained with the melanogaster subgroup: the divergence of nuclear rRNA appears lower, that of the mtDNA higher whereas genetic distances (allozymes) and sncDNA distances are similar. Noticeable variability of evolutionary rates can be observed even in low taxonomical levels. Phylogenetic trees for the obscura group are in general agreement with those obtained with other characters.},
}
@article {pmid1399706,
year = {1992},
author = {Birt, TP and Friesen, VL and Green, JM and Montevecchi, WA and Davidson, WS},
title = {Cytochrome-b sequence variation among parrots.},
journal = {Hereditas},
volume = {117},
number = {1},
pages = {67-72},
doi = {10.1111/j.1601-5223.1992.tb00009.x},
pmid = {1399706},
issn = {0018-0661},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/physiology ; Molecular Sequence Data ; Parrots/*genetics ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {The nucleotide sequence of a 307 bp fragment of the mitochondrial cytochrome-b gene was determined for 12 species of parrot, using the polymerase chain reaction and direct sequencing. Sequence divergence ranged from 26-54 differences in pairwise comparisons, with the majority of base substitutions occurring at third positions of codons. The transition:transversion ratio was determined to be higher (approximately 24.3:1) in recently divergent parrot lineages than has generally been observed in other groups. Strongly biased base composition, particularly at the third position of codons, is evident among the sequences. Phylogenetic relationships among more divergent taxa were estimated, using only transversion substitutions, while all the substitutions were useful for closely related taxa. The African genera Psittacus and Poicephalus are closely related, in contrast to the Australian genera Nymphicus, Purpureicephalus and Melopsittacus, which represent more divergent lineages. The cockatoos appear to represent an ancient lineage within the parrots.},
}
@article {pmid1413112,
year = {1992},
author = {Korobov, VN and Nazarenko, VI and Radomskiĭ, NF and Starodub, NF},
title = {[Comparative analysis of the spatial organization of myoglobins. I. Hydrophobicity profiles].},
journal = {Ukrainskii biokhimicheskii zhurnal (1978)},
volume = {64},
number = {2},
pages = {22-26},
pmid = {1413112},
issn = {0201-8470},
mesh = {Alligators and Crocodiles ; Animals ; Humans ; Mitochondria/*metabolism ; Mollusca ; Myoglobin/*chemistry ; Oxygen/*metabolism ; *Phylogeny ; Protein Conformation ; Rodentia ; Water ; Whales ; },
abstract = {Hydrophobicity profiles of myoglobins in the animal species far remote in the evolutionary series are considerably similar. A complete coincidence as to the arrangement of hydrophobic zones along the polypeptide chain in myoglobins of the compared species (from a man to mollusc) is revealed at the beginning of alpha-helix of B-segment and in the area corresponding to a cluster which embodies a heme- bound water molecule, distal histidine E7 being directed to this cluster. The mollusc myoglobin with two absent (as compared to myoglobins of other species) hydrophobic sites differs in the profile of hydrophobicity most of all. It is supposed that hydrophobic nuclei forming the heme circumference create a globule "skeleton" thus pre-setting general spatial structure of the myoglobin molecule, which is very significant for its functional activity.},
}
@article {pmid1426143,
year = {1992},
author = {Roten, CA and Karamata, D},
title = {Endogenous synthesis of peptidoglycan in eukaryotic cells; a novel concept involving its essential role in cell division, tumor formation and the biological clock.},
journal = {Experientia},
volume = {48},
number = {10},
pages = {921-931},
pmid = {1426143},
issn = {0014-4754},
mesh = {Animals ; Bacteria/metabolism ; Carbohydrate Sequence ; Humans ; Molecular Sequence Data ; Peptidoglycan/*biosynthesis/chemistry/metabolism ; Periodicity ; Phylogeny ; Plants/metabolism ; },
abstract = {Degradation products of peptidoglycan, the universal bacterial cell wall constituent, were previously found in animal tissues and urine. Reassessment and quantitative analysis of available data lead to an original concept, i.e. that eukaryotic cells synthesize peptidoglycan. We present a model in which this endogenously synthesized peptidoglycan is essential for the processes of eukaryotic cell division and sleep induction in animals. Genes for peptidoglycan metabolism, like those for lysine biosynthesis in plants, are probably inherited from endosymbiotic bacteria, the ancestors of mitochondria and chloroplasts. Corollaries of this concept, i.e. roles for peptidoglycan metabolism in tumor formation and in the biological clock, are supported by abundant evidence. We propose that many interactions between bacteria and eukaryotes are conditioned by their common genetic heritage.},
}
@article {pmid1469708,
year = {1992},
author = {Mandrup, S and Hummel, R and Ravn, S and Jensen, G and Andreasen, PH and Gregersen, N and Knudsen, J and Kristiansen, K},
title = {Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes. A typical housekeeping gene family.},
journal = {Journal of molecular biology},
volume = {228},
number = {3},
pages = {1011-1022},
doi = {10.1016/0022-2836(92)90888-q},
pmid = {1469708},
issn = {0022-2836},
mesh = {Animals ; Base Sequence ; Carrier Proteins/*genetics ; Cloning, Molecular ; Diazepam Binding Inhibitor ; Exons ; Introns ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Pseudogenes/*genetics ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Antisense ; Rats ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; },
abstract = {Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous modulator of the GABAA receptor in brain membranes. ACBP/DBI, or proteolytically derived polypeptides of ACBP/DBI, have also been implicated in the control of steroidogenesis in mitochondria and glucose-stimulated insulin secretion. Thus, it appears that ACBP/DBI is a remarkable, versatile protein. Now we have molecularly cloned and characterized the ACBP/DBI gene family in rat. The rat ACBP/DBI gene family comprises one expressed gene and four processed pseudogenes of which one was shown to exist in two allelic forms. The expressed gene is organized into four exons and three introns. There is a remarkable correspondence between the structural modules of ACBP/DBI as determined by 1H nuclear magnetic resonance spectroscopy and the exon-intron architecture of the ACBP/DBI gene. Detailed analyses of transcription of the ACBP/DBI gene in brain and liver were performed to map transcription initiation sites and to examine if transcripts from the ACBP/DBI gene were subject to alternative processing. In both brain and liver, transcription is initiated from two major and multiple minor initiation sites. No evidence for alternative splicing was obtained. The promoter region of the ACBP/DBI gene is located in a CpG island and lacks a canonical TATA box. Thus, the ACDB/DBI gene exhibits all the hallmarks of a typical housekeeping gene.},
}
@article {pmid1473724,
year = {1992},
author = {Moum, T and Johansen, S},
title = {The mitochondrial NADH dehydrogenase subunit 6 (ND6) gene in Murres: relevance to phylogenetic and population studies among birds.},
journal = {Genome},
volume = {35},
number = {6},
pages = {903-906},
doi = {10.1139/g92-139},
pmid = {1473724},
issn = {0831-2796},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Birds/*genetics/metabolism ; DNA, Mitochondrial ; *Genetics, Population ; Mitochondria/*enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; *Phylogeny ; Sequence Homology, Nucleic Acid ; },
abstract = {The nucleotide sequences of the mitochondrial ND6 and tRNA(Glu) genes and part of the displacement loop region in two closely related seabird species are presented. A chicken type gene organization in which the tRNA(Glu), ND6, and displacement loop are localized next to each other was found in these species and suggests that this is a conserved feature of avian mitochondrial DNA. The nucleotide and amino acid divergences of ND6 at different taxonomic levels are assessed, and its relevance to phylogenetic studies in birds is discussed.},
}
@article {pmid1533253,
year = {1992},
author = {Recipon, H and Perasso, R and Adoutte, A and Quetier, F},
title = {ATP synthase subunit c/III/9 gene sequences as a tool for interkingdom and metaphytes molecular phylogenies.},
journal = {Journal of molecular evolution},
volume = {34},
number = {4},
pages = {292-303},
pmid = {1533253},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Eukaryotic Cells/enzymology ; Genome ; Humans ; Molecular Sequence Data ; Organelles/*enzymology ; *Phylogeny ; Prokaryotic Cells/enzymology ; Proton-Translocating ATPases/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {The 38 sequences of the ATPase c/III/9 gene determined in bacteria, fungi, mammals, and higher plants have been used to construct phylogenetic trees by distance matrix and parsimony methods (checked by bootstrapping); alignments have been performed on the deduced amino-acid sequences and then transferred back to the nucleotide sequences. Three lineages stand out: (1) eubacteria (except cyanobacteria and alpha purple bacteria), (2) chloroplasts, together with cyanobacteria, and (3) mitochondria together with nuclei and alpha purple bacteria. The clear monophyly of the mitochondrial/nuclear lineage, taken all together, strongly suggests that the nuclear copies of the gene now residing in the eukaryotic nucleus originate from a mitochondrial transfer. Within this lineage, metaphytes emerge late and as a cohesive group, after fungi (as a dispersed group) and metazoa, yielding an order that markedly differs from that obtained through typical RNA nuclear molecules. The possible biphyletic origin of mitochondria based on mitochondrial rRNA sequences is not evidenced by these sequences. Internal branches within both the chloroplastic and the mitochondrial lineages are consistent with botanical evolutionary schemes based on morphological characters. In spite of its relatively small size, the ATPase c/III/9 gene therefore displays remarkable properties as a phylogenetic index and adds a new tool for molecular evolutionary reconstructions, especially within the metaphytes.},
}
@article {pmid1584013,
year = {1992},
author = {Gatesy, J and Yelon, D and DeSalle, R and Vrba, ES},
title = {Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.},
journal = {Molecular biology and evolution},
volume = {9},
number = {3},
pages = {433-446},
doi = {10.1093/oxfordjournals.molbev.a040734},
pmid = {1584013},
issn = {0737-4038},
mesh = {Animals ; Artiodactyla/*classification/genetics ; Base Sequence ; DNA ; DNA, Ribosomal/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; },
abstract = {Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.},
}
@article {pmid1588598,
year = {1992},
author = {Karlovsky, P and Fartmann, B},
title = {Genetic code and phylogenetic origin of oomycetous mitochondria.},
journal = {Journal of molecular evolution},
volume = {34},
number = {3},
pages = {254-258},
pmid = {1588598},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Base Sequence ; Codon ; DNA, Fungal ; DNA, Mitochondrial ; *Mitochondria ; Molecular Sequence Data ; *Phylogeny ; Phytophthora/classification/*genetics ; Sequence Alignment ; },
abstract = {We sequenced the 3'-terminal part of the COX3 gene encoding cytochrome c oxidase subunit 3 from mitochondria of Phytophthora parasitica (phylum Oomycota, kingdom Protoctista). Comparison of the sequence with known COX3 genes revealed that UGG is used as a tryptophan codon in contrast to UGA in the mitochondrial codes of most organisms other than green plants. A very high AT mutation pressure operates on the mitochondrial genome of Phytophthora, as revealed by codon usage and by A+T content of noncoding regions, which seems paradoxical because AT pressure causes tryptophan codon reassignment from UGG to UGA in mitochondria of most species. The genetic code and other data suggest that mitochondria of Oomycota share a direct common ancestor with mitochondria of plants and that mitochondria of the ancestor of Planta and Oomycota were acquired in a second endosymbiotic event, which occurred later than the acquisition of mitochondria by other eukaryotes.},
}
@article {pmid1648084,
year = {1991},
author = {Lundin, M and Baltscheffsky, H and Ronne, H},
title = {Yeast PPA2 gene encodes a mitochondrial inorganic pyrophosphatase that is essential for mitochondrial function.},
journal = {The Journal of biological chemistry},
volume = {266},
number = {19},
pages = {12168-12172},
pmid = {1648084},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Base Sequence ; Catalysis ; Chromosomes, Fungal ; *Genes, Fungal ; Mitochondria/*enzymology/physiology ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Pyrophosphatases/*genetics ; Restriction Mapping ; Saccharomyces cerevisiae/*genetics ; Sequence Alignment ; },
abstract = {We have cloned a gene encoding a mitochondrial inorganic pyrophosphatase (PPase) in the yeast Saccharomyces cerevisiae by low stringency hybridization to PPA1, the yeast gene for cytoplasmic PPase. The new gene, PPA2, is located on chromosome 13 and encodes a protein whose sequence is 49% identical to the cytoplasmic enzyme. The protein differs from cytoplasmic PPase in that it has a leader sequence enriched in basic and hydroxylated residues, which is typically found in mitochondrial proteins. Yeast cells overproducing PPA2 had a 47-fold increase in mitochondrial PPase activity. This activity was further stimulated 3-fold by the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone, which suggests that PPA2 is part of an energy-linked enzyme. Using gene disruptions, we found that PPA1 is required for cell growth. In contrast, cells disrupted for PPA2 are viable, but unable to grow on respiratory carbon sources. Fluorescence microscopy revealed that these cells have lost their mitochondrial DNA. We conclude that the mitochondrial PPase encoded by PPA2 is essential for mitochondrial function and maintenance of the mitochondrial genome.},
}
@article {pmid1663569,
year = {1991},
author = {Normark, BB and McCune, AR and Harrison, RG},
title = {Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences.},
journal = {Molecular biology and evolution},
volume = {8},
number = {6},
pages = {819-834},
doi = {10.1093/oxfordjournals.molbev.a040685},
pmid = {1663569},
issn = {0737-4038},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/chemistry/genetics ; DNA ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/chemistry/genetics ; Fishes/classification/*genetics ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; },
abstract = {To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.},
}
@article {pmid1679525,
year = {1991},
author = {Perl, A and Aviv, D and Galun, E},
title = {Nuclear-organelle interaction in Solanum: interspecific cybridizations and their correlation with a plastome dendrogram.},
journal = {Molecular &amp; general genetics : MGG},
volume = {228},
number = {1-2},
pages = {193-200},
pmid = {1679525},
issn = {0026-8925},
mesh = {Blotting, Southern ; Cell Nucleus/chemistry ; Chloroplasts ; Cloning, Molecular ; DNA/*analysis/isolation &amp; purification ; DNA, Mitochondrial ; Extrachromosomal Inheritance ; Hybridization, Genetic ; *Phylogeny ; *Plants, Edible ; Polymorphism, Restriction Fragment Length ; Protoplasts ; },
abstract = {Alloplasmic compatibility, namely the functional interaction between the nuclear genome of a given species with plastomes and chondriomes of alien species, is of considerable relevance in plant biology. The genus Solanum encompasses a wide spectrum of species and is therefore suitable for a study of this compatibility. We thus chose the nuclear genome of Solanum tuberosum (potato) and organelles (chloroplast and mitochondria) from 14 other Solanum species to initiate an investigation of intrageneric nucleus/organelle interactions. An assessment of the diversity of the chloroplast DNAs from these 15 species resulted in the construction of a plastome dendrogram (phylogenetic tree). In parallel we extended a previous study and performed ten additional fusion combinations by the "donor-recipient protoplast fusion" procedure, using potato protoplasts as recipients and protoplasts from any of ten other Solanum species as donors. We found that two fusion combinations did not yield cybrids and that the chloroplasts of S. polyadenium and the mitochondria (or mitochondrial components) from S. tarijense could not be transferred to cybrids bearing potato nuclei. In general, there is a correlation, albeit not perfect, between the cybridization data and the plastome dendrogram. These results furnish valuable information toward future transfer of plasmone-encoded breeding traits from wild Solanum species into potato. This information should also be useful for the planning of asymmetric protoplast fusion between potato and wild accessions for the improvement of pathogen and stress resistance of potato cultivars.},
}
@article {pmid1692773,
year = {1990},
author = {Wolff, G and Kück, U},
title = {The structural analysis of the mitochondrial SSUrRNA implies a close phylogenetic relationship between mitochondria from plants and from the heterotrophic alga Prototheca wickerhamii.},
journal = {Current genetics},
volume = {17},
number = {4},
pages = {347-351},
pmid = {1692773},
issn = {0172-8083},
mesh = {Base Sequence ; Chlamydomonas/genetics ; Genes ; Mitochondria/*analysis ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/genetics/ultrastructure ; Prototheca/*genetics/ultrastructure ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {The gene for the mitochondrial small subunit rRNA (SSUrRNA) from the heterotrophic alga Prototheca wickerhamii has been isolated from a gene library of extranuclear DNA. Sequence and structural analyses allow the determination of a secondary structure model for this rRNA. In addition, several sequence motifs are present which are typically found in SSUrRNAs of various mitochondrial origins. Unexpectedly, the Prototheca RNA sequence has more features in common with mitochondrial SSUrRNAs from plants than with that from the green alga Chlamydomonas reinhardtii. The phylogenetic relationship between mitochondria from plants and algae is discussed.},
}
@article {pmid1756976,
year = {1991},
author = {Hegedus, DD and Pfeifer, TA and MacPherson, JM and Khachatourians, GG},
title = {Cloning and analysis of five mitochondrial tRNA-encoding genes from the fungus Beauveria bassiana.},
journal = {Gene},
volume = {109},
number = {1},
pages = {149-154},
doi = {10.1016/0378-1119(91)90601-7},
pmid = {1756976},
issn = {0378-1119},
mesh = {Base Sequence ; Cloning, Molecular ; Genetic Code ; Mitochondria/*chemistry ; Mitosporic Fungi/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics ; RNA, Transfer, Ile/genetics ; RNA, Transfer, Pro/genetics ; RNA, Transfer, Ser/genetics ; RNA, Transfer, Trp/genetics ; RNA, Transfer, Val/genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; },
abstract = {Five mitochondrial (mt) tRNA genes from the filamentous fungus, Beauveria bassiana, were cloned and sequenced. The genes encoding the Val-, Ile-, Ser-, Trp- and Pro-accepting tRNAs were found clustered in the region 5' to the lrRNA-encoding gene. The genes were 64-77% homologous with the equivalent genes from other filamentous fungi, 49-58% to yeasts with the exception of the Val-accepting tRNA-encoding gene which was 76%, and only slightly homologous with Escherichia coli. The B. bassiana mt genetic code was found to be similar to that of other fungal mitochondria in that the UGA codon is used as a signal for Trp rather than as a stop codon. Transcript analysis has revealed that the genes present in tRNA cluster are transcribed and processed into tRNA-size products. Secondary structure models proposed for the gene products show that conservation of tRNA secondary structure also exists. The presence of a GGC sequence rather than a GGU sequence in the D-loop of the tRNA(Trp)-encoding gene is a feature unique to the B. bassiana mt tRNA. An unconventional G-A base pair present in the D-stem of the tRNA(Ser)-encoding gene is a feature conserved in the mt tRNA of other filamentous fungi. Comparison of the B. bassiana tRNA-encoding genes with those of two other filamentous fungi and two yeasts revealed that the differences between closely related species favoured transition-type mutations.},
}
@article {pmid1779435,
year = {1991},
author = {Pesole, G and Sbisá, E and Mignotte, F and Saccone, C},
title = {The branching order of mammals: phylogenetic trees inferred from nuclear and mitochondrial molecular data.},
journal = {Journal of molecular evolution},
volume = {33},
number = {6},
pages = {537-542},
pmid = {1779435},
issn = {0022-2844},
mesh = {Animals ; Databases, Factual ; Genetic Variation ; Humans ; Mammals/*genetics ; Markov Chains ; Mitochondria/*metabolism ; *Phylogeny ; },
abstract = {In order to clarify some controversial phylogenies such as those regarding the triplet of human, rodent, and cow and the evolutionary position of Lagomorpha with respect to other mammals, we have analyzed both nuclear and mitochondrial genes using the stationary Markov model developed in our laboratory. We found that the two sets of genes give different results. In particular the mitochondrial tree showed rabbit linked first to rodents and the rabbit-rodents branch linked to artiodactyls with human as the outgroup. The most favorite nuclear tree showed human linked first to artiodactyls and the human-artiodactyls branch linked to rabbit with rodents as the outgroup. The obvious questions, (1) which tree is the correct one, or (2) both trees can be incorrect, and (3) how can we explain such an evolutionary pattern, are discussed on the basis of our limited knowledge of factors that influence the clocklike behavior of biological macromolecules.},
}
@article {pmid1854909,
year = {1991},
author = {Spiegel, FW},
title = {A proposed phylogeny of the flagellated protostelids.},
journal = {Bio Systems},
volume = {25},
number = {1-2},
pages = {113-120},
doi = {10.1016/0303-2647(91)90017-f},
pmid = {1854909},
issn = {0303-2647},
mesh = {Animals ; Eukaryota/*classification ; Flagella ; Mitochondria ; *Phylogeny ; Terminology as Topic ; },
abstract = {The flagellated members of the group of mycetozoans known as protostelids have been recognized for some time to be members of a monophyletic group which also includes the myxomycetes. This inference was based primarily upon comparisons of the flagellar apparatus of the amoeboflagellate state. However, more detailed comparisons based on the whole life history and comparisons with an outgroup were necessary to have information sufficient to determine the interrelationships within the group. Recent studies of the other states of the life history of protostelids have provided a wealth of additional morphological and developmental characters such that an in depth phylogenetic analysis is possible. The results show that the group can be resolved into two major clades, one of which contains the myxomycetes and the myxomycete-like protostelid genera, Protosporangium, Clastostelium, and Ceratiomyxa, and another which contains the protostelid genera Planoprotostelium, Cavostelium, and Ceratiomyxella. As the myxomycetes appear to be part of the ingroup, and not a sister group to the protostelids, L.S. Olive's subclass Protostelia must be considered paraphyletic.},
}
@article {pmid1854912,
year = {1991},
author = {Cavalier-Smith, T},
title = {Archamoebae: the ancestral eukaryotes?.},
journal = {Bio Systems},
volume = {25},
number = {1-2},
pages = {25-38},
doi = {10.1016/0303-2647(91)90010-i},
pmid = {1854912},
issn = {0303-2647},
mesh = {Amoeba ; Animals ; *Eukaryota ; *Eukaryotic Cells ; Organelles ; *Phylogeny ; },
abstract = {The archezoan phylum Archamoebae Cavalier-Smith, 1983 is here modified by adding a new order Phreatamoebida (presently containing only Phreatamoeba) and removing the family Entamoebidae. Entamoebidae are instead tentatively placed as a class Entamoebea together with the classes Heterolobosea, Percolomonadea and Pseudociliatea in the new protozoan phylum Percolozoa Cavalier-Smith, 1991. Thus emended the phylum Archamoebae is more homogeneous; it is more distinguished from the other two phyla of the primitively amitochondrial kingdom and superkingdom Archezoa (i.e. Metamonada and Microsporidia) by having kinetids with only a single flagellum and basal body and a flagellar root consisting of a cone of evenly spaced microtubules. This unikont character of the archamoebae suggests that they may be ancestral to the tetrakont Metamonada, from which the non-flagellate Microsporidia possibly evolved. Higher eukaryotes (superkingdom Metakaryota) probably evolved from a tetrakont metamonad by the symbiotic origin of mitochondria and peroxisomes. If so, the Archamoebae are the most primitive extant phylum of eukaryotes; if molecular phylogenetic studies confirm this idea, Archamoebae will deserve intensive study, which could reveal much about the origin of the eukaryote condition and also establish what is truly universal among eukaryotes. Archamoebae, like other Archezoa, lack mitochondria and peroxisomes and have no obvious Golgi dictyosomes. Their evolutionary significance is discussed and a detailed classification is presented in which the two earlier classes are merged into a single one: Pelobiontea Page, 1976 stat. nov., containing two orders Mastigamoebida Frenzel, 1892 (Syn. Rhizo-Flagellata Kent, 1880 non Rhizomastigida auct.) (including Mastigamoeba, Mastigina, Mastigella, Pelomyxa and probably a few other genera, which have one or more flagella or cilia (motile or immotile, 9 + 2 or otherwise) in the amoeboid trophic phase), and Phreatamoebida ord. nov. (including only Phreatamoeba in the new family Phreatamoebidae, which has alternating phases of non-flagellate amoebae and uniflagellate cells). Mastigamoebida are divided into three families: Mastigamoebidae Goldschmidt, 1907; Mastigellidae fam. nov.; Pelomyxidae Schulze, 1877. Archamoebae may be uni- or multi-nucleate and either gut parasites or (more usually) free-living in soil, freshwater, or marine habitats. Some can form cysts that would probably fossilize; the earliest (1450 My old) smooth-walled fossil cells large enough to be probable eukaryotes might therefore be archamoebal cysts.},
}
@article {pmid1917282,
year = {1991},
author = {Rohde, K and Watson, NA and Cribb, T},
title = {Ultrastructure of sperm and spermatogenesis of Lobatostoma manteri (Trematoda, Aspidogastrea).},
journal = {International journal for parasitology},
volume = {21},
number = {4},
pages = {409-419},
doi = {10.1016/0020-7519(91)90098-r},
pmid = {1917282},
issn = {0020-7519},
mesh = {Animals ; Male ; Microscopy, Electron ; Phylogeny ; Spermatogenesis ; Spermatozoa/*ultrastructure ; Trematoda/physiology/*ultrastructure ; },
abstract = {Mature sperm has two axonemes of the 9 + '1' pattern incorporated in the sperm body, a row of peripheral microtubules interrupted along part of the sperm by the axonemes, some microtubules in the interior of the sperm and a long lateral extension (lobe) of the sperm body, an elongate nucleus and mitochondrion, and many dense rod-like structures. A supporting rod extends underneath a specialized region consisting of alternating thin and thick transverse rows of irregular dense patches, and with surface ridges around (all or) most of the surface of the sperm. Primary spermatocytes in the prophase of the first meiotic division have synaptonemal complex(es), and are rich in mitochondria. In early spermiogenesis, mitochondria are arranged around the surface of the nucleus, a dense layer appears at one pole of the nucleus, close to an apposed dense layer at the cell membrane in which a row of microtubules develops. The intercentriolar (= central) body develops close to the nucleus. The fully developed intercentriolar body has a regular striation and is located perpendicular and close to the surface of the nucleus. Two flagella extend into the space surrounding the outgoing median process, their basal bodies are located perpendicular to the intercentriolar body and their cross-striated rootlets extend along the surface of the rounded nucleus. At a later stage, rootlets and flagella become more parallel with the intercentriolar body, the nucleus and the fused mitochondria migrate into the median process, and the flagella become incorporated into the median process (= sperm body). The outgrowing spermatozoa are connected to the cytoplasm of the cytophore by dense arching membranes. Finally, rootlets of flagella are resorbed and the spermatozoa are pinched off close to the basal bodies. Two species (Lobatostoma and Multicotyle) of the same family differ strongly in the type of spermiogenesis, although their mature sperm is of the same basic type, i.e. spermiogenesis is not necessarily more useful for phylogenetic considerations than sperm structure.},
}
@article {pmid2002767,
year = {1991},
author = {Smith, MF and Patton, JL},
title = {Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae).},
journal = {Molecular biology and evolution},
volume = {8},
number = {1},
pages = {85-103},
doi = {10.1093/oxfordjournals.molbev.a040638},
pmid = {2002767},
issn = {0737-4038},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Electrophoresis, Polyacrylamide Gel ; Genes ; *Genetic Variation ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Muridae/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; South America ; },
abstract = {A 401-bp fragment of the mitochondrial cytochrome b gene was sequenced from polymerase chain reaction-amplified products for 20 natural populations representing 12 species of South American akodontine rodents (Muridae). Variation among these taxa increased with their hierarchical position, from comparisons within local populations to those among different genera. Two individuals from the same local population differed by less than 1% sequence divergence. Sequence divergence among geographic samples within a species was 0.25%-8%, while that among species was 3%-21%. Comparisons of the akodontine sequences with that for the house mouse show 21%-25% sequence difference. A parsimony-based phylogenetic analysis of the data supports the placement of the taxon Microxus within Akodon (sensu stricto), of Bolomys just outside the Akodon cluster, and of Chroeomys as a separate genus quite distinct from the other members of this group. This phylogenetic hypothesis is identical to that determined from electrophoretic data but is quite divergent from the present taxonomy of the group.},
}
@article {pmid2025303,
year = {1991},
author = {Ozawa, T and Tanaka, M and Ino, H and Ohno, K and Sano, T and Wada, Y and Yoneda, M and Tanno, Y and Miyatake, T and Tanaka, T},
title = {Distinct clustering of point mutations in mitochondrial DNA among patients with mitochondrial encephalomyopathies and with Parkinson's disease.},
journal = {Biochemical and biophysical research communications},
volume = {176},
number = {2},
pages = {938-946},
doi = {10.1016/s0006-291x(05)80276-1},
pmid = {2025303},
issn = {0006-291X},
mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*chemistry ; Female ; Humans ; Male ; Middle Aged ; Mitochondria, Muscle/*pathology ; *Multigene Family ; *Mutation ; Parkinson Disease/*genetics ; Phylogeny ; },
abstract = {The total sequence data for mitochondrial DNA (mtDNA) revealed distinct clustering of point mutations (pms) in mtDNA among one patient with myoclonus epilepsy with ragged-red fibers (MERRF), two patients with Parkinson's disease (PD), two patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and one patient with fatal infantile cardiomyopathy (FICM). Among 33 to 62 pms found in each patients, sequentially diverged five clusters of pms were detected and designated as C-1 to C-5. C-1, consisted of fourteen pms, existed in the MERRF patient, C-1 and C-2 (nine pms) in one PD patient, C-1 to C-3 (seven pms) in another PD patient, C-1 to C-4 (one pm) in one MELAS patient and C-1 to C-5 (three pms) in another MELAS patient and the FICM patient. From these clustering of pms, a phylogenetic tree of mitochondrial encephalomyopathies (ME) was constructed. This tree clearly indicated that the ME and PD patients are members of the same gene family, and the MELAS and FICM patients are each others' closest relative. Each patient's unique pms (14 to 28 pms) were detected and, from their characteristic features, the types of the mutations specific for the disease were classified as mit- + syn- for MERRF, mit- + p- for PD, and syn- + mit- for MELAS. An inverse relation was found between the total number of pms and life span of the MELAS and FICM patients.},
}
@article {pmid2068786,
year = {1991},
author = {Cavalier-Smith, T},
title = {Intron phylogeny: a new hypothesis.},
journal = {Trends in genetics : TIG},
volume = {7},
number = {5},
pages = {145-148},
pmid = {2068786},
issn = {0168-9525},
mesh = {Animals ; *Introns ; *Phylogeny ; RNA Splicing ; RNA, Transfer/genetics/metabolism ; },
abstract = {The three major classes of intron are clearly of unequal antiquity. Structured (often self-splicing and sometimes mobile) introns are the most ancient, probably dating (at least for group I) from the ancestral (eubacterial) cell 3500 million years ago, and were originally restricted to tRNA. Protein-spliced introns (usually in tRNA) probably evolved from them by a radical change in splicing mechanism in the common ancestor of eukaryotes and archaebacteria, perhaps only about 1700 million years ago. Spliceosomal introns probably evolved from group-II-like self-splicing introns after the origin of the nucleus between 1700 and 1000 million years ago, and were probably mostly inserted into previously unsplit protein-coding genes after the origin of mitochondria 1000 million years ago.},
}
@article {pmid2085956,
year = {1990},
author = {Eisenstein, RS and Miller, RH and Hoganson, G and Harper, AE},
title = {Phylogenetic comparisons of the branched-chain alpha-ketoacid dehydrogenase complex.},
journal = {Comparative biochemistry and physiology. B, Comparative biochemistry},
volume = {97},
number = {4},
pages = {719-726},
doi = {10.1016/0305-0491(90)90113-8},
pmid = {2085956},
issn = {0305-0491},
support = {AM-10748/AM/NIADDK NIH HHS/United States ; },
mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide) ; Animals ; Antibodies/pharmacology ; Cattle ; Chickens ; Immunoblotting ; Ketone Oxidoreductases/antagonists &amp; inhibitors/immunology/*metabolism ; Kidney/enzymology ; Mitochondria/enzymology ; Mitochondria, Liver/enzymology ; Multienzyme Complexes/antagonists &amp; inhibitors/immunology/*metabolism ; Peptide Fragments/metabolism ; *Phylogeny ; Rats ; Rats, Inbred Strains ; Serine Endopeptidases/metabolism ; Sheep ; Species Specificity ; Trout ; },
abstract = {1. Antibodies against the E1b and E2b components of bovine branched-chain alpha-ketoacid (BCKA) dehydrogenase (BCKAD) complex completely inhibited BCKA oxidation in mammalian and avian mitochondria. BCKA oxidation by salmonid mitochondria was less affected and the enzyme from Pseudomonas putida was unaffected. 2. In rodents, anti-E1b E2b IgG inhibited oxidation of all three BCKA in a similar dose-dependent manner: oxidation of alpha-ketobutyrate and alpha-keto-y-methiolbutyrate was also partially inhibited. 3. Except for the salmonid BCKAD, a similar Mr for the E2b and E1b alpha proteins was observed in these species. 4. After digestion with V-8 protease similar immunoreactive peptides were observed for the human and rodent complex.},
}
@article {pmid2166594,
year = {1990},
author = {Kostetsky, P and Vladimirova, R},
title = {Identification of significant conservative and variable regions in homologous protein sequences.},
journal = {Biochimie},
volume = {72},
number = {4},
pages = {295-297},
doi = {10.1016/0300-9084(90)90087-w},
pmid = {2166594},
issn = {0300-9084},
mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/genetics ; *Genetic Variation ; Humans ; Mitochondria/analysis ; Phospholipases A/genetics ; *Phylogeny ; Proteins/*genetics ; Rats ; Sequence Homology, Nucleic Acid ; Snake Venoms/genetics ; Sodium-Potassium-Exchanging ATPase/genetics ; Swine ; },
abstract = {A set of aligned homologous protein sequences is divided into 2 groups consisting of m and n sequences. Each group contains sequences from the most related species. Value of the position variability of homologous proteins sequences is defined as a number of failures to coincide in comparison of all possible m.n pairs of amino acid residues (each from a different group) in that position divided by m.n. The variability value plotted vs the sequence position number with a window of 10 positions gives the intergroup variability profile (VP). Area of the figure included between the VP and its mean value line characterizes the overall irregularity of amino acid substitutions along the protein sequences. If the area value S is greater than the average area Sr for 1000 random VPs by more than 2 standard deviation units (sigma), the real VP extrema containing the surplus of area S-(Sr + 2 sigma) are cut off. The cut-off stretches are likely to be significant variable and conservative regions. Intergroup comparisons of protein sequences reveal high overall irregularity of amino acid substitutions and identify variable and conservative regions for all considered families of proteins: phospholipases A2, aspartate aminotransferases, alpha-subunits of Na+,K(+)-ATPase, L- and M-subunits of photosynthetic bacteria photoreaction centre, and human rhodopsins.},
}
@article {pmid2216410,
year = {1990},
author = {Soto, MA and Toha, J},
title = {Phylogenetic tree of tRNAs using a simple algorithm.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {20},
number = {2},
pages = {161-166},
pmid = {2216410},
issn = {0169-6149},
mesh = {*Algorithms ; Amino Acid Sequence ; Animals ; Base Sequence ; Chloroplasts ; Codon ; Escherichia coli/genetics ; Genetic Code ; Humans ; Mitochondria ; Molecular Sequence Data ; Phenylalanine/genetics ; Phylogeny ; Plants/genetics ; RNA, Transfer/*classification ; },
abstract = {A simple method for phylogenetic tree construction is described. In this method each node is calculated considering the distance between the elements and the difference between these elements and an average element, allowing the selection of the most probable node. Two examples of tRNA phylogenies (E. coli set and Phe family) are analyzed, giving both reliable trees. Data from these dendrograms give support to the idea of an early cloverleaf arising.},
}
@article {pmid2246114,
year = {1990},
author = {Bereiter-Hahn, J},
title = {Behavior of mitochondria in the living cell.},
journal = {International review of cytology},
volume = {122},
number = {},
pages = {1-63},
doi = {10.1016/s0074-7696(08)61205-x},
pmid = {2246114},
issn = {0074-7696},
mesh = {Animals ; Cell Cycle ; Cell Nucleus/physiology ; Cytoskeleton/physiology ; Endoplasmic Reticulum/physiology ; Mitochondria/metabolism/*physiology/ultrastructure ; Phylogeny ; },
}
@article {pmid2266771,
year = {1990},
author = {Grace, SC},
title = {Phylogenetic distribution of superoxide dismutase supports an endosymbiotic origin for chloroplasts and mitochondria.},
journal = {Life sciences},
volume = {47},
number = {21},
pages = {1875-1886},
doi = {10.1016/0024-3205(90)90399-c},
pmid = {2266771},
issn = {0024-3205},
mesh = {Animals ; Chloroplasts/*enzymology ; Isoenzymes/genetics/*physiology ; Mitochondria/*enzymology ; *Phylogeny ; Plants/enzymology ; Species Specificity ; Superoxide Dismutase/genetics/*physiology ; Symbiosis/genetics ; },
abstract = {Three isozymes of superoxide dismutase (SOD) have been identified and characterized. The iron and manganese isozymes (Fe-SOD and Mn-SOD, respectively) show extensive primary sequence and structural homology, suggesting a common evolutionary ancestor. In contrast, the copper/zinc isozyme (CuZn-SOD) shows no homology with Fe-SOD or Mn-SOD, suggesting an independent origin for this enzyme. The three isozymes are unequally distributed throughout the biological kingdoms and are located in different subcellular compartments. Obligate anaerobes and aerobic diazotrophs contain Fe-SOD exclusively. Facultative aerobes contain either Fe-SOD or Mn-SOD or both. Fe-SOD is found in the cytosol of cyanobacteria while the thylakoid membranes of these organisms contain a tightly bound Mn-SOD. Similarly, most eukaryotic algae contain Fe-SOD in the chloroplast stroma and Mn-SOD bound to the thylakoids. Most higher plants contain a cytosol-specific and a chloroplast-specific CuZn-SOD, and possibly a thylakoid-bound Mn-SOD as well. Plants also contain Mn-SOD in their mitochondria. Likewise, animals and fungi contain a cytosolic CuZn-SOD and a mitochondrial Mn-SOD. The Mn-SOD found in the mitochondria of eukaryotes shows strong homology to the prokaryotic form of the enzyme. Taken together, the phylogenetic distribution and subcellular localization of the SOD isozymes provide strong support for the hypothesis that the chloroplasts and mitochondria of eukaryotic cells arose from prokaryotic endosymbionts.},
}
@article {pmid2483246,
year = {1986},
author = {Godinot, C and Moradi-Ameli, M and Gautheron, DC},
title = {Monoclonal antibodies to F1-ATPase subunits as probes of structure, conformation, and functions of isolated or membrane-bound F1.},
journal = {Methods in enzymology},
volume = {126},
number = {},
pages = {761-769},
doi = {10.1016/s0076-6879(86)26075-9},
pmid = {2483246},
issn = {0076-6879},
mesh = {Animals ; *Antibodies, Monoclonal ; Antigen-Antibody Complex ; Epitopes/analysis ; Kinetics ; Macromolecular Substances ; Mitochondria, Heart/enzymology ; Phylogeny ; Protein Conformation ; Proton-Translocating ATPases/immunology/isolation &amp; purification/*metabolism ; Swine ; },
}
@article {pmid2570428,
year = {1989},
author = {Healy, JM},
title = {Spermatozoa of the deep-sea cephalopod Vampyroteuthis infernalis Chun: ultrastructure and possible phylogenetic significance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {323},
number = {1219},
pages = {589-600},
doi = {10.1098/rstb.1989.0038},
pmid = {2570428},
issn = {0962-8436},
mesh = {Animals ; Male ; Microscopy, Electron ; Mollusca/*physiology ; Octopodiformes/physiology ; *Phylogeny ; Species Specificity ; Spermatogenesis ; Spermatozoa/*ultrastructure ; },
abstract = {Sperm ultrastructure in the rare deep-sea cephalopod Vampyroteuthis infernalis is described, based on formalin-fixed material held in the Australian Museum (Sydney). The species is the sole member of the coleoidean order Vampyromorpha, which represents a level of organization intermediate between that of the Sepioidea-Teuthoidea and the Octopoda. Spermatozoa of Vampyroteuthis, the simplest observed in any cephalopod, exhibit the following features: (1) a spheroidal acrosome lacking any complex substructure; (2) a short (8.5 microns) fusiform nucleus with a deep (2.2-2.5 microns) basal invagination (containing an extensive plug of dense material); (3) two triplet centrioles arranged parallel to the sperm longitudinal axis; (4) a short (1 micron) midpiece composed of a triangular cluster of mitochondria surrounding the centrioles; and (5) a tail (length 130-135 microns) that is continuous with one of the centrioles (here considered as a 'distal' centriole). An annulus and membranous skirt are absent, though the coarse fibres do fuse into a ring at the tail-midpiece junction). These cells show some resemblance to sperm or spermatids of sepioids and teuthoids (spheroidal acrosome, short nucleus) but are also remarkably similar to mid-spermatids of Octopus (with the exception of the uncondensed nucleus in Octopus spermatids). Sperm morphology supports the current assignment of Vampyroteuthis to a separate coleoidean order--Vampyromorpha--and also suggests that a close link exists between the Vampyromorpha and Octopoda.},
}
@article {pmid2684776,
year = {1989},
author = {Michel, F and Umesono, K and Ozeki, H},
title = {Comparative and functional anatomy of group II catalytic introns--a review.},
journal = {Gene},
volume = {82},
number = {1},
pages = {5-30},
doi = {10.1016/0378-1119(89)90026-7},
pmid = {2684776},
issn = {0378-1119},
mesh = {Animals ; Base Sequence ; Chloroplasts/analysis ; DNA, Mitochondrial/genetics ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/*genetics ; RNA Precursors/genetics ; *RNA Splicing ; RNA, Catalytic ; RNA, Fungal/*genetics ; RNA, Ribosomal/*genetics ; },
abstract = {The 70 published sequences of group II introns from fungal and plant mitochondria and plant chloroplasts are analyzed for conservation of primary sequence, secondary structure and three-dimensional base pairings. Emphasis is put on structural elements with known or suspected functional significance with respect to self-splicing: the exon-binding and intron-binding sites, the bulging A residue involved in lariat formation, structural domain V and two isolated base pairs, one of them involving the last intron nucleotide and the other one, the first nt of the 3' exon. Separate sections are devoted to the 29 group II-like introns from Euglena chloroplasts and to the possible relationship of catalytic group II introns to nuclear premessenger introns. Alignments of all available sequences of group II introns are provided in the APPENDIX.},
}
@article {pmid2856125,
year = {1986},
author = {Ljungdahl, PO and Pennoyer, JD and Trumpower, BL},
title = {Purification of cytochrome bc1 complexes from phylogenically diverse species by a single method.},
journal = {Methods in enzymology},
volume = {126},
number = {},
pages = {181-191},
doi = {10.1016/s0076-6879(86)26020-6},
pmid = {2856125},
issn = {0076-6879},
mesh = {Animals ; Cattle ; Cell Membrane/enzymology ; Chromatography, DEAE-Cellulose/methods ; Chromatography, Ion Exchange/methods ; Electron Transport Complex III/*isolation &amp; purification/metabolism ; Indicators and Reagents ; Kinetics ; Mitochondria, Heart/*enzymology ; Phylogeny ; Rhodobacter sphaeroides/*enzymology ; Saccharomyces cerevisiae/*enzymology ; Species Specificity ; Submitochondrial Particles/enzymology ; },
}
@article {pmid2978296,
year = {1988},
author = {Amann, R and Ludwig, W and Schleifer, KH},
title = {Beta-subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of eubacteria.},
journal = {Journal of general microbiology},
volume = {134},
number = {10},
pages = {2815-2821},
doi = {10.1099/00221287-134-10-2815},
pmid = {2978296},
issn = {0022-1287},
mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Bacteroides fragilis/*genetics ; Base Sequence ; Cytophaga/*genetics ; Flavobacterium/*genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; },
abstract = {The genes encoding the beta-subunits of ATP-synthases (ATPases) from Bacteroides fragilis DSM 2151, Cytophaga lytica DSM 2039 and 'Taxeobacter ocellatus' were cloned. The nucleotide sequences were determined completely for the genes of the first two organisms and to a major part for that of 'T. ocellatus'. The predicted amino acid sequences were compared with previously published amino acid sequences of beta-subunits. Two characteristic insertions were found in genes from organisms belonging to the so-called bacteroides-cytophaga-flavo-bacterium group. The remaining structure shows a high degree of sequence similarity within this group. These data support the conclusions drawn from comparative 16S rRNA sequence analyses that organisms in this phenotypically heterogeneous group are phylogenetically related. A phylogenetic tree was constructed based on a distance matrix of optimally aligned amino acid sequences of beta-subunits of ATPases of various eubacteria, chloroplasts and mitochondria. It is in good agreement with a tree derived from 16S rRNA sequence analyses.},
}
@article {pmid2992672,
year = {1985},
author = {Opperdoes, FR},
title = {Biochemical peculiarities of trypanosomes, African and South American.},
journal = {British medical bulletin},
volume = {41},
number = {2},
pages = {130-136},
doi = {10.1093/oxfordjournals.bmb.a072039},
pmid = {2992672},
issn = {0007-1420},
mesh = {Animals ; Cyclic AMP/metabolism ; DNA, Mitochondrial ; Glutathione Reductase/metabolism ; Glycolysis ; Microbodies/metabolism ; Mitochondria/metabolism ; Phylogeny ; Protein Biosynthesis ; Purines/metabolism ; Pyrimidines/biosynthesis ; Trypanosoma/genetics ; Trypanosoma brucei brucei/*metabolism ; Trypanosoma cruzi/*metabolism ; },
}
@article {pmid3001728,
year = {1986},
author = {Meyer, TE and Cusanovich, MA and Kamen, MD},
title = {Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {83},
number = {2},
pages = {217-220},
pmid = {3001728},
issn = {0027-8424},
support = {GM21277/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; *Bacterial Proteins ; *Cytochrome c Group/genetics ; Mitochondria ; *Phylogeny ; RNA, Ribosomal/genetics ; },
abstract = {It has been proposed that phylogenetic trees, intended to show divergence of eukaryotic protein and nucleic acid sequences, be extended to include those from bacteria. However, we have compared the amino acid sequences of 18 of the most divergent mitochondrial cytochromes c with those of 18 bacterial cytochromes c2 and have found that the average percentage difference between these mitochondrial cytochromes c and cytochromes c2 was not significantly greater than that among the cytochromes c2 alone. The large discontinuities in physical-chemical properties recognized between the prokaryote and eukaryote cytochromes render it highly improbable that members of the two classes should be no more different from one another than members of either class alone, assuming that sequence differences can accurately reveal evolutionary divergence. Instead, we propose that divergent amino acid sequences approach a limit of change considerably less than for comparison of random sequences. This limit of change presumably is determined by the structure/function relationship. When two homologous protein sequences have reached such a limit, convergence or back-mutations and parallel mutations become as frequent as divergent mutations. As two diverging proteins approach this steady-state condition, sequence differences no longer reflect the numbers of mutations resulting in amino acid substitution and therefore species cannot be positioned on a phylogenetic tree. Insertions and deletions are less reversible than are amino acid substitutions and, provided they are well-documented, might be more reliable indicators of bacterial relationships. Nevertheless, we suggest that data available on bacterial protein sequences do not permit construction of all-inclusive phylogenetic trees. Comparisons of protein and rRNA trees suggest that similar restrictions apply to use of rRNA sequence data.},
}
@article {pmid3006116,
year = {1985},
author = {Senn, H and Wüthrich, K},
title = {Amino acid sequence, haem-iron co-ordination geometry and functional properties of mitochondrial and bacterial c-type cytochromes.},
journal = {Quarterly reviews of biophysics},
volume = {18},
number = {2},
pages = {111-134},
doi = {10.1017/s0033583500005151},
pmid = {3006116},
issn = {0033-5835},
mesh = {Amino Acid Sequence ; Animals ; Bacteria/*metabolism ; *Cytochrome c Group/metabolism ; Heme/analysis ; Histidine ; Iron/analysis ; Ligands ; Methionine ; Mitochondria/*metabolism ; Phylogeny ; Protein Binding ; Protein Conformation ; },
}
@article {pmid3032252,
year = {1987},
author = {Ljungdahl, PO and Pennoyer, JD and Robertson, DE and Trumpower, BL},
title = {Purification of highly active cytochrome bc1 complexes from phylogenetically diverse species by a single chromatographic procedure.},
journal = {Biochimica et biophysica acta},
volume = {891},
number = {3},
pages = {227-241},
doi = {10.1016/0005-2728(87)90218-0},
pmid = {3032252},
issn = {0006-3002},
support = {GM 20379/GM/NIGMS NIH HHS/United States ; GM 27309/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Cattle ; Chromatography, Gel ; Chromatography, Ion Exchange ; Electron Transport Complex III/genetics/*isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Mitochondria/*enzymology ; Mitochondria, Heart/*enzymology ; *Phylogeny ; Rhodobacter sphaeroides/*enzymology ; Rhodopseudomonas/*enzymology ; Saccharomyces cerevisiae/*enzymology ; Species Specificity ; },
abstract = {A method has been developed for purification of highly active ubiquinol-cytochrome c oxidoreductase (cytochrome bc1) complexes from wild-type Rhodobacter sphaeroides, Rhodobacter capsulatus MT1131, bovine heart and yeast mitochondria. This is the first report of the isolation of cytochrome bc1 complex from a wild-type strain of Rb. sphaeroides and from any strain of Rb. capsulatus. The purification involves extraction of membranes with dodecyl maltoside and two successive DEAE column chromatography steps. All of the resulting bc1 complexes are free of succinate dehydrogenase and cytochrome c oxidase activities. The purified bc1 complexes from both photosynthetic bacteria contain four polypeptide subunits, although the molecular weights of some of their subunits differ. They are also free of reaction center and light-harvesting pigments and polypeptides. The turnover number of the Rb. sphaeroides complex is 128 s-1, and that of the Rb. capsulatus complex is 64 s-1. The bc1 complex from bovine heart contains eight polypeptides and has a turnover number of 1152 s-1, while the yeast complex contains nine polypeptides and has a turnover number of 219 s-1. The activities of these complexes are equal to or better than those commonly obtained by previously reported methods. This method of purification is relatively simple, reproducible, and yields cytochrome bc1 complexes which largely retain the turnover number of the starting material and are pure on the basis of optical spectra, enzymatic activities and polypeptide composition. The purification of cytochrome bc1 complexes from energy-transducing membranes which differ markedly in their lipid and protein composition makes it likely that with minor modifications this method could be applied to species other than those described here.},
}
@article {pmid3038859,
year = {1987},
author = {Okamura, K and Miyata, T and Iwanaga, S and Takamiya, K and Nishimura, M},
title = {Complete amino acid sequence of cytochrome c551 from Erythrobacter species strain OCh 114.},
journal = {Journal of biochemistry},
volume = {101},
number = {4},
pages = {957-966},
doi = {10.1093/oxfordjournals.jbchem.a121965},
pmid = {3038859},
issn = {0021-924X},
mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Bacteria, Aerobic/classification/*enzymology ; *Bacterial Proteins ; *Cytochrome c Group ; Mitochondria/enzymology ; Oxidation-Reduction ; Peptide Fragments/analysis ; Photosynthesis ; Phylogeny ; },
abstract = {The complete amino acid sequence of cytochrome c551 isolated from an aerobic photosynthetic bacterium, Erythrobacter sp. strain OCh 114, was determined. The cytochrome molecule was composed of a total of 119 amino acid residues and its molecular weight including heme was calculated to be 13,235. The sequence was (Sequence: see text). Its molecular weight indicates that this cytochrome is of the L-type. Sequence alignment with other bacterial cytochromes c shows that this cytochrome is similar to cytochromes c of Rhodobacter capsulatus, Rhodobacter sphaeroides, and Paracoccus denitrificans, which were grouped into the alpha-3 subcluster from the 16S rRNA sequence analysis.},
}
@article {pmid3134965,
year = {1988},
author = {Canning, EU},
title = {Nuclear division and chromosome cycle in microsporidia.},
journal = {Bio Systems},
volume = {21},
number = {3-4},
pages = {333-340},
doi = {10.1016/0303-2647(88)90030-5},
pmid = {3134965},
issn = {0303-2647},
mesh = {Animals ; Apicomplexa/*cytology/ultrastructure ; *Cell Cycle ; *Cell Division ; Cell Nucleus/*ultrastructure ; Chromosomes/*ultrastructure ; Microscopy, Electron ; Phylogeny ; },
abstract = {Nuclear division and chromosome cycle of microsporidia are reviewed in the light of recent speculation that the group diverged as an early branch in the eukaryotic line of descent. Microsporidia are primitive eukaryotes with simple cytoplasmic organisation, lacking mitochondria, peroxisomes and a classical Golgi apparatus. The ribosomes resemble prokaryotic ribosomes in size and in having sequences complementary to the eukaryotic 5.8S rRNA contained within their large (23S) ribosomal subunit, rather than a separate 5.8S molecule. Nuclei may be isolated or closely appressed as a diplokaryotic pair which divide synchronously. Mitosis is intranuclear: there are no centrioles but spindle termini are electron dense plaques in pores in the nuclear envelope. Some genera have isolated nuclei throughout the life cycle, while others have diplokaryotic nuclei throughout: meiosis is not known in either of these categories of genera. In contrast, certain polymorphic species, which are transmitted horizontally between copepods and mosquitoes and vertically between generations of mosquitoes, alternate between stages with isolated nuclei and stages with diplokaryotic nuclei. Haploid spores in copepods are infective to mosquito larvae, in which gametogenesis and plasmogamy occur to give diplokaryotic (diploid) stages. Stages remain diplokaryotic through transovarial transmission to the next generation, when an unusual form of meiosis is initiated in both nuclei of the diplokaryon (as indicated by synaptonemal complexes), and mingling of chromosomes occurs when the two nuclei fuse during pachytene.},
}
@article {pmid3238378,
year = {1988},
author = {Kogaya, Y and Furuhashi, K},
title = {Comparison of the calcium distribution pattern among several kinds of hard tissue forming cells of some living vertebrates.},
journal = {Scanning microscopy},
volume = {2},
number = {4},
pages = {2029-2043},
pmid = {3238378},
issn = {0891-7035},
mesh = {Ameloblasts/*analysis/ultrastructure ; Amphibians ; Animals ; Antimony ; Calcium/*analysis ; Cartilage/analysis/*cytology/ultrastructure ; Fishes ; Microscopy, Electron/instrumentation/methods ; Odontoblasts/*analysis/ultrastructure ; Osteoblasts/*analysis/ultrastructure ; Phylogeny ; Rats ; Reptiles ; Spectrum Analysis/methods ; },
abstract = {We investigated the ultrastructural distribution of calcium in several kinds of hard tissue forming cells (secretory and maturation ameloblasts, odontoblasts osteoblasts, chondrocytes, and osteodentine forming cells) of mammals, amphibians, and fish by use of the potassium pyroantimonate technique. The calcium distribution pattern is compared among these cells, and its biological significance is discussed. Except for mammalian odontoblasts, all types of the hard tissue forming cells exhibited fundamentally the same distribution pattern of calcium; the antimonate reaction product was mainly localized on the inner face of the plasmalemma and inside mitochondria. On the other hand, in mammalian odontoblasts, the reaction product was found within secretory granules and in the intercellular spaces. Thus, the calcium distribution pattern in odontoblasts of lower vertebrates differed from that of mammalian odontoblasts and was similar to that of the osteoblasts or chondrocytes of the vertebrates examined. The differences in calcium distribution pattern among these hard tissue forming cells were not related to their origin, ectodermal or mesodermal (ectomesenchymal). We suggest on the basis of previous studies cited in this paper and of the present data that they are closely associated with the phylogeny and physiological system of Ca-ATPase.},
}
@article {pmid3242866,
year = {1988},
author = {Boer, PH and Gray, MW},
title = {Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria.},
journal = {Current genetics},
volume = {14},
number = {6},
pages = {583-590},
pmid = {3242866},
issn = {0172-8083},
mesh = {Base Sequence ; Chlamydomonas/*genetics ; Codon/genetics ; DNA, Mitochondrial/genetics ; Genes ; *Genetic Code ; *Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics ; Restriction Mapping ; Transcription, Genetic ; },
abstract = {Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA(Met) gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs(Met) are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.},
}
@article {pmid3275942,
year = {1988},
author = {Storey, KB and Storey, JM},
title = {Freeze tolerance in animals.},
journal = {Physiological reviews},
volume = {68},
number = {1},
pages = {27-84},
doi = {10.1152/physrev.1988.68.1.27},
pmid = {3275942},
issn = {0031-9333},
mesh = {*Adaptation, Physiological ; Animals ; Anura/metabolism ; Avoidance Learning ; Cryoprotective Agents/metabolism ; *Freezing ; Ice ; Insecta/metabolism ; Membrane Proteins/physiology ; Mitochondria/physiology ; Phylogeny ; Proteins/physiology ; Water ; },
}
@article {pmid3395680,
year = {1988},
author = {Wolters, J and Erdmann, VA},
title = {Cladistic analysis of ribosomal RNAs--the phylogeny of eukaryotes with respect to the endosymbiotic theory.},
journal = {Bio Systems},
volume = {21},
number = {3-4},
pages = {209-214},
doi = {10.1016/0303-2647(88)90015-9},
pmid = {3395680},
issn = {0303-2647},
mesh = {Base Sequence ; Eukaryota/*genetics ; Information Systems ; Models, Biological ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/*genetics ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 5S/genetics ; Symbiosis ; },
abstract = {A strict cladistic analysis of 5S and 16S rRNA secondary and primary structure confirms particular hypotheses concerning the phylogeny of eukaryotes: plastids of Euglena, green algae and land plants, and the cyanelle of Cyanophora share a specific character and are closely related to cyanobacteria of the Synechococcus-type. Angiosperm mitochondria share specific signatures with the alpha subdivision of rhodobacteria. Cyanophora is a member of the Euglenozoa, the Oomycetes are derived from a group of heterokont algae.},
}
@article {pmid3446957,
year = {1987},
author = {Arquès, DG and Michel, CJ},
title = {A purine-pyrimidine motif verifying an identical presence in almost all gene taxonomic groups.},
journal = {Journal of theoretical biology},
volume = {128},
number = {4},
pages = {457-461},
doi = {10.1016/s0022-5193(87)80190-x},
pmid = {3446957},
issn = {0022-5193},
mesh = {Base Sequence ; DNA/classification ; *Genes ; Phylogeny ; Probability ; *Purines ; *Pyrimidines ; },
abstract = {A statistical parameter identifies, with a high degree of significance, a motif which is present in protein-coding sequences of eukaryotes, prokaryotes, chloroplasts, mitochondria, viral introns, ribosomal RNA genes, and transfer RNA genes. The random probability of occurrence of such a situation is 10(-12). This motif has the following properties: (i) its significant presence in almost all present-day genes explains why it can be considered as primitive oligonucleotide, (ii) its nucleotide order is: YRY (N)6YRY, R being a purine base, Y a pyrimidine one and N any base, (iii) its length and its terminal trinucleotides YRY suggest a primordial function related to the spatial structure of the DNA sequences. This motif is found in some viral protein-coding genes, but not in eukaryotic introns.},
}
@article {pmid3561476,
year = {1987},
author = {Cavalier-Smith, T},
title = {Eukaryotes with no mitochondria.},
journal = {Nature},
volume = {326},
number = {6111},
pages = {332-333},
doi = {10.1038/326332a0},
pmid = {3561476},
issn = {0028-0836},
mesh = {Animals ; Base Sequence ; Cells/*ultrastructure ; Chloroplasts ; Eukaryota/genetics/*ultrastructure ; Eukaryotic Cells/*ultrastructure ; *Mitochondria ; Phylogeny ; RNA, Ribosomal/genetics ; },
}
@article {pmid3892535,
year = {1985},
author = {Yang, D and Oyaizu, Y and Oyaizu, H and Olsen, GJ and Woese, CR},
title = {Mitochondrial origins.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {82},
number = {13},
pages = {4443-4447},
pmid = {3892535},
issn = {0027-8424},
support = {AM-34527/AM/NIADDK NIH HHS/United States ; },
mesh = {Base Sequence ; Escherichia coli/genetics ; *Mitochondria ; Phylogeny ; Pseudomonas/*ultrastructure ; RNA, Ribosomal/analysis ; Rhizobium/*ultrastructure ; },
abstract = {The 16S ribosomal RNA sequences from Agrobacterium tumefaciens and Pseudomonas testosteroni have been determined to further delimit the origin of the endosymbiont that gave rise to the mitochondrion. These two prokaryotes represent the alpha and beta subdivisions, respectively, of the so-called purple bacteria. The endosymbiont that gave rise to the mitochondrion belonged to the alpha subdivision, a group that also contains the rhizobacteria, the agrobacteria, and the rickettsias--all prokaryotes that have developed intracellular or other close relationships with eukaryotic cells.},
}
@article {pmid3959152,
year = {1986},
author = {Rouse, GW and Robson, SK},
title = {An ultrastructural study of megachiropteran (Mammalia: Chiroptera) spermatozoa: implications for chiropteran phylogeny.},
journal = {Journal of submicroscopic cytology},
volume = {18},
number = {1},
pages = {137-152},
pmid = {3959152},
issn = {0022-4782},
mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Chiroptera/*classification/physiology ; Eulipotyphla/classification ; Male ; Microscopy, Electron ; Phylogeny ; Primates/classification ; Sperm Head/ultrastructure ; Spermatozoa/*ultrastructure ; },
abstract = {The fine structure of epididymal or electro-ejaculated spermatozoa of Pteropus poliocephalus, P. scapulatus, P. conspiculatus, P. alecto and Syconycteris australis is described. The sperm of all species were found to be very similar. The head is extremely flattened and spatulate; the nucleus is capped by a long acrosome that comprises the proximal half of the head and covers two-thirds of the nucleus area, and a prominent sub-acrosomal space possesses a unique 'anvil'-like shape. Redundant nuclear envelope forms a 'scroll' in a restricted region of the neck, next to the base of the proximal centriole and the most proximal of the mitochondria. The axoneme is atypical for mammals, the central singlets arising distal to the outer doublets. Coarse fibres 1, 5, 6 and 9 are larger than the remainder, a feature shared with the Microchiroptera, most insectivores and the Primates. The large sub-acrosomal space of the megachiropteran sperm is significantly is different from that of the Microchiroptera. We consider that the difference in sperm ultrastructure between the chiropteran sub-orders is not inconsistent with theories of a di-phyletic origin for this group. The use of sperm ultrastructure as a phylogenetic tool is discussed and comparisons with the spermatozoa of other closely related Eutheria are made.},
}
@article {pmid6179895,
year = {1982},
author = {Kuroiwa, T},
title = {Mitochondrial nuclei.},
journal = {International review of cytology},
volume = {75},
number = {},
pages = {1-59},
doi = {10.1016/s0074-7696(08)61001-3},
pmid = {6179895},
issn = {0074-7696},
mesh = {Animals ; Cell Cycle ; Chloroplasts/ultrastructure ; Chromatin/analysis ; Chromosomes ; *DNA, Mitochondrial/analysis ; Fungi/ultrastructure ; Humans ; Mitochondria/analysis/physiology/*ultrastructure ; Models, Biological ; Molecular Weight ; Phylogeny ; Proteins/analysis/physiology ; RNA/analysis ; RNA, Ribosomal/analysis ; },
}
@article {pmid6261575,
year = {1981},
author = {Bhattacharyya, TK and Butler, DG and Youson, JH},
title = {Distribution and structure of the adrenocortical homologue in the garpike.},
journal = {The American journal of anatomy},
volume = {160},
number = {3},
pages = {231-246},
doi = {10.1002/aja.1001600302},
pmid = {6261575},
issn = {0002-9106},
mesh = {3-Hydroxysteroid Dehydrogenases/analysis ; Adrenal Cortex/anatomy &amp; histology/drug effects/*ultrastructure ; Adrenocorticotropic Hormone/pharmacology ; Animals ; Female ; Fishes/*anatomy &amp; histology ; Histocytochemistry ; Inclusion Bodies/ultrastructure ; Lipids ; Male ; Microscopy, Electron ; Organoids/ultrastructure ; Phylogeny ; },
abstract = {The microanatomy of the yellow corpuscles (adrenocortical homologue, AH) in the holostean fish, Lepisosteus spp. was studied by serial sectioning, steroid histochemistry, and electron microscopy. The modification of this tissue to short-term ACTH treatment was also observed. The distribution of the AH within the renal tissue of the garpike phylogenetically represents a more advanced condition than that seen in its closest holostean relative, the bowfin, and appears to approximate that in teleosts. The homology of this tissue of vertebrate adrenocortical tissue was established by the positive identification of the enzyme, gamma 5-3 beta-hydroxysteroid dehydrogenase, and by the ultrastructural features of the cells before and after ACTH administration. The AH cells possess fine structural features characteristic of steroidogenic cells, namely, polymorphic mitochondria with tubular cristae, abundant tubules of smooth endoplasmic reticulum, a prominent Golgi complex, and lipid droplets. Other interesting features include the presence of annulate lamellae and a variety of dense bodies. Digitonin perfusion results in the deposition of presumed, cholesterol-digitonide crystalline spicules on the surface microplicae of the cells and as dense accumulations in association with smooth endoplasmic reticulum. ACTH administration results in swelling of mitochondria, a loss of their cristae, and a smooth decrease in electron density of their matrices. Alterations also occur in the smooth and rough endoplasmic reticulum, and large osmiophilic inclusions of irregular profile appear. Some of the ACTH-induced modifications are similar to those observed in the adrenocortical cells of other vertebrate groups following comparable stimulation.},
}
@article {pmid6310133,
year = {1983},
author = {Johnson, MJ and Wallace, DC and Ferris, SD and Rattazzi, MC and Cavalli-Sforza, LL},
title = {Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns.},
journal = {Journal of molecular evolution},
volume = {19},
number = {3-4},
pages = {255-271},
pmid = {6310133},
issn = {0022-2844},
mesh = {DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Gene Frequency ; Genetic Variation ; Humans ; Mathematics ; Models, Genetic ; Phylogeny ; *Racial Groups ; },
abstract = {Human mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns were analyzed using total blood cell DNA isolated from 200 individuals representing five different populations. Thirty-two fragment patterns (morphs) were observed with the enzymes Hpa I, Bam HI, Hae II, Msp I and Ava II yielding thirty-five different combinations of fragment patterns (mt DNA types). The major ethnic groups exhibit quantitative as well as qualitative differences in their mtDNA types, all of which are related to each other by a tree in which the closely related mtDNA types cluster according to geographic origin. Three mtDNA types are postulated to be 'central' to ethnic radiations due to their high frequencies, their appearance in more than one ethnic group, or their presence in other primate species. Genetic distances among populations were computed and employed in construction of an average linkage tree. If one of the three central mtDNA types is the root of the tree, differences in evolutionary rates among the branches become apparent. In particular, the Bushmen appear to have a higher evolutionary rate for mtDNA than the other four populations. Comparisons with nuclear gene frequencies suggest that this higher evolutionary rate may be the product of an elevated mutation rate or fixation of mutations in mtDNA.},
}
@article {pmid6365337,
year = {1983},
author = {Tashiro, Y},
title = {Subcellular compartments and protein topogenesis.},
journal = {Cell structure and function},
volume = {8},
number = {2},
pages = {91-107},
doi = {10.1247/csf.8.91},
pmid = {6365337},
issn = {0386-7196},
mesh = {Bacteria/metabolism/*ultrastructure ; Bacterial Proteins/*metabolism ; Biological Transport ; *Cell Compartmentation ; Cell Membrane/metabolism ; Cell Nucleus/metabolism ; Cells/*ultrastructure ; Chloroplasts/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells/metabolism/*ultrastructure ; Intracellular Membranes/metabolism ; Membrane Proteins/metabolism ; Microbodies/metabolism ; Mitochondria/metabolism ; Models, Biological ; Phylogeny ; Proteins/*metabolism ; Ribosomes/metabolism ; Symbiosis ; Terminology as Topic ; },
abstract = {A cell is surrounded by a plasma membrane. It contains various organelles, most of which are enclosed by limiting membranes. The intracellular space is thus divided into a number of subcellular compartments. Structurally, a cell is composed of membranes and the spaces enclosed by those membranes. In order to classify these compartments, the extracellular space has been designated S1 and whenever a unit membrane structure is crossed to arrive at the next space, one is added to term; the cytoplasmic space becomes S2, the intraluminal space of the endoplasmic reticulum and the intermembrane space of the mitochondria S3, and the matrix space of the mitochondria S4. Similarly, the plasma membrane is M1, the outer membrane of the mitochondria M2, and the inner counterpart M3. This classification of the subcellular compartments is useful in understanding a number of complicated cellular structures and functions. The intracellular transport of newly synthesized protein (protein topogenesis) and the probable development of subcellular organelles during phylogenesis of eukaryotic cells is discussed in terms of these subcellular compartments.},
}
@article {pmid6709501,
year = {1984},
author = {Van Knippenberg, PH and Van Kimmenade, JM and Heus, HA},
title = {Phylogeny of the conserved 3' terminal structure of the RNA of small ribosomal subunits.},
journal = {Nucleic acids research},
volume = {12},
number = {6},
pages = {2595-2604},
pmid = {6709501},
issn = {0305-1048},
mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Fungi/genetics ; Humans ; Nucleic Acid Conformation ; *Phylogeny ; Plants/genetics ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; Species Specificity ; },
abstract = {The strongest conserved part of the RNA of small ribosomal subunits is probably located near the 3' end. This paper reviews the primary and secondary structures of some 40 sequenced 3' termini and tries to classify these structures according to common features and differences. The regions under consideration contain at the 5' side an almost universal, supposedly single-stranded stretch of nucleotides with the sequence--AAGUCGUAACAAGGU--. This is followed by a stem-loop structure. The stem always contains 9 basepairs (including U-G pairs) and no mismatches or bulged nucleotides. The loop of the hairpin is either (m2)GGm62Am62A (bacteria, chloroplasts and mitochondria) or UGm62Am62A (cytoplasm). The hairpin is, in most cases, followed at the 3' side by--GGAUCA--. Next to it bacteria and chloroplasts contain the so-called "Shine and Dalgarno" sequence --CCUCC--. The stem region of the hairpin contains a conserved A-U U-G junction. The two basepairs between this junction and the loop are either of type 1 (G-C G-C) or type 2 (C-G C-G). Classification according to type links certain bacteria with mitochondria of yeast and plants and others with chloroplasts and with animal mitochondria.},
}
@article {pmid6785727,
year = {1981},
author = {Küntzel, H and Heidrich, M and Piechulla, B},
title = {Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences.},
journal = {Nucleic acids research},
volume = {9},
number = {6},
pages = {1451-1461},
pmid = {6785727},
issn = {0305-1048},
mesh = {Bacteria/*analysis ; Base Sequence ; Chloroplasts/*analysis ; Computers ; Cyanobacteria/*analysis ; Cytosol/analysis ; Mitochondria/analysis ; *Phylogeny ; Plants/*analysis ; *RNA, Ribosomal/genetics ; Species Specificity ; Thermus/analysis ; },
abstract = {A phylogenetic tree was constructed by computer analysis of 47 completely determined 5S rRNA sequences. The wheat mitochondrial sequence is significantly more related to prokaryotic than to eukaryotic sequences, and its affinity to that of the thermophilic Gram-negative bacterium Thermus aquaticus is comparable to the affinity between Anacystis nidulans and chloroplastic sequences. This strongly supports the idea of an endosymbiotic origin of plant mitochondria. A comparison of the plant cytosol and chloroplast sub-trees suggests a similar rate of nucleotide substitution in nuclear genes and chloroplastic genes. Other features of the tree are a common precursor of protozoa and metazoa, which appears to be more related to the fungal than to the plant protosequence, and an early divergence of the archebacterial sequence (Halobacterium cutirubrum) from the prokaryotic branch.},
}
@article {pmid7198422,
year = {1981},
author = {Euzet, L and Swiderski, Z and Mokhtar-Maamouri, F},
title = {[Comparative fine structure of the cestode spermatozoon. Relationship to phylogenesis].},
journal = {Annales de parasitologie humaine et comparee},
volume = {56},
number = {3},
pages = {247-259},
pmid = {7198422},
issn = {0003-4150},
mesh = {Animals ; Cell Nucleus/ultrastructure ; Cestoda/classification/*ultrastructure ; Cytoplasm/ultrastructure ; Male ; Microscopy, Electron ; Microtubules/ultrastructure ; Phylogeny ; Species Specificity ; Spermatozoa/ultrastructure ; },
abstract = {The comparison of the ultrastructure of spermatozoa in Cestodes from seven different orders shows that they have the same general pattern of organization. The main common features are following: (a) a long thread-like body; (b) an elongated nucleus; (c) cortical microtubules underlying plasma membrane; (d) the absence of mitochondria and of a typical acrosome. The mode of spermatozoon differentiation indicates an inversion of the polarity. The number of axonemes of the 9 + "1" pattern, characteristic of the platyhelminthes, allow us to distinguish two types of spermatozoa among cestodes: --The "two-axonemes"-type is considered as primitive as it has also been found in the free-living platyhelminths. This type has been observed in the Pseudophyllidea, Proteocephalidea, Tetrarhynchidea and Tetraphyllidea (Onchobothriidae). --The "one-axoneme"-type has been found in the Cyclophyllidea, Caryophyllaeidea, Diphyllidea and Tetraphyllidea (Phyllobothriidae). It has been proved that the one axoneme type of the spermatozoon, observed in Tetraphyllidea, Phyllobothriidae arises from the two axoneme type by early abortion of the second axoneme. In all the tetraphyllidean species studied so far, we found an helicoidal body forming so-called "crested body" or "spiral crest" at the proximal end of the spermatozoon, which is opposite to the nuclear part. This division of the cestodes into two groups, according to the number of axonemes in the spermatozoon is compared with the phylogenetic diagrammes of Cestoda proposed by Freeman (1973) and Euzet (1974). As result, two hypothesis can be forwarded to explain the relationships between the Tetraphyllidea, Proteocephalidea and Cyclophyllidea. The importance of data on the cestode spermatozoa as a criterion in analysis of cestode phylogenesis is drawn and discussed.},
}
@article {pmid7325033,
year = {1981},
author = {},
title = {Phylogeny, structure and composition of cell membranes.},
journal = {Advances in experimental medicine and biology},
volume = {140},
number = {},
pages = {1-53},
doi = {10.1007/978-1-4684-4112-3_1},
pmid = {7325033},
issn = {0065-2598},
mesh = {Animals ; Biological Transport, Active ; Calcium/metabolism ; Cell Membrane/*physiology ; Erythrocyte Membrane/physiology ; Humans ; Intracellular Membranes/*physiology ; Lipid Bilayers ; Liposomes ; Membrane Lipids/physiology ; Membrane Proteins/physiology ; Mitochondria/physiology ; *Phylogeny ; },
}
@article {pmid7337818,
year = {1981},
author = {Cavalier-Smith, T},
title = {Eukaryote kingdoms: seven or nine?.},
journal = {Bio Systems},
volume = {14},
number = {3-4},
pages = {461-481},
doi = {10.1016/0303-2647(81)90050-2},
pmid = {7337818},
issn = {0303-2647},
mesh = {Animals ; Bacteria/classification ; Euglena/classification ; Eukaryota/*classification ; Fungi/*classification ; Phycobilisomes ; *Phylogeny ; Plants/classification ; },
abstract = {The primary taxa of eukaryote classification should be monophyletic and based on fundamental cell structure rather than nutritional adaptive zones. The classical two kingdom classification into "plants" and "animals" and the newer four kingdom classifications into "protis", "fungi" "animals" and "plants" are therefore both unsatisfactory. Eukaryotes can be classified into nine kingdoms each defined in terms of a unique constellation of cell structures. Five kingdoms have plate-like mitochondrial cristae: (1) Eufungi (the non-ciliated fungi, which unlike the other eight kingdoms have unstacked Golgi cisternae), (2) Ciliofungi (the posteriorly ciliated fungi), (3) Animalia (Animals, sponges, mesozoa, and choanociliates; phagotrophs with basically posterior ciliation), (4) Biliphyta (Non-phagotrophic, phycobilisome-containing, algae; i.e. theGlaucophyceae and Rhodophyceae), (5) Viridiplantae (Non-phagotrophic green plants, with starch-containing plastids). Kingdom (6), the Euglenozoa, has disc-shaped cristae and an intraciliary dense rod and may be phagotrophic and/or phototrophic with plastids with three-membraned envelopes. Kingdom (7), the cryptophyta, has flattened tubular cristae, tubular mastigonemes on both cilia,m and starch in thecompartment between the plastid endoplasmic reticulum and the plastid envelope; their plastids, if present, have phycobilins inside the paired thylakoids and chlorophyll c2. Kingdom (8), the Chromophyta, has tubular cristae, together with tubular mastigonemes on one anterior cilum and/or a plastid endoplasmic reticulum and chlorophyll c1 + c2. Members of the ninth kingdom, the Protozoa, are mainly phagotrophic, and have tubular or vesicular cristae (or lack mitochondria altogether), and lack tubular mastigonemes on their (primitively anterior) cilia; plastids if present have three-envelop membranes, chlorophyll c2, and no internal starch, and a plastid endoplasmic reticulum is absent. Kingdoms 4-9 are primitively anteriorly biciliate. Detailed definitions of the new kingdoms and lists of the phyla comprising them are given. Advantages of the new system and its main phylogenetic implications are discussed. A simpler system of five kingdoms suitable for very elementary teaching is possible by grouping the photosynthetic and fungal kindoms in pairs. Various compromises are possible between the nine and five kingdoms systems; it is suggested that the best one for general scientific use is a system of seven kingdoms in which the Eufungi and Ciliofungi become subkingdoms of the Kingdom Fungi, and the Cryptophyta andChromophyta subkingdoms of th Kingdom Chromista; the Fungi, Viridiplantae, Biliphyta, and Chromista can be subject to the Botanical Code of Nomenclature, while the Zoological Code can govern the Kingdoms Animalia, Protozoa and Euglenozoa...},
}
@article {pmid7377628,
year = {1980},
author = {Rohde, K},
title = {Some aspects of the ultrastructure of Gotocotyla secunda and Hexostoma euthynni.},
journal = {Angewandte Parasitologie},
volume = {21},
number = {1},
pages = {32-48},
pmid = {7377628},
issn = {0003-3162},
mesh = {Animals ; Cecum/ultrastructure ; Cell Nucleus/ultrastructure ; Cilia/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Golgi Apparatus/ultrastructure ; Male ; Membranes/ultrastructure ; Microscopy, Electron ; Mitochondria/ultrastructure ; Organoids/ultrastructure ; Phylogeny ; Spermatozoa/ultrastructure ; Trematoda/*ultrastructure ; },
abstract = {The ultrastructure of the spermatozoon, the protonephridia, the intestine and the tegument of Gotocotyla secunda (Monogenea, Gotocotylidae) and of the intestine of Hexostoma euthynni (Monogenea, Hexostomatidae) is described. The "connecting cells" in the intestine of at least some Monogenea show secretory activity and are possibly involved in extracellular digestion. Sloughing of whole haematin cells appears to be common and may be an important component in the digestive process. Flame cells appear to be a very conservative element and their more or less identical structure in all major groups of parasitic platyhelminths indicates that parasitic platyhelminths have originated from one or a few closely related groups of freeliving Turbellaria with the same type of flame cell.},
}
@article {pmid7499431,
year = {1995},
author = {Gudi, R and Bowker-Kinley, MM and Kedishvili, NY and Zhao, Y and Popov, KM},
title = {Diversity of the pyruvate dehydrogenase kinase gene family in humans.},
journal = {The Journal of biological chemistry},
volume = {270},
number = {48},
pages = {28989-28994},
doi = {10.1074/jbc.270.48.28989},
pmid = {7499431},
issn = {0021-9258},
support = {DK 47844/DK/NIDDK NIH HHS/United States ; GM 51262/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Catalysis ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary ; Escherichia coli/genetics ; *Genetic Variation ; Humans ; Isoenzymes/chemistry/*genetics/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Kinases/chemistry/*genetics/metabolism ; Protein Serine-Threonine Kinases ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Rats ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Recent evidence from this laboratory indicates that at least two isoenzymic forms of pyruvate dehydrogenase kinase (PDK1 and PDK2) may be involved in the regulation of enzymatic activity of mammalian pyruvate dehydrogenase complex by phosphorylation (Popov, K.M., Kedishvili, N.Y., Zhao, Y., Gudi, R., and Harris, R.A. (1994) J. Biol. Chem. 269, 29720-29724). The present study was undertaken to further explore the diversity of the pyruvate dehydrogenase kinase gene family. Here we report the deduced amino acid sequences of three isoenzymic forms of PDK found in humans. In terms of their primary structures, two isoenzymes identified in humans correspond to rat PDK1 and PDK2, whereas a third gene (PDK3) encodes for a new isoenzyme that shares 68% and 67% of amino acid identities with PDK1 and PDK2, respectively. PDK3 cDNA expressed in Eschierichia coli directs the synthesis of a polypeptide with a molecular mass of approximately 45,000 Da that possesses catalytic activity toward kinase-depleted pyruvate dehydrogenase. PDK3 appears to have the highest specific activity among the three isoenzymes tested as recombinant proteins. Tissue distribution of all three isoenzymes of human PDK was characterized by Northern blot analysis. The highest amount of PDK2 mRNA was found in heart and skeletal muscle, the lowest amount in placenta and lung. Brain, kidney, pancreas, and liver expressed an intermediate amount of PDK2 (brain > kidney = pancreas > liver). The tissue distribution of PDK1 mRNA differs markedly from PDK2. The message for PDK1 was expressed predominantly in heart with only modest levels of expression in other tissues (skeletal muscle > liver > pancreas > brain > placenta = lung > kidney). In contrast to PDk1 and PDK2, which are expressed in all tissues tested, the message for PDK3 was found almost exclusively in heart and skeletal muscle, indicating that PDK3 may serve specialized functions characteristic of muscle tissues. In all tissues tested thus far, the level of expression of PDK2 mRNA was essentially higher than that of PDK1 and PDK3, consistent with the idea that PDK2 is a major isoenzyme responsible for regulation of pyruvate dehydrogenase in human tissues.},
}
@article {pmid7507251,
year = {1994},
author = {Hiesel, R and von Haeseler, A and Brennicke, A},
title = {Plant mitochondrial nucleic acid sequences as a tool for phylogenetic analysis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {2},
pages = {634-638},
pmid = {7507251},
issn = {0027-8424},
mesh = {Base Sequence ; DNA, Complementary/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genes, Plant ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/classification/*genetics/metabolism ; RNA/chemistry/genetics ; RNA Editing ; RNA, Mitochondrial ; Species Specificity ; },
abstract = {To evaluate the potential of mitochondrial nucleic acid sequences as a phylogenetic tool, we have analyzed cytochrome oxidase subunit III (coxIII) coding sequences in representatives of the major groups of land plants. The phylogenetic tree derived from these mitochondrial sequences confirms the monophyletic origin of land plant mitochondria with the general order and descent of land plants deduced by other molecular, physiological, and morphological traits. The mitochondrial sequences strongly suggest a close phylogenetic relationship between Bryophyta and Lycopodiatae, whereas Psilophytatae cluster with the other vascular plants. In addition to the high sequence similarity, both Hepaticophytina and Lycopodiatae contain a related intron in the coxIII gene that, to our knowledge, is not found in any other plant species. The slowly evolving mitochondrial sequences of plants are shown to provide a useful phylogenetic tool to evaluate distant evolutionary relationships within this kingdom.},
}
@article {pmid7521532,
year = {1994},
author = {Polashock, JJ and Hillman, BI},
title = {A small mitochondrial double-stranded (ds) RNA element associated with a hypovirulent strain of the chestnut blight fungus and ancestrally related to yeast cytoplasmic T and W dsRNAs.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {18},
pages = {8680-8684},
pmid = {7521532},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Ascomycota/*genetics/pathogenicity ; Base Sequence ; *Genes, Viral ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Plant Viruses/*genetics ; RNA/genetics ; RNA, Double-Stranded/*genetics ; RNA, Fungal/*genetics ; RNA, Mitochondrial ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trees ; Viral Structural Proteins/*genetics ; },
abstract = {A small double-stranded (ds) RNA element was isolated from a moderately hypovirulent strain of the chestnut blight fungus Cryphonectria parasitica (Murr.) Barr. from eastern New Jersey. Virulence was somewhat lower in the dsRNA-containing strain than in a virulent dsRNA-free control strain, but colony morphology and sporulation levels were comparable. A library of cDNA clones was constructed, and overlapping clones representing the entire genome were sequenced. The 2728-bp dsRNA was considerably smaller than previously characterized C. parasitica dsRNAs, which are 12-13 kb and ancestrally related to the Potyviridae family of plant viruses. Sequence analysis revealed one large open reading frame, but only if mitochondrial codon usage (UGA = Trp) was invoked. Nuclease assays of purified mitochondria confirmed that the dsRNA was localized within mitochondria. Assuming mitochondrial translation, the deduced amino acid sequence had landmarks typical of RNA-dependent RNA polymerases. Alignments of the conserved regions indicate that this dsRNA is more closely related to yeast T and W dsRNAs and single-stranded RNA bacteriophages such as Q beta than to other hypovirulence-associated dsRNAs.},
}
@article {pmid7521869,
year = {1994},
author = {Nosek, J and Fukuhara, H},
title = {NADH dehydrogenase subunit genes in the mitochondrial DNA of yeasts.},
journal = {Journal of bacteriology},
volume = {176},
number = {18},
pages = {5622-5630},
pmid = {7521869},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Base Sequence ; Candida/enzymology/*genetics ; DNA, Fungal/analysis/genetics ; DNA, Mitochondrial/*genetics ; Genes, Fungal/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Nucleic Acid Hybridization ; Phylogeny ; RNA/analysis ; RNA, Fungal/analysis ; RNA, Mitochondrial ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription, Genetic ; Yeasts/enzymology/*genetics ; },
abstract = {The genes encoding the NADH dehydrogenase subunits of respiratory complex I have not been identified so far in the mitochondrial DNA (mtDNA) of yeasts. In the linear mtDNA of Candida parapsilosis, we found six new open reading frames whose sequences were unambiguously homologous to those of the genes known to code for NADH dehydrogenase subunit proteins of different organisms, i.e., ND1, ND2, ND3, ND4L, ND5, and ND6. The gene for ND4 also appears to be present, as judged from hybridization experiments with a Podospora gene probe. Specific transcripts from these open reading frames (ND genes) could be detected in the mitochondria. Hybridization experiments using C. parapsilosis genes as probes suggested that ND genes are present in the mtDNAs of a wide range of yeast species including Candida catenulata, Pichia guilliermondii, Clavispora lusitaniae, Debaryomyces hansenii, Hansenula polymorpha, and others.},
}
@article {pmid7528198,
year = {1994},
author = {Falah, M and Gupta, RS},
title = {Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence.},
journal = {Journal of bacteriology},
volume = {176},
number = {24},
pages = {7748-7753},
pmid = {7528198},
issn = {0021-9193},
mesh = {Amino Acid Sequence ; Burkholderia cepacia/classification/*genetics ; Chloroplasts/genetics ; Cloning, Molecular ; Conserved Sequence ; Cyanobacteria/genetics ; *Escherichia coli Proteins ; Genes, Bacterial/*genetics ; Gram-Negative Bacteria/classification/genetics ; HSP70 Heat-Shock Proteins/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/classification/*genetics ; },
abstract = {The genes for hsp70 (or dnaK) have been cloned and sequenced from Rhizobium meliloti and Pseudomonas cepacia, two bacterial species belonging to the alpha- and beta-subdivisions of gram-negative proteobacteria, respectively. On the basis of global alignment of HSP70 proteins, several sequence signatures have been identified that are distinctive of mitochondrial homologs and gram-negative proteobacteria on the one hand and the chloroplasts and cyanobacteria on the other. Detailed phylogenetic analyses of HSP70 sequences from various eubacteria and eukaryotic organellar and cytosolic homologs support the inference regarding the origin of mitochondria from a member of the alpha-proteobacteria and of chloroplasts from cyanobacteria. The analysis presented here also suggests a monophyletic origin of the mitochondrial homologs.},
}
@article {pmid7528811,
year = {1994},
author = {Okimoto, R and Macfarlane, JL and Wolstenholme, DR},
title = {The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.},
journal = {Journal of molecular evolution},
volume = {39},
number = {6},
pages = {598-613},
pmid = {7528811},
issn = {0022-2844},
support = {GM-18375/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Ascaris suum/*genetics ; Base Composition ; Base Sequence ; Caenorhabditis elegans/*genetics ; *Consensus Sequence ; *Conserved Sequence ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; },
abstract = {The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.},
}
@article {pmid7529407,
year = {1994},
author = {Watanabe, Y and Kawai, G and Yokogawa, T and Hayashi, N and Kumazawa, Y and Ueda, T and Nishikawa, K and Hirao, I and Miura, K and Watanabe, K},
title = {Higher-order structure of bovine mitochondrial tRNA(SerUGA): chemical modification and computer modeling.},
journal = {Nucleic acids research},
volume = {22},
number = {24},
pages = {5378-5384},
pmid = {7529407},
issn = {0305-1048},
mesh = {Alkylating Agents ; Animals ; Anticodon/chemistry ; Base Sequence ; Cattle ; *Computer Simulation ; Diethyl Pyrocarbonate ; Mitochondria/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry ; RNA, Mitochondrial ; RNA, Transfer, Ser/*chemistry/genetics ; Sequence Alignment ; Sulfuric Acid Esters ; },
abstract = {On the basis of enzymatic probing and phylogenetic comparison, we have previously proposed that mammalian mitochondrial tRNA(sSer) (anticodon UGA) possess a slightly altered cloverleaf structure in which only one nucleotide exists between the acceptor stem and D stem (usually two nucleotides) and the anticodon stem consists of six base pairs (usually five base pairs) [Yokogawa et al. (1991) Nucleic Acids Res. 19, 6101-6105]. To ascertain whether such tRNA(sSer) can be folded into a normal L-shaped tertiary structure, the higher-order structure of bovine mitochondrial tRNA(SerUGA) was examined by chemical probing using dimethylsulfate and diethylpyrocarbonate, and on the basis of the results a tertiary structure model was obtained by computer modeling. It was found that a one-base-pair elongation in the anticodon stem was compensated for by multiple-base deletions in the D and extra loop regions of the tRNA(SerUGA), which resulted in preservation of an L-shaped tertiary structure similar to that of conventional tRNAs. By summarizing the findings, the general structural requirements of mitochondrial tRNAs necessary for their functioning in the mitochondrial translation system are considered.},
}
@article {pmid7543951,
year = {1995},
author = {van der Kuyl, AC and Kuiken, CL and Dekker, JT and Perizonius, WR and Goudsmit, J},
title = {Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.},
journal = {Journal of molecular evolution},
volume = {40},
number = {6},
pages = {652-657},
pmid = {7543951},
issn = {0022-2844},
mesh = {Animals ; Base Sequence ; Cercocebus ; DNA/*genetics ; DNA Primers ; Humans ; Molecular Sequence Data ; Mummies ; Papio/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Primates/genetics ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; },
abstract = {Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.},
}
@article {pmid7545947,
year = {1994},
author = {Rensing, SA and Maier, UG},
title = {Phylogenetic analysis of the stress-70 protein family.},
journal = {Journal of molecular evolution},
volume = {39},
number = {1},
pages = {80-86},
pmid = {7545947},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Animals ; Consensus Sequence ; Databases, Factual ; Heat-Shock Proteins/*genetics ; Humans ; Molecular Sequence Data ; *Multigene Family ; *Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {The eukaryotic cyto-/nucleoplasmatic 70-kDa heat-shock protein (HSP70) has homologues in the endoplasmic reticulum as well as in bacteria, mitochondria, and plastids. We selected a representative subset from the large number of sequenced stress-70 family members which covers all known branches of the protein family and calculated and manually improved an alignment. Here we present the consensus sequence of the aligned proteins and putative nuclear localization signals (NLS) in the eukaryotic HSP70 homologues. The phylogenetic relationships of the stress-70 group family members were estimated by use of different computation methods. We present a phylogenetic tree containing all known stress-70 subfamilies and demonstrate the usefulness of stress-70 protein sequences for the estimation of intertaxonic phylogeny.},
}
@article {pmid7603983,
year = {1995},
author = {Rich, SM and Caporale, DA and Telford, SR and Kocher, TD and Hartl, DL and Spielman, A},
title = {Distribution of the Ixodes ricinus-like ticks of eastern North America.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {14},
pages = {6284-6288},
pmid = {7603983},
issn = {0027-8424},
support = {AI 19693/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Demography ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Population ; RNA, Ribosomal, 16S/*genetics ; Ticks/classification/*genetics ; United States ; },
abstract = {We analyzed the geographic distribution of the Ixodes ricinus-like ticks in eastern North America by comparing the mitochondrial 16S rDNA sequences of specimens sampled directly from the field during the 1990s. Two distinct lineages are evident. The southern clade includes ticks from the southeastern and middle-eastern regions of the United States. The range of the northern clade, which appears to have been restricted to the northeastern region until the mid-1900s, now extends throughout the northeastern and middle-eastern regions. These phyletic units correspond to northern and southern taxa that have previously been assigned specific status as Ixodes dammini and Ixodes scapularis, respectively. The expanding range of I. dammini appears to drive the present outbreaks of zoonotic disease in eastern North America that include Lyme disease and human babesiosis.},
}
@article {pmid7604025,
year = {1995},
author = {Clark, CG and Roger, AJ},
title = {Direct evidence for secondary loss of mitochondria in Entamoeba histolytica.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {14},
pages = {6518-6521},
pmid = {7604025},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Cattle ; Consensus Sequence ; Eimeria tenella/genetics ; Entamoeba histolytica/*classification/*genetics/metabolism ; Escherichia coli/genetics ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; NADP Transhydrogenases/chemistry/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Rhodospirillum rubrum/enzymology ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {Archezoan protists are though to represent lineages that diverged from other eukaryotes before acquisition of the mitochondrion and other organelles. The parasite Entamoeba histolytica was originally included in this group. Ribosomal RNA based phylogenies, however, place E. histolytica on a comparatively recent branch of the eukaryotic tree, implying that its ancestors had these structures. In this study, direct evidence for secondary loss of mitochondrial function was obtained by isolating two E. histolytica genes encoding proteins that in other eukaryotes are localized in the mitochondrion: the enzyme pyridine nucleotide transhydrogenase and the chaperonin cpn60. Phylogenetic analysis of the E. histolytica homolog of cpn60 confirmed that it is specifically related to the mitochondrial lineage. The data suggest that a mitochondrial relic may persist in this organism. Similar studies are needed in archezoan protists to ascertain which, if any, eukaryotic lineages primitively lack mitochondria.},
}
@article {pmid7604961,
year = {1995},
author = {Jamieson, BG and Koehler, L and Todd, BJ},
title = {Spermatozoal ultrastructure in three species of parrots (aves, Psittaciformes) and its phylogenetic implications.},
journal = {The Anatomical record},
volume = {241},
number = {4},
pages = {461-468},
doi = {10.1002/ar.1092410404},
pmid = {7604961},
issn = {0003-276X},
mesh = {Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; In Vitro Techniques ; Male ; Microscopy, Electron ; *Parrots ; Phylogeny ; Spermatozoa/*ultrastructure ; },
abstract = {BACKGROUND: DNA-DNA hybridization studies suggest that Psittaciformes are highly, but not the most, derived nonpasserines. Multilocus protein electrophoresis indicates that cockatoos (Cacatuinae) form a monophyletic lineage distant from the other Australo-Papuan psittacids (Psittacinae).<br><br>METHODS: Transmission electron microscope procedures are applied to the spermatozoa of three parrots, in the Cacatuninae and Psittacinae, to investigate these relationships.<br><br>RESULTS: Psittaciform sperm have the following characteristics: (1) conical acrosome vesicle; rodlike perforatorium; cylindrical, highly condensed nucleus; proximal and distal centriole embedded in dense material; elongate periaxonemal mitochondrial midpiece, (2) nine dense peripheral axonemal fibers (coarse fibers), (3) no fibrous sheath around the axoneme, (4) mitochondria with linear cristae, lacking intra- (or inter-) mitochondrial dense bodies, (5) restriction of the endonuclear perforatorial canal to the anterior region of the nucleus, (6) a short distal centriole, and (7) nucleus abutting on but not penetrating the acrosome.<br><br>CONCLUSIONS: (1) These features are tetrapod symplesiomorphies, (2) is an amniote synapomorphy; the fibers differ from those of reptiles in being uniform in size, (3) loss of the fibrous sheath is an apomorphy known elsewhere only in columbiforms, (4) are apomorphies relative to basal aminiotes (Chelonia, Sphenodon, and Crocodilia), (5) is an apomorphic condition shared with other nonpasserines (galliforms and the white-naped crane) and crocodilians, (6) the latter taxa differ from parrots in a plesiomorphic elongation of the distal centriole, and (7) is a unique apomorphy of parrot sperm relative to other nonpasserines and reptiles. The short midpiece of N. hollandicus distinguishes this cacatuine from the two psittacines.},
}
@article {pmid7632440,
year = {1995},
author = {Yamagata, T and Ohishi, K and Faruque, MO and Masangkay, JS and Ba-Loc, C and Vu-Binh, D and Mansjoer, SS and Ikeda, H and Namikawa, T},
title = {Genetic variation and geographic distribution on the mitochondrial DNA in local populations of the musk shrew, Suncus murinus.},
journal = {Idengaku zasshi},
volume = {70},
number = {3},
pages = {321-337},
doi = {10.1266/jjg.70.321},
pmid = {7632440},
issn = {0021-504X},
mesh = {Animals ; Animals, Wild/genetics ; Asia ; DNA, Mitochondrial/*genetics ; Demography ; *Genetic Variation ; Haplotypes ; Kidney ; Mitochondria, Liver/genetics ; Phylogeny ; Polymorphism, Genetic ; Shrews/*genetics ; },
abstract = {The musk shrew (Suncus Murinus) is widely distributed throughout Asia and East Africa. The mitochondrial DNA (mtDNA) of this species was analyzed in individuals from 31 local populations in nine Asian countries and Mauritius, using 17 restriction endonucleases. Although fourteen and nine mtDNA haplotypes were detected from Bangladesh and Nepal, respectively, one to four haplotypes were found in each Southeast Asian country, and one common haplotype existed in Japan, Philippines, Vietnam, Thailand and Indonesia. Clustering analysis of mtDNA haplotypes classified shrew populations to three groups--continental group (Bangladesh and Nepal), islands' group (insular countries and Vietnam) and Malay group. The average nucleotide diversity among these three groups was calculated to be about 3.5%. These results indicate that the origin of feral populations in this species might be old and their population sizes are extremely large in the continent, and suggest a rapid spread of this animal throughout the islands. Although we have not shown yet an evidence of close relationships between islands' and continental mtDNA haplotypes, it is likely that the musk shrew had migrated from the continent in South Asia to the islands in Southeast Asia recently.},
}
@article {pmid7640891,
year = {1995},
author = {Hayashi, M and De Bellis, L and Alpi, A and Nishimura, M},
title = {Cytosolic aconitase participates in the glyoxylate cycle in etiolated pumpkin cotyledons.},
journal = {Plant &amp; cell physiology},
volume = {36},
number = {4},
pages = {669-680},
pmid = {7640891},
issn = {0032-0781},
mesh = {Aconitate Hydratase/genetics/immunology/*metabolism ; Amino Acid Sequence ; Animals ; Antibodies/immunology ; Antibody Specificity ; Base Sequence ; Cotyledon/enzymology ; Cytosol/enzymology ; DNA, Plant ; Escherichia coli ; Fruit/*enzymology ; Germination ; Glyoxylates/metabolism ; Iron-Regulatory Proteins ; Molecular Sequence Data ; Phylogeny ; RNA-Binding Proteins/metabolism ; Recombinant Fusion Proteins/genetics/immunology/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Two different aconitases are known to be expressed after the germination of oil-seed plants. One is a mitochondrial aconitase that is involved in the tricarboxylic acid cycle. The other participates in the glyoxylate cycle, playing a role in gluconeogenesis from stored oil. We isolated and characterized a cDNA for an aconitase from etiolated pumpkin cotyledons. The cDNA was 3,145 bp long and capable of encoding a protein of 98 kDa. N-terminal and C-terminal amino acid sequences deduced from the cDNA did not contain mitochondrial or glyoxysomal targeting signals. A search of protein databases suggested that the cDNA encoded a cytosolic aconitase. Immunoblotting analysis with a specific antibody against the aconitase expressed in Escherichia coli revealed that developmental changes in the amount of the aconitase were correlated with changes in levels of other enzymes of the glyoxylate cycle during growth of seedlings. Further analysis by subcellular fractionation and immunofluorescence microscopy revealed that aconitase was present only the cytosol and mitochondria. No glyoxysomal aconitase was found in etiolated cotyledons even though all the other enzymes of the glyoxylate cycle are known to be localized in glyoxysomes. Taken together, the data suggest that the cytosolic aconitase participates in the glyoxylate cycle with four glyoxysomal enzymes.},
}
@article {pmid7647296,
year = {1995},
author = {Zhou, YH and Ragan, MA},
title = {Characterization of the nuclear gene encoding mitochondrial aconitase in the marine red alga Gracilaria verrucosa.},
journal = {Plant molecular biology},
volume = {28},
number = {4},
pages = {635-646},
pmid = {7647296},
issn = {0167-4412},
mesh = {Aconitate Hydratase/*genetics ; Amino Acid Sequence ; Base Sequence ; Cell Compartmentation/*genetics ; Cell Nucleus/*genetics ; Gene Dosage ; Genomic Library ; Introns/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Sorting Signals/genetics ; Protein Structure, Secondary ; RNA Splicing ; Regulatory Sequences, Nucleic Acid/genetics ; Restriction Mapping ; Rhodophyta/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; Transcription, Genetic ; },
abstract = {We have cloned a nuclear gene from the marine red alga Gracilaria verrucosa that encodes the complete 779 amino-acid mitochondrial aconitase (m-ACN), the first characterized from a photosynthetic organism. The N-terminal 28 deduced amino acids are predicted to constitute the mitochondrial transit peptide, the first described from a red alga. Putative transcriptional cis-acting elements were identified in the upstream untranslated region. The G. verrucosa m-ACN gene (m-ACN) is present in a single copy and is located ca. 1.5 kb upstream from the single-copy polyubiquitin gene. The single spliceosomal intron is located near the 5' end of the region encoding the mature m-ACN in precisely the same location and phase as intron 2 in Caenorhabditis elegans m-ACN; sequences at its 3' and 5' splice junctions and at the predicted lariat branch point conform well to the eukaryote consensus sequences. Multiple protein-sequence alignment of m-ACN, bacterial aconitase (b-ACN) and iron-responsive element-binding protein (IRE-BP), and phylogenetic analyses, revealed that m-ACN does not share a recent common ancestry with either b-ACN or IRE-BP.},
}
@article {pmid7678563,
year = {1993},
author = {Schmitt, ME and Bennett, JL and Dairaghi, DJ and Clayton, DA},
title = {Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {7},
number = {1},
pages = {208-213},
doi = {10.1096/fasebj.7.1.7678563},
pmid = {7678563},
issn = {0892-6638},
support = {GM07365-15/GM/NIGMS NIH HHS/United States ; GM08294-04/GM/NIGMS NIH HHS/United States ; GM33088-22/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Binding Sites ; Endoribonucleases/*chemistry/genetics ; Humans ; Mitochondria/*chemistry ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry ; RNA, Catalytic/chemistry ; Ribonuclease P ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; },
abstract = {RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. The bulk of RNase MRP activity is found in the nucleus where its function remains unknown. Two different approaches have resulted in predictions of distinct secondary structures for RNase MRP RNA. In order to analyze more definitively the higher-order structure of RNase MRP RNA, we have conducted a phylogenetic comparison of the available RNase MRP RNA sequences from human, mouse, rat, cow, toad, and yeast. The resulting secondary structure shares features in common with previously described structures for prokaryotic and eukaryotic RNase P RNAs (1) and RNase MRP RNAs (2, 3). In addition, the phylogenetic structure is consistent with available chemical modification data on RNase MRP RNA and with the detailed analysis of the To antigen binding domain located near the 5' end of the RNase MRP RNA. The structure is not limited to RNase MRP RNAs, but can be expanded to cover both eukaryotic RNase P RNAs and RNase P/MRP RNAs from plants.},
}
@article {pmid7680126,
year = {1993},
author = {Wolff, G and Burger, G and Lang, BF and Kück, U},
title = {Mitochondrial genes in the colourless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns.},
journal = {Nucleic acids research},
volume = {21},
number = {3},
pages = {719-726},
pmid = {7680126},
issn = {0305-1048},
mesh = {Amino Acid Sequence ; Animals ; Ascomycota/genetics ; Base Sequence ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Exons ; *Genes, Fungal ; *Genes, Plant ; Humans ; *Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Prototheca/*genetics ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Homology, Amino Acid ; },
abstract = {The mitochondrial DNA from the colourless alga Prototheca wickerhamii contains two mosaic genes as was revealed from complete sequencing of the circular extranuclear genome. The genes for the large subunit of the ribosomal RNA (LSUrRNA) as well as for subunit I of the cytochrome oxidase (coxI) carry two and three intronic sequences respectively. On the basis of their canonical nucleotide sequences they can be classified as group I introns. Phylogenetic comparisons of the coxI protein sequences allow us to conclude that the P.wickerhamii mtDNA is much closer related to higher plant mtDNAs than to those of the chlorophyte alga C.reinhardtii. The comparison of the intron sequences revealed several unusual features: (1) The P.wickerhamii introns are structurally related to mitochondrial introns from various ascomycetous fungi. (2) Phylogenetic analyses indicate a close relationship between fungal and algal intronic sequences. (3) The P. wickerhamii introns are located at positions within the structural genes which can be considered as preferred intron insertion sites in homologous mitochondrial genes from fungi or liverwort. In all cases, the sequences adjacent to the insertion sites are very well conserved over large evolutionary distances. Our finding of highly similar introns in fungi and algae is consistent with the idea that introns have already been present in the bacterial ancestors of present day mitochondria and evolved concomitantly with the organelles.},
}
@article {pmid7704116,
year = {1994},
author = {Van Syoc, RJ},
title = {Genetic divergence between subpopulations of the eastern Pacific goose barnacle Pollicipes elegans: mitochondrial cytochrome c subunit 1 nucleotide sequences.},
journal = {Molecular marine biology and biotechnology},
volume = {3},
number = {6},
pages = {338-346},
pmid = {7704116},
issn = {1053-6426},
mesh = {Animals ; Base Sequence ; Cytochrome c Group/chemistry/*genetics ; DNA, Mitochondrial ; *Genetic Variation ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Thoracica/*genetics ; },
abstract = {Nucleotide sequence data derived from polymerase chain reaction products from the cytochrome oxidase subunit 1 gene of mitochondrial DNA provide evidence for interrupted gene flow and subsequent genetic divergence between geographically separate subpopulations of the edible goose barnacle, Pollicipes elegans, with a 4400-km latitudinal distribution in the eastern Pacific Ocean. The amphitropical subpopulations of Pollicipes elegans have a net nucleotide sequence divergence of about 1.2%. A range of mutation rates are applied to calculate estimates for the timing of this divergence. The earliest estimated time of divergence agrees with a Pliocene time of general warming in the eastern Pacific. The latest estimated times coincide with the Pleistocene epoch and periods of cooling and warming that could have allowed for a series of expansions and contractions of P. elegans populations in the eastern tropical Pacific. These expansions and contractions may, therefore, represent alternating periods of genetic exchange and isolation of the two populations.},
}
@article {pmid7714914,
year = {1995},
author = {Arnason, U and Bodin, K and Gullberg, A and Ledje, C and Mouchaty, S},
title = {A molecular view of pinniped relationships with particular emphasis on the true seals.},
journal = {Journal of molecular evolution},
volume = {40},
number = {1},
pages = {78-85},
pmid = {7714914},
issn = {0022-2844},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Seals, Earless/*genetics ; Sequence Analysis ; },
abstract = {Phylogenetic analysis of conservative nucleotide substitutions in 18 complete sequences of the mitochondrial cytochrome b gene of Phocidae (true seals), Odobenidae (walruses), and Otariidae (sea lions and fur seals), plus three ursid and three felid sequences, identified the pinnipeds as monophyletic with Otariidae and Odobenidae on a common evolutionary branch. Analysis of total nucleotide differences separated the evolutionary lineages of northern and southern phocids. Both lineages are distinct from the most ancestral phocid genus, Monachus (monk seals), represented by the Hawaiian monk seal. The inclusion of the Hawaiian monk seal in the subfamily Monachinae makes the subfamily paraphyletic. Among the northern phocids, the hooded seal (genus Cystophora, chromosome number 2n = 34) is sister taxon to the Phoca complex. The Phoca complex, which is characterized by the chromosome number 2n = 32, includes genus Phoca and the monotypic genus Halichoerus (grey seal). The comparison does not support a generic distinction of Halichoerus within the Phoca complex. The present data suggest that Cystophora and Phoca separated > or = 6 million years ago. Among the southern phocids the close molecular relationship of the Weddell and leopard seals relative to their morphological distinction exemplifies rapid adaptation to different ecological niches. This result stands in contrast to the limited morphological differentiation relative to the pronounced molecular distinctions that may occur within the Phoca complex.},
}
@article {pmid7731996,
year = {1995},
author = {Authier, F and Bergeron, JJ and Ou, WJ and Rachubinski, RA and Posner, BI and Walton, PA},
title = {Degradation of the cleaved leader peptide of thiolase by a peroxisomal proteinase.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {9},
pages = {3859-3863},
pmid = {7731996},
issn = {0027-8424},
mesh = {Acetyl-CoA C-Acetyltransferase/biosynthesis/*metabolism ; Amino Acid Sequence ; Animals ; Antibodies ; CHO Cells ; Cell Line ; Cricetinae ; Endopeptidases/biosynthesis/genetics/*metabolism ; Liver/enzymology ; Microbodies/*enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptides/chemical synthesis/immunology ; Phylogeny ; Protein Processing, Post-Translational ; Protein Sorting Signals/*metabolism ; Rats ; Recombinant Proteins/biosynthesis/metabolism ; Transfection ; },
abstract = {A peroxisomal location for insulin-degrading enzyme (IDE) has been defined by confocal immunofluorescence microscopy of stably transfected CHO cells overexpressing IDE and digitonin-permeabilization studies in normal nontransfected fibroblasts. The functional significance of IDE in degrading cleaved leader peptides of peroxisomal proteins targeted by the type II motif was evaluated with a synthetic peptide corresponding to the type II leader peptide of prethiolase. The peptide effectively competed for degradation and cross-linking of the high-affinity substrate 125I-labeled insulin to IDE. Direct proteolysis of the leader peptide of prethiolase was confirmed by HPLC; degradation was inhibited by immunodepletion with an antibody to IDE. Phylogenetic analysis of proteinases related to IDE revealed sequence similarity to mitochondrial processing peptidases.},
}
@article {pmid7766262,
year = {1995},
author = {Heidrich, P and König, C and Wink, M},
title = {Molecular phylogeny of South American screech owls of the Otus atricapillus complex (Aves: Strigidae) inferred from nucleotide sequences of the mitochondrial cytochrome b gene.},
journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences},
volume = {50},
number = {3-4},
pages = {294-302},
doi = {10.1515/znc-1995-3-420},
pmid = {7766262},
issn = {0939-5075},
mesh = {Animals ; Base Sequence ; Birds/*classification/*genetics ; Chickens/genetics ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; South America ; },
abstract = {The cytochrome b gene of 6 South American screech owls of the genus Otus (O. choliba, O. atricapillus, O. usta, O. sanctaecatarinae, O. guatemalae, and O. hoyi) and two Old World species (Otus scops and Otus leucotis) was amplified by polymerase chain reaction (PCR) and partially sequenced (300 nucleotides). Otus atricapillus, O. guatemalae, O. hoyi and O. sanctaecatarinae which are morphologically very similar, have been treated as belonging to a single species. A. atricapillus (Sibley and Monroe, 1990). Nucleotide sequences differ substantially between these taxa (6.3 to 8.8% nucleotide substitutions) indicating that they represent well established and distinct species which had been implicated already from ecological and bioacoustical analyses (König, 1991, 1994). The importance of vocal and ecological characters for the taxonomy of nocturnal birds is thus confirmed by our molecular analysis. Phylogenetic relationships were reconstructed between Old and New World owls using character state ("maximum parsimony"; PAUP 3.1.1) and distance matrix methods (neighbour-joining; MEGA).},
}
@article {pmid7766872,
year = {1995},
author = {Thompson, MD and Paavola, CD and Lenvik, TR and Gantt, JS},
title = {Chlamydomonas transcripts encoding three divergent plastid chaperonins are heat-inducible.},
journal = {Plant molecular biology},
volume = {27},
number = {5},
pages = {1031-1035},
pmid = {7766872},
issn = {0167-4412},
support = {GM38769/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chaperonins/*biosynthesis/genetics ; Chlamydomonas/*genetics/*metabolism ; *Gene Expression Regulation, Plant ; Hot Temperature ; Kinetics ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plants/metabolism ; Plastids/*metabolism ; RNA, Plant/biosynthesis ; *Transcription, Genetic ; },
abstract = {Three cDNAs encoding plastid cpn60 chaperonin subunits have been isolated from the unicellular green alga Chlamydomonas reinhardtii. Based on comparisons of the predicted amino acid sequences, we conclude that Chlamydomonas, like higher plants, contains divergent plastid cpn60-alpha and cpn60-beta subunits. The predicted amino acid sequences of the two Chlamydomonas cpn60-beta subunits differ significantly (24% divergent), indicating that the two cpn60-beta subunits have been selectively maintained for a considerable period of time. Unlike plastid chaperonin transcripts in higher plants, heat shock conditions (42 degrees C) lead to a rapid increase (10- to 30-fold) in the level of each of the three plastid transcripts.},
}
@article {pmid7881821,
year = {1994},
author = {Yang, SY},
title = {The large subunit of the pig heart mitochondrial membrane-bound beta-oxidation complex is a long-chain enoyl-CoA hydratase: 3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology},
volume = {109},
number = {4},
pages = {557-566},
doi = {10.1016/0305-0491(94)90117-1},
pmid = {7881821},
issn = {1096-4959},
support = {DK 47392/DK/NIDDK NIH HHS/United States ; },
mesh = {3-Hydroxyacyl CoA Dehydrogenases/*isolation &amp; purification/metabolism ; Amino Acid Sequence ; Animals ; Cell Membrane ; Enoyl-CoA Hydratase/*isolation &amp; purification/metabolism ; Mitochondria, Heart/*enzymology ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Phylogeny ; Sequence Alignment ; Swine ; },
abstract = {The subunit locations of the component enzymes of the pig heart trifunctional mitochondrial beta-oxidation complex are suggested by analyzing the primary structure of the large subunit of this membrane-bound multienzyme complex [Yang S.-Y. et al. (1994) Biochem. biophys. Res. Commun. 198, 431-437] with those of the subunits of the E. coli fatty acid oxidation complex and the corresponding mitochondrial matrix beta-oxidation enzymes. Long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase are located in the amino-terminal and the central regions of the 79 kDa polypeptide, respectively, whereas the long-chain 3-ketoacyl-CoA thiolase is associated with the 46 kDa subunit of this complex. The pig heart mitochondrial bifunctional beta-oxidation enzyme is more homologous to the large subunit of the prokaryotic fatty acid oxidation complex than to the peroxisomal trifunctional beta-oxidation enzyme. The evolutionary trees of 3-hydroxyacyl-CoA dehydrogenases and enoyl-CoA hydratases suggest that the mitochondrial inner membrane-bound bifunctional beta-oxidation enzyme and the corresponding matrix monofunctional beta-oxidation enzymes are more remotely related to each other than to their corresponding prokaryotic enzymes, and that the genes of E. coli multifunctional fatty acid oxidation protein and pig heart mitochondrial bifunctional beta-oxidation enzyme diverged after the appearance of eukaryotic cells.},
}
@article {pmid7883039,
year = {1995},
author = {Murgia, I and Maciver, SK and Morandini, P},
title = {An actin-related protein from Dictyostelium discoideum is developmentally regulated and associated with mitochondria.},
journal = {FEBS letters},
volume = {360},
number = {3},
pages = {235-241},
doi = {10.1016/0014-5793(95)00111-l},
pmid = {7883039},
issn = {0014-5793},
mesh = {Actins/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Compartmentation ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/genetics ; Dictyostelium/*genetics ; Gene Expression Regulation, Developmental ; *Genes, Fungal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; },
abstract = {An actin-related protein (ACLA) has been identified in the cellular slime mould Dictyostelium discoideum. The complete cDNA sequence indicates that within the actin superfamily it belongs to the ARP3 family of actin-related proteins together with Arp66B from Drosophila melanogaster, Actin2 from Bos taurus, act2 from Schizosaccharomyces pombe and possibly act2 from Caenorhabditis elegans. The ACLA mRNA is regulated during development, showing a maximum between 2 and 4 h after starvation. The protein has been expressed in E. coli and antibodies raised against it. Immunofluorescence microscopy shows that ACLA protein co-localises with mitochondria; the protein copurifies with Dictyostelium mitochondria.},
}
@article {pmid7883436,
year = {1994},
author = {Watson, NA and Rohde, K},
title = {Ultrastructure of sperm and spermiogenesis in the monocotylid monogeneans Monocotyle helicophallus and Calicotyle australiensis (Platyhelminthes).},
journal = {International journal for parasitology},
volume = {24},
number = {7},
pages = {1019-1030},
doi = {10.1016/0020-7519(94)90168-6},
pmid = {7883436},
issn = {0020-7519},
mesh = {Animals ; Cell Nucleus/ultrastructure ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Models, Structural ; Phylogeny ; Platyhelminths/*classification/*ultrastructure ; Sperm Tail/ultrastructure ; Spermatids/ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; },
abstract = {Spermiogenesis in Monocotyle helicophallus involves formation of free flagella which rotate to lie parallel before fusing. There is no median cytoplasmic process. A small number of microtubules (usually 2-4) is associated with the axonemes in the zone of differentiation. Nucleus and a fused mitochondrion migrate alongside the axonemes and one basal body moves distally. A coil of nucleus, originally in the cytophore, also moves out along the shaft. The mature spermatozoan has only a single axoneme for a short distance at each end, with two associated microtubules at the proximal end, as well as one axoneme, nucleus and mitochondrion throughout most of its length (the nucleus being enlarged and roughly coiled in one region), and a short region of two overlapping axonemes. We interpret our findings as two axonemes arranged almost end to end, one extending from the proximal end to some point in the mid-region, where the second axoneme begins and continues to the distal end of the sperm. Spermatozoa of Calicotyle australiensis develop from a zone of differentiation which has two basal bodies and a complete ring of cortical microtubules. Two initially free axonemes fuse with each other and there is no median cytoplasmic process. Spermatids form within parallel canals in the cytophore, by backward movement of the zone of differentiation. Prior to detachment, an electron-dense spiral end-piece forms around and proximal to the basal body region. Sixty-four spermatids are present in each isogenic group. With the study of spermiogenesis in more species of Monogenea Monopisthocotylea, it is apparent that the previously designated sperm patterns 2 and 3 are not distinct and should be combined and re-defined. Species previously designated as having sperm patterns 2 and 3 can all be accommodated by the description "two normal axonemes or one normal and one shortened, altered or displaced axoneme, and none, one or a few cortical microtubules remaining in a region of the sperm derived from the zone of differentiation in which a few or a complete ring of microtubules was present".},
}
@article {pmid7910968,
year = {1994},
author = {Burton, RS and Lee, BN},
title = {Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {11},
pages = {5197-5201},
pmid = {7910968},
issn = {0027-8424},
mesh = {Animals ; Base Sequence ; Cell Nucleus ; Crustacea/*classification/enzymology/genetics ; DNA ; Electron Transport Complex IV/*genetics ; Female ; Isoenzymes/*genetics ; Mitochondria ; Molecular Sequence Data ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; },
abstract = {The genetic structure of natural populations is frequently inferred from geographic distributions of alleles at multiple gene loci. Surveys of allozyme polymorphisms in the tidepool copepod Tigriopus californicus have revealed sharp genetic differentiation of populations, indicating that gene flow among populations is highly restricted. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial gene genealogies. DNA sequences of the mtDNA-encoded cytochrome-c oxidase subunit I gene from 21 isofemale lines derived from seven populations reveal a phylogeographic break between populations north and south of Point Conception, California, with sequence divergence across the break exceeding 18%, the highest level of mtDNA divergence yet reported among conspecific populations. Divergence between populations based on 22 sequences of the nuclear histone H1 gene is geographically concordant with the mitochondrial sequences. In contrast with previously studied nuclear genes in other sexually reproducing metazoans, the H1 gene genealogy from T. californicus shows no evidence of recombination. The apparent absence of intragenic recombinants probably results from the persistent lack of gene flow among geographically separated populations, a conclusion strongly supported by allozyme data and the mitochondrial gene genealogy. Despite strong population differentiation at allozyme loci, the phylogeographic break identified by the DNA sequences was not evident in the allozyme data.},
}
@article {pmid7912616,
year = {1994},
author = {Giuffra, E and Bernatchez, L and Guyomard, R},
title = {Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy.},
journal = {Molecular ecology},
volume = {3},
number = {2},
pages = {161-171},
doi = {10.1111/j.1365-294x.1994.tb00117.x},
pmid = {7912616},
issn = {0962-1083},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Genetic Variation ; Genotype ; Italy ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Homology, Nucleic Acid ; Trout/*genetics ; },
abstract = {The Pô River basin of northern Italy is the home of distinctive and endemic morphological forms of brown trout Salmo trutta. We used PCR-direct sequencing and RFLP techniques to study variation in the mitochondrial control region of 225 trout in order to assess genetic relatedness among 18 populations from that region. The distribution analysis of these genotypes among north Italian populations confirmed the phylogenetic differentiation of marbled trout Salmo trutta marmoratus populations and the postglacial origin of S. t. carpio. Extensive genetic heterogeneity was observed among morphologically identical S. t. fario populations. Introgression with domestic strains of Atlantic basin origin was detected in all forms. In order to assess the phylogenetic congruence detected in coding and noncoding regions of the mitochondrial genome, we also analysed sequence variation in segments of the cytochrome b and ATPase subunit VI genes among representatives of all variants detected in the analysis of the control region. Variation in protein coding genes was only slightly less than that observed in the control region of the same individuals, both in terms of number of variants detected and of pairwise sequence divergence estimates among variants. Phylogenetic analysis based on protein coding genes sequences identified the same phylogenetic groupings defined by the control region analysis and also allowed a partial resolution of their phyletic relationships that was previously unresolved. However, coding and noncoding segments differed substantially in the transition-transversion ratio (17:0 in coding segments vs. 17:6 in control region segments).},
}
@article {pmid7937116,
year = {1994},
author = {Thanaraj, TA},
title = {Phylogenetically preserved inter-rRNA base pairs: involvement in ribosomal subunit association.},
journal = {Nucleic acids research},
volume = {22},
number = {19},
pages = {3936-3942},
pmid = {7937116},
issn = {0305-1048},
mesh = {Animals ; Bacteria/genetics ; *Base Composition ; Base Sequence ; Binding Sites ; Eukaryotic Cells/chemistry ; Humans ; Mitochondria/chemistry ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*chemistry ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/metabolism ; },
abstract = {Intermolecular complementary base pairs, that can be formed between the bases from single-stranded and weak stem regions on 16S rRNA and those on 23S rRNA, were located and checked for preservation in a variety of species covering the complete phylogenetic spectrum. Putative base pairs that exhibited two 'compensatory base pair changes' (a requisite as dictated by the approach of 'comparative sequence data analysis') were picked up. Potential base pairs were selected by assessing the frequency and taxonomy specificity of the occurrence of compensatory base pair changes against those of other types of base pair changes. The selected base pairs were classified as universal, non-mitochondrial, and prokaryote-specific. The positions of the proposed base pairs occur near the structurally and functionally important regions on rRNAs.},
}
@article {pmid7948926,
year = {1994},
author = {Taniguchi, M and Mori, J and Sugiyama, T},
title = {Structure of genes that encode isozymes of aspartate aminotransferase in Panicum miliaceum L., a C4 plant.},
journal = {Plant molecular biology},
volume = {26},
number = {2},
pages = {723-734},
pmid = {7948926},
issn = {0167-4412},
mesh = {Animals ; Aspartate Aminotransferases/*biosynthesis/genetics ; Bacteria/enzymology/genetics ; Base Sequence ; Blotting, Southern ; Cytosol/enzymology ; DNA Primers ; DNA, Plant/isolation &amp; purification/metabolism ; Exons ; *Genes, Plant ; Genomic Library ; Humans ; Introns ; Isoenzymes/*biosynthesis/genetics ; Mice ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Plants/enzymology/*genetics ; Regulatory Sequences, Nucleic Acid ; Restriction Mapping ; },
abstract = {The cytosolic and mitochondrial isozymes of aspartate aminotransferase (AspAT) function in the C4 photosynthetic cycle in NAD-malic enzyme-type C4 plants and are expressed at high levels in mesophyll cells and bundle sheath cells, respectively. We constructed a genomic library from Panicum miliaceum, a NAD-malic enzyme-type C4 plant, and cloned the genes for these isozymes. The sequence of the cloned gene for cytosolic AspAT spans 7800 bp and consists of 12 exons. The sequence of the cloned gene for mitochondrial AspAT spans 9000 bp and consists of 10 exons. The results of primer-extension analysis suggest that transcription may be initiated from multiple adjacent sites. Both genes have significant GC-rich regions around the site of initiation of transcription, and these regions showed no CpG suppression. The 5'- flanking regions of both genes include several short sequences similar to the regulatory elements found in other genes for components of the photosynthetic machinery. In particular, the cytosolic AspAT gene contains sequences similar to nuclear protein-binding sites in other mesophyll-expressed C4 photosynthetic genes and the mitochondrial AspAT gene contains elements for light-sensitive and constitutive expression of a bundle sheath-expressed gene. The results of Southern analysis indicated that there are at least two genes that encode each isozyme in the genome of P. miliaceum. A comparison of intron-insertion positions between AspAT genes of plants and animals revealed that several introns are located at identical positions. On the basis of a phylogenetic tree among AspATs and tyrosine aminotransferase, we have shown that the introns of aminotransferase genes antedate the divergence of eubacteria, archaebacteria, and eukaryotes.},
}
@article {pmid7961755,
year = {1994},
author = {Saito, K and Tatsuguchi, K and Takagi, Y and Murakoshi, I},
title = {Isolation and characterization of cDNA that encodes a putative mitochondrion-localizing isoform of cysteine synthase (O-acetylserine(thiol)-lyase) from Spinacia oleracea.},
journal = {The Journal of biological chemistry},
volume = {269},
number = {45},
pages = {28187-28192},
pmid = {7961755},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Cysteine Synthase/*biosynthesis/genetics ; DNA Primers ; DNA, Complementary/isolation &amp; purification/metabolism ; Escherichia coli/enzymology ; Genetic Complementation Test ; Isoenzymes/*biosynthesis ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Recombinant Proteins/biosynthesis/genetics ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology ; },
abstract = {The cDNA clones that encode a putative mitochondrion-localizing isoform of cysteine synthase (O-acetyl-L-serine(thiol)-lyase, O-acetyl-L-serine acetate-lyase (adding hydrogen sulfide), EC 4.2.99.8), which is denoted as cysteine synthase C, were isolated from spinach (Spinacia oleracea L.). The cDNA encodes a polypeptide of 368 amino acids containing a putative transit peptide of 30-40 amino acids at the N terminus. This leader peptide sequence exhibited several structural features common to other mitochondrion-targeting transit peptides. Homology was also detected between the putative transit peptide sequence of cysteine synthase C and other mitochondrion-targeting leader sequences. A deduced amino acid sequence of cysteine synthase C exhibited a homology of 61% with cytoplasmic isoform A and 63% with chloroplastic isoform B. A bacterial expression vector of the cDNA clone could genetically complement an Escherichia coli auxotroph lacking cysteine synthase loci and could produce the functionally active and immunoreactive cysteine synthase in E. coli. DNA blot hybridization analysis showed the presence of one or two copies of cysC gene in the genome of spinach. RNA blot hybridization analysis indicated that the expression level of cysC gene was lower than those of cysA and cysB and that the mode of cysC expression was constitutive in green and etiolated seedlings of spinach. The molecular evolutionary study of cysteine synthase proteins from plants and bacteria suggested that a common ancestor cysteine synthase gene has evolved into five cysteine synthase gene families, plant isoform A family, plant isoform B family, plant isoform C family, bacterial cysK family, and bacterial cysM family.},
}
@article {pmid7971961,
year = {1994},
author = {Shigenaga, MK and Hagen, TM and Ames, BN},
title = {Oxidative damage and mitochondrial decay in aging.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {91},
number = {23},
pages = {10771-10778},
pmid = {7971961},
issn = {0027-8424},
support = {CA39910/CA/NCI NIH HHS/United States ; ESO1896/ES/NIEHS NIH HHS/United States ; },
mesh = {*Aging ; Animals ; DNA, Mitochondrial/chemistry ; Electron Transport ; Energy Metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Immune System/metabolism ; Intracellular Membranes/chemistry ; Lipids/chemistry ; Longevity ; Mitochondria/*physiology ; Mutation ; Neurons/metabolism ; Oxidation-Reduction ; Phylogeny ; Proteins/chemistry ; Superoxides/metabolism ; },
abstract = {We argue for the critical role of oxidative damage in causing the mitochondrial dysfunction of aging. Oxidants generated by mitochondria appear to be the major source of the oxidative lesions that accumulate with age. Several mitochondrial functions decline with age. The contributing factors include the intrinsic rate of proton leakage across the inner mitochondrial membrane (a correlate of oxidant formation), decreased membrane fluidity, and decreased levels and function of cardiolipin, which supports the function of many of the proteins of the inner mitochondrial membrane. Acetyl-L-carnitine, a high-energy mitochondrial substrate, appears to reverse many age-associated deficits in cellular function, in part by increasing cellular ATP production. Such evidence supports the suggestion that age-associated accumulation of mitochondrial deficits due to oxidative damage is likely to be a major contributor to cellular, tissue, and organismal aging.},
}
@article {pmid8018725,
year = {1994},
author = {Johansen, S and Johansen, T},
title = {Sequence analysis of 12 structural genes and a novel non-coding region from mitochondrial DNA of Atlantic cod, Gadus morhua.},
journal = {Biochimica et biophysica acta},
volume = {1218},
number = {2},
pages = {213-217},
doi = {10.1016/0167-4781(94)90015-9},
pmid = {8018725},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA/*genetics ; Enzymes/chemistry/genetics ; Fishes/*genetics/metabolism ; *Genes ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; },
abstract = {We have determined the nucleotide sequences of 12 structural genes from the mitochondrial DNA of Atlantic cod, Gadus morhua. These genes encode the proteins NADH dehydrogenase subunit 2, cytochrome c oxidase subunit I, cytochrome c oxidase subunit II, and apocytochrome b, as well as the transfer RNAs tRNA(Ile), tRNA(Gln), tRNA(Met), tRNA(Ser) (UCN), tRNA(Asp), tRNA(Glu), tRNA(Thr) and tRNA(Pro). The apocytochrome b sequences were used to construct a phylogenetic tree revealing the evolutionary divergence between modern bony fishes, sturgeon and sharks. We found that bony fishes display the same slow amino acid substitution rates in the mitochondrial encoded proteins as cartilaginous fishes (sharks). A novel non-coding region of 74 base pairs not found in other fishes where sequence data are available is located between the genes encoding tRNA(Thr) and tRNA(Pro). This region contains both direct and inverted repeat motifs that may function in termination of the H-strand transcript.},
}
@article {pmid8121281,
year = {1994},
author = {Brown, JM and Pellmyr, O and Thompson, JN and Harrison, RG},
title = {Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data.},
journal = {Molecular biology and evolution},
volume = {11},
number = {1},
pages = {128-141},
doi = {10.1093/oxfordjournals.molbev.a040087},
pmid = {8121281},
issn = {0737-4038},
mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genes, Insect ; Genetic Variation ; Lepidoptera/anatomy &amp; histology/*enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; },
abstract = {The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from nucleotide sequence variation across a 765-bp region in the cytochrome oxidase I and II genes of the mitochondrial genome. Most parsimonious relationships of 25 haplotypes from 16 Greya species and two outgroup genera (Tetragma and Prodoxus) showed substantial congruence with the species relationships indicated by morphological variation. Differences between mitochondrial and morphological trees were found primarily in the positions of two species, G. variabilis and G. pectinifera, and in the branching order of the three major species groups in the genus. Conflicts between the data sets were examined by comparing levels of homoplasy in characters supporting alternative hypotheses. The phylogeny of Greya species suggests that host-plant association at the family level and larval feeding mode are conservative characters. Transition/transversion ratios estimated by reconstruction of nucleotide substitutions on the phylogeny had a range of 2.0-9.3, when different subsets of the phylogeny were used. The decline of this ratio with the increase in maximum sequence divergence among taxa indicates that transitions are masked by transversions along deeper internodes or long branches of the phylogeny. Among transitions, substitutions of A-->G and T-->C outnumbered their reciprocal substitutions by 2-6 times, presumably because of the approximately 4:1 (77%) A+T-bias in nucleotide base composition. Of all transversions, 73%-80% were A<-->T substitutions, 85% of which occurred at third positions of codons; these estimates did not decrease with an increase in maximum sequence divergence of taxa included in the analysis. The high frequency of A<-->T substitutions is either a reflection or an explanation of the 92% A+T bias at third codon positions.},
}
@article {pmid8132485,
year = {1993},
author = {Klingenberg, M},
title = {Dialectics in carrier research: the ADP/ATP carrier and the uncoupling protein.},
journal = {Journal of bioenergetics and biomembranes},
volume = {25},
number = {5},
pages = {447-457},
pmid = {8132485},
issn = {0145-479X},
mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Adipose Tissue, Brown/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Biological Transport ; Carrier Proteins/chemistry/*physiology ; *Energy Metabolism ; Intracellular Membranes/*metabolism ; Ion Channels ; Mammals/metabolism ; Membrane Proteins/chemistry/*physiology ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*physiology ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protons ; Structure-Activity Relationship ; Uncoupling Protein 1 ; },
abstract = {A concise review is given of the research in our laboratory on the ADP/ATP carrier (AAC) and the uncoupling protein (UCP). Although homologous proteins, their widely different functions and contrasts are stressed. The pioneer role of research on the AAC, not only for the mitochondrial but also for other carriers, and the present state of their structure-function relationship is reviewed. The function of UCP as a highly regulated H+ carrier is described in contrast to the largely unregulated ADP/ATP exchange in AAC. General principles of carrier catalysis as derived from studies on the AAC and UCP are elucidated.},
}
@article {pmid8136921,
year = {1993},
author = {DeWalt, TS and Sudman, PD and Hafner, MS and Davis, SK},
title = {Phylogenetic relationships of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {2},
number = {3},
pages = {193-204},
doi = {10.1006/mpev.1993.1020},
pmid = {8136921},
issn = {1055-7903},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; Genetic Variation ; Kidney/metabolism ; Mitochondria/*metabolism ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Rodentia/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {Phylogenetic relationships among 7 of the 10 species of pocket gophers in the genera Pappogeomys and Cratogeomys were addressed using nucleotide sequence data from the entire cytochrome b gene of the mitochondrial genome (1140 base pairs). Results of parsimony analysis were concordant with the results of morphological analysis (R. J. Russell, Univ. Kans. Pub. Mus. Nat. Hist. 16: 581-776, 1968), but differed somewhat from the conclusions drawn from an allozymic study of these species (R. L. Honeycutt and S. L. Williams, J. Mammal. 63: 208-217, 1982). Phylogenetic analysis indicated that Cratogeomys is monophyletic, as are the two species groups within this genus. Estimates of levels of nucleotide sequence divergence between species of these genera indicated that the cytochrome b gene of pocket gophers may have evolved at a dramatically higher rate than in organisms examined previously (D. M. Irwin, T. D. Kocher, and A. C. Wilson, J. Mol. Evol. 32: 128-144, 1991).},
}
@article {pmid8136924,
year = {1993},
author = {da Silva, MN and Patton, JL},
title = {Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha).},
journal = {Molecular phylogenetics and evolution},
volume = {2},
number = {3},
pages = {243-255},
doi = {10.1006/mpev.1993.1023},
pmid = {8136924},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Brazil ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; *Genetic Variation ; Geography ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; *Phylogeny ; Rodentia/classification/*genetics ; Species Specificity ; },
abstract = {Patterns of evolutionary relationships among haplotype clades of sequences of the mitochondrial cytochrome b DNA gene are examined for five genera of arboreal rodents of the Caviomorph family Echimyidae from the Amazon Basin. Data are available for 798 bp of sequence from a total of 24 separate localities in Peru, Venezuela, Bolivia, and Brazil for Mesomys, Isothrix, Makalata, Dactylomys, and Echimys. Sequence divergence, corrected for multiple hits, is extensive, ranging from less than 1% for comparisons within populations of over 20% among geographic units within genera. Both the degree of differentiation and the geographic patterning of the variation suggest that more than one species composes the Amazonian distribution of the currently recognized Mesomys hispidus, Isothrix bistriata, Makalata didelphoides, and Dactylomys dactylinus. There is general concordance in the geographic range of haplotype clades for each of these taxa, and the overall level of differentiation within them is largely equivalent. These observations suggest that a common vicariant history underlies the respective diversification of each genus. However, estimated times of divergence based on the rate of third position transversion substitutions for the major clades within each genus typically range above 1 million years. Thus, allopatric isolation precipitating divergence must have been considerably earlier than the late Pleistocene forest fragmentation events commonly invoked for Amazonian biota.},
}
@article {pmid8136925,
year = {1993},
author = {Graybeal, A},
title = {The phylogenetic utility of cytochrome b: lessons from bufonid frogs.},
journal = {Molecular phylogenetics and evolution},
volume = {2},
number = {3},
pages = {256-269},
doi = {10.1006/mpev.1993.1024},
pmid = {8136925},
issn = {1055-7903},
mesh = {Amino Acid Sequence ; Animals ; Bufonidae/*classification/*genetics ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; North America ; *Phylogeny ; Sequence Homology, Amino Acid ; Species Specificity ; Xenopus laevis/classification/genetics ; },
abstract = {The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.},
}
@article {pmid8253773,
year = {1993},
author = {Kamijo, T and Aoyama, T and Miyazaki, J and Hashimoto, T},
title = {Molecular cloning of the cDNAs for the subunits of rat mitochondrial fatty acid beta-oxidation multienzyme complex. Structural and functional relationships to other mitochondrial and peroxisomal beta-oxidation enzymes.},
journal = {The Journal of biological chemistry},
volume = {268},
number = {35},
pages = {26452-26460},
pmid = {8253773},
issn = {0021-9258},
mesh = {3-Hydroxyacyl CoA Dehydrogenases/*genetics/metabolism ; Acetyl-CoA C-Acyltransferase/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Carbon-Carbon Double Bond Isomerases ; Cells, Cultured ; Cloning, Molecular ; DNA, Complementary ; Enoyl-CoA Hydratase/*genetics/metabolism ; Fatty Acids/*metabolism ; Isomerases/*genetics/metabolism ; Microbodies/*enzymology ; Mitochondria, Liver/*enzymology ; Mitochondrial Trifunctional Protein ; Molecular Sequence Data ; Multienzyme Complexes/*genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Racemases and Epimerases/*genetics/metabolism ; Rats ; Sequence Homology, Amino Acid ; },
abstract = {Rat liver mitochondrial fatty acid oxidation multienzyme complex consists of 4 mol of the alpha-subunit and 4 mol of the beta-subunit, and has three enzyme activities of long chain enoyl-CoA hydratase, long chain 3-hydroxyacyl-CoA dehydrogenase, and long chain 3-ketoacyl-CoA thiolase. The following cDNA clones for the rat enzyme complex were isolated, sequenced, and expressed: 1) the 2,789-base pair (bp) cDNA clone had a 2,289-bp open reading frame encoding a 82,511-Da precursor and a 78,637-Da mature subunit. The deduced amino acid sequence of this subunit revealed that this cDNA encodes the alpha-subunit and had regions similar to the structure of rat mitochondrial enoyl-CoA hydratase and rat mitochondrial enoyl-CoA isomerase on the amino-terminal side, and a part similar to that of pig mitochondrial 3-hydroxyacyl-CoA dehydrogenase on the carboxyl-terminal side. Expression of this cDNA in COS-1 cells yielded a protein with long chain enoyl-CoA hydratase and long chain 3-hydroxyacyl-CoA dehydrogenase activities. 2) The 1,943-bp cDNA clone had a 1,425-bp open reading frame encoding a 51,413-Da precursor and a 47,583-Da mature subunit. A high similarity of the structure to 3-ketoacyl-CoA thiolases and acetoacetyl-CoA thiolases from various sources suggests that this clone encodes the beta-subunits. Expression of this cDNA in COS-1 cells yielded a protein with long chain 3-ketoacyl-CoA thiolase activity. By phylogenetic analysis of the deduced amino acid sequences of the alpha- and beta-subunits with those of other beta-oxidation enzymes, it was suggested that the alpha-subunit is a descendant of short chain enoyl-CoA hydratase and short chain 3-hydroxyacyl-CoA dehydrogenase while the beta-subunit first diverged from a common ancestor gene of the thiolase family.},
}
@article {pmid8300282,
year = {1993},
author = {Rohde, K and Watson, NA},
title = {Spermatogenesis in Udonella (Platyhelminthes, Udonellidea) and the phylogenetic position of the genus.},
journal = {International journal for parasitology},
volume = {23},
number = {6},
pages = {725-735},
doi = {10.1016/0020-7519(93)90068-a},
pmid = {8300282},
issn = {0020-7519},
mesh = {Animals ; Male ; Microscopy, Electron ; Phylogeny ; Platyhelminths/*classification/physiology ; Spermatids/ultrastructure ; Spermatogenesis/*physiology ; Testis/ultrastructure ; Trematoda/*classification/physiology ; },
abstract = {Spermatids are joined (cytophores). Two centrioles lateral and/or proximal to the nucleus form axonemes, arranged parallel with each other, that extend into a short distal cytoplasmic process. The nucleus elongates, and mitochondria fuse to form a single elongate mitochondrion. The part of the spermatid containing the axonemes, nucleus and mitochondrion elongates to a thread-like spermatozoon, surrounded at its base (at the level near the basal bodies) by an arching membrane where the sperm detaches from the residual cytoplasm. At no stage are there free flagella (except for short free flagellar tips), an intercentriolar body or a median cytoplasmic process. A few peripheral microtubules and a compact dense body, not membrane bound and closely associated with the mitochondrion, were seen in spermatids. Spermiogenesis in Udonella is interpreted as derived from proximo-distal fusion by a shifting of the basal bodies deeper into the cytoplasm and a consequent loss of the median cytoplasmic process. Both the ultrastructure of the protonephridia and spermiogenesis indicate that Udonella does not represent the sister group of all other neodermatans, but is a secondarily modified "advanced" neodermatan. Lack of convincing synapomorphies indicates that the taxon Cercomeridea as a defined by Brooks (1989a, b) is invalid.},
}
@article {pmid8326863,
year = {1993},
author = {Riley, DE and Campbell, LA and Puolakkainen, M and Krieger, JN},
title = {Trichomonas vaginalis and early evolving DNA and protein sequences of the CDC2/28 protein kinase family.},
journal = {Molecular microbiology},
volume = {8},
number = {3},
pages = {517-519},
doi = {10.1111/j.1365-2958.1993.tb01595.x},
pmid = {8326863},
issn = {0950-382X},
support = {R01 DK38955/DK/NIDDK NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; CDC2 Protein Kinase/*genetics ; CDC28 Protein Kinase, S cerevisiae/*genetics ; DNA, Protozoan/*genetics ; *Genes ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Trichomonas vaginalis/enzymology/*genetics ; },
abstract = {The human sexually transmitted parasite Trichomonas vaginalis is a representative of one of the three earliest evolving eukaryotic lineages. We investigated whether T. vaginalis has DNA sequences and peptides related to cell division control molecules universal among yeasts and higher eukaryotes. A T. vaginalis cell division control (CDC2/28) homologue was amplified by the polymerase chain reaction and sequenced. The absolute similarity with other CDC2/28 genes was 47%, with conservative replacement similarity of 67%. Western blots demonstrated a single T. vaginalis peptide reactive with antiserum to the PSTAIRE peptide, an expressed component of CDC2/28 genes in higher eukaryotes. Although eukaryotic, T. vaginalis has properties similar to those of bacteria and is the earliest evolving eukaryote reported to possess CDC2/28 DNA and peptide homologues. These observations suggest that the molecular origins of cell division control in eukaryotes preceded mitochondria, 28S ribosomes and regulated glycolysis.},
}
@article {pmid8345516,
year = {1993},
author = {Guo, HC and De Abreu, DM and Tillier, ER and Saville, BJ and Olive, JE and Collins, RA},
title = {Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA.},
journal = {Journal of molecular biology},
volume = {232},
number = {2},
pages = {351-361},
doi = {10.1006/jmbi.1993.1395},
pmid = {8345516},
issn = {0022-2836},
mesh = {Base Sequence ; Consensus Sequence ; DNA Mutational Analysis ; Genetic Variation ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Neurospora/genetics/*metabolism ; Phylogeny ; Plasmids/genetics ; *RNA Processing, Post-Transcriptional ; RNA, Catalytic/genetics/*metabolism ; RNA, Fungal/genetics/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Structure-Activity Relationship ; },
abstract = {We have used several complementary approaches to investigate the minimal contiguous sequence required for the in vitro self cleavage reaction performed by Neurospora VS RNA. Deletion analysis and site-directed mutagenesis revealed that only a single nucleotide is required upstream of the self-cleavage site, and that the identity of this nucleotide is not critical. This distinguishes VS RNA from all currently known ribozymes except hepatitis delta virus RNA. The shortest contiguous sequence capable of cleavage contains 153 nt downstream of the cleavage site. Linker insertion mutagenesis suggests that much of this downstream sequence is important for self-cleavage. Comparative sequence analysis of the VS plasmid from six natural isolates supports the importance in vivo of the minimal region determined by in vitro methods. Also, phylogenetic analysis raises the possibility of a recent horizontal transfer of the VS plasmid from Neurospora intermedia to Neurospora sitophila.},
}
@article {pmid8370534,
year = {1993},
author = {Vodkin, MH and Gordon, VR and McLaughlin, GL},
title = {A ribosomal protein in Acanthamoeba polyphaga is conserved in eukaryotic nuclei, organelles and bacteria.},
journal = {Gene},
volume = {131},
number = {1},
pages = {141-144},
doi = {10.1016/0378-1119(93)90683-t},
pmid = {8370534},
issn = {0378-1119},
support = {R01 EYO8205/EY/NEI NIH HHS/United States ; },
mesh = {Acanthamoeba/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Archaea/chemistry/genetics ; Bacteria/chemistry/genetics ; Base Sequence ; Chloroplasts/chemistry ; Cloning, Molecular ; Conserved Sequence ; DNA, Mitochondrial/analysis/*genetics ; Eukaryotic Cells/chemistry ; Molecular Sequence Data ; Open Reading Frames ; *Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; Sequence Alignment ; },
abstract = {An EcoRI fragment from the mitochondrial DNA of Acanthamoeba polyphaga was cloned and partly sequenced, and the conceptual translation product of the open reading frame (partial sequence) was found to have similarities with rp114, a ribosomal protein. Phylogenetic analysis based on the amino acid (aa) sequences of this conserved protein resolved four branches that consisted of: (1) eubacteria and the chloroplasts of algae and higher plants, (2) ciliate mitochondria, (3) Acanthamoeba, and (4) archaebacteria and the nuclei of eukaryotes. The groupings based on the rp114 aa sequences were consistent with the phylogenies derived by rRNA analysis of these organisms.},
}
@article {pmid8394320,
year = {1993},
author = {Graham, LA and Brandt, U and Sargent, JS and Trumpower, BL},
title = {Mutational analysis of assembly and function of the iron-sulfur protein of the cytochrome bc1 complex in Saccharomyces cerevisiae.},
journal = {Journal of bioenergetics and biomembranes},
volume = {25},
number = {3},
pages = {245-257},
pmid = {8394320},
issn = {0145-479X},
mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; Catalysis ; Electron Transport ; Electron Transport Complex III/genetics/*physiology ; Fungal Proteins/genetics/*metabolism ; Iron-Sulfur Proteins/genetics/*physiology ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; *Mutagenesis ; Oxidation-Reduction ; Phylogeny ; Plant Proteins/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/*enzymology/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Ubiquinone/analogs &amp; derivatives/metabolism ; },
abstract = {The iron-sulfur protein of the cytochrome bc1 complex oxidizes ubiquinol at center P in the protonmotive Q cycle mechanism, transferring one electron to cytochrome c1 and generating a low-potential ubisemiquinone anion which reduces the low-potential cytochrome b-566 heme group. In order to catalyze this divergent transfer of two reducing equivalents from ubiquinol, the iron-sulfur protein must be structurally integrated into the cytochrome bc1 complex in a manner which facilitates electron transfer from the iron-sulfur cluster to cytochrome c1 and generates a strongly reducing ubisemiquinone anion radical which is proximal to the b-566 heme group. This radical must also be sequestered from spurious reactivities with oxygen and other high-potential oxidants. Experimental approaches are described which are aimed at understanding how the iron-sulfur protein is inserted into center P, and how the iron-sulfur cluster is inserted into the apoprotein.},
}
@article {pmid8462546,
year = {1993},
author = {Miyata, A and Yoshida, T and Yamaguchi, K and Yokoyama, C and Tanabe, T and Toh, H and Mitsunaga, T and Izumi, Y},
title = {Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2.},
journal = {European journal of biochemistry},
volume = {212},
number = {3},
pages = {745-750},
doi = {10.1111/j.1432-1033.1993.tb17713.x},
pmid = {8462546},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology/genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular/methods ; DNA, Bacterial/genetics/isolation &amp; purification ; Escherichia coli/genetics ; *Genes, Bacterial ; Glycine Hydroxymethyltransferase/*genetics/isolation &amp; purification/*metabolism ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Phylogeny ; Rabbits ; Recombinant Proteins/isolation &amp; purification/metabolism ; Restriction Mapping ; Sequence Homology, Amino Acid ; },
abstract = {The gene encoding serine hydroxymethyltransferase (SHMT), one of the key enzymes of the one-carbon-compound assimilation of a methylotroph, Hyphomicrobium methylovorum GM2, and its flanking regions were isolated using a DNA fragment encoding Escherichia coli SHMT as a probe. Nucleotide sequencing of the recombinant plasmids revealed the SHMT gene codes for the 434-amino-acid protein with a calculated molecular mass of 46,068 Da. The amino-acid sequence of the enzyme showed identity to the sequences of the enzymes from E. coli (55%) and rabbit liver (44%). The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223-3, was introduced to an SHMT-deficient E. coli mutant ME5427 (glyA-). The transformed E. coli cells expressed SHMT, which was immunologically and enzymologically indistinguishable from the enzyme isolated from H. methylovorum GM2.},
}
@article {pmid8520584,
year = {1995},
author = {Gilson, P and Waller, R and McFadden, G},
title = {Preliminary characterisation of chlorarachniophyte mitochondrial DNA.},
journal = {The Journal of eukaryotic microbiology},
volume = {42},
number = {6},
pages = {696-701},
doi = {10.1111/j.1550-7408.1995.tb01618.x},
pmid = {8520584},
issn = {1066-5234},
mesh = {Animals ; Bacteria/classification/genetics ; Chloroplasts/metabolism ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; DNA, Protozoan/*genetics/isolation &amp; purification ; Eukaryota/classification/*genetics ; Fungi/classification/genetics ; Humans ; In Situ Hybridization ; Karyotyping ; Mitochondria/metabolism ; *Phylogeny ; Plants/classification/genetics ; Transcription, Genetic ; },
abstract = {The division Chlorarachniophyte comprises amoeboflagellate protists with complex chloroplasts derived from the endosymbiosis of a eukaryotic alga. Analysis of chlorarachniophyte chromosomal DNAs by pulsed-field gel electrophoresis revealed an apparently linear 36-kb chromosome that could not be ascribed to either the host or endosymbiont nuclei. A single eubacterial-like small subunit ribosomal RNA gene is encoded on this chromosome and phylogenetic analyses places this gene within a clade of mitochondrial genes from other eukaryotes. High resolution in situ hybridization demonstrates that transcripts of the small subunit ribosomal RNA gene encoded by the 36-kb chromosome are exclusively located in the mitochondria. The 36-kb chromosome thus likely represents a linear mitochondrial genome. Small amounts of an apparently dimeric (72 kb) form are also detectable in pulsed-field gel electrophoresis.},
}
@article {pmid8524824,
year = {1995},
author = {Hedges, SB and Simmons, MD and van Dijk, MA and Caspers, GJ and de Jong, WW and Sibley, CG},
title = {Phylogenetic relationships of the hoatzin, an enigmatic South American bird.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {92},
number = {25},
pages = {11662-11665},
pmid = {8524824},
issn = {0027-8424},
mesh = {Animals ; Base Sequence ; Birds/*classification/genetics ; Crystallins/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; South America ; },
abstract = {The hoatzin (Opisthocomus hoazin) lives in the humid lowlands of northern and central South America, often in riparian habitats. It is a slender bird approximately 65 cm in length, brownish with lighter streaks and buffy tips to the long tail feathers. The small head has a ragged, bristly crest of reddish-brown feathers, and the bare skin of the face is bright blue. It resembles a chachalaca (Ortalis, Cracidae) in size and shape, but its plumage and markings are similar to those of the smaller guira cuckoo (Guira guira). The hoatzin (pronounced Watson) has been a taxonomic puzzle since it was described in 1776. It usually has been viewed as related to the gallinaceous birds, but alliances to other groups have been suggested, including the cuckoos. We present DNA sequence evidence from the 12S and 16S rRNA mitochondrial genes, and from the nuclear gene that codes for the eye lens protein, alpha A-crystallin. The results indicate that the hoatzin is most closely related to the typical cuckoos and that the divergence occurred at or near the base of the cuculiform phylogenetic tree.},
}
@article {pmid8550293,
year = {1995},
author = {Gozar, MM and Bagnara, AS},
title = {An organelle-like small subunit ribosomal RNA gene from Babesia bovis: nucleotide sequence, secondary structure of the transcript and preliminary phylogenetic analysis.},
journal = {International journal for parasitology},
volume = {25},
number = {8},
pages = {929-938},
doi = {10.1016/0020-7519(95)00022-t},
pmid = {8550293},
issn = {0020-7519},
mesh = {Animals ; Babesia ; Babesia bovis/*genetics ; Bacteria/genetics ; Base Sequence ; Cyanobacteria/genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; *Genes, Protozoan ; Genome ; Mitochondria/physiology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Organelles/physiology ; *Phylogeny ; Piroplasmida ; Plasmodium falciparum/genetics ; Plastids/physiology ; Polymerase Chain Reaction ; RNA, Protozoan/chemistry/*genetics ; RNA, Ribosomal/chemistry/*genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; },
abstract = {Investigations aimed at identifying the mitochondrial genome of Babesia bovis using the polymerase chain reaction (PCR) have established the existence of an organelle-like small subunit ribosomal RNA (SSU rRNA) gene in the parasite. The sequence, compiled from three main PCR products, was 1448 bp in length (including the primer regions), had a 73% A+T content and showed significant similarity (68% sequence identity) to the "organellar" SSU rRNA gene from Plasmodium falciparum. The proposed secondary structure of the transcript showed several features which were consistent with a eubacterial origin for the organelle-like gene. The presence of putative binding sites for streptomycin and tetracycline also supported an "organellar" location for the gene and suggested that the SSU rRNA transcript is functional in protein synthesis because tetracycline has anti-babesial activity. Phylogenetic analyses based on the conserved regions of the SSU-like rRNA genes from a wide variety of organisms showed only a weak association of the babesial sequence with its mitochondrial homologues and an even weaker association with the corresponding genes of plastid origin. The origin of this organelle-like gene in B. bovis therefore remains unresolved, as is the case for its homologue from P. falciparum.},
}
@article {pmid8555450,
year = {1995},
author = {Kessler, U and Zetsche, K},
title = {Physical map and gene organization of the mitochondrial genome from the unicellular green alga Platymonas (Tetraselmis) subcordiformis (Prasinophyceae).},
journal = {Plant molecular biology},
volume = {29},
number = {5},
pages = {1081-1086},
pmid = {8555450},
issn = {0167-4412},
mesh = {Chlorophyta/*genetics ; Cloning, Molecular ; *DNA, Mitochondrial ; Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Restriction Mapping ; },
abstract = {The entire mitochondrial genome (mt genome) of the unicellular green alga Platymonas subcordiformis (synonym Tetraselmis subcordiformis; Prasinophyceae) was cloned and a physical map for the four restriction enzymes Hind III, Eco RI, Bg/II and Xba I was constructed. The mt genome of P. subcordiformis is a 42.8 kb circular molecule, coding for at least 23 genes. Hybridization and sequence analysis revealed the presence of a ca. 1.5 kb inverted repeat on the mt genome of P. subcordiformis. Phylogenetic analyses based on sequences of several coxI genes were carried out. Our data indicate that mitochondria from P. subcordiformis and from land plants form a natural, monophyletic group.},
}
@article {pmid8557473,
year = {1995},
author = {Tang, J and Toé, L and Back, C and Unnasch, TR},
title = {Mitochondrial alleles of Simulium damnosum sensu lato infected with Onchocerca volvulus.},
journal = {International journal for parasitology},
volume = {25},
number = {10},
pages = {1251-1254},
doi = {10.1016/0020-7519(95)00047-6},
pmid = {8557473},
issn = {0020-7519},
support = {AI 33008/AI/NIAID NIH HHS/United States ; },
mesh = {*Alleles ; Animals ; Base Sequence ; DNA, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; *Onchocerca volvulus/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Simuliidae/*genetics/parasitology ; },
abstract = {Onchocerca volvulus infected Simulium damnosum s.l. were analysed by directed heteroduplex analysis. Of 73 infected flies, 68 produced heteroduplex products identical to those previously identified. All 6 major sibling species, except S. leonense, were present in this group. In the 5 remaining flies, 2 new heteroduplex patterns were noted. Molecular phylogenetic analysis of these samples suggested that they belonged to the S. squamosum/S. yahense subcomplex. The ability to reliably genotype adult flies will permit studies of the vectorial capacity of the sibling species of S. damnosum s.l. for the blinding and non-blinding strains of O. volvulus.},
}
@article {pmid8581162,
year = {1996},
author = {Blair, A and Ngo, L and Park, J and Paulsen, IT and Saier, MH},
title = {Phylogenetic analyses of the homologous transmembrane channel-forming proteins of the F0F1-ATPases of bacteria, chloroplasts and mitochondria.},
journal = {Microbiology (Reading, England)},
volume = {142 (Pt 1)},
number = {},
pages = {17-32},
doi = {10.1099/13500872-142-1-17},
pmid = {8581162},
issn = {1350-0872},
support = {2RO1 AI 14176/AI/NIAID NIH HHS/United States ; 5RO1 AI 21702/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/*genetics ; Chloroplasts/classification/enzymology/*genetics ; Macromolecular Substances ; Mitochondria/classification/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Protein Conformation ; Proton-Translocating ATPases/classification/*genetics ; Sequence Alignment/methods ; Sequence Homology, Amino Acid ; },
abstract = {Sequences of the three integral membrane subunits (subunits a, b and c) of the F0 sector of the proton-translocating F-type (F0F1-) ATPases of bacteria, chloroplasts and mitochondria have been analysed. All homologous-sequenced proteins of these subunits, comprising three distinct families, have been identified by database searches, and the homologous protein sequences have been aligned and analysed for phylogenetic relatedness. The results serve to define the relationships of the members of each of these three families of proteins, to identify regions of relative conservation, and to define relative rates of evolutionary divergence. Of these three subunits, c-subunits exhibited the slowest rate of evolutionary divergence, b-subunits exhibited the most rapid rate of evolutionary divergence, and a-subunits exhibited an intermediate rate of evolutionary divergence. The results allow definition of the relative times of occurrence of specific events during evolutionary history, such as the intragenic duplication event that gave rise to large c-subunits in eukaryotic vacuolar-type ATPases after eukaryotes diverged from archaea, and the extragenic duplication of F-type ATPase b-subunits that occurred in blue-green bacteria before the advent of chloroplasts. The results generally show that the three F0 subunits evolved as a unit from a primordial set of genes without appreciable horizontal transmission of the encoding genetic information although a few possible exceptions were noted.},
}
@article {pmid8589847,
year = {1995},
author = {Howland, DE and Hewitt, GM},
title = {Phylogeny of the Coleoptera based on mitochondrial cytochrome oxidase I sequence data.},
journal = {Insect molecular biology},
volume = {4},
number = {3},
pages = {203-215},
doi = {10.1111/j.1365-2583.1995.tb00026.x},
pmid = {8589847},
issn = {0962-1075},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Coleoptera/*classification/enzymology/genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/classification/*genetics ; Genes, Insect ; Genetic Variation ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {A 400 base pair region of the mitochondrial cytochrome oxidase I gene (COI) was sequenced for thirty-seven species of beetle, representing fifteen families. The sequence was found to be highly variable, with 12-18% divergence within families, and up to 27% divergence between families. Phylogenetic analysis using the neighbour-joining method shows the Carabidae (Adephaga) as a distinct clade, but also shows that all other beetles (Polyphaga) diverged soon after the Adephaga/Polyphaga split. Whilst some species are grouped within their respective families, others are too diverged for easy resolution. The main disagreement with trees constructed using comparative morphology and the fossil record is the position of the Coccinellidae. Whilst COI may be an informative gene for molecular systematics at lower taxonomic levels, or in other insects, improved resolution of this particular phylogeny will require a more highly conserved sequence.},
}
@article {pmid8595866,
year = {1996},
author = {Markos, A and Morris, A and Rozario, C and Müller, M},
title = {Primary structure of a cytosolic malate dehydrogenase of the amitochondriate eukaryote, Trichomonas vaginalis.},
journal = {FEMS microbiology letters},
volume = {135},
number = {2-3},
pages = {259-264},
doi = {10.1111/j.1574-6968.1996.tb07998.x},
pmid = {8595866},
issn = {0378-1097},
support = {AI 11942/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytosol/*enzymology ; Genes, Protozoan/genetics ; Malate Dehydrogenase/*chemistry/genetics/isolation &amp; purification ; Molecular Sequence Data ; Peptide Fragments/chemistry ; Phylogeny ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/classification/*enzymology/genetics ; },
abstract = {The nucleotide sequence of a gene coding for a 37 kDa subunit of a cytosolic malate dehydrogenase of Trichomonas vaginalis was established. The sequence of a gDNA clone and a cDNA clone, which lacked seven amino-terminal codons, were identical, indicating an absence of introns from the gene. Cell fractionation combined with sequencing of peptide fragments of the purified enzyme showed that the gene codes for an expressed cytosolic enzyme. The derived amino acid sequence was closely related to cytosolic malate dehydrogenases from animals and plants and from the eubacteria Thermus aquaticus and Mycobacterium leprae and was more distant from the enzyme of mitochondria and from Escherichia coli and certain other eubacteria. In phylogenetic reconstructions this enzyme shared a most recent common ancestor with other cytosolic enzymes.},
}
@article {pmid8626323,
year = {1996},
author = {Imlay, KR and Imlay, JA},
title = {Cloning and analysis of sodC, encoding the copper-zinc superoxide dismutase of Escherichia coli.},
journal = {Journal of bacteriology},
volume = {178},
number = {9},
pages = {2564-2571},
pmid = {8626323},
issn = {0021-9193},
support = {GM49640/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Escherichia coli/*enzymology/genetics ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; RNA, Bacterial/biosynthesis ; RNA, Messenger/biosynthesis ; Restriction Mapping ; Sequence Alignment ; Sequence Analysis ; Sequence Analysis, DNA ; Superoxide Dismutase/chemistry/*genetics/metabolism ; },
abstract = {Benov and Fridovich recently reported the existence of a copper- and zinc-containing superoxide dismutase (CuZnSOD) in Escherichia coli (L. T. Benov and I. Fridovich, J. Biol. Chem. 269:25310-25314,1994). We have used the N-terminal protein sequence to isolate the gene encoding this enzyme. The gene, denoted sodC, is located at 37.1 min on the chromosome, adjacent to lhr and sodB. A monocistronic transcript of sodC accumulates only in stationary phase. The presence of a conventional leader sequence is consistent with physical data indicating that the E. coli enzyme, like other bacterial CuZnSODs, is secreted into the periplasm. Because superoxide cannot cross membranes, this localization indicates that the enzyme has evolved to defend periplasmic biomolecules against an extracytoplasmic superoxide source. Neither the source nor the target of the superoxide is known. Although once considered an exclusively eukaryotic enzyme, CuZnSOD has now been found in species that span three subdivisions of the purple bacteria. The bacterial CuZnSODs are more homologous to one another than to the eukaryotic enzymes, but active-site residues and structural motifs are clearly shared by both families of enzymes. The use of copper and an invariant disulfide bond suggest that the ancestral gene of present-day CuZnSODs evolved in an aerobic environment, long after the evolutionary split between the eukaryotes and the eubacteria. If so, a CuZnSOD gene must have been transferred laterally between members of these domains. The eukaryotic SODs most closely resemble that of Caulobacter crescentus, a relatively close descendant of the mitochondrial ancestor, suggesting that sodC may have entered the eukaryotes during the establishment of mitochondria.},
}
@article {pmid8626705,
year = {1996},
author = {Marty, L and Fort, P},
title = {A delayed-early response nuclear gene encoding MRPL12, the mitochondrial homologue to the bacterial translational regulator L7/L12 protein.},
journal = {The Journal of biological chemistry},
volume = {271},
number = {19},
pages = {11468-11476},
doi = {10.1074/jbc.271.19.11468},
pmid = {8626705},
issn = {0021-9258},
mesh = {3T3 Cells ; Amino Acid Sequence ; Animals ; Bacterial Proteins/metabolism ; Base Sequence ; *Cell Cycle Proteins ; Cell Division ; Cell Line ; Cell Nucleus ; Chlorocebus aethiops ; Chloroplasts/metabolism ; Cloning, Molecular ; Cricetinae ; DNA, Complementary ; Escherichia coli/metabolism ; Gene Expression ; Geobacillus stearothermophilus/metabolism ; Glutathione Transferase/biosynthesis ; HeLa Cells ; Humans ; Mice ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/*biosynthesis/*genetics/metabolism ; Oligodeoxyribonucleotides ; Phylogeny ; Protein Biosynthesis ; Recombinant Fusion Proteins/biosynthesis/metabolism ; Ribosomal Proteins/*biosynthesis/*genetics/*metabolism ; Ribosomes ; Sequence Homology, Amino Acid ; Spinacia oleracea ; },
abstract = {We have characterized a new delayed-early response mRNA encoding a 21-kDa product (MRPL12) that accumulates during the G1 phase of growth-stimulated cells. MRPL12 is the mammalian homologue to chloroplastic and bacterial L12 ribosomal proteins. Immunofluorescence microscopy and cell fractionation indicate a predominant mitochondrial localization in various mammalian cell lines. The NH2-terminal 49 amino acids are necessary and sufficient to target the protein within the mitochondria and are probably cleaved off during import. MRPL12 proteins associated in vitro and cofractionate with ribosomal structures, as is the case for prokaryotic L12 proteins. Expression of a dominant inhibitory truncated protein leads to a severe reduction in cell growth by inhibiting mitochondrial ATP production. MRPL12 is the first mammalian mitochondrial ribosomal protein to be characterized.},
}
@article {pmid8637872,
year = {1996},
author = {Burger, G and Lang, BF and Reith, M and Gray, MW},
title = {Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {6},
pages = {2328-2332},
pmid = {8637872},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry ; *DNA, Mitochondrial ; Electron Transport Complex II ; Eukaryota/*genetics ; Fungal Proteins/chemistry ; Genes ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Rhodophyta/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Succinate Dehydrogenase/*genetics ; },
abstract = {Although mitochondrial DNA is known to encode a limited number (<20) of the polypeptide components of respiratory complexes I, III, IV, and V, genes for components of complex II [succinate dehydrogenase (ubiquinone); succinate:ubiquinone oxidoreductase, EC 1.3.5.1] are conspicuously lacking in mitochondrial genomes so far characterized. Here we show that the same three subunits of complex II are encoded in the mitochondrial DNA of two phylogenetically distant eukaryotes, Porphyra purpurea (a photosynthetic red alga) and Reclinomonas americana (a heterotrophic zooflagellate). These complex II genes, sdh2, sdh3, and sdh4, are homologs, respectively, of Escherichia coli sdhB, sdhC, and sdhD. In E. coli, sdhB encodes the iron-sulfur subunit of succinate dehydrogenase (SDH), whereas sdhC and sdhD specify, respectively, apocytochrome b558 and a hydrophobic 13-kDa polypeptide, which together anchor SDH to the inner mitochondrial membrane. Amino acid sequence similarities indicate that sdh2, sdh3, and sdh4 were originally encoded in the protomitochondrial genome and have subsequently been transferred to the nuclear genome in most eukaryotes. The data presented here are consistent with the view that mitochondria constitute a monophyletic lineage.},
}
@article {pmid8660427,
year = {1996},
author = {Xia, X and Hafner, MS and Sudman, PD},
title = {On transition bias in mitochondrial genes of pocket gophers.},
journal = {Journal of molecular evolution},
volume = {43},
number = {1},
pages = {32-40},
pmid = {8660427},
issn = {0022-2844},
mesh = {Analysis of Variance ; Animals ; Base Sequence ; Consensus Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Mathematics ; Mitochondria/metabolism ; *Models, Genetic ; Mutation ; *Phylogeny ; Probability ; Rodentia/*genetics ; },
abstract = {The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (micros Ps)/(microv Pv), where micros and microv denote mutation rate of transitions and transversions, respectively, and Ps and Pv denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, Ps/Pv approximately 1 at fourfold degenerate sites, so that the s/v ratio at fourfold degenerate sites is approximately micros/microv, which is a measure of mutational contribution to transition bias. Similarly, the s/v ratio at nondegenerate sites is also an estimate of micros/microv if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) in pocket gophers, the s/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the micros/microv ratio is about 2, the Ps/Pv ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of protein-coding genes.},
}
@article {pmid8660972,
year = {1996},
author = {Lopez, JV and Cevario, S and O'Brien, SJ},
title = {Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome.},
journal = {Genomics},
volume = {33},
number = {2},
pages = {229-246},
doi = {10.1006/geno.1996.0188},
pmid = {8660972},
issn = {0888-7543},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cats/*genetics ; Cell Nucleus ; DNA Transposable Elements ; *DNA, Mitochondrial ; Genome ; Humans ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; },
abstract = {The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species.},
}
@article {pmid8662206,
year = {1996},
author = {Hayashi-Ishimaru, Y and Ohama, T and Kawatsu, Y and Nakamura, K and Osawa, S},
title = {UAG is a sense codon in several chlorophycean mitochondria.},
journal = {Current genetics},
volume = {30},
number = {1},
pages = {29-33},
doi = {10.1007/s002940050096},
pmid = {8662206},
issn = {0172-8083},
mesh = {Alanine/genetics ; Amino Acid Sequence ; Base Sequence ; Chlorophyta/classification/enzymology/*genetics ; Codon/*genetics ; DNA Primers/genetics ; Electron Transport Complex IV/chemistry/genetics ; Leucine/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3-8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined.},
}
@article {pmid8675018,
year = {1996},
author = {Couzin, N and Trézéguet, V and Le Saux, A and Lauquin, GJ},
title = {Cloning of the gene encoding the mitochondrial adenine nucleotide carrier of Schizosaccharomyces pombe by functional complementation in Saccharomyces cerevisiae.},
journal = {Gene},
volume = {171},
number = {1},
pages = {113-117},
doi = {10.1016/0378-1119(96)00095-9},
pmid = {8675018},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; Chromosomes, Fungal/genetics ; Cloning, Molecular/methods ; DNA, Complementary/genetics ; DNA, Fungal/analysis ; Fungal Proteins/*genetics ; Gene Dosage ; Genes, Fungal/*genetics ; Genetic Complementation Test ; Mitochondria ; *Mitochondrial ADP, ATP Translocases ; Molecular Sequence Data ; Nuclear Proteins/*genetics ; Phylogeny ; Restriction Mapping ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Schizosaccharomyces/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Transcription Factor TFIID ; },
abstract = {We describe the isolation and sequencing of both cDNA and genomic clones encoding the mitochondrial ADP/ATP carrier (Anc) of Schizosaccharomyces pombe (Sp). The cDNA clone was isolated from a cDNA library of this fission yeast by complementation of a Saccharomyces cerevisiae (Sc) strain defective in adenine nucleotide carrier. The predicted amino acid (aa) sequence (322 aa) shared similarity with the known Anc sequences. It is more closely related to Neurospora crassa (Nc) Anc than to ScAnc1, 2, or 3 or Kluyveromyces lactis (Kl) Anc. Hybridization experiments with ordered libraries of Sp genomic DNA led to the physical mapping (chromosome II, NotI-B region) and the isolation of the Sp ANC1 gene. We also conclude that a single-copy gene encodes the Sp Anc.},
}
@article {pmid8702755,
year = {1996},
author = {Eden, A and Simchen, G and Benvenisty, N},
title = {Two yeast homologs of ECA39, a target for c-Myc regulation, code for cytosolic and mitochondrial branched-chain amino acid aminotransferases.},
journal = {The Journal of biological chemistry},
volume = {271},
number = {34},
pages = {20242-20245},
doi = {10.1074/jbc.271.34.20242},
pmid = {8702755},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Cytoplasm/enzymology ; Fungal Proteins ; Gene Expression ; Genes, Fungal ; Humans ; Mice ; Mitochondria/enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; Proto-Oncogene Proteins c-myc/*physiology ; RNA, Messenger/genetics ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction ; Transaminases/*genetics ; },
abstract = {ECA39 was isolated as a target gene for c-Myc regulation in mice. We identified two homologs for the murine ECA39 in the yeast Saccharomyces cerevisiae, ECA39 and ECA40, as well as two human homologs. These genes show a significant homology to prokaryotic branched-chain amino acid aminotransferase (BCAT) (EC). To understand the function of eukaryotic ECA39 and ECA40, we deleted either gene from the yeast genome. Activity of branched-chain amino acid aminotransferase was measured in the wild-type and mutants with either leucine, isoleucine, or valine as substrates. The results demonstrate that in S. cerevisiae ECA39 and ECA40 code for mitochondrial and cytosolic branched-chain amino acid aminotransferases, respectively. ECA39 is highly expressed during log phase and is down-regulated during the stationary phase of growth, while ECA40 shows an inverse pattern of gene expression. In agreement with these results, while we previously showed that deletion of ECA39 affected the cell cycle in proliferating cells, we do not observe a growth phenotype in eca40Delta cells. We suggest that BCAT is a target for c-Myc activity and discuss the evolutionary conservation of prokaryotic and eukaryotic BCATs and their possible involvement in regulation of cell proliferation.},
}
@article {pmid8728387,
year = {1996},
author = {Pedersen, BV},
title = {A phylogenetic analysis of cuckoo bumblebees (Psithyrus, Lepeletier) and bumblebees (Bombus, Latreille) inferred from sequences of the mitochondrial gene cytochrome oxidase I.},
journal = {Molecular phylogenetics and evolution},
volume = {5},
number = {2},
pages = {289-297},
doi = {10.1006/mpev.1996.0024},
pmid = {8728387},
issn = {1055-7903},
mesh = {Animals ; Base Sequence ; Bees/classification/enzymology/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria, Muscle/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Point Mutation ; Polymerase Chain Reaction ; Probability ; Sequence Homology, Nucleic Acid ; },
abstract = {PCR amplification and direct sequencing of a 532-bp region of the mt CO-1 (cytochrome oxidase I) gene from five true bumblebee species and six cuckoo bumblebee species were performed. The sequences were then aligned to the corresponding sequence in the honey bee. Phylogenetic analyses based on parsimony and maximum likelihood indicate that the cuckoo bumblebees form a monophyletic group within the true bumblebees. The Bombus lucorum group (subgenus Bombus) falls out as the sister group to a clade comprising the cuckoo bumblebees and the remaining true bumblebees. A strong A + T bias (A + T = 75%) was recorded. Comparisons of all the sequences show a high-transversion bias (A<-->T) even among closely related species. The bias is most pronounced in third positions.},
}
@article {pmid8742633,
year = {1996},
author = {Pawlowski, J and Bolivar, I and Fahrni, JF and Cavalier-Smith, T and Gouy, M},
title = {Early origin of foraminifera suggested by SSU rRNA gene sequences.},
journal = {Molecular biology and evolution},
volume = {13},
number = {3},
pages = {445-450},
doi = {10.1093/oxfordjournals.molbev.a025605},
pmid = {8742633},
issn = {0737-4038},
mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Eukaryota/classification/*genetics ; Fossils ; Macromolecular Substances ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/genetics ; RNA, Ribosomal/*genetics ; },
abstract = {Foraminifera are one of the largest groups of unicellular eukaryotes with probably the best known fossil record. However, the origin of foraminifera and their phylogenetic relationships with other eukaryotes are not well established. In particular, two recent reports, based on ribosomal RNA gene sequences, have reached strikingly different conclusions about foraminifera's evolutionary position within eukaryotes. Here, we present the complete small subunit (SSU) rRNA gene sequences of three species of foraminifera. Phylogenetic analysis of these sequences indicates that they branch very deeply in the eukaryotic evolutionary tree: later than those of the amitochondrial Archezoa, but earlier than those of the Euglenozoa and other mitochondria-bearing phyla. Foraminifera are clearly among the earliest eukaryotes with mitochondria, but because of the peculiar nature of their SSU genes we cannot be certain that they diverged first, as our data suggest.},
}
@article {pmid8747299,
year = {1995},
author = {Emerson, BC and Wallis, GP},
title = {Phylogenetic relationships of the Prodontria (Coleoptera; Scarabaeidae; subfamily Melolonthinae), derived from sequence variation in the mitochondrial cytochrome oxidase II gene.},
journal = {Molecular phylogenetics and evolution},
volume = {4},
number = {4},
pages = {433-447},
doi = {10.1006/mpev.1995.1040},
pmid = {8747299},
issn = {1055-7903},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Coleoptera/classification/enzymology/*genetics ; DNA/genetics ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {The beetle genus Prodontria is of importance to New Zealand conservation programs. All Prodontria species are brachypterous (having reduced wings), and the genus presents some interesting evolutionary and biogeographic questions that are testable using phylogenetic reconstruction. A phylogeny was produced for 14 flightless Prodontria species, 2 macropterous (fully winged) Odontria species, and single representatives of 2 outgroup genera using sequence data from the mitochondrial COII gene. The data support probable conspecificity of the morphologically similar P. modesta and P. bicolorata but do not support their hypothesized sister-species relationship with the geographically proximate P. lewisi. The alpine P. capito is found to be a paraphyletic group, with the most eastern population diverging after the western populations made their appearance. Many interesting biogeographic disjunctions are here proposed to be anomalous and the result of morphological convergence. The data do not support the idea of a common flightless ancester for Prodontria, but suggest that brachyptery has evolved numerous times. In some instances, this appears to have led to contemporaneous speciation resulting in little resolution of phylogenetic relationships in some parts of the tree. These data allow for a new interpretation of the origin and diversification of the southern New Zealand flightless melolonthine fauna. Multiple speciation events involving wing reduction are suggested to involve at least one widespread flighted ancestor that has given rise to brachypterous forms.},
}
@article {pmid8748016,
year = {1995},
author = {Nee, S and Holmes, EC and Rambaut, A and Harvey, PH},
title = {Inferring population history from molecular phylogenies.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {349},
number = {1327},
pages = {25-31},
doi = {10.1098/rstb.1995.0087},
pmid = {8748016},
issn = {0962-8436},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {*Genetics, Population ; Genome, Viral ; Humans ; Mathematics ; Mitochondria/genetics ; Molecular Biology ; *Phylogeny ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.},
}
@article {pmid8765228,
year = {1996},
author = {Pawelek, PD and MacKenzie, RE},
title = {Methylenetetrahydrofolate dehydrogenase-cyclohydrolase from Photobacterium phosphoreum shares properties with a mammalian mitochondrial homologue.},
journal = {Biochimica et biophysica acta},
volume = {1296},
number = {1},
pages = {47-54},
doi = {10.1016/0167-4838(96)00052-0},
pmid = {8765228},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Enzyme Activation/drug effects ; Genetic Complementation Test ; Humans ; Kinetics ; Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry/*genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleotides/metabolism ; Phosphates/metabolism/pharmacology ; Photobacterium/*enzymology ; Phylogeny ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {The marine bioluminescent bacterium Photobacterium phosphoreum expresses a bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase with dual cofactor specificity. An investigation of the kinetic parameters of the P. phosphoreum enzyme indicate that its utilization of dinucleotide cofactors shares similarities with the human mitochondrial dehydrogenase-cyclohydrolase. Both enzymes exhibit dual cofactor specificity and the NAD(+)-dependent dehydrogenase activities from both enzymes can be activated by inorganic phosphate. Furthermore, an analysis of multiply aligned dehydrogenase-cyclohydrolase sequences from 11 species revealed that bacterial and mitochondrial enzymes are more closely related to each other than to the dehydrogenase-cyclohydrolase domains from eukaryotic trifunctional enzymes, and that the bacterial and mitochondrial enzymes share a common point of divergence. Since the NADP+ cofactor is kinetically favoured by a factor of 18 over NAD+, and is therefore likely to be the preferred in vivo cofactor, we propose that the P. phosphoreum enzyme and the human mitochondrial enzyme evolved from a common ancestral dehydrogenase-cyclohydrolase with dual cofactor specificity, but that cofactor preference in these two enzymes diverged in response to different metabolic requirements.},
}
@article {pmid8776869,
year = {1996},
author = {Parker, A and Kornfield, I},
title = {An improved amplification and sequencing strategy for phylogenetic studies using the mitochondrial large subunit rRNA gene.},
journal = {Genome},
volume = {39},
number = {4},
pages = {793-797},
doi = {10.1139/g96-099},
pmid = {8776869},
issn = {0831-2796},
mesh = {Animals ; Base Sequence ; Birds/genetics ; Conserved Sequence ; DNA Primers/*chemistry ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/genetics ; Fishes/genetics ; Genetic Variation ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nephropidae/genetics ; *Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {Numerous molecular systematic studies have employed variation in the mitochondrial large subunit (16s) rRNA gene to infer patterns of relationship among species and higher taxa. The primers most commonly employed in 16s rRNA amplification and sequencing bracket an approximately 600 bp portion of this gene. However, most of the informative variation occurs within a 200 bp subset of this segment. We describe a novel primer pair designed to amplify this variable region in a wide range of taxa, allowing broader application and considerable streamlining of data acquisition for studies using this gene.},
}
@article {pmid8812436,
year = {1996},
author = {Sampson, MJ and Lovell, RS and Davison, DB and Craigen, WJ},
title = {A novel mouse mitochondrial voltage-dependent anion channel gene localizes to chromosome 8.},
journal = {Genomics},
volume = {36},
number = {1},
pages = {192-196},
doi = {10.1006/geno.1996.0445},
pmid = {8812436},
issn = {0888-7543},
support = {1P30-HD27823/HD/NICHD NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping/*methods ; Cloning, Molecular ; Crosses, Genetic ; DNA, Complementary/genetics ; Ion Channels/*genetics ; Membrane Proteins/*genetics ; Mice ; Mice, Inbred C57BL ; *Mitochondria ; Molecular Sequence Data ; Muridae ; Organ Specificity ; Phylogeny ; *Porins ; RNA, Messenger/analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic/genetics ; Voltage-Dependent Anion Channels ; },
abstract = {Voltage-dependent anion channels (VDACs) are small pore-forming channels found in the outer membrane of mitochondria. VDACs translocate adenine nucleotides and are the binding sites for several cytosolic kinases important in intermediary metabolism. Recently two human VDAC cDNAs (HVDAC1 and HVDAC2) were isolated, and possible orthologues of these genes have been isolated from mouse, bovine, and rat tissues. We report the isolation of a novel third VDAC cDNA from the mouse, designated MVDAC3. The deduced MVDAC3 protein is approximately 70% identical to the previously isolated MVDAC1 and MVDAC2 proteins. The MVDAC3 gene was mapped by an interspecies backcross panel to mouse chromosome 8. A database search using the mouse VDACs identified a second yeast VDAC-like gene that retains about 20% amino acid sequence identity with the mouse VDAC genes and 50% identity with the previously isolated yeast VDAC gene. The phylogenetic relationship of the eukaryotic VDAC genes is presented.},
}
@article {pmid8813670,
year = {1996},
author = {Nakamura, Y and Hashimoto, T and Yoshikawa, H and Kamaishi, T and Nakamura, F and Okamoto, K and Hasegawa, M},
title = {Phylogenetic position of Blastocystis hominis that contains cytochrome-free mitochondria, inferred from the protein phylogeny of elongation factor 1 alpha.},
journal = {Molecular and biochemical parasitology},
volume = {77},
number = {2},
pages = {241-245},
doi = {10.1016/0166-6851(96)02600-x},
pmid = {8813670},
issn = {0166-6851},
mesh = {Animals ; Base Composition ; Blastocystis hominis/*classification/*genetics ; Cytochromes ; Mitochondria ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; RNA, Messenger/genetics ; RNA, Protozoan/genetics ; },
}
@article {pmid8824418,
year = {1995},
author = {Craig, E and Ziegelhoffer, T and Nelson, J and Laloraya, S and Halladay, J},
title = {Complex multigene family of functionally distinct Hsp70s of yeast.},
journal = {Cold Spring Harbor symposia on quantitative biology},
volume = {60},
number = {},
pages = {441-449},
doi = {10.1101/sqb.1995.060.01.049},
pmid = {8824418},
issn = {0091-7451},
support = {2 RO1 GM-278760/GM/NIGMS NIH HHS/United States ; 5 RO1 GM-31107/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Transport, Active ; *Calcium-Transporting ATPases ; Carrier Proteins/metabolism ; Fungal Proteins/metabolism ; *Genes, Fungal ; HSP70 Heat-Shock Proteins/*genetics/*metabolism ; *Heat-Shock Proteins ; *Membrane Transport Proteins ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Molecular Chaperones/metabolism ; *Multigene Family ; Phylogeny ; Saccharomyces cerevisiae/*genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; },
}
@article {pmid8876236,
year = {1996},
author = {Ragan, MA and Goggin, CL and Cawthorn, RJ and Cerenius, L and Jamieson, AV and Plourde, SM and Rand, TG and Söderhäll, K and Gutell, RR},
title = {A novel clade of protistan parasites near the animal-fungal divergence.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {21},
pages = {11907-11912},
pmid = {8876236},
issn = {0027-8424},
support = {GM 48207/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Conserved Sequence ; Crustacea/parasitology ; Eukaryota/*classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics ; *Genes, Protozoan ; Gills/parasitology ; Microscopy, Electron ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/chemistry/genetics ; Salmon/parasitology ; Trout/parasitology ; },
abstract = {Sequences of nuclear-encoded small-subunit rRNA genes have been determined for representatives of the enigmatic genera Dermocystidium, Ichthyophonus, and Psorospermium, protistan parasites of fish and crustaceans. The small-subunit rRNA genes from these parasites and from the "rosette agent" (also a parasite of fish) together form a novel, statistically supported clade. Phylogenetic analyses demonstrate this clade to diverge near the animal-fungal dichotomy, although more precise resolution is problematic. In the most parsimonious and maximally likely phylogenetic frameworks inferred from the most stably aligned sequence regions, the clade constitutes the most basal branch of the metazoa; but within a limited range of model parameters, and in some analyses that incorporate less well-aligned sequence regions, an alternative topology in which it diverges immediately before the animal-fungal dichotomy was recovered. Mitochondrial cristae of Dermocystidium spp. are flat, whereas those of Ichthyophonus hoferi appear tubulovesiculate. These results extend our understanding of the types of organisms from which metazoa and fungi may have evolved.},
}
@article {pmid8876257,
year = {1996},
author = {Eriksson, M and Karlsson, J and Ramazanov, Z and Gardeström, P and Samuelsson, G},
title = {Discovery of an algal mitochondrial carbonic anhydrase: molecular cloning and characterization of a low-CO2-induced polypeptide in Chlamydomonas reinhardtii.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {21},
pages = {12031-12034},
pmid = {8876257},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carbon Dioxide ; Carbonic Anhydrases/*biosynthesis/*chemistry ; Chlamydomonas reinhardtii/classification/*enzymology ; Cyanobacteria/classification/enzymology ; Enzyme Induction ; Escherichia coli/classification/enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Plants/classification/*enzymology ; Sequence Homology, Amino Acid ; },
abstract = {In green unicellular algae, several polypeptides are induced upon exposure to limiting CO2. We report here on the localization and characterization of one of these, a 22-kDa polypeptide in Chlamydomonas reinhardtii. This nuclear-encoded polypeptide is induced in the mitochondria by a lowering of the partial pressure of CO2 in the growth medium from 5% to air CO2 levels. Sequencing of two different cDNA clones coding for the polypeptide identified it as a 20.7-kDa beta-type carbonic anhydrase (CA; carbonate dehydratase, carbonate hydro-lyase, EC 4.2.1.1). The two clones differ in their nucleotide sequences but code for identical proteins, showing that this CA is encoded by at least two genes. Northern blot hybridization reveals that mRNA transcripts are only present in cells transferred to air CO2 levels. A comparison of the deduced amino acid sequence with those of other beta-CAs shows the largest degree of similarity with CA from the cyanobacterium Synechocystis (50% identity and 66% similarity). To our knowledge, this is the first identification and characterization of a mitochondrial CA from a photosynthetic organism.},
}
@article {pmid8881281,
year = {1996},
author = {Garcia-Machado, E and Dennebouy, N and Suarez, MO and Mounolou, JC and Monnerot, M},
title = {Partial sequence of the shrimp Penaeus notialis mitochondrial genome.},
journal = {Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie},
volume = {319},
number = {6},
pages = {473-486},
pmid = {8881281},
issn = {0764-4469},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*chemistry ; Drosophila/genetics ; Genetic Code ; *Genome ; Mitochondria/genetics ; Molecular Sequence Data ; Penaeidae/*genetics ; Phylogeny ; RNA, Transfer/chemistry/ultrastructure ; *Sequence Homology, Nucleic Acid ; },
abstract = {About half of the mitochondrial DNA of the shrimp Penaeus notialis (Crustacea: Decapoda) has been cloned (in 2 overlapping fragments of 7.9 kb and 1 kb) and partially sequenced. The gene content and arrangement are identical to that of the homologous domain in Drosophila yakuba. Intergenic nucleotides are scarce and a 982 bp non-coding sequence exhibit features similar to that of mtDNA control regions. The gene organization and the tRNA structures differentiate the Penaeus notialis mitochondrial genome from that of Artemia franciscana. Paraphyletism of crustacean mtDNA with respect to Insecta is discussed. A secondary structure of s-rRNA is proposed.},
}
@article {pmid8896379,
year = {1996},
author = {Jenkins, TM and Basten, CJ and Anderson, WW},
title = {Mitochondrial gene divergence of Colombian Drosophila pseudoobscura.},
journal = {Molecular biology and evolution},
volume = {13},
number = {9},
pages = {1266-1275},
doi = {10.1093/oxfordjournals.molbev.a025692},
pmid = {8896379},
issn = {0737-4038},
mesh = {Animals ; Colombia ; *DNA, Mitochondrial ; Drosophila/*genetics ; Genes, Insect ; *Genetic Variation ; Genetics, Population ; Mexico ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; RNA, Ribosomal ; Sequence Homology, Nucleic Acid ; },
abstract = {Isolated populations of drosophila pseudoobscura, separated from North American populations by about 2,400 km, were found in Colombia in 1960. We compared for sequences of the small ribosomal RNA (srRNA) gene on the mitochondria between North American and Colombian D. pseudoobscura in order to clarify the age of the Colombian isolates. The North American populations were not genetically different from each other but were genetically different from the Colombian populations. The Mexican strains represent the area from which the Colombian founders might have come. The estimated net nucleotide divergence between Mexican and Colombian D. pseudoobscura indicates that the Colombian population is not an ancient lineage. Phylogenies using both distance and parsimony methodologies reinforced this conclusion. The Colombian samples group together with both methods but, according to the bootstrap analysis, not significantly. It appears that the populations have not been separated long enough for their DNA sequences to show much divergence.},
}
@article {pmid8920004,
year = {1996},
author = {Kohl, L and Drmota, T and Thi, CD and Callens, M and Van Beeumen, J and Opperdoes, FR and Michels, PA},
title = {Cloning and characterization of the NAD-linked glycerol-3-phosphate dehydrogenases of Trypanosoma brucei brucei and Leishmania mexicana mexicana and expression of the trypanosome enzyme in Escherichia coli.},
journal = {Molecular and biochemical parasitology},
volume = {76},
number = {1-2},
pages = {159-173},
doi = {10.1016/0166-6851(95)02556-1},
pmid = {8920004},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Gene Expression ; Glycerol-3-Phosphate Dehydrogenase (NAD+) ; Glycerolphosphate Dehydrogenase/*chemistry/genetics ; Leishmania mexicana/*enzymology/genetics ; Molecular Sequence Data ; NAD/metabolism ; Phylogeny ; Sequence Homology ; Trypanosoma brucei brucei/*enzymology/genetics ; },
abstract = {A polyclonal antiserum raised against the purified glycosomal glycerol-3-phosphate dehydrogenase of Trypanosoma brucei brucei has been used to identify the corresponding cDNA clone in a T.b. brucei expression library. This cDNA was subsequently used to obtain genomic clones containing glycerol-3-phosphate dehydrogenase genes. Two tandemly arranged genes were detected in these clones. Characterization of one of the genes showed that it codes for a polypeptide of 353 amino acids, with a molecular mass of 37,651 Da and a calculated net charge of +8. Using the T.b. brucei gene as a probe, a corresponding glycerol-3-phosphate dehydrogenase gene was also identified in a genomic library of Leishmania mexicana mexicana. The L.m. mexicana gene codes for a polypeptide of 365 amino acids, with a molecular mass of 39,140 Da and a calculated net charge of +8. The amino-acid sequences of both polypeptides are 63% identical and carry a type-1 peroxisomal targeting signal (PTS1) SKM and -SKL at their respective C-termini. Moreover, the L.m. mexicana polypeptide also carries a short N-terminal extension reminiscent of a mitochondrial transit sequence. Subcellular localisation analysis showed that in L.m. mexicana the glycerol-3-phosphate dehydrogenase activity co-fractionated both with mitochondria and with glycosomes. This is not the case in T. brucei, where the enzyme is predominantly glycosomal. The two trypanosomatid sequences resemble their prokaryotic homologues (32-36%) more than their eukaryotic counterparts (25-31%) and carry typical prokaryotic signatures. The possible reason for this prokaryotic nature of a trypanosomatid glycerol-3-phosphate dehydrogenase is discussed.},
}
@article {pmid8940916,
year = {1996},
author = {Suzuki, T and Yuasa, H and Machida, Y},
title = {Phylogenetic position of the Japanese river otter Lutra nippon inferred from the nucleotide sequence of 224 bp of the mitochondrial cytochrome b gene.},
journal = {Zoological science},
volume = {13},
number = {4},
pages = {621-626},
doi = {10.2108/zsj.13.621},
pmid = {8940916},
issn = {0289-0003},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA ; Fossils ; Mitochondria/*enzymology ; Molecular Sequence Data ; Otters/*classification/genetics ; *Phylogeny ; Polymerase Chain Reaction ; },
abstract = {A 224 bp fragment of the mitochondrial cytochrome b gene has been amplified from a 30-year-old mummy-like specimen of the Japanese river otter Lutra nippon by polymerase chain reaction (PCR). The amplified products were subcloned in the Smal site of pUC 18 and sequenced. The sequence was different from those of the congeneric Eurasian otters Lutra lutra (Latvia) and Lutra lutra (China) in 7-9 nucleotides, all of which were located at the third position of a codon and identified as transitional differences A<-->G or C<-->T. The phylogenetic analysis using the 224 bp sequences of Lutra nippon, Lutra lutra (Lativa), Lutra lutra (China), Aonyx cinerea (Asian small-clawed otter), Mustela sibirica and Mustela itatsi (weasels) supports the recent morphological study that the Japanese river otter is not a subspecies of Lutra lutra, but a distinct species, Lutra nippon. We found that Lutra nippon and Lutra lutra contain the cytochrome b-like sequences, that appear to be a pseudo-form of cytochrome b gene. The sequences are characterized by the presence of deletion and termination codons by the presence of several types of sequences with minor variations, and by the faster evolutionary rate compared with that of the mitochondrial cytochrome b gene. The genes would present in the nuclear DNA rather than in the mitochondrial DNA, as in the case of the nonfunctional cytochrome b-like sequences previously reported in a rodent.},
}
@article {pmid8962101,
year = {1996},
author = {Germot, A and Philippe, H and Le Guyader, H},
title = {Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
number = {25},
pages = {14614-14617},
pmid = {8962101},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Animals ; DNA, Mitochondrial/*genetics ; HSP70 Heat-Shock Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis ; Trichomonas vaginalis/*genetics ; },
abstract = {Molecular phylogenetic analyses, based mainly on ribosomal RNA, show that three amitochondriate protist lineages, diplomonads, microsporidia, and trichomonads, emerge consistently at the base of the eukaryotic tree before groups having mitochondria. This suggests that these groups could have diverged before the mitochondrial endosymbiosis. Nevertheless, since all these organisms live in anaerobic environments, the absence of mitochondria might be due to secondary loss, as demonstrated for the later emerging eukaryote Entamoeba histolytica. We have now isolated from Trichomonas vaginalis a gene encoding a chaperone protein (HSP70) that in other lineages is addressed to the mitochondrial compartment. The phylogenetic reconstruction unambiguously located this HSP70 within a large set of mitochondrial sequences, itself a sister-group of alpha-purple bacteria. In addition, the T. vaginalis protein exhibits the GDAWV sequence signature, so far exclusively found in mitochondrial HSP70 and in proteobacterial dnaK. Thus mitochondrial endosymbiosis could have occurred earlier than previously assumed. The trichomonad double membrane-bounded organelles, the hydrogenosomes, could have evolved from mitochondria.},
}
@article {pmid8979399,
year = {1996},
author = {La Cognata, U and Landschütze, V and Willmitzer, L and Müller-Röber, B},
title = {Structure and expression of mitochondrial citrate synthases from higher plants.},
journal = {Plant &amp; cell physiology},
volume = {37},
number = {7},
pages = {1022-1029},
doi = {10.1093/oxfordjournals.pcp.a029033},
pmid = {8979399},
issn = {0032-0781},
mesh = {Amino Acid Sequence ; Citrate (si)-Synthase/chemistry/*genetics ; Cloning, Molecular ; Crystallography, X-Ray ; DNA, Complementary ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Plants/classification/*enzymology ; Protein Conformation ; Sequence Homology, Amino Acid ; },
abstract = {Mitochondrial citrate synthase (EC 4.1.3.7) represents the first enzyme of the tricarboxylic acid cycle, catalyzing the condensation of acetyl-CoA and oxaloacetate, finally yielding citrate and CoA. We report here the isolation of cDNA clones encoding citrate synthase from Nicotiana tabacum, Beta vulgaris and Populus. Nucleotide and deduced amino acid sequences were compared with previously published sequences of mitochondrial citrate synthases from Arabidopsis thaliana and potato, as well as with the sequence of glyoxysomal citrate synthase from pumpkin. Homologies between the various plant mitochondrial enzymes were in the range from 77.2% (potato vs. Arabidopsis) to 94.2% (potato vs. tobacco) on the nucleotide level (coding regions only), and in the range from 70.1% to 90.4% (potato vs. Arabidopsis, and potato vs. tobacco, respectively) on the amino acid level. Identities of the mitochondrial isozymes to the pumpkin glyoxysomal enzyme were below 30% on the nucleotide and amino acid level. In Northern blot experiments citrate synthase mRNA was detected in all tissues analyzed. However, levels of expression showed tissue dependency despite the fact that citrate synthase is usually considered a house-keeping enzyme. Whether these different levels of expression reflect tissue-specific variations with respect to basic metabolism awaits further analysis.},
}
@article {pmid9000384,
year = {1997},
author = {Ogawa, S and Matsuo, K and Angata, K and Yanagisawa, K and Tanaka, Y},
title = {Group-I introns in the cytochrome c oxidase genes of Dictyostelium discoideum: two related ORFs in one loop of a group-I intron, a cox1/2 hybrid gene and an unusually large cox3 gene.},
journal = {Current genetics},
volume = {31},
number = {1},
pages = {80-88},
doi = {10.1007/s002940050179},
pmid = {9000384},
issn = {0172-8083},
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/*genetics ; Dictyostelium/*genetics ; Electron Transport Complex IV/*genetics ; Endonucleases/genetics ; Endoribonucleases/genetics ; *Introns ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Molecular Structure ; Nucleotidyltransferases/genetics ; *Open Reading Frames ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Viral Proteins/*genetics ; },
abstract = {The DNA sequences of cytochrome oxidase (subunits 1, 2 and 3) genes of the cellular slime mold Dictyostelium discoideum mitochondria were determined. The genes for subunits 1 and 2 have a single continuous ORF (COX1/2) which contains four group-I introns. The insertion sites of the two group-I introns (DdOX1/2.2 and DdOX1/2.3) coincide with those of fungal and algal group-I introns, as well as a liverwort group-I intron, in the cytochrome oxidase subunit 1. Interestingly, intron DdOX1/2.2 has two free-standing ORFs in a loop (L8) which have similar amino-acid sequences and are homologous to ai4 DNA endonuclease (I-Sce II) and bi4 RNA maturase found in group-I introns of Saccharomyces cerevisiae mitochondrial DNA. Two group-I introns (DdOX1/2.3 and DdOX1/2.4) also have a free-standing ORF in loop 1 and loop 2, respectively. These results show that these group-I introns and the intronic ORFs have evolved from the same ancestral origin, but that these ORFs have been propagated independently.},
}
@article {pmid9004216,
year = {1997},
author = {van der Giezen, M and Rechinger, KB and Svendsen, I and Durand, R and Hirt, RP and Fèvre, M and Embley, TM and Prins, RA},
title = {A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria.},
journal = {Molecular microbiology},
volume = {23},
number = {1},
pages = {11-21},
doi = {10.1046/j.1365-2958.1997.1891553.x},
pmid = {9004216},
issn = {0950-382X},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Base Sequence ; DNA, Complementary ; DNA, Fungal ; Fungi/*enzymology/genetics ; Gene Library ; Humans ; Malate Dehydrogenase/classification/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Signal Transduction ; },
abstract = {The hydrogenosomal malic enzyme (ME) was purified from the anaerobic fungus Neocallimastix frontalis. Using reverse genetics, the corresponding cDNA was isolated and characterized. The deduced amino acid sequence of the ME showed high similarity to ME from metazoa, plants and protists. Putative functional domains for malate and NAD+/NADP+ binding were identified. Phylogenetic analysis of the deduced amino acid sequence of the new ME suggests that it is homologous to reference bacterial and eukaryotic ME. Most interestingly, the cDNA codes for a protein which contains a 27-amino-acid N-terminus which is not present on the purified mature protein. This presequence shares features with known mitochondrial targeting signals, including an enrichment in Ala, Leu, Ser, and Arg, and the presence of an Arg at position-2 relative to amino acid 1 of the mature protein. This is the first report of a mitochondrial-like targeting signal on a hydrogenosomal enzyme from an anaerobic fungus and provides support for the hypothesis that hydrogenosomes in Neocallimastix frontalis might be modified mitochondria.},
}
@article {pmid9019132,
year = {1996},
author = {Margulis, L and Olendzenski, L and Dolan, M and MacIntyre, F and , },
title = {Diversity of eukaryotic microorganisms: computer-based resources, "The Handbook of Protoctista" and its "Glossary".},
journal = {Microbiologia (Madrid, Spain)},
volume = {12},
number = {1},
pages = {29-42},
pmid = {9019132},
issn = {0213-4101},
mesh = {Animals ; Archaea/classification ; *CD-ROM ; *Classification ; Dictionaries as Topic ; Eukaryota/classification/ultrastructure ; *Eukaryotic Cells/ultrastructure ; *Phylogeny ; *Reference Books ; },
abstract = {The kingdom Protoctista comprises some 30 phyla, including the eukaryotic anaerobes that permanently lack mitochondria, the Phylum Archaeprotista, with its three classes: (i) Archamoebae, e.g., Pelomyxa, Mastigina, (ii) Metamonada, e.g., Giardia, Pyrsonympha, and (iii) Parabasalia, e.g., Trichomonas, Calonympha, and the Phylum Microspora (Microsporidia), e.g., Vairimorpha. These and all algae, protozoa, labyrinthulids, "water molds" (oomycota, plasmodiophorans, hyphochytrids, chytrids, etc.) and other eukaryotes excluded from plants, animals and fungi are detailed in the Handbook of Protoctista. The Illustrated Glossary of Protoctista contains descriptions of the morphology and taxonomy of these microorganisms, including the many equivalent and homologous structures with different names. The Glossary has also been made into a Macintosh-compatible CD-ROM disk.},
}
@article {pmid9022265,
year = {1996},
author = {Salomone, N and Frati, F and Bernini, F},
title = {Investigation on the taxonomic status of Steganacarus magnus and Steganacarus anomalus (Acari:Oribatida) using mitochondrial DNA sequences.},
journal = {Experimental &amp; applied acarology},
volume = {20},
number = {11},
pages = {607-615},
pmid = {9022265},
issn = {0168-8162},
mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; DNA, Complementary ; *DNA, Mitochondrial ; Electron Transport Complex IV/classification/*genetics ; Mites/classification/*enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {To test the previously suggested synonymization of S. anomalus with the older S. magnus, a fragment of the mitochondrial COI gene was amplified via the polymerase chain reaction and sequenced. The sequence variation was examined in a total of 327 base pairs for four steganacarid mite populations, two of which belong to S. anomalus, one to S. magnus and one to S. hirsutus. The sequence variation suggests that S. magnus and S. anomalus are not distinct species and that the population from Fioreta (Siena) is more similar to that from Apulia than to the nearer population from the Apuan Alps. The results show the usefulness of this molecular approach as a tool for determining taxonomic status and for suggesting faunistic movements in the past millions of years.},
}
@article {pmid9034326,
year = {1997},
author = {Lecrenier, N and Van Der Bruggen, P and Foury, F},
title = {Mitochondrial DNA polymerases from yeast to man: a new family of polymerases.},
journal = {Gene},
volume = {185},
number = {1},
pages = {147-152},
doi = {10.1016/s0378-1119(96)00663-4},
pmid = {9034326},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA-Directed DNA Polymerase/classification/*genetics ; Drosophila melanogaster ; Exonucleases/genetics ; Gene Library ; Humans ; Melanoma/*genetics ; Mice ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Pichia ; Repetitive Sequences, Nucleic Acid ; Saccharomyces cerevisiae ; Schizosaccharomyces ; Sequence Alignment ; Sequence Homology, Amino Acid ; Xenopus laevis ; },
abstract = {We report the sequence of a 4.5-kb cDNA clone isolated from a human melanoma library which bears high amino acid sequence identity to the yeast mitochondrial (mt) DNA polymerase (Mip1p). This cDNA contains a 3720-bp open reading frame encoding a predicted 140-kDa polypeptide that is 43% identical to Mip1p. The N-terminal part of the sequence contains a 13 glutamine stretch encoded by a CAG trinucleotide repeat which is not found in the other DNA polymerases gamma (Pol gamma). Multiple amino acid sequence alignments with Pol gamma from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Drosophila melanogaster, Xenopus laevis and Mus musculus show that these DNA polymerases form a family strongly conserved from yeast to man and are only loosely related to the Family A DNA polymerases.},
}
@article {pmid9037043,
year = {1997},
author = {Janke, A and Xu, X and Arnason, U},
title = {The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {94},
number = {4},
pages = {1276-1281},
pmid = {9037043},
issn = {0027-8424},
mesh = {Animals ; Anticodon/genetics ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; Gene Rearrangement ; Genome ; Likelihood Functions ; Mammals/classification/*genetics ; Marsupialia/classification/*genetics ; Mitochondria/*genetics ; Models, Biological ; Molecular Sequence Data ; Monotremata/classification/genetics ; *Phylogeny ; RNA Editing ; RNA, Transfer, Asp/genetics ; RNA, Transfer, Lys/genetics ; RNA, Transfer, Ser/genetics ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {The complete mitochondrial DNA (mtDNA) (16,896 nt) of the wallaroo (Macropus robustus) was sequenced. The concatenated amino acid sequences of 12 mitochondrial protein-coding genes of the wallaroo plus those of a number of other mammals were included in a phylogenetic study of early mammalian divergences. The analysis joined monotremes and marsupials (the Marsupionta hypothesis) to the exclusion of eutherians. The analysis rejected significantly the commonly acknowledged Theria hypothesis, according to which Marsupialia and Eutheria are grouped together to the exclusion of Monotremata. The region harboring the gene for lysine tRNA (tRNA-Lys) in the mtDNA of other vertebrates is in the wallaroo occupied by a sequence (tRNA-Lys) that lacks both an anticodon loop as well as the anticodon for the amino acid lysine. An alternative tRNA-Lys gene was not identified in any other region of the mtDNA of the wallaroo, suggesting that a tRNA-Lys of nuclear origin is imported into marsupial mitochondria. Previously described RNA editing of tRNA-Asp and rearrangement of some tRNA genes were reconfirmed in the mtDNA of the wallaroo. The divergence between Monotremata/Marsupialia and Eutheria was timed to approximately 130 million years before present (MYBP). The same calculations suggested that Monotremata and Marsupialia diverged approximately 115 MYBP and that Australian and American marsupials separated approximately 75 MYBP. The findings also show that many, probably most, extant eutherian orders had their origin in middle to late Cretaceous times, 115-65 MYBP.},
}
@article {pmid9060394,
year = {1997},
author = {Foster, PG and Jermiin, LS and Hickey, DA},
title = {Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria.},
journal = {Journal of molecular evolution},
volume = {44},
number = {3},
pages = {282-288},
doi = {10.1007/pl00006145},
pmid = {9060394},
issn = {0022-2844},
mesh = {Amino Acids/*analysis ; Animals ; Bees ; Chickens ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine) and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes. This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content.},
}
@article {pmid9060401,
year = {1997},
author = {Yasuhira, S and Simpson, L},
title = {Phylogenetic affinity of mitochondria of Euglena gracilis and kinetoplastids using cytochrome oxidase I and hsp60.},
journal = {Journal of molecular evolution},
volume = {44},
number = {3},
pages = {341-347},
doi = {10.1007/pl00006152},
pmid = {9060401},
issn = {0022-2844},
mesh = {Animals ; Chaperonin 60/*genetics ; Cloning, Molecular ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Euglena gracilis/*genetics ; Kinetoplastida/*genetics ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI cDNAs from E. gracilis possess short 5' and 3' untranslated transcribed sequences and lack a 3' poly[A] tail. The COI gene does not require uridine insertion/ deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional, and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [alpha-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3' end structures of mRNAs, phylogenetic analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using nuclear ribosomal RNA sequences.},
}
@article {pmid9061940,
year = {1997},
author = {Bessho, Y and Tamura, S and Hori, H and Tanaka, H and Ohama, T and Osawa, S},
title = {Planarian mitochondria sequence heterogeneity: relationships between the type of cytochrome c oxidase subunit I gene sequence, karyotype and genital organ.},
journal = {Molecular ecology},
volume = {6},
number = {2},
pages = {129-136},
doi = {10.1046/j.1365-294x.1997.00162.x},
pmid = {9061940},
issn = {0962-1083},
mesh = {Animals ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genes, Helminth/genetics ; Genetic Variation/*genetics ; Genitalia ; Japan ; Karyotyping ; Molecular Sequence Data ; Phylogeny ; Planarians/*genetics/physiology ; Sequence Analysis, DNA ; Taiwan ; },
abstract = {Freshwater planarians Dugesia japonica from three localities were examined for cytochrome c oxidase subunit I (COI) gene sequence, karyotype and the presence of genital organ. The planarians from Mt Fujiwara in Japan were composed of two different groups; one revealed inter- and intraindividual COI gene heterogeneity, while another revealed no sequence heterogeneity. The sequence in planarians from Mt Alishan in Taiwan was homogeneous, while that from the Kenting National Park in Taiwan revealed a considerable heterogeneity. All the planarians having the homogeneous gene sequences carry the 2X karyotype and many of them had genital organs. These are assumed to belong to the sexual lineage. In contrast, almost all planarians having heterogeneous sequences carry the karyotype of either 3X plus 2X (mixoploid) or 3X, and all of them lack genital organs. These lineages are assumed to be asexual. The heterogeneity of COI gene sequences in the presumed asexual lineages would have resulted from an accumulation of mutations by repeated asexual reproduction.},
}
@article {pmid9099578,
year = {1997},
author = {Zhang, DX and Hewitt, GM},
title = {Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects.},
journal = {Insect molecular biology},
volume = {6},
number = {2},
pages = {143-150},
doi = {10.1111/j.1365-2583.1997.tb00082.x},
pmid = {9099578},
issn = {0962-1075},
mesh = {*Conserved Sequence ; DNA Primers ; *DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Insect Proteins/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {A set of mitochondrial COI primers has been studied by genomic PCR and many primer combinations shown to work universally well across Insecta. They are able to amplify various amplicons with different variability which enables the selection of a particular amplicon as a suitable DNA marker for a project. The potential usefulness of different amplicons is examined, with analysis on published study cases employing these regions. With respect to their variability, amplicons UEA5/UEA6, UEA7/UEA8 and UEA5/UEA8 could be useful for low- to mid-level phylogenetic analysis, i.e. from species, genus to perhaps family level depending on taxa involved. UEA5/UEA6 will be too conserved for intraspecific studies. Amplicons UEA3/UEA4 and UEA9/UEA10 would be better suited to low-level phylogenetic investigations, such a analysis of relationships among closely related species and population genetic studies. However, these guidelines should not be over-generalized for the reasons given. Amplification conditions of various primer combinations, and general problems in the use of conserved PCR primers are discussed.},
}
@article {pmid9099850,
year = {1997},
author = {Milon, L and Rousseau-Merck, MF and Munier, A and Erent, M and Lascu, I and Capeau, J and Lacombe, ML},
title = {nm23-H4, a new member of the family of human nm23/nucleoside diphosphate kinase genes localised on chromosome 16p13.},
journal = {Human genetics},
volume = {99},
number = {4},
pages = {550-557},
doi = {10.1007/s004390050405},
pmid = {9099850},
issn = {0340-6717},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Chromosome Mapping ; *Chromosomes, Human, Pair 16 ; DNA, Complementary ; Humans ; Molecular Sequence Data ; *Monomeric GTP-Binding Proteins ; Multigene Family ; NM23 Nucleoside Diphosphate Kinases ; Nucleoside Diphosphate Kinase D ; Nucleoside-Diphosphate Kinase/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Transcription Factors/*genetics ; },
abstract = {A novel human nm23/nucleoside diphosphate (NDP) kinase gene, called nm23-H4, was identified by screening a human stomach cDNA library with a probe generated by amplification by reverse transcription-polymerase chain reaction. The primers were designed from publicly available database cDNA sequences selected according to their homology to the human nn23-H1 putative metastasis suppressor gene. The full-length cDNA sequence predicts a 187 amino acid protein possessing the region homologous to NDP kinases with all residues crucial for nucleotide binding and catalysis, strongly suggesting that Nm23-H4 possesses NDP kinase activity. It shares 56, 55 and 60% identity with Nm23-H1, Nm23-H2 and DR-Nm23, respectively, the other human Nm23 proteins isolated so far. Compared with these proteins, Nm23-H4 contains an additional NH2-terminal region that is rich in positively charged residues and could indicate routing to mitochondria. The nm23-H4 gene has been localised to human chromosomal band 16p13.3. The corresponding 1.2 kb mRNA is widely distributed and expressed in a tissue-dependent manner, being found at very high levels in prostate, heart, liver, small intestine and skeletal muscle tissues and in low amounts in the brain and in blood leucocytes. Nm23-H4 naturally possesses the Pro-Ser substitution equivalent to the K-pn mutation (P97S) of Drosophila.},
}
@article {pmid9108143,
year = {1997},
author = {Topczewski, J and Sienko, M and Paszewski, A},
title = {Cloning and characterization of the Aspergillus nidulans cysB gene encoding cysteine synthase.},
journal = {Current genetics},
volume = {31},
number = {4},
pages = {348-356},
doi = {10.1007/s002940050215},
pmid = {9108143},
issn = {0172-8083},
mesh = {Amino Acid Sequence ; Amino Acids, Sulfur/genetics/metabolism ; Aspergillus nidulans/*genetics/*metabolism ; Base Sequence ; Cloning, Molecular ; Cysteine Synthase/*genetics/*metabolism ; DNA, Complementary/genetics ; Mitochondria/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {The cysB gene of A. nidulans was cloned by complementation of a cysB mutation. This is the first cloned eukaryotic genomic sequence coding for cysteine synthase. The gene contains one 71-bp intron and codes for a protein of 370 amino acids. Its N-terminal region has characteristic features of transit peptides, suggesting mitochondrial localisation of the enzyme. The protein shows homology with bacterial and plant cysteine synthases among which it occupies a remote phylogenetic position and apparently represents a distinct subfamily. Transcription of the cysB gene is not appreciably regulated by the concentration of methionine in the growth medium.},
}
@article {pmid9117996,
year = {1997},
author = {Müller, EC and Wittmann-Liebold, B},
title = {Phylogenetic relationship of organisms obtained by ribosomal protein comparison.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {53},
number = {1},
pages = {34-50},
doi = {10.1007/pl00000578},
pmid = {9117996},
issn = {1420-682X},
mesh = {Amino Acid Sequence ; Animals ; Archaea/classification ; Bacteria/classification ; Conserved Sequence ; Fungi/classification ; Humans ; Mitochondria/chemistry ; Molecular Sequence Data ; *Phylogeny ; Plants/classification ; Protein Conformation ; Ribosomal Proteins/chemistry/*classification ; Sequence Homology, Amino Acid ; },
abstract = {The evolutionary relationships of ribosomal proteins from eubacteria, archaea, eukaryotes, chloroplasts and mitochondria were examined by their degree of conservation, their structural and functional properties and by the occurrence of conserved structural elements. The structural domains formed by the different protein families were studied. The occurrence of monophyletic groups was investigated for each protein family within the archaea. Phylogenetic trees were constructed between these organisms and together with the homologous sequences of the other phylogenetic domains. All organisms belonging to the archaea clearly formed a monophyletic group. The conserved sequence motifs were checked for the potential to form similar secondary structural elements.},
}
@article {pmid9143492,
year = {1997},
author = {Crnogorac-Jurcevic, T and Brown, JR and Lehrach, H and Schalkwyk, LC},
title = {Tetraodon fluviatilis, a new puffer fish model for genome studies.},
journal = {Genomics},
volume = {41},
number = {2},
pages = {177-184},
doi = {10.1006/geno.1997.4646},
pmid = {9143492},
issn = {0888-7543},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/classification/*genetics ; DNA, Complementary ; Fishes, Poisonous/classification/*genetics ; Genome ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {The puffer fish Fugu rubripes rubripes was recently introduced by S. Brenner et al. (1993, Nature 366: 265-268) as a new model for genomic studies. Due to difficulties in obtaining material from this Japanese marine puffer, we have started work on Tetraodon fluviatilis, a small, freshwater puffer fish that can be kept and bred in an aquarium. It was originally described by E. Hinegardner (1968, Am. Nat. 102(928) 517-523) as the teleost with the smallest amount of DNA per cell (0.4 pg, 380 Mb). To estimate the extent of divergence between T. fluviatilis and F. r. rubripes, part of the mitochondrial cytochrome b (cyt b) gene from both fishes was cloned and sequenced. A comparison of these two sequences indicated that F.r. rubripes and T. fluviatilis diverged approximately 18-30 million years ago, and phylogenetic analysis placed both fishes at the base of the Perciformes lineage. To facilitate and extend further the use of the puffer fish as a model for genome studies, we have constructed and characterized a T. fluviatilis cDNA library.},
}
@article {pmid9175861,
year = {1997},
author = {Schneider, R and Brors, B and Massow, M and Weiss, H},
title = {Mitochondrial fatty acid synthesis: a relic of endosymbiontic origin and a specialized means for respiration.},
journal = {FEBS letters},
volume = {407},
number = {3},
pages = {249-252},
doi = {10.1016/s0014-5793(97)00360-8},
pmid = {9175861},
issn = {0014-5793},
mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/genetics/metabolism ; Acyl Carrier Protein/genetics/metabolism ; Animals ; Electron Transport Complex I ; Fatty Acids/*biosynthesis ; Humans ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/metabolism ; NADH, NADPH Oxidoreductases/metabolism ; Oxygen Consumption ; Phospholipids/metabolism ; Phylogeny ; Symbiosis ; },
abstract = {Genes that encode mitochondrial homologues to the bacterial enzymes of fatty acid synthesis were found in various eukaryotic species. Inactivation of these genes leads to a disturbed mitochondrial respiration and an increase in mitochondrial lysophospholipids. We postulate that there is a mitochondrial biosynthetic system providing fatty acids for phospholipid repair. The mitochondrial acyl carrier protein may also play another role, supporting the formation of the respiratory NADH:ubiquinone oxidoreductase.},
}
@article {pmid9178508,
year = {1997},
author = {el Moualij, B and Duyckaerts, C and Lamotte-Brasseur, J and Sluse, FE},
title = {Phylogenetic classification of the mitochondrial carrier family of Saccharomyces cerevisiae.},
journal = {Yeast (Chichester, England)},
volume = {13},
number = {6},
pages = {573-581},
doi = {10.1002/(SICI)1097-0061(199705)13:6&lt;573::AID-YEA107&gt;3.0.CO;2-I},
pmid = {9178508},
issn = {0749-503X},
mesh = {Amino Acid Sequence ; Base Sequence ; Carrier Proteins/chemistry/*classification/genetics ; DNA, Fungal ; Fungal Proteins/chemistry/*classification/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Saccharomyces cerevisiae/*chemistry ; },
abstract = {The screening of the open reading frames identified in the whole yeast genome has allowed us to discover 34 proteins belonging to the mitochondrial carrier family. By phylogenetic study, they can be divided into 27 subfamilies including ADP/ATP, phosphate and citrate carriers, putative oxoglutarate and GDC carriers and 22 new subfamilies. Topology predictions using the 'positive inside rule' approach have shown that the yeast carriers are similarly oriented with both extremities exposed to the cytosol. In each subfamily, a strict conservation of the charged residues in the six transmembrane alpha-helices is observed, suggesting a functional role for these residues and the existence of 27 functionally distinct carriers.},
}
@article {pmid9214748,
year = {1997},
author = {Härlid, A and Janke, A and Arnason, U},
title = {The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds.},
journal = {Molecular biology and evolution},
volume = {14},
number = {7},
pages = {754-761},
doi = {10.1093/oxfordjournals.molbev.a025815},
pmid = {9214748},
issn = {0737-4038},
mesh = {Animals ; Base Composition ; Base Sequence ; Birds/*genetics ; Chickens/*genetics ; DNA, Mitochondrial/*genetics ; Genes ; Mitochondria, Heart ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Regulatory Sequences, Nucleic Acid ; },
abstract = {The complete mitochondrial DNA (mtDNA) molecule of the ostrich, Struthio camelus, was sequenced. The size of the molecule is 16,591 nucleotides. Since the ostrich represents the paleognathous birds, comparison with the mtDNA of the neognathous chicken, the only avian species reported so far in databases, made it possible to identify common and, probably, general avian mtDNA characteristics. Relative to other vertebrates, the avian NADH6 and tRNA-Glu genes are positioned upstream of the control region rather than the cytochrome b gene. The NADH3 gene of the ostrich is terminated by a stop codon at position 207. Thus, the gene is about 140 nucleotides shorter than in other vertebrates. The sequence for L-strand origin of replication is missing in both birds, and four transfer RNA genes of the two avian mtDNAs deviate from common characteristics of tRNAs of vertebrate mtDNAs by having an adenine (and not a thymidine) at position 8. Due to the absence of suitable fossils, most paleontological datings of avian divergences are conjectural. Molecular dating of the divergence between the ostrich and the chicken indicates that these two avian lineages separated 80-90 MYA. Phylogenetic analysis of complete cytochrome b genes of six avian orders showed that Passeriformes represent the earliest divergence among recent birds, contradicting the commonly accepted notion of a basal position of the Palaeognathae among recent birds.},
}
@article {pmid9236270,
year = {1997},
author = {Ehara, M and Hayashi-Ishimaru, Y and Inagaki, Y and Ohama, T},
title = {Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum.},
journal = {Journal of molecular evolution},
volume = {45},
number = {2},
pages = {119-124},
pmid = {9236270},
issn = {0022-2844},
mesh = {DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Eukaryota/classification/*genetics ; *Genetic Code ; Isoleucine/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae, on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla. We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two, Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms, especially when it is considered with the results obtained through a molecular phylogenetic tree.},
}
@article {pmid9242608,
year = {1997},
author = {Hedtke, B and Börner, T and Weihe, A},
title = {Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis.},
journal = {Science (New York, N.Y.)},
volume = {277},
number = {5327},
pages = {809-811},
doi = {10.1126/science.277.5327.809},
pmid = {9242608},
issn = {0036-8075},
mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/genetics ; Cell Nucleus/genetics ; Chloroplasts/*enzymology ; Cloning, Molecular ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Exons ; *Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; T-Phages/enzymology ; },
abstract = {In addition to the RNA polymerases (RNAPs) transcribing the nuclear genes, eukaryotic cells also require RNAPs to transcribe the genes of the mitochondrial genome and, in plants, of the chloroplast genome. The plant Arabidopsis thaliana was found to contain two nuclear genes similar to genes encoding the mitochondrial RNAP from yeast and RNAPs of bacteriophages T7, T3, and SP6. The putative transit peptides of the two polymerases were capable of targeting fusion proteins to mitochondria and chloroplasts, respectively, in vitro. The results indicate that the mitochondrial RNAP in plants is a bacteriophage-type enzyme. A gene duplication event may have generated the second RNAP, which along with the plastid-encoded eubacteria-like RNAP could transcribe the chloroplast genome.},
}
@article {pmid9247927,
year = {1997},
author = {Germot, A and Philippe, H and Le Guyader, H},
title = {Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae.},
journal = {Molecular and biochemical parasitology},
volume = {87},
number = {2},
pages = {159-168},
doi = {10.1016/s0166-6851(97)00064-9},
pmid = {9247927},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; Eukaryotic Cells ; Genes, Protozoan ; HSP70 Heat-Shock Proteins/*genetics ; Microsporida/*genetics/ultrastructure ; Mitochondria/*genetics ; Molecular Sequence Data ; Nosema/*genetics/ultrastructure ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Protozoan Proteins/genetics ; Sequence Homology, Amino Acid ; },
abstract = {In molecular phylogenies based on ribosomal RNA, three amitochondriate protist lineages, Microsporidia, Metamonada (including diplomonads) and Parabasala (including trichomonads), are the earliest offshoots of the eukaryotic tree. As an explantation for the lack of mitochondria in these organisms, the hypothesis that they have diverged before the mitochondrial endosymbiosis is preferred to the less parsimonious hypothesis of several independent losses of the organelle. Nevertheless, if they had descended from mitochondrion-containing ancestors, it may be possible to find in their nuclear DNA genes that derive from the endosymbiont which gave rise to mitochondria. Based on similar evidence, secondary losses of mitochondria have recently been suggested for Entamoeba histolytica and for Trichomonas vaginalis. In this study, we have isolated a gene encoding a chaperone protein (HSP70, 70 kDa heat shock protein) from the microspordian Nosema locustae. In phylogenetic trees, this HSP70 was located within a group of sequences that in other lineages is targetted to the mitochondrial compartment, itself included in the proteobacterial clade. In addition, the N. locustae protein contained the GDAW(V) motif shared by mitochondrial and proteobacterial sequences, with only one conservative substitution. Moreover, microsporidia, a phylum which was assumed to emerge close to the base of the eukaryotic tree, appears as the sister-group of fungi in the HSP70 phylogeny, in agreement with some ultrastructural characters and phylogenies based on alpha- and beta-tubulins. Loss of mitochondria, now demonstrated for several amitochondriate groups, indicates that the common ancestor of all the extant eukaryotic species could have been a mitochondriate eukaryote.},
}
@article {pmid9252184,
year = {1997},
author = {Naylor, GJ and Brown, WM},
title = {Structural biology and phylogenetic estimation.},
journal = {Nature},
volume = {388},
number = {6642},
pages = {527-528},
doi = {10.1038/41460},
pmid = {9252184},
issn = {0028-0836},
mesh = {Animals ; Mitochondria/*genetics ; *Phylogeny ; },
}
@article {pmid9260887,
year = {1997},
author = {Singh, B and Soltys, BJ and Wu, ZC and Patel, HV and Freeman, KB and Gupta, RS},
title = {Cloning and some novel characteristics of mitochondrial Hsp70 from Chinese hamster cells.},
journal = {Experimental cell research},
volume = {234},
number = {2},
pages = {205-216},
doi = {10.1006/excr.1997.3609},
pmid = {9260887},
issn = {0014-4827},
mesh = {Amino Acid Sequence ; Animals ; Antibody Specificity ; Base Sequence ; Biological Transport ; *CHO Cells ; Cloning, Molecular ; Cricetinae ; DNA, Complementary/genetics ; Escherichia coli ; HSP70 Heat-Shock Proteins/*analysis/*genetics/metabolism ; Mitochondria/*chemistry ; Mitochondria, Heart/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Processing, Post-Translational ; Rats ; Recombinant Fusion Proteins ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {The cDNA for Chinese hamster mitochondrial Hsp70 (mHsp70) was cloned and sequenced using a polymerase chain reaction probe based on conserved regions in the Hsp70 family of proteins. The encoded protein consists of 679 amino acids which includes a N-terminal mitochondrial targeting sequence of 46 amino acids. The mHsp70 protein contains several sequence signatures that are characteristics of prokaryotic and eukaryotic organellar Hsp70 homologs. In a phylogenetic tree based on Hsp70 sequences, it branches with the gram-negative proteobacteria, supporting the endosymbiotic origin of mitochondria from this group of prokaryotes. The mHsp70 cDNA was transcribed and translated in vitro and its import into isolated rat heart mitochondria was examined. The precursor mHsp70 was converted into a mature form of lower molecular mass (approximately 71 kDa) which became resistant to trypsin digestion. The import of mHsp70 into mitochondria was not observed in the presence of an uncoupler of energy metabolism or when the N-terminal presequence was lacking. The cDNA for mHsp70 was expressed in Escherichia coli and a polyclonal antibody to the purified recombinant protein was raised. The antibody shows no cross-reactivity to recombinant cytosolic Hsp70 protein and in 2-D gel blots it reacted specifically with the mHsp70 protein only. In immunofluorescence experiments, the antibody predominantly labeled mitochondria, and the observed labeling pattern was identical to that seen with a monoclonal antibody to the mitochondrial Hsp60 chaperonin. The affinity-purified antibody to mHsp70 was also employed to examine the subcellular distribution of the protein by cryoelectron microscopy and the immunogold-labeling technique. In these experiments, in addition to mitochondria, labeling with mitochondrial Hsp70 antibody was also observed on the plasma membrane and in unidentified cytoplasmic vesicles and granules. These studies raise the possibility that similar to the Hsp60 chaperonin and a number of other mitochondrial proteins, mHsp70 may have an extramitochondrial role.},
}
@article {pmid9302321,
year = {1997},
author = {Guimarães, RC and Trifonov, EN and Lagunez-Otero, J},
title = {Taxonomy of 5 S ribosomal RNA by the linguistic technique: probing with mitochondrial and mammalian sequences.},
journal = {Journal of molecular evolution},
volume = {45},
number = {3},
pages = {271-277},
doi = {10.1007/pl00006230},
pmid = {9302321},
issn = {0022-2844},
mesh = {Animals ; Bacteria/genetics ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells ; Fungi/genetics ; Mammals/*genetics ; *Models, Genetic ; Phylogeny ; Plants/genetics ; RNA, Ribosomal, 5S/*classification ; Sensitivity and Specificity ; Glycine max/genetics ; },
abstract = {Linguistic similarities and dissimilarities between 5 S rRNA sequences allowed taxonomical separation of species and classes. Comparisons with the molecule from mammals distinguished fungi and plants from protists and animals. Similarities to mammalians progressively increased from protists to invertebrates and to somatic-type molecules of the vertebrates lineage. In this, deviations were detected in avian, oocyte type, and pseudogene sequences. Among bacteria, actinobacteria were most similar to the mammalians, which could be related to the high frequency of associations among members of these groups. Some archaebacterial species most similar to the mammalians belonged to the Thermoproteales and Halobacteria groups. Comparisons with the soybean mitochondrial molecule revealed high internal homogeneity among plant mitochondria. The eubacterial groups most similar to it were Thermus and Rhodobacteria gamma-1 and alpha-2. Other procedures have already indicated similarities of Rhodobacteria alpha to mitochondria but the linguistic similarities were on the average higher with the first two groups.},
}
@article {pmid9304815,
year = {1997},
author = {Weekers, PH and Kleyn, J and Vogels, GD},
title = {Phylogenetic position of Psalteriomonas lanterna deduced from the SSU rDNA sequence.},
journal = {The Journal of eukaryotic microbiology},
volume = {44},
number = {5},
pages = {467-470},
doi = {10.1111/j.1550-7408.1997.tb05725.x},
pmid = {9304815},
issn = {1066-5234},
mesh = {Animals ; Base Composition ; Cloning, Molecular ; DNA, Protozoan/analysis/chemistry ; DNA, Ribosomal/analysis/chemistry ; Eukaryota/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/*genetics ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The small subunit ribosomal DNA sequence (SSU rDNA) of the microaerophilic free-living amoeboflagellate Psalteriomonas lanterna has been sequenced and analyzed. The gene is 1,945 bp long and has a G + C content of 33.4%. Based upon ultrastructural studies, P. lanterna has been placed in the class Lyromonadea within the phylum Percolozoa Cavalier-Smith, 1991. However, based upon cytological characteristics, this microaerophilic free-living amoeboflagellate appears to be very primitive. It shares certain characteristics in common with some archezoans, i.e. it lacks mitochondria and dictyosomes but contains hydrogenosomes. Despite sharing these characteristics with the amitochondriate taxa, P. lanterna is not related to any of these taxa but instead to the Vahlkampfiidae. Therefore, we used primary sequence data and the secondary structure of the SSU rDNA gene to determine the placement P. lanterna in the phylogenetic tree. Our analyses showed that P. lanterna groups as a sister taxon to the Vahlkampfiidae but probably diverged from them quite early.},
}
@article {pmid9381856,
year = {1997},
author = {Malikov, NG and Grachev, MA and Mertvetsov, NP},
title = {[An estimation of the time of divergence of the seals Phoca vitulina, Phoca largha and Phoca sibirica from a common ancestral species].},
journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii},
volume = {33},
number = {2},
pages = {252-254},
pmid = {9381856},
issn = {0044-4529},
mesh = {Animals ; Base Sequence ; Cytochrome b Group/genetics ; DNA, Mitochondrial/genetics ; Mitochondria, Liver/genetics ; Molecular Sequence Data ; Phylogeny ; Seals, Earless/*classification/genetics ; Time Factors ; },
}
@article {pmid9409151,
year = {1997},
author = {Zumft, WG},
title = {Cell biology and molecular basis of denitrification.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {61},
number = {4},
pages = {533-616},
pmid = {9409151},
issn = {1092-2172},
mesh = {Amino Acid Sequence ; Bacteria/genetics/*metabolism ; Fungi/genetics/*metabolism ; Gene Expression ; Genes, Bacterial ; Genes, Fungal ; Heme/metabolism ; Molecular Sequence Data ; Multigene Family ; Nitric Oxide/metabolism ; Nitrites/metabolism ; Nitrogen/*metabolism ; Nitrous Oxide/metabolism ; Phylogeny ; },
abstract = {Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.},
}
@article {pmid9461620,
year = {1998},
author = {Souri, M and Aoyama, T and Cox, GF and Hashimoto, T},
title = {Catalytic and FAD-binding residues of mitochondrial very long chain acyl-coenzyme A dehydrogenase.},
journal = {The Journal of biological chemistry},
volume = {273},
number = {7},
pages = {4227-4231},
doi = {10.1074/jbc.273.7.4227},
pmid = {9461620},
issn = {0021-9258},
mesh = {Acyl-CoA Dehydrogenase, Long-Chain/*chemistry/genetics ; Amino Acid Sequence ; Binding Sites ; Flavin-Adenine Dinucleotide/*metabolism ; Humans ; Kinetics ; Mitochondria, Liver/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Palmitoyl Coenzyme A/metabolism ; Phylogeny ; Protein Binding ; Protein Folding ; Recombinant Proteins/genetics ; Sequence Alignment ; Trypsin/metabolism ; },
abstract = {Very long-chain acyl-CoA dehydrogenase (VLCAD) is one of four flavoproteins which catalyze the initial step of the mitochondrial beta-oxidation spiral. By sequence comparison with other acyl-CoA dehydrogenases, Glu-422 of VLCAD has been presumed to be the catalytic residue that abstracts the alpha-proton in the alphabeta-dehydrogenation reaction. Replacing Glu-422 with glutamine (E422Q) caused a loss of enzyme activity by preventing the formation of a charge transfer complex between VLCAD and palmitoyl-CoA. This result provides further evidence for Glu-422 being part of the active site of VLCAD. F418L is a disease-causing mutation in human VLCAD deficiency. Unlike wild-type VLCAD, F418L and F418V contained no bound FAD when expressed at extremely high levels in the baculovirus expression system. Although F418T and F418Y bound FAD at a level similar to that of wild-type VLCAD, both showed reduced Vmax values toward palmitoyl-CoA, most likely due to a decrease in the rate of enzyme-bound FAD reduction. These data suggest that Phe-418 is involved in the binding and subsequent reduction of FAD. FAD-deficient VLCADs (F418L, F418V, and apo-VLCAD) showed increased sensitivity to trypsinization. Loss of FAD may change the folding of VLCAD subunit.},
}
@article {pmid9464882,
year = {1998},
author = {Mannen, H and Kojima, T and Oyama, K and Mukai, F and Ishida, T and Tsuji, S},
title = {Effect of mitochondrial DNA variation on carcass traits of Japanese Black cattle.},
journal = {Journal of animal science},
volume = {76},
number = {1},
pages = {36-41},
doi = {10.2527/1998.76136x},
pmid = {9464882},
issn = {0021-8812},
mesh = {Animals ; Base Sequence ; Body Composition/*genetics ; Breeding ; Cattle/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/analysis/chemistry/*genetics ; *Genetic Variation ; Haplotypes ; Male ; Meat/*standards ; Molecular Sequence Data ; Mutation ; Phylogeny ; },
abstract = {Japanese Black fattening steers were used to examine relationships between carcass traits and mitochondria displacement loop (D-loop) variations. The D-loop region of Japanese Black cattle was sequenced and revealed 26 mitochondrial haplotypes defined by 25 polymorphic sites. The haplotypes were classified into five mitochondrial types (type 1 to 5) using the unweighted pair-group method with arithmetic means. Carcass weight, longissimus muscle area (LMA), rib thickness, subcutaneous fat thickness, yield estimate, and beef marbling score (BMS) were compared among five mitochondrial types with BLUP procedures. Significant differences between mitochondria types were detected for LMA and BMS. Difference (P < . 05) was observed between mitochondrial types 2 and 4 for LMA. There was a highly significant difference (P < .01) in BMS between types 2 and 4. Difference (P < .05) was also found between types 1 and 4 on BMS. These results suggest that cytoplasmic genetic effects are important sources of variation for carcass traits in Japanese Black cattle.},
}
@article {pmid9481814,
year = {1998},
author = {Gray, MW and Lang, BF},
title = {Transcription in chloroplasts and mitochondria: a tale of two polymerases.},
journal = {Trends in microbiology},
volume = {6},
number = {1},
pages = {1-3},
doi = {10.1016/S0966-842X(97)01182-7},
pmid = {9481814},
issn = {0966-842X},
mesh = {Arabidopsis/genetics ; Bacterial Proteins/genetics ; Chloroplasts/*genetics ; *DNA-Binding Proteins ; DNA-Directed RNA Polymerases/*genetics ; Gene Expression ; Mitochondria/*genetics ; Organelles ; *Phylogeny ; Plants/genetics ; Sigma Factor/genetics ; T-Phages/genetics ; *Transcription, Genetic ; },
}
@article {pmid9512533,
year = {1998},
author = {Helm, M and Brulé, H and Degoul, F and Cepanec, C and Leroux, JP and Giegé, R and Florentz, C},
title = {The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA.},
journal = {Nucleic acids research},
volume = {26},
number = {7},
pages = {1636-1643},
pmid = {9512533},
issn = {0305-1048},
mesh = {Cloning, Organism ; Female ; Genetic Variation ; Humans ; Methylation ; Mitochondria/*metabolism ; Models, Molecular ; Mutagenesis, Site-Directed ; *Nucleic Acid Conformation ; Phylogeny ; Placenta/metabolism ; Polymerase Chain Reaction ; Pregnancy ; RNA/biosynthesis/*chemistry ; RNA Editing ; RNA, Mitochondrial ; RNA, Transfer, Lys/biosynthesis/*chemistry ; *Transcription, Genetic ; },
abstract = {Direct sequencing of human mitochondrial tRNALysshows the absence of editing and the occurrence of six modified nucleotides (m1A9, m2G10, Psi27, Psi28 and hypermodified nucleotides at positions U34 and A37). This tRNA folds into the expected cloverleaf, as confirmed by structural probing with nucleases. The solution structure of the corresponding in vitro transcript unexpectedly does not fold into a cloverleaf but into an extended bulged hairpin. This non-canonical fold, established according to the reactivity to a large set of chemical and enzymatic probes, includes a 10 bp aminoacyl acceptor stem (the canonical 7 bp and 3 new pairs between residues 8-10 and 65-63), a 13 nt large loop and an anticodon-like domain. It is concluded that modified nucleotides have a predominant role in canonical folding of human mitochondrial tRNALys. Phylogenetic comparisons as well as structural probing of selected in vitro transcribed variants argue in favor of a major contribution of m1A9 in this process.},
}
@article {pmid9573371,
year = {1998},
author = {Moriya, S and Ohkuma, M and Kudo, T},
title = {Phylogenetic position of symbiotic protist Dinenympha [correction of Dinemympha] exilis in the hindgut of the termite Reticulitermes speratus inferred from the protein phylogeny of elongation factor 1 alpha.},
journal = {Gene},
volume = {210},
number = {2},
pages = {221-227},
doi = {10.1016/s0378-1119(98)00078-x},
pmid = {9573371},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Digestive System ; *Diplomonadida ; In Situ Hybridization ; *Insecta ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; *Symbiosis ; },
abstract = {The phylogenetic position of the symbiotic oxymonad Dinenympha exilis, found in the hindgut of the lower termite Reticulitermes speratus, was determined by analysis of translation elongation factor 1 alpha (EF-1 alpha). cDNA corresponding to a major part of the amino acid coding region of EF-1 alpha mRNA was amplified by the reverse transcription polymerase chain reaction (RT-PCR) method from total mRNA of termite hindgut microorganisms without cultivation. The product was cloned into a plasmid vector, pGEM-T, and the clones were isolated and sequenced. One of the EF-1 alpha clones isolated was assigned to the protist D. exilis by whole-cell in-situ hybridization using a specific oligonucleotide probe with enzymatic signal amplification. The deduced amino acid sequence was aligned with those of other eukaryotic and archaeabacterial EF-1 alpha s, and the phylogenetic relationships among early branching eukaryotes were inferred by using the distance matrix method and the maximum parsimony method. The phylogenetic analysis indicated that the D. exilis offshoot occurred before mitochondria-containing organisms and D. exilis branched out after the diplomonads clade. These results indicate that the oxymonad D. exilis is one of the early branching organisms and suggest that the oxymonads form a lineage independent of other early branching organisms.},
}
@article {pmid9600982,
year = {1998},
author = {Lakshman, DK and Jian, J and Tavantzis, SM},
title = {A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {95},
number = {11},
pages = {6425-6429},
pmid = {9600982},
issn = {0027-8424},
mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Complementary/analysis/genetics ; DNA, Fungal/*genetics ; Fungal Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/*genetics ; Rhizoctonia/*genetics/pathogenicity ; Sequence Analysis ; Virulence ; },
abstract = {M2 is a double-stranded RNA (dsRNA) element occurring in the hypovirulent isolate Rhs 1A1 of the plant pathogenic basidiomycete Rhizoctonia solani. Rhs 1A1 originated as a sector of the virulent field isolate Rhs 1AP, which contains no detectable amount of the M2 dsRNA. The complete sequence (3,570 bp) of the M2 dsRNA has been determined. A 6.9-kbp segment of total DNA from either Rhs 1A1 or Rhs 1AP hybridizes with an M2-specific cDNA probe. The sequences of M2 dsRNA and of PCR products generated from Rhs 1A1 total DNA were found to be identical. Thus this report describes a fungal host containing full-length DNA copies of a dsRNA element. A major portion of the M2 dsRNA is located in the cytoplasm, whereas a smaller amount is found in mitochondria. Based on either the universal or the mitochondrial genetic code of filamentous fungi, one strand of M2 encodes a putative protein of 754 amino acids. The resulting polypeptide has all four motifs of a dsRNA viral RNA-dependent RNA polymerase (RDRP) and is phylogenetically related to the RDRP of a mitochondrial dsRNA associated with hypovirulence in strain NB631 of Cryphonectria parasitica, incitant of chestnut blight. This polypeptide also has significant sequence similarity with two domains of a pentafunctional polypeptide, which catalyzes the five central steps of the shikimate pathway in yeast and filamentous fungi.},
}
@article {pmid9615624,
year = {1998},
author = {Onuma, M and Kusakabe, T and Kusakabe, S},
title = {Phylogenetic positions of insectivora in eutheria inferred from mitochondrial cytochrome c oxidase subunit II gene.},
journal = {Zoological science},
volume = {15},
number = {1},
pages = {139-145},
doi = {10.2108/zsj.15.139},
pmid = {9615624},
issn = {0289-0003},
mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; Eulipotyphla/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {For the elucidation of the phylogenetic position of insectivora in eutheria, we have sequenced the cytochrome c oxidase subunit II (COII) gene of mitochondria for three insectivoran species [musk screw (Suncus murinus), shrew mole (Urotrichus talpoides), Japanese mole (Mogera wogura)] and analyzed these amino acid sequences with neighbor-joining (NJ) method and maximum likelihood (ML) method. NJ analysis shows polyphyly of Insectivora and Chiroptera. Assuming that each of Primates, Ferungulata, Chiroptera, Insectivora and Rodentia is a monophyletic group, ML analysis suggests that Chiroptera is a sister group of Insectivora and that Ferungulata is the closest outgroup to the (Insectivora and Chiroptera) clade.},
}
@article {pmid9615625,
year = {1998},
author = {Kobayashi, N and Tamura, K and Aotsuka, T and Katakura, H},
title = {Molecular phylogeny of twelve Asian species of epilachnine ladybird beetles (Coleoptera, Coccinellidae) with notes on the direction of host shifts.},
journal = {Zoological science},
volume = {15},
number = {1},
pages = {147-151},
doi = {10.2108/zsj.15.147},
pmid = {9615625},
issn = {0289-0003},
mesh = {Amino Acid Sequence ; Animals ; Coleoptera/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {We determined the nucleotide sequences of a part of the mitochondrial cytochrome c oxidase I gene (1,000 bp) for twelve species of Asian phytophagous ladybird beetles belonging to the genus Epilachna, and constructed molecular phylogenetic trees for ten "Henosepilachna" species, using two "Epilachna" species as outgroups. Based on the suggested phylogenetic trees, we discussed taxonomic issues and the direction of host shift in these epilachnines.},
}
@article {pmid9618503,
year = {1998},
author = {Hashimoto, T and Sánchez, LB and Shirakura, T and Müller, M and Hasegawa, M},
title = {Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {95},
number = {12},
pages = {6860-6865},
pmid = {9618503},
issn = {0027-8424},
support = {R01 AI011942/AI/NIAID NIH HHS/United States ; AI11942/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Giardia lamblia/*genetics/*ultrastructure ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Trichomonas vaginalis/*genetics/*ultrastructure ; Valine-tRNA Ligase/*genetics ; },
abstract = {Nuclear-coded valyl-tRNA synthetase (ValRS) of eukaryotes is regarded of mitochondrial origin. Complete ValRS sequences obtained by us from two amitochondriate protists, the diplomonad, Giardia lamblia and the parabasalid, Trichomonas vaginalis were of the eukaryotic type, strongly suggesting an identical history of ValRS in all eukaryotes studied so far. The findings indicate that diplomonads are secondarily amitochondriate and give further evidence for such conclusion reached recently concerning parabasalids. Together with similar findings on other amitochondriate groups (microsporidia and entamoebids), this work provides critical support for the emerging notion that no representatives of the premitochondrial stage of eukaryotic phylogenesis exist among the species living today.},
}
@article {pmid9650294,
year = {1998},
author = {Jian, JH and Lakshman, DK and Tavantzis, SM},
title = {A virulence-associated, 6.4-kb, double-stranded RNA from Rhizoctonia solani is phylogenetically related to plant bromoviruses and electron transport enzymes.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {11},
number = {7},
pages = {601-609},
doi = {10.1094/MPMI.1998.11.7.601},
pmid = {9650294},
issn = {0894-0282},
mesh = {Amino Acid Sequence ; Base Sequence ; Bromovirus/*genetics ; Conserved Sequence ; Cytosol/metabolism ; DNA, Complementary/chemistry ; Electron Transport ; Electron Transport Complex IV/chemistry ; Fabaceae/virology ; Mitochondria/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plants, Medicinal ; RNA, Bacterial/chemistry/genetics ; RNA, Double-Stranded/chemistry/*genetics ; Rhizoctonia/*genetics/*pathogenicity ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Proteins/biosynthesis/chemistry ; Virulence ; },
abstract = {We have recently shown that acquisition of a 6.4-kb, double-stranded (ds) RNA (M1) by hyphal anastomosis is associated with enhanced vigor and virulence, whereas its removal by hyphal tipping correlates with diminished virulence in the plant-pathogenic basidiomycete Rhizoctonia solani. The M1 dsRNA is not encapsidated by a typical nucleocapsid, has a circular and/or concatemeric form, and is associated with the mitochondrial and cytosolic fractions. M1 possesses six open reading frames (ORFs) the longest of which (ORF 2) is located on the (+) strand, and encodes a putative polypeptide consisting of 1,747 amino acids or 199.4 kDa. This polypeptide has a significant amino acid sequence similarity, including six conserved helicase domains and an ATP/GTP binding motif, with the 1A protein of broad bean mottle virus (BBMV) and other bromoviruses. ORF 5, which is located on the (-) strand of M1 and is complementary to a region of ORF 2, codes for a putative polypeptide that has a significant amino acid sequence similarity with the cytochrome c oxidase assembly factor. This complementarity provides direct evidence suggesting that the long-standing hypothesis of viruses evolving from cellular genes may be valid.},
}
@article {pmid9651529,
year = {1998},
author = {Nowitzki, U and Flechner, A and Kellermann, J and Hasegawa, M and Schnarrenberger, C and Martin, W},
title = {Eubacterial origin of nuclear genes for chloroplast and cytosolic glucose-6-phosphate isomerase from spinach: sampling eubacterial gene diversity in eukaryotic chromosomes through symbiosis.},
journal = {Gene},
volume = {214},
number = {1-2},
pages = {205-213},
doi = {10.1016/s0378-1119(98)00229-7},
pmid = {9651529},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/genetics ; Base Sequence ; Chloroplasts/enzymology/genetics ; Cloning, Molecular ; Cyanobacteria/classification/enzymology/genetics ; Cytosol/enzymology ; DNA Primers/genetics ; Escherichia coli/enzymology/genetics ; *Genes, Bacterial ; *Genes, Plant ; Genetic Variation ; Glucose-6-Phosphate Isomerase/*genetics ; Haemophilus/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology/*genetics/microbiology ; Symbiosis/genetics ; },
abstract = {Higher plants possess two distinct nuclear-encoded glucose-6-phosphate isomerase (GPI) isoenzymes, a cytosolic enzmye of the Embden-Meyerhof pathway and a chloroplast enzyme essential to storage and mobilization of carbohydrate fixed by the Calvin cycle. We have purified spinach chloroplast GPI to homogeneity, determined amino acid sequences from the active enzyme, and cloned cDNAs for chloroplast and cytosolic GPI isoenzymes from spinach. Sequence comparisons reveal three distantly related families of GPI genes that are non-uniformly distributed among contemporary eubacteria and archaebacteria, suggesting that ancient gene diversity existed for this glycolytic enzyme. Spinach chloroplast GPI is much more similar to its homologue from the cyanobacterium Synechocystis PCC6803 than it is to the enzyme from any other source, providing strong evidence that the gene for chloroplast GPI was acquired by the nucleus via endosymbiotic gene transfer from the cyanobacterial antecedants of chloroplasts. Eukaryotic nuclear genes for cytosolic GPI are more similar to eubacterial than to archaebacterial homologues, suggesting that these too were acquired by eukaryotes from eubacteria, probably during the course of the endosymbiotic origin of mitochondria. Chloroplast and cytosolic GPI provide evidence for a eubacterial origin of yet another component of the eukaryotic glycolytic pathway.},
}
@article {pmid9689214,
year = {1996},
author = {Andersson, SG and Eriksson, AS and Näslund, AK and Andersen, MS and Kurland, CG},
title = {The Rickettsia prowazekii genome: a random sequence analysis.},
journal = {Microbial &amp; comparative genomics},
volume = {1},
number = {4},
pages = {293-315},
pmid = {9689214},
issn = {1090-6592},
mesh = {Base Sequence ; Citric Acid Cycle/genetics ; DNA, Mitochondrial/genetics ; Electron Transport/genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Mitochondrial ADP, ATP Translocases/genetics ; Molecular Sequence Data ; Phylogeny ; Rickettsia prowazekii/*genetics ; Sequence Analysis ; },
abstract = {We describe here the first general survey of the genomic content and the coding capacity of the 1.1 Mb genome of Rickettsia prowazekii based on an analysis of a total of 200 kb of unique sequence data collected in a random manner. Based on nucleotide distribution profiles, we estimate that the R. prowazekii genome may have a coding density of 60%-70% and that it may contain a total of circa 800 genes. Here, we have tentatively identified and classified 173 of these genes. Our analysis suggests that the R. prowazekii genome is a highly derived, reduced genome that has lost many genes involved in amino acid biosynthetic pathways and regulatory functions. Furthermore, the R. prowazekii genome seems to lack glycolytic genes, but it does contain genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system. We have also encountered a family of homologous genes coding for ATP/ADP translocases, as observed in several mitochondrial genomes. We relate these findings to previous phylogenetic studies that suggest that Rickettsia and mitochondria share a common ancestor.},
}
@article {pmid9711305,
year = {1998},
author = {Sicheritz-Pontén, T and Kurland, CG and Andersson, SG},
title = {A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae.},
journal = {Biochimica et biophysica acta},
volume = {1365},
number = {3},
pages = {545-551},
doi = {10.1016/s0005-2728(98)00099-1},
pmid = {9711305},
issn = {0006-3002},
mesh = {Amino Acids ; Base Composition ; Cloning, Molecular ; Cytochrome b Group/*genetics ; DNA, Bacterial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Genes, Bacterial/genetics ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Rickettsia prowazekii/enzymology/genetics ; Rickettsiaceae/enzymology/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {We have cloned and sequenced the genes encoding cytochrome b (cob) and cytochrome c oxidase subunit I (cox1) from Rickettsia prowazekii, a member of the alpha-proteobacteria. The phylogenetic analysis supports the hypothesis that mitochondria are derived from the alpha-proteobacteria and more specifically from within the Rickettsiaceae. We have estimated that the common ancestor of mitochondria and Rickettsiaceae dates back to more than 1500 million years ago.},
}
@article {pmid9718722,
year = {1998},
author = {Budin, K and Philippe, H},
title = {New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences.},
journal = {Molecular biology and evolution},
volume = {15},
number = {8},
pages = {943-956},
doi = {10.1093/oxfordjournals.molbev.a026010},
pmid = {9718722},
issn = {0737-4038},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Ciliophora/*genetics ; Cloning, Molecular ; Cytosol/metabolism ; DNA Primers/genetics ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells ; Euplotes/genetics ; Genes, Protozoan ; Genetic Markers ; HSP70 Heat-Shock Proteins/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Multigene Family ; Paramecium tetraurelia/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; },
abstract = {The current framework of the eukaryotic phylogeny is based on the analysis of a comprehensive set of sequences of the small subunit ribosomal RNA. However, phylogenies based on protein-encoding genes are not completely congruent with this picture. Since congruence between different markers is the best tool to determine evolutionary history, we focused on Hsp70 (heat-shock protein of 70 kDa), a chaperone protein which is highly conserved and is a potentially reliable phylogenetic marker. We used a PCR-based approach to sequence Hsp70s in two distinct classes of Ciliates. Seven Hsp70s were identified from Paramecium tetraurelia (Oligohymenophora) and six Hsp70s from Euplotes aediculatus (Hypotricha), encompassing orthologous genes for all major Hsp70 classes of Eukaryotes, i.e., those localized in cytosol, in endoplasmic reticulum, and in mitochondria. Three independent phylogenies of eukaryotes, based on each set of orthologous genes, have been constructed using different tree reconstruction methods. A significant advantage of Hsp70s is the existence of outgroups close to Eukaryotes for these major classes, reducing the long-branch attraction artifact due to the outgroup. The monophyly of Ciliates is supported by good bootstrap proportions in the phylogenetic reconstructions, and this phylum is generally a sister-group of Sporozoa, forming the expected Alveolates clade. The Hsp70 seems to be a suitable phylogenetic marker since it recovers all the monophyletic groups, undoubtedly defined by morphological criteria. The Hsp70 trees are, however, notably different from the rRNA ones and do not show two aspects of the classical topology, i.e., the successive emergence of deeply branching groups and the vast assembly of the major eukaryotic groups, emerging at the tip of the tree, i.e., the "terminal crown". More precisely, the Hsp70 trees do not resolve the relationships between the major groups of Eukaryotes with confidence, in keeping with the hypothesis that all these groups emerged in a great radiation that occurred at the origin of all the extant Eukaryotes.},
}
@article {pmid9763293,
year = {1998},
author = {Keddie, EM and Higazi, T and Unnasch, TR},
title = {The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis.},
journal = {Molecular and biochemical parasitology},
volume = {95},
number = {1},
pages = {111-127},
doi = {10.1016/s0166-6851(98)00102-9},
pmid = {9763293},
issn = {0166-6851},
support = {P01-AI28780/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Ascaris suum/genetics ; Base Sequence ; Caenorhabditis elegans/genetics ; Chromosome Mapping ; Codon ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/*analysis/genetics ; Genes, rRNA/genetics ; *Genome ; Helminth Proteins/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Onchocerca volvulus/*genetics ; *Phylogeny ; Protein Biosynthesis ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; },
abstract = {The complete DNA sequence of the mitochondrial genome of Onchocerca volvulus is described. The O. volvulus mitochondrial genome is 13747 bp, slightly smaller than the mitochondrial genomes of the nematodes Ascaris suum and Caenorhabditis elegans, and the smallest metazoan mitochondrial DNA molecule reported to date. The O. volvulus mitochondrial genome contains genes for two ribosomal RNAs, 22 transfer RNAs and 12 proteins. Consistent with the small size of the genome, four gene pairs overlap and eight contain no intergenic regions. Only 17 intergenic regions are found, ranging in size from 1 to 46 bp. As in C. elegans and A. suum, the O. volvulus mitochondrial genome lacks an open reading frame encoding ATPase subunit 8, and all genes are apparently transcribed in the same direction. However, the mitochondrial gene order of O. volvulus differs from that of A. suum, C. elegans and other metazoan mitochondrial genomes. A total of 20 of the 22 transfer RNAs encoded in the O. volvulus mitochondrial genome have the potential to fold into secondary structures lacking the TpsiC arm, as has been reported in other nematodes. The genome exhibits a striking codon bias, with 15/20 amino acids having a single codon preference of > 70%.},
}
@article {pmid9821489,
year = {1998},
author = {McNiff, BE and Allard, MW},
title = {A test of Archonta monophyly and the phylogenetic utility of the mitochondrial gene 12S rRNA.},
journal = {American journal of physical anthropology},
volume = {107},
number = {3},
pages = {225-241},
doi = {10.1002/(SICI)1096-8644(199811)107:3&lt;225::AID-AJPA1&gt;3.0.CO;2-N},
pmid = {9821489},
issn = {0002-9483},
mesh = {Animals ; Genetic Markers ; Mammals/classification/genetics ; Mitochondria/*genetics ; Molecular Biology ; *Phylogeny ; Primates/*classification/genetics ; RNA, Ribosomal/classification/*genetics ; Sequence Analysis, RNA ; },
abstract = {The relationships within the superorder Archonta, which contains the orders Dermoptera (flying lemurs), Scandentia (tree shrews), Chiroptera (bats), and Primates, were examined through the analysis of five newly derived and complete mitochondrial 12S rRNA sequences. The new data is combined with 83 additional known mammalian sequences to provide a full phylogenetic sampling. Phylogenetic hypotheses are generated using PAUP 3.1.1 (Swofford [1993] Illinois Natural History Survey, Champaign, IL) through analyses of all characters equally weighted, transversions only, and the effect of alignment gaps on phylogeny. The Parsimony Jackknifer (Farris et al. [1996] Cladistics 12:99-124) was used to assess the level of ambiguity present in the sequence data, and therefore the strength of the tree topologies. The conclusions of Springer and Douzery (1996, J. Mol. Evol. 43:357-373) which states that 12S rRNA is reliable to a time depth of 100 mya is unsupported by these analyses. The usefulness of 12S rRNA to aid in solving Archonta relationships and others of similar time depth is found to be suspect.},
}
@article {pmid9837879,
year = {1998},
author = {Artigues, A and Crawford, DL and Iriarte, A and Martinez-Carrion, M},
title = {Divergent Hsc70 binding properties of mitochondrial and cytosolic aspartate aminotransferase. Implications for their segregation to different cellular compartments.},
journal = {The Journal of biological chemistry},
volume = {273},
number = {50},
pages = {33130-33134},
doi = {10.1074/jbc.273.50.33130},
pmid = {9837879},
issn = {0021-9258},
support = {GM-38341/GM/NIGMS NIH HHS/United States ; HL-38412/HL/NHLBI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/chemistry/classification/*metabolism ; Binding Sites ; Carrier Proteins/*metabolism ; Cattle ; Cell Compartmentation ; Cytosol/*enzymology ; HSC70 Heat-Shock Proteins ; *HSP70 Heat-Shock Proteins ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; },
abstract = {Cytosolic Hsc70 discriminates between the homologous mitochondrial and cytosolic isozymes of aspartate aminotransferase, binding exclusively the mitochondrial form. By screening a library of synthetic peptides spanning the sequence of the mitochondrial enzyme, we have identified binding sites in this polypeptide that interact with Hsc70. These potential binding sites are scattered over the entire sequence and map to secondary structure elements, particularly the alpha-helix, that are partly exposed on the surface of the native protein. Several peptides corresponding to analogous positions in the cytosolic enzyme sequence do not bind to Hsc70. Phylogenetic analyses suggest that Hsc70 binding sequences have diverged as a consequence of biochemical specialization ensuring differential interaction of each isozyme with the cellular machinery in charge of protein folding and translocation.},
}
@article {pmid9873084,
year = {1999},
author = {Rasmussen, AS and Arnason, U},
title = {Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes.},
journal = {Journal of molecular evolution},
volume = {48},
number = {1},
pages = {118-123},
doi = {10.1007/pl00006439},
pmid = {9873084},
issn = {0022-2844},
mesh = {Animals ; DNA, Mitochondrial/*chemistry/*genetics ; Dogfish/genetics ; Fishes/*classification/*genetics ; Genome ; Likelihood Functions ; Mitochondria, Liver/chemistry ; Molecular Sequence Data ; *Phylogeny ; },
abstract = {It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish, Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved. The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant bony fishes.},
}
@article {pmid9878234,
year = {1998},
author = {Gleeson, DM and Rowell, DM and Tait, NN and Briscoe, DA and Higgins, AV},
title = {Phylogenetic relationships among onychophora from Australasia inferred from the mitochondrial cytochrome oxidase subunit I gene.},
journal = {Molecular phylogenetics and evolution},
volume = {10},
number = {2},
pages = {237-248},
doi = {10.1006/mpev.1998.0512},
pmid = {9878234},
issn = {1055-7903},
mesh = {Animals ; Asia ; Australia ; Base Sequence ; Electron Transport Complex IV/*genetics ; Invertebrates/*classification/enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Nucleotide sequence variation in a region of the mitochondrial cytochrome oxidase subunit I (COI) gene (456 bp) was examined for 26 onychophorans representing 15 genera of the family Peripatopsidae from Australasia. Sequence analysis revealed high intergeneric COI sequence divergence (up to 20.6% corrected) but low amino acid substitution rates, with high levels of transitional saturation evident. Among unambiguously alignable sequences, parsimony and distance analyses revealed a broadly congruent tree topology, robust to various algorithms and statistical analysis. There are two major groupings. One, largely unresolved, consists entirely of Australian mainland taxa. The other, for which there is convincing support, includes all of the New Zealand and Tasmanian taxa together with one mainland Australian species. In respect of the two major groupings, this topology is consistent with previous morphologically based phylogenies and provides further evidence for an ancient radiation within the mainland Australian Onychophora. The biogeographic implications of the close affinities revealed between the Tasmanian and New Zealand taxa are discussed.},
}
@article {pmid9878631,
year = {1999},
author = {Wu, D and Wright, DA and Wetzel, C and Voytas, DF and Rodermel, S},
title = {The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis.},
journal = {The Plant cell},
volume = {11},
number = {1},
pages = {43-55},
pmid = {9878631},
issn = {1040-4651},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; *Arabidopsis Proteins ; Base Sequence ; Chloroplasts/*genetics ; Cloning, Molecular ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/*genetics/metabolism ; Oxidoreductases/*genetics ; Phylogeny ; Pigmentation/*genetics ; Plant Leaves/genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {Nuclear gene-induced variegation mutants provide a powerful system to dissect interactions between the genetic systems of the nucleus-cytoplasm, the chloroplast, and the mitochondrion. The immutans (im) variegation mutation of Arabidopsis is nuclear and recessive and results in the production of green- and white-sectored leaves. The green sectors contain cells with normal chloroplasts, whereas the white sectors are heteroplastidic and contain cells with abnormal, pigment-deficient plastids as well as some normal chloroplasts. White sector formation can be promoted by enhanced light intensities, but sectoring becomes irreversible early in leaf development. The white sectors accumulate the carotenoid precursor phytoene. We have positionally cloned IM and found that the gene encodes a 40.5-kD protein with sequence motifs characteristic of alternative oxidase, a mitochondrial protein that functions as a terminal oxidase in the respiratory chains of all plants. However, phylogenetic analyses revealed that the IM protein is only distantly related to these other alternative oxidases, suggesting that IM is a novel member of this protein class. We sequenced three alleles of im, and all are predicted to be null. Our data suggest a model of variegation in which the IM protein functions early in chloroplast biogenesis as a component of a redox chain responsible for phytoene desaturation but that a redundant electron transfer function is capable of compensating for IM activity in some plastids and cells.},
}
@article {pmid9952445,
year = {1999},
author = {Krath, BN and Hove-Jensen, B},
title = {Organellar and cytosolic localization of four phosphoribosyl diphosphate synthase isozymes in spinach.},
journal = {Plant physiology},
volume = {119},
number = {2},
pages = {497-506},
pmid = {9952445},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Base Sequence ; Chloroplasts/enzymology ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Escherichia coli/genetics ; Genetic Complementation Test ; Isoenzymes/genetics/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Organelles/enzymology ; Pisum sativum/enzymology ; Phylogeny ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Ribose-Phosphate Pyrophosphokinase/genetics/*metabolism ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology/genetics ; },
abstract = {Four cDNAs encoding phosphoribosyl diphosphate (PRPP) synthase were isolated from a spinach (Spinacia oleracea) cDNA library by complementation of an Escherichia coli Deltaprs mutation. The four gene products produced PRPP in vitro from ATP and ribose-5-phosphate. Two of the enzymes (isozymes 1 and 2) required inorganic phosphate for activity, whereas the others were phosphate independent. PRPP synthase isozymes 2 and 3 contained 76 and 87 amino acid extensions, respectively, at their N-terminal ends in comparison with other PRPP synthases. Isozyme 2 was synthesized in vitro and shown to be imported and processed by pea (Pisum sativum) chloroplasts. Amino acid sequence analysis indicated that isozyme 3 may be transported to mitochondria and that isozyme 4 may be located in the cytosol. The deduced amino acid sequences of isozymes 1 and 2 and isozymes 3 and 4 were 88% and 75% identical, respectively. In contrast, the amino acid identities of PRPP synthase isozyme 1 or 2 with 3 or 4 was modest (22%-25%), but the sequence motifs for binding of PRPP and divalent cation-nucleotide were identified in all four sequences. The results indicate that PRPP synthase isozymes 3 and 4 belong to a new class of PRPP synthases that may be specific to plants.},
}
@article {pmid9952460,
year = {1999},
author = {Thelen, JJ and Miernyk, JA and Randall, DD},
title = {Molecular cloning and expression analysis of the mitochondrial pyruvate dehydrogenase from maize.},
journal = {Plant physiology},
volume = {119},
number = {2},
pages = {635-644},
pmid = {9952460},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Conformation ; Pyruvate Dehydrogenase Complex/chemistry/*genetics ; Sequence Homology, Amino Acid ; Zea mays/*enzymology/*genetics ; },
abstract = {Four cDNAs, one encoding an alpha-subunit and three encoding beta-subunits of the mitochondrial pyruvate dehydrogenase, were isolated from maize (Zea mays L.) libraries. The deduced amino acid sequences of both alpha- and beta-subunits are approximately 80% identical with Arabidopsis and pea (Pisum sativum L.) homologs. The mature N terminus was determined for the beta-subunit by microsequencing the protein purified from etiolated maize shoot mitochondria and was resolved by two-dimensional gel electrophoresis. This single isoelectric species comprised multiple isoforms. Both alpha- and beta-subunits are encoded by multigene families in maize, as determined by Southern-blot analyses. RNA transcripts for both alpha- and beta-subunits were more abundant in roots than in young leaves or etiolated shoots. Pyruvate dehydrogenase activity was also higher in roots (5-fold) compared with etiolated shoots and leaves. Both subunits were present at similar levels in all tissues examined, indicating coordinated gene regulation. The protein levels were highest in heterotrophic organs and in pollen, which contained about 2-fold more protein than any other organ examined. The relative abundance of these proteins in nonphotosynthetic tissues may reflect a high cellular content of mitochondria, a high level of respiratory activity, or an extra plastidial requirement for acetate.},
}
@article {pmid10027191,
year = {1998},
author = {Ragan, MA and Gaasterland, T},
title = {Microbial genescapes: a prokaryotic view of the yeast genome.},
journal = {Microbial &amp; comparative genomics},
volume = {3},
number = {4},
pages = {219-235},
doi = {10.1089/omi.1.1998.3.219},
pmid = {10027191},
issn = {1090-6592},
mesh = {Archaea/genetics ; Bacteria/genetics ; Computational Biology ; DNA, Fungal/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Genes, Fungal ; *Genome, Fungal ; Open Reading Frames ; Phylogeny ; Saccharomyces cerevisiae/*genetics/metabolism ; },
abstract = {We examine the translated open reading frames (ORFs) of the yeast Saccharomyces cerevisiae, focusing on those that have FASTA matches in phyletically defined sets of completely sequenced genomes. On this basis, we identify archaeal yeast, bacterial yeast, universal yeast, and yeast ORFs that do not have a match in any of nine prokaryote genomes. Similarly, we examine the yeast mitochondrial genome and the subset of the yeast nuclear ORFs identified as being involved in mitochondrial biogenesis. For the yeast ORFs that match one or more ORFs in these prokaryote genomes, we examine the phyletic and functional distributions of these matches as a function of match strength. These results provide genome level insights into the origin of the eukaryotic cell and the origin of mitochondria. More generally, they exemplify how the growing database of prokaryote genome sequences can help us understand eukaryote genomes.},
}
@article {pmid10082615,
year = {1999},
author = {Chippindale, PT and Davé, VK and Whitmore, DH and Robinson, JV},
title = {Phylogenetic relationships of North American damselflies of the genus Ischnura (Odonata: Zygoptera: Coenagrionidae) based on sequences of three mitochondrial genes.},
journal = {Molecular phylogenetics and evolution},
volume = {11},
number = {1},
pages = {110-121},
doi = {10.1006/mpev.1998.0559},
pmid = {10082615},
issn = {1055-7903},
mesh = {Animals ; Cytochrome b Group/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Insecta/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Species Specificity ; Statistics as Topic ; },
abstract = {Relationships of North American damselflies of the genus Ischnura (Odonata: Zygoptera: Coenagrionidae) were investigated using a total of 1205 bp from portions of three mitochondrial genes: cytochrome b, cytochrome oxidase II, and 12S ribosomal DNA. Parsimony and neighbor joining analyses reveal a monophyletic group consisting of I. damula, I. demorsa, I. perparva, I. posita posita, I. posita atezca, I. verticalis, and probably I. denticollis, likely reflecting a recent radiation in North America. Ischnura kellicotti, I. barberi, I. prognata, I. hastata, I. ramburii, and I. capreola appear to represent much earlier divergences in the group. Many previous hypotheses of relationships among North American species of Ischnura are not supported by the molecular-based analyses. However, there is agreement in many respects between the results of the molecular phylogenetic analyses and the morphologically based conclusions of Kennedy (1919, "The Phylogeny of the Zygoptera," Ph.D. Dissertation, Cornell University, Ithaca). Although results of single-gene phylogenetic analyses often differ, there are very few cases in which there is strong support for conflicting relationships using different partitions of the data. Combined analysis of all three genes yields trees with stronger support overall than the single-gene analyses, and the combined data trees that result from diverse data treatments are congruent with one another in most respects.},
}
@article {pmid10092866,
year = {1999},
author = {Bof, M and Brandolin, G and Satre, M and Klein, G},
title = {The mitochondrial adenine nucleotide translocator from Dictyostelium discoideum. Functional characterization and DNA sequencing.},
journal = {European journal of biochemistry},
volume = {259},
number = {3},
pages = {795-800},
doi = {10.1046/j.1432-1327.1999.00088.x},
pmid = {10092866},
issn = {0014-2956},
mesh = {Animals ; Atractyloside/analogs &amp; derivatives/pharmacology ; Cell Differentiation/genetics ; Cell Division/drug effects ; Cloning, Molecular ; Dictyostelium/*genetics ; Enzyme Inhibitors/pharmacology ; Gene Expression Regulation, Developmental/genetics ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics ; Phylogeny ; Protozoan Proteins/chemistry/*genetics ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {The mitochondrial adenine nucleotide translocator (ANT) catalyses the exchange of ATP and ADP between the mitochondria and the cytosol. We have cloned and sequenced the gene encoding the Dictyostelium discoideum ANT (DdANT) and analysed its transcriptional regulation. The single copy D. discoideum ant gene encodes a protein of 309 amino acid residues with a predicted molecular mass of 33,469 Da and a pI of 9.85. These values are comparable to those of ANTs from mammals, insects and fungi. The long N-terminal extension characteristic of plant ANT is absent in DdANT. The protein coding region of the D. discoideum ant gene is interrupted by three introns. Polyclonal antibodies directed against the beef heart mitochondrial ANT or its C-terminal peptide recognized the D. discoideum protein. Northern blot analysis revealed that the expression of the D. discoideum ant gene decreased rapidly during the first hours of multicellular development but the amount of protein remained stable throughout differentiation.},
}
@article {pmid10093219,
year = {1999},
author = {Steinhauser, S and Beckert, S and Capesius, I and Malek, O and Knoop, V},
title = {Plant mitochondrial RNA editing.},
journal = {Journal of molecular evolution},
volume = {48},
number = {3},
pages = {303-312},
doi = {10.1007/pl00006473},
pmid = {10093219},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Base Sequence ; Chloroplasts/metabolism ; DNA Primers ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics ; Plants/classification/*genetics ; Polymerase Chain Reaction ; RNA/*genetics ; *RNA Editing ; RNA, Mitochondrial ; Sequence Homology, Amino Acid ; },
abstract = {RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene (1104 nt) was analyzed in a large collection of bryophytes and green algae (Charles). The genomic nad5 sequences predict editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae, on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.},
}
@article {pmid10093228,
year = {1999},
author = {DeWoody, JA and Chesser, RK and Baker, RJ},
title = {A translocated mitochondrial cytochrome b pseudogene in voles (Rodentia: Microtus).},
journal = {Journal of molecular evolution},
volume = {48},
number = {3},
pages = {380-382},
doi = {10.1007/pl00013154},
pmid = {10093228},
issn = {0022-2844},
mesh = {Animals ; Arvicolinae/classification/*genetics ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; *Pseudogenes ; Sequence Homology, Nucleic Acid ; *Translocation, Genetic ; },
abstract = {A full-length cytochrome b pseudogene was found in rodents; it has apparently been translocated from a mitochondrion to the nuclear genome in the subfamily Arvicolinae. The pseudogene (psi cytb) differed from its mitochondrial counterpart at 201 of 1143 sites (17.6%) and by four indels. Cumulative evidence suggests that the pseudogene has been translocated to the nucleus. Phylogenetic reconstruction indicates that the pseudogene arose before the diversification of M. arvalis/M. rossiaemeridionalis from M. oeconomus, but after the divergence of the peromyscine/sigmodontine/ arvicoline clades some approximately 10 MYA. Published rates of divergence between mitochondrial genes and their nuclear pseudogenes suggest that the translocation of this mitochondrial gene to the nuclear genome occurred some 6 MYA, in agreement with the phylogenetic evidence.},
}
@article {pmid10222164,
year = {1999},
author = {Murrell, A and Campbell, NJ and Barker, SC},
title = {Mitochondrial 12S rDNA indicates that the Rhipicephalinae (Acari: Ixodida) is paraphyletic.},
journal = {Molecular phylogenetics and evolution},
volume = {12},
number = {1},
pages = {83-86},
doi = {10.1006/mpev.1998.0595},
pmid = {10222164},
issn = {1055-7903},
mesh = {Animals ; Ixodes/*classification/*genetics ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, RNA ; },
}
@article {pmid10319184,
year = {1999},
author = {Hesse, H and Lipke, J and Altmann, T and Höfgen, R},
title = {Molecular cloning and expression analyses of mitochondrial and plastidic isoforms of cysteine synthase (O-acetylserine(thiol)lyase) from Arabidopsis thaliana.},
journal = {Amino acids},
volume = {16},
number = {2},
pages = {113-131},
doi = {10.1007/BF01321531},
pmid = {10319184},
issn = {0939-4451},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Cloning, Molecular ; Cysteine Synthase/*genetics/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; *Protein Isoforms ; Recombinant Fusion Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Time Factors ; Tissue Distribution ; },
abstract = {Cysteine synthase, the key enzyme for fixation of inorganic sulfide, catalyses the formation of cysteine from O-acetylserine and inorganic sulfide. Here we report the cloning of cDNAs encoding cysteine synthase isoforms from Arabidopsis thaliana. The isolated cDNA clones encode for a mitochondrial and a plastidic isoform of cysteine synthase (O-acetylserine (thiol)-lyase, EC 4.2.99.8), designated cysteine synthase C (AtCS-C, CSase C) and B (AtCS-B; CSase B), respectively. AtCS-C and AtCS-B, having lengths of 1569-bp and 1421-bp, respectively, encode polypeptides of 430 amino acids (approximately 45.8 kD) and of 392 amino acids (approximately 41.8 kD), respectively. The deduced amino acid sequences of the mitochondrial and plastidic isoforms exhibit high homology even with respect to the presequences. The predicted presequence of AtCS-C has a N-terminal extension of 33 amino acids when compared to the plastidic isoform. Northern blot analysis showed that AtCS-C is higher expressed in roots than in leaves whereas the expression of AtCS-B is stronger in leaves. Furthermore, gene expression of both genes was enhanced by sulfur limitation which in turn led to an increase in enzyme activity in crude extracts of plants. Expression of the AtCS-B gene is regulated by light. The mitochondrial, plastidic and cytosolic (Hesse and Altmann, 1995) isoforms of cysteine synthase of Arabidopsis are able to complement a cysteine synthase-deficient mutant of Escherichia coli unable to grow on minimal medium without cysteine, indicating synthesis of functional plant proteins in the bacterium. Two lines of evidence proved that AtCS-C encodes a mitochondrial form of cysteine synthase; first, import of in vitro translation products derived from AtCS-C in isolated intact mitochondria and second, Western blot analysis of mitochondria isolated from transgenic tobacco plants expressing AtCS-C cDNA/c-myc DNA fusion protein.},
}
@article {pmid10335652,
year = {1999},
author = {Takezaki, N and Gojobori, T},
title = {Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences.},
journal = {Molecular biology and evolution},
volume = {16},
number = {5},
pages = {590-601},
doi = {10.1093/oxfordjournals.molbev.a026141},
pmid = {10335652},
issn = {0737-4038},
mesh = {Amino Acids/genetics ; Animals ; DNA, Mitochondrial/*genetics ; Humans ; *Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Vertebrates/*physiology ; },
abstract = {Concatenated sequences of all protein-coding genes in mitochondria recovered a known phylogeny of 11 vertebrate species correctly with statistical significance. However, when it was rooted by lampreys or sea urchins, the root of the vertebrate tree was placed between the mammal cluster and the chicken-frog-fish cluster or between the mammal-chicken cluster and the frog-fish cluster, depending on the tree-making method used. Although the frog-fish or chicken-frog-fish cluster was biologically incorrect, it was again supported with a significantly high bootstrap value. In this study, we investigated the reasons why this happened. It has been suggested that an incorrect phylogeny may be constructed due to a change of amino acid composition in different lineages or due to homoplasies at sites with hydrophobic amino acids. However, our results indicated that these were not the causes of the incorrect rooting of the vertebrate tree. Rather, it was important to take into account an extensive rate variation across sites and different probabilities of substitution among different amino acids. The substitution rates for mitochondrial sequences vary considerably for different vertebrate lineages. In such a case, it is known to be important to use the model that reflects the actual substitution probability to obtain a correct tree topology. The correct rooting of the vertebrate tree was recovered when rate variation across sites was properly accounted for.},
}
@article {pmid10361311,
year = {1999},
author = {Akhmanova, A and Voncken, FG and Hosea, KM and Harhangi, H and Keltjens, JT and op den Camp, HJ and Vogels, GD and Hackstein, JH},
title = {A hydrogenosome with pyruvate formate-lyase: anaerobic chytrid fungi use an alternative route for pyruvate catabolism.},
journal = {Molecular microbiology},
volume = {32},
number = {5},
pages = {1103-1114},
doi = {10.1046/j.1365-2958.1999.01434.x},
pmid = {10361311},
issn = {0950-382X},
mesh = {Acetyltransferases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Anaerobiosis ; Base Sequence ; Blotting, Northern ; Blotting, Western ; DNA, Complementary ; DNA, Fungal ; Endopeptidase K/metabolism ; Gene Library ; Genes, Fungal ; Hydrogen/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Organelles/*enzymology ; Phylogeny ; Piromyces/*enzymology/genetics ; Pyruvic Acid/*metabolism ; Sequence Alignment ; },
abstract = {The chytrid fungi Piromyces sp. E2 and Neocallimastix sp. L2 are obligatory amitochondriate anaerobes that possess hydrogenosomes. Hydrogenosomes are highly specialized organelles engaged in anaerobic carbon metabolism; they generate molecular hydrogen and ATP. Here, we show for the first time that chytrid hydrogenosomes use pyruvate formate-lyase (PFL) and not pyruvate:ferredoxin oxidoreductase (PFO) for pyruvate catabolism, unlike all other hydrogenosomes studied to date. Chytrid PFLs are encoded by a multigene family and are abundantly expressed in Piromyces sp. E2 and Neocallimastix sp. L2. Western blotting after cellular fractionation, proteinase K protection assays and determinations of enzyme activities reveal that PFL is present in the hydrogenosomes of Piromyces sp. E2. The main route of the hydrogenosomal carbon metabolism involves PFL; the formation of equimolar amounts of formate and acetate by isolated hydrogenosomes excludes a significant contribution by PFO. Our data support the assumption that chytrid hydrogenosomes are unique and argue for a polyphyletic origin of these organelles.},
}
@article {pmid10366551,
year = {1999},
author = {Campbell, RB},
title = {The coalescent time in the presence of background fertility selection.},
journal = {Theoretical population biology},
volume = {55},
number = {3},
pages = {260-269},
doi = {10.1006/tpbi.1998.1402},
pmid = {10366551},
issn = {0040-5809},
mesh = {Female ; *Fertility ; Gene Frequency/*genetics ; Genetic Linkage/genetics ; Genetic Variation/*genetics ; Haploidy ; Humans ; Male ; Markov Chains ; Mitochondria/genetics ; *Models, Genetic ; Pedigree ; Phylogeny ; Poisson Distribution ; Reproducibility of Results ; *Selection, Genetic ; Sex Characteristics ; Time Factors ; Y Chromosome/genetics ; },
abstract = {Selection ultimately entails differential reproductive success over several generations. This can be measured as a correlation of the number of progeny an individual has with the number of progeny its parent had. This correlation could have a genetic or a cultural basis. The effect of such a correlation is to multiply the single generation sampling variance (Vdeltap) in the diffusion approximation for fixation time by (1-b)+bx(1+r)/(1-r), where bxrn is the correlation between the number of progeny of an individual and its ancestor n generations ago (e.g., b is the heritability and br is the resultant parent-offspring progeny number correlation if the progeny number is genetically determined). This results in a reduction of the fixation or coalescent time by division by this factor. Sex differences in this correlation have been observed, and this provides an explanation for the difference of coalescent times of y-chromosomes and mitochondria.},
}
@article {pmid10419971,
year = {1999},
author = {Westenberg, DJ and Guerinot, ML},
title = {Succinate dehydrogenase (Sdh) from Bradyrhizobium japonicum is closely related to mitochondrial Sdh.},
journal = {Journal of bacteriology},
volume = {181},
number = {15},
pages = {4676-4679},
pmid = {10419971},
issn = {0021-9193},
mesh = {Animals ; Base Sequence ; Bradyrhizobium/classification/*enzymology/genetics ; Cloning, Molecular ; Consensus Sequence ; Genetic Complementation Test ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Operon ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Glycine max/microbiology ; Succinate Dehydrogenase/chemistry/*genetics/metabolism ; Symbiosis ; },
abstract = {The sdhCDAB operon, encoding succinate dehydrogenase, was cloned from the soybean symbiont Bradyrhizobium japonicum. Sdh from B. japonicum is phylogenetically related to Sdh from mitochondria. This is the first example of a mitochondrion-like Sdh functionally expressed in Escherichia coli.},
}
@article {pmid10437831,
year = {1999},
author = {Takabatake, R and Hata, S and Taniguchi, M and Kouchi, H and Sugiyama, T and Izui, K},
title = {Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopis.},
journal = {Plant molecular biology},
volume = {40},
number = {3},
pages = {479-486},
pmid = {10437831},
issn = {0167-4412},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Cloning, Molecular ; DNA, Complementary/*genetics/*isolation &amp; purification ; DNA, Plant/*genetics/*isolation &amp; purification ; Escherichia coli/genetics ; Gene Expression ; Mitochondria/metabolism ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phosphate-Binding Proteins ; Phosphates/*metabolism ; Phylogeny ; Plants/*genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Glycine max/genetics/metabolism ; Zea mays/genetics/metabolism ; },
abstract = {cDNA clones encoding mitochondrial phosphate transporters were isolated from four herbaceous plants. The cDNAs for the soybean, maize and rice transporters contained entire coding regions, whereas the Arabidopsis cDNA lacked the 5' portion. The hydropathy profiles of the deduced amino acid sequences predicted the existence of six membrane-spanning domains which are highly conserved in the mitochondrial transporter family. In soybeans, the mRNA level for the transporter was high in tissues containing dividing cells. It was suggested that there are multiple copies of transporter genes in both dicots and monocots. The soybean transporter was expressed as inclusion bodies in Escherichia coli, solubilized with detergents, and then reconstituted into liposomes. The resulting proteoliposomes exhibited high phosphate transport activity. The activity was inhibited by N-ethylmaleimide, like those of mammalian phosphate transporters.},
}
@article {pmid10447674,
year = {1999},
author = {Pineda, AO and Ellington, WR},
title = {Structural and functional implications of the amino acid sequences of dimeric, cytoplasmic and octameric mitochondrial creatine kinases from a protostome invertebrate.},
journal = {European journal of biochemistry},
volume = {264},
number = {1},
pages = {67-73},
doi = {10.1046/j.1432-1327.1999.00577.x},
pmid = {10447674},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Creatine Kinase/*chemistry ; Cytoplasm/*enzymology ; DNA Primers ; DNA, Complementary ; Dimerization ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Polychaeta/*enzymology ; Sequence Homology, Amino Acid ; },
abstract = {The cDNA and deduced amino-acid sequences for dimeric and octameric isoforms of creatine kinase (CK) from a protostome, the polychaete Chaetopterus variopedatus, were elucidated and then analysed in the context of available vertebrate CK sequences and the recently determined crystal structure of chicken sarcomeric mitochondrial CK (MiCK). As protostomes last shared a common ancestor with vertebrates roughly 700 million years ago, observed conserved residues may serve to confirm or reject contemporary hypotheses about the roles of particular amino acids in functional/structural processes such as dimer/octamer formation and membrane binding. The isolated cDNA from the dimeric CK consisted of 1463 nucleotides with an open reading frame of 1116 nucleotides encoding a 372-amino-acid protein having a calculated molecular mass of 41.85 kDa. The percentage identity of C. variopedatus dimeric CK to vertebrate CK is as high as 69%. The octameric MiCK cDNA is composed of 1703 nucleotides with an open reading frame of 1227 nucleotides. The first 102 nucleotides of the open reading frame encode a 34-amino-acid leader peptide whereas the mature protein is composed of 375 amino acids with a calculated molecular mass of 42.17 kDa. The percentage identity of C. variopedatus MiCK to vertebrate CK is as high as 71%. This similarity is also evident in residues purported to be important in the structure and function of dimeric and octameric CK: (a) presence of seven basic amino acids in the C-terminal end thought to be important in binding of MiCK to membranes; (b) presence of a lysine residue (Lys110 in chicken MiCK) also thought to be involved in membrane binding; and (c) presence of a conserved tryptophan thought to be important in dimer stabilization which is present in all dimeric and octameric guanidino kinases. However, C. variopedatus MiCK lacks the N-terminal heptapeptide present in chicken MiCK, which is thought to mediate octamer stabilization. In contrast with vertebrate MiCK, polychaete octamers are very stable indicating that dimer binding into octamers may be mediated by additional and/or other residues. Phylogenetic analyses showed that both octamer and dimer evolved very early in the CK lineage, well before the divergence of deuterostomes and protostomes. These results indicate that the octamer is a primitive feature of CK rather than being a derived and advanced character.},
}
@article {pmid10449446,
year = {1999},
author = {Herr, RA and Ajello, L and Taylor, JW and Arseculeratne, SN and Mendoza, L},
title = {Phylogenetic analysis of Rhinosporidium seeberi's 18S small-subunit ribosomal DNA groups this pathogen among members of the protoctistan Mesomycetozoa clade.},
journal = {Journal of clinical microbiology},
volume = {37},
number = {9},
pages = {2750-2754},
pmid = {10449446},
issn = {0095-1137},
mesh = {DNA, Ribosomal/*chemistry ; Microscopy, Electron ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Rhinosporidium/*classification/genetics/ultrastructure ; },
abstract = {For the past 100 years the phylogenetic affinities of Rhinosporidium seeberi have been controversial. Based on its morphological features, it has been classified as a protozoan or as a member of the kingdom Fungi. We have amplified and sequenced nearly a full-length 18S small-subunit (SSU) ribosomal DNA (rDNA) sequence from R. seeberi. Using phylogenetic analysis, by parsimony and distance methods, of R. seeberi's 18S SSU rDNA and that of other eukaryotes, we found that this enigmatic pathogen of humans and animals clusters with a novel group of fish parasites referred to as the DRIP clade (Dermocystidium, rossete agent, Ichthyophonus, and Psorospermium), near the animal-fungal divergence. Our phylogenetic analyses also indicate that R. seeberi is the sister taxon of the two Dermocystidium species used in this study. This molecular affinity is remarkable since members of the genus Dermocystidium form spherical structures in infected hosts, produce endospores, have not been cultured, and possess mitochondria with flat cristae. With the addition of R. seeberi to this clade, the acronym DRIP is no longer appropriate. We propose to name this monophyletic clade Mesomycetozoa to reflect the group's phylogenetic association within the Eucarya.},
}
@article {pmid10455226,
year = {1999},
author = {Shi, NQ and Davis, B and Sherman, F and Cruz, J and Jeffries, TW},
title = {Disruption of the cytochrome c gene in xylose-utilizing yeast Pichia stipitis leads to higher ethanol production.},
journal = {Yeast (Chichester, England)},
volume = {15},
number = {11},
pages = {1021-1030},
doi = {10.1002/(SICI)1097-0061(199908)15:11&lt;1021::AID-YEA429&gt;3.0.CO;2-V},
pmid = {10455226},
issn = {0749-503X},
support = {R01 GM12702/GM/NIGMS NIH HHS/United States ; },
mesh = {Antifungal Agents/chemistry/metabolism ; Base Sequence ; Blotting, Southern ; Cytochrome c Group/chemistry/*genetics ; DNA Primers ; DNA, Fungal/chemistry ; Electron Transport/genetics ; Ethanol/*metabolism ; Fermentation ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Pichia/genetics/growth &amp; development/*metabolism ; Polymerase Chain Reaction ; Salicylamides/chemistry/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Xylose/*metabolism ; },
abstract = {The xylose-utilizing yeast, Pichia stipitis, has a complex respiratory system that contains cytochrome and non-cytochrome alternative electron transport chains in its mitochondria. To gain primary insights into the alternative respiratory pathway, a cytochrome c gene (PsCYC1, Accession No. AF030426) was cloned from wild-type P. stipitis CBS 6054 by cross-hybridization to CYC1 from Saccharomyces cerevisiae. The 333 bp open reading frame of PsCYC1 showed 74% and 69% identity to ScCYC1 and ScCYC7, respectively, at the DNA level. Disruption of PsCYC1 resulted in a mutant that uses the salicylhydroxamic acid (SHAM)-sensitive respiratory pathway for aerobic energy production. Cytochrome spectra revealed that cytochromes c and a.a(3) both disappeared in the cyc1-Delta mutant, so no electron flow through the cytochrome c oxidase was possible. The cyc1-Delta mutant showed 50% lower growth rates than the parent when grown on fermentable sugars. The cyc1-Delta mutant was also found to be unable to grow on glycerol. Interestingly, the mutant produced 0.46 g/g ethanol from 8% xylose, which was 21% higher in yield than the parental strain (0.38 g/g). These results suggested that the alternative pathway might play an important role in supporting xylose conversion to ethanol under oxygen-limiting conditions.},
}
@article {pmid10480381,
year = {1999},
author = {Ikeda, TM and Gray, MW},
title = {Identification and characterization of T3/T7 bacteriophage-like RNA polymerase sequences in wheat.},
journal = {Plant molecular biology},
volume = {40},
number = {4},
pages = {567-578},
pmid = {10480381},
issn = {0167-4412},
mesh = {Amino Acid Sequence ; Bacteriophage T3/*enzymology ; Bacteriophage T7/*enzymology ; Base Sequence ; Cloning, Molecular ; DNA-Directed RNA Polymerases/*genetics ; Genes, Plant/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Triticum/chemistry/enzymology/*genetics ; },
abstract = {Using PCR-based methods, we assembled two wheat cDNA sequences, wheat-G and wheat-C, that encode T3/T7 bacteriophage-like RNA polymerases (RNAPs) sharing 45% amino acid identity. In phylogenetic analyses using maximum likelihood, parsimony and distance methods, the predicted protein sequence of wheat-G (1005 amino acids, 113 kDa) clusters with sequences of previously assigned mitochondrial RNAPs from dicotyledonous plants (Arabidopsis thaliana, Chenopodium album); likewise, in such analyses, the wheat-C sequence (949 amino acids, 107 kDa) affiliates specifically with the Arabidopsis sequence that encodes a phage-like RNAP thought to function in chloroplasts. To confirm biochemically the assignment of the gene encoding the putative wheat mitochondrial RNAP, we isolated a ca. 100 kDa wheat mitochondrial protein that is enriched in fractions displaying specific in vitro transcription activity and that reacts with an antibody raised against a recombinant maize phage-type RNAP. Internal peptide sequence information obtained from the 100-kDa polypeptide revealed that it corresponds to the predicted wheat-G cDNA sequence, providing direct evidence that the wheat-G gene (which we propose to call RpoTm) encodes the wheat mitochondrial RNAP.},
}
@article {pmid10497022,
year = {1999},
author = {Schulte, U and Haupt, V and Abelmann, A and Fecke, W and Brors, B and Rasmussen, T and Friedrich, T and Weiss, H},
title = {A reductase/isomerase subunit of mitochondrial NADH:ubiquinone oxidoreductase (complex I) carries an NADPH and is involved in the biogenesis of the complex.},
journal = {Journal of molecular biology},
volume = {292},
number = {3},
pages = {569-580},
doi = {10.1006/jmbi.1999.3096},
pmid = {10497022},
issn = {0022-2836},
mesh = {Electron Spin Resonance Spectroscopy ; Electron Transport ; Electron Transport Complex I ; Electrophoresis, Polyacrylamide Gel ; Gene Deletion ; Kinetics ; Mitochondria/*enzymology ; NAD/chemistry ; NAD(P)H Dehydrogenase (Quinone)/*biosynthesis ; NADH, NADPH Oxidoreductases/*chemistry/genetics ; NADP/*chemistry ; Neurospora crassa/*enzymology/genetics ; Oxidation-Reduction ; Phylogeny ; Protein Binding ; Spectrophotometry ; },
abstract = {Respiratory chains of bacteria and mitochondria contain closely related forms of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I. The bacterial complex I consists of 14 subunits, whereas the mitochondrial complex contains some 25 extra subunits in addition to the homologues of the bacterial subunits. One of these extra subunits with a molecular mass of 40 kDa belongs to a heterogeneous family of reductases/isomerases with a conserved nucleotide binding site. We deleted this subunit in Neurospora crassa by gene disruption. In the mutant nuo 40, a complex I lacking the 40 kDa subunit is assembled. The mutant complex I does not contain tightly bound NADPH present in wild-type complex I. This NADPH cofactor is not connected to the respiratory electron pathway of complex I. The mutant complex has normal NADH dehydrogenase activity and contains the redox groups known for wild-type complex I, one flavin mononucleotide and four iron-sulfur clusters detectable by electron paramagnetic resonance spectroscopy. In the mutant complex these groups are all readily reduced by NADH. However, the mutant complex is not capable of reducing ubiquinone. A recently described redox group identified in wild-type complex I by UV-visible spectroscopy is not detectable in the mutant complex. We propose that the reductase/isomerase subunit with its NADPH cofactor takes part in the biosynthesis of this new redox group.},
}
@article {pmid10519246,
year = {1999},
author = {Riordan, CE and Langreth, SG and Sanchez, LB and Kayser, O and Keithly, JS},
title = {Preliminary evidence for a mitochondrion in Cryptosporidium parvum: phylogenetic and therapeutic implications.},
journal = {The Journal of eukaryotic microbiology},
volume = {46},
number = {5},
pages = {52S-55S},
pmid = {10519246},
issn = {1066-5234},
support = {AI 43020/AI/NIAID NIH HHS/United States ; },
mesh = {Adenylate Kinase/genetics ; Amino Acid Sequence ; Animals ; Chaperonins/genetics ; Cryptosporidium parvum/drug effects/*genetics/metabolism/*ultrastructure ; DNA, Protozoan/genetics ; Mitochondria/drug effects/*genetics/*metabolism ; Molecular Sequence Data ; Naphthoquinones/pharmacology ; Phylogeny ; Sequence Analysis, DNA ; Valine-tRNA Ligase/genetics ; },
}
@article {pmid10542417,
year = {1999},
author = {Boore, JL and Fuerstenberg, SI},
title = {Entamoeba histolytica: a derived, mitochondriate eukaryote?.},
journal = {Trends in microbiology},
volume = {7},
number = {11},
pages = {426-428},
doi = {10.1016/s0966-842x(99)01606-6},
pmid = {10542417},
issn = {0966-842X},
mesh = {Animals ; Cell Nucleus/genetics ; Entamoeba histolytica/*classification/*genetics/metabolism/ultrastructure ; *Eukaryotic Cells ; Mitochondria/*genetics ; Organelles/physiology ; Phylogeny ; },
}
@article {pmid10546224,
year = {1999},
author = {Emel'ianov, VV},
title = {[Hypothetic molecular basis of obligate parasitism of Rickettsiae].},
journal = {Molekuliarnaia biologiia},
volume = {33},
number = {4},
pages = {684-687},
pmid = {10546224},
issn = {0026-8984},
mesh = {DNA, Bacterial/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Rickettsiaceae/*genetics ; },
}
@article {pmid10552927,
year = {1999},
author = {Jin, H and Kendall, E and Freeman, TC and Roberts, RG and Vetrie, DL},
title = {The human family of Deafness/Dystonia peptide (DDP) related mitochondrial import proteins.},
journal = {Genomics},
volume = {61},
number = {3},
pages = {259-267},
doi = {10.1006/geno.1999.5966},
pmid = {10552927},
issn = {0888-7543},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Blotting, Northern ; Carrier Proteins/*genetics/metabolism ; Chromosome Mapping ; Chromosomes, Artificial, Yeast ; Deafness/*genetics ; Dystonia/*genetics ; Humans ; In Situ Hybridization, Fluorescence ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Yeasts/genetics/metabolism ; },
abstract = {The gene responsible for the human genetic neurodegenerative disorder DFN-1/MTS encodes a small protein known as deafness/dystonia peptide (DDP). It bears a strong resemblance to a recently characterized set of zinc-binding yeast proteins (Tim8p, Tim9p, Tim10p, Tim12p, and Tim13p) that are implicated in the import of a class of transmembrane carrier proteins from the cytoplasm to the mitochondrial inner membrane. We describe here the human complement of DDP/Tim-like proteins and establish the likely orthologous relationships between sequences from human, yeast, and other organisms. We also describe the expression patterns and chromosomal locations of their genes, which are candidate loci for autosomal recessive neurodegenerative disorders.},
}
@article {pmid10564443,
year = {1999},
author = {Ross, TK},
title = {Phylogeography and conservation genetics of the Iowa pleistocene snail.},
journal = {Molecular ecology},
volume = {8},
number = {9},
pages = {1363-1373},
doi = {10.1046/j.1365-294x.1999.00696.x},
pmid = {10564443},
issn = {0962-1083},
mesh = {Animals ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Genes, rRNA ; Genetic Variation ; Genetics, Population ; Geography ; Iowa ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*genetics/physiology ; },
abstract = {The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.},
}
@article {pmid10581290,
year = {1999},
author = {Yokobori, Si and Ueda, T and Feldmaier-Fuchs, G and Pääbo, S and Ueshima, R and Kondow, A and Nishikawa, K and Watanabe, K},
title = {Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).},
journal = {Genetics},
volume = {153},
number = {4},
pages = {1851-1862},
pmid = {10581290},
issn = {0016-6731},
mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Codon ; DNA, Mitochondrial/*genetics ; *Genome ; Humans ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer, Gly/chemistry/genetics ; Urochordata/*genetics ; },
abstract = {The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.},
}
@article {pmid10601861,
year = {2000},
author = {Papenbrock, J and Schmidt, A},
title = {Characterization of a sulfurtransferase from Arabidopsis thaliana.},
journal = {European journal of biochemistry},
volume = {267},
number = {1},
pages = {145-154},
doi = {10.1046/j.1432-1327.2000.00980.x},
pmid = {10601861},
issn = {0014-2956},
mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*enzymology ; Blotting, Southern ; Chloroplasts/enzymology ; Cloning, Molecular ; Cyanides/metabolism ; Cysteine/*analogs &amp; derivatives/metabolism ; Expressed Sequence Tags ; Genes, Plant/genetics ; Hydrogen-Ion Concentration ; Isoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Sorting Signals/chemistry/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Deletion/genetics ; Substrate Specificity ; Sulfurtransferases/chemistry/genetics/isolation &amp; purification/*metabolism ; Thiosulfate Sulfurtransferase/chemistry/genetics ; Thiosulfates/*metabolism ; },
abstract = {A database search for similarities between sequenced parts of the Arabidopsis thaliana genome with known sulfurtransferase sequences from Escherichia coli and mammals was undertaken to obtain information about plant sulfurtransferase-like proteins. One gene and several homologous EST clones were identified. One of the EST clones was used for screening an Arabidopsis cDNA library. The isolated full-length clone consists of 1134 bp and encodes a 42.6 kDa protein that includes a putative transit peptide sequence of about 7.1 kDa. Sequence comparisons with known sulfurtransferases from different organisms confirmed high homology between them and the existence of several highly conserved regions. Results of a Southern blot performed with genomic Arabidopsis DNA showed the occurrence of at least two sulfurtransferase-like isozymes in Arabidopsis. Recombinant proteins with and without the putative transit peptide were expressed in E. coli with an N-terminal His6-tag, purified by affinity chromatography and tested for enzyme activity using different sulfur donors and acceptors. Both recombinant proteins catalyzed the formation of SCN- from thiosulfate and cyanide as a rhodanese per definition; however, both recombinant proteins preferred 3-mercaptopyruvate to thiosulfate. A monospecific antibody produced by using the mature recombinant protein as an antigen recognized a single protein band in total extracts of Arabidopsis plants equating to the full-length protein size. A single band equating to the size of the mature protein was detected from purified Arabidopsis mitochondria, but there was no antigenic reaction with any protein from chloroplasts. The function of the protein is still speculative. Now tools are available to elucidate the roles and substrates of this sulfurtransferase in higher plants.},
}
@article {pmid10605113,
year = {1999},
author = {Vavre, F and Fleury, F and Lepetit, D and Fouillet, P and Boulétreau, M},
title = {Phylogenetic evidence for horizontal transmission of Wolbachia in host-parasitoid associations.},
journal = {Molecular biology and evolution},
volume = {16},
number = {12},
pages = {1711-1723},
doi = {10.1093/oxfordjournals.molbev.a026084},
pmid = {10605113},
issn = {0737-4038},
mesh = {Animals ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Data Interpretation, Statistical ; Drosophila/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wolbachia/*genetics ; },
abstract = {Endosymbiotic Wolbachia infect a number of arthropod species in which they can affect the reproductive system. While maternally transmitted, unlike mitochondria their molecular phylogeny does not parallel that of their hosts. This strongly suggests horizontal transmission among species, the mechanisms of which remain unknown. Such transfers require intimate between-species relationships, and thus host-parasite associations are outstandingly appropriate for study. Here, we demonstrate that hymenopteran parasitoids of frugivorous Drosophila species are especially susceptible to Wolbachia infection. Of the five common European species, four proved to be infected; furthermore, multiple infections are common, with one species being doubly infected and two triply infected (first report). Phylogenetic statuses of the Wolbachia infecting the different species of the community have been studied using the gene wsp, a highly variable gene recently described. This study reveals exciting similarities between the Wolbachia variants found in parasitoids and their hosts. These arguments strongly support the hypothesis of frequent natural Wolbachia transfers into other species and open a new field for genetic exchanges among species, especially in host-parasitoid associations.},
}
@article {pmid10607403,
year = {1999},
author = {Escobar Galvis, ML and Håkansson, G and Alexciev, K and Knorpp, C},
title = {Cloning and characterisation of a pea mitochondrial NDPK.},
journal = {Biochimie},
volume = {81},
number = {12},
pages = {1089-1096},
doi = {10.1016/s0300-9084(99)00353-3},
pmid = {10607403},
issn = {0300-9084},
mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Gene Expression ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/*genetics ; Pisum sativum/*enzymology/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; },
abstract = {Here we report the cloning of a cDNA encoding the first nucleoside diphosphate kinase (NDPK) isolated from plant mitochondria. Amplification of a 317 nt product was performed by PCR, using oligonucleotide primers based on partial amino acid sequences of the pea mitochondria NDPK and other NDPK isoforms. By screening of a pea cDNA library with this PCR product, a full length clone was obtained. Northern analysis revealed the presence of a 1.1 kb single transcript, with high expression in young leaves and reproductive tissues. The clone encodes a precursor protein of 232 amino acids (26 kDa), including an N-terminal extension of 80 amino acids (9 kDa). Analysis of the deduced amino acid sequence confirmed its identity with the sequences obtained from the purified mature pea mitochondrial NDPK. In vitro import experiments carried out in isolated pea mitochondria showed targeting and processing of the 27 kDa precursor into a 16.5 kDa mature form. Phylogenetic analysis of some vertebrate and plant isoforms of NDPK showed that the pea mtNDPK groups together with the NDPK3 isoform from A. thaliana and the chloroplastic NDPK III from spinach. We suggest that it is possible to design a novel classification of the different NDPK isoforms according to their subcellular localisation and origin.},
}
@article {pmid10609758,
year = {1999},
author = {Hwang, JS and Lee, JS and Goo, TW and Yun, EY and Sohn, HR and Kim, HR and Kwon, OY},
title = {Molecular genetic relationships between Bombycidae and Saturniidae based on the mitochondria DNA encoding of large and small rRNA.},
journal = {Genetic analysis : biomolecular engineering},
volume = {15},
number = {6},
pages = {223-228},
doi = {10.1016/s1050-3862(99)00008-x},
pmid = {10609758},
mesh = {Animals ; Base Sequence ; Bombyx/*classification/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Molecular Sequence Data ; Moths/*classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; },
abstract = {The phylogenetic relationships between Bombycidae (Bombyx mori and Bombyx mandarina) and Saturniidae (Antheraea yamamai and Antheraea pernyi) were investigated based on large and small mitochondiral rRNA genes. About 430 bp of four kinds of PCR-amplified fragments were sequenced and aligned. For the 16S rRNA gene, B. mori shared a 98, 87 and 86% sequence homology with B. mandarina, A. yamamai and A. pernyi, and for the 12S rRNA gene, B. mori shared a 99, 89 and 88% sequence homology with B. mandarina, A. yamamai and A. pernyi, respectively. DNA sequence data were also used for a phylogenetic analysis. All of the trees showed monophyly for both Bombycidae and Saturniidae. The monophyly confidence limits of these trees were estimated using bootstrapping tests and measured more than 99% for all trees for both Bombycidae and Saturniidae.},
}
@article {pmid10618092,
year = {2000},
author = {Sanson, GF and Briones, MR},
title = {Typing of Candida glabrata in clinical isolates by comparative sequence analysis of the cytochrome c oxidase subunit 2 gene distinguishes two clusters of strains associated with geographical sequence polymorphisms.},
journal = {Journal of clinical microbiology},
volume = {38},
number = {1},
pages = {227-235},
pmid = {10618092},
issn = {0095-1137},
mesh = {*Bacterial Proteins ; Bacteriocins ; Base Sequence ; Brazil ; Candida/*classification/enzymology/genetics ; Candidiasis/epidemiology/*microbiology ; Cluster Analysis ; Cytotoxins/*genetics ; DNA Primers ; Electron Transport Complex IV/*genetics ; *Genes, Bacterial ; Geography ; Mitochondria/enzymology/genetics ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Sequence Homology, Nucleic Acid ; Species Specificity ; United States ; },
abstract = {We tested whether comparative sequence analysis of the mitochondrion-encoded cytochrome c oxidase subunit 2 gene (COX2) could be used to distinguish intraspecific variants of Candida glabrata. Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intraspecific variation. For this survey we used 11 clinical isolates of C. glabrata from three different geographical locations in Brazil, 10 isolates from one location in the United States, 1 American Type Culture Collection strain as an internal control, and the published sequence of strain CBS 138. The complete coding region of COX2 was amplified from total cellular DNA, and both strands were sequenced twice for each strain. These sequences were aligned with published sequences from other fungi, and the numbers of substitutions and phylogenetic relationships were determined. Typing of these strains was done by using 17 substitutions, with 8 being nonsynonymous and 9 being synonymous. Also, cDNAs made from purified mitochondrial polyadenylated RNA were sequenced to confirm that our sequences correspond to the expressed copies and not nuclear pseudogenes and that a frameshift mutation exists in the 3' end of the coding region (position 673) relative to the Saccharomyces cerevisiae sequence and the previously published C. glabrata sequence. We estimated the average evolutionary rate of COX2 to be 11.4% sequence divergence/10(8) years and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of COX2 sequences enables typing of C. glabrata strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphism that discriminates strains isolated in the United States and strains isolated in Brazil. This provides for the first time a means of typing of Candida strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.},
}
@article {pmid10635118,
year = {1999},
author = {Watanabe, A and Nakazono, M and Tsutsumi, N and Hirai, A},
title = {AtUCP2: a novel isoform of the mitochondrial uncoupling protein of Arabidopsis thaliana.},
journal = {Plant &amp; cell physiology},
volume = {40},
number = {11},
pages = {1160-1166},
doi = {10.1093/oxfordjournals.pcp.a029501},
pmid = {10635118},
issn = {0032-0781},
mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Base Sequence ; Cloning, Molecular ; Cold Temperature ; DNA, Complementary ; Ion Channels ; *Membrane Transport Proteins ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms/chemistry/genetics/*metabolism ; Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Uncoupling Protein 2 ; },
abstract = {Mitochondrial uncoupling proteins (UCPs) play a central role in adaptive thermogenesis in mammals. The UCPs dissipate the proton gradient formed through respiration without ATP synthesis, and the freed energy is readily converted to heat, helping the animals to maintain their body temperature in cold environments. Recently, it was found that UCPs also function in plant mitochondria. Subsequently, a cDNA clone encoding a UCP in potato was isolated. Whereas the UCP gene constitutes a multigene family in mammals, only a single cDNA sequence has been reported so far for the potato UCP. Moreover, it has been recently suggested that Arabidopsis has only a single nuclear gene for UCP. Here we report the existence of another UCP gene in the Arabidopsis genome, showing for the first time the occurrence of a multigene family for the protein in higher plants. A cDNA analysis of this gene showed that the novel isoform possesses all typical features reported for known UCPs. However, the new gene, unlike the other gene in Arabidopsis and the gene in potato, did not appear to respond to low temperature.},
}
@article {pmid10644738,
year = {2000},
author = {Saas, J and Ziegelbauer, K and von Haeseler, A and Fast, B and Boshart, M},
title = {A developmentally regulated aconitase related to iron-regulatory protein-1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei.},
journal = {The Journal of biological chemistry},
volume = {275},
number = {4},
pages = {2745-2755},
doi = {10.1074/jbc.275.4.2745},
pmid = {10644738},
issn = {0021-9258},
mesh = {Aconitate Hydratase/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cytoplasm/*enzymology ; DNA, Complementary ; *Gene Expression Regulation, Enzymologic ; Iron Regulatory Protein 1 ; Iron-Regulatory Proteins ; Iron-Sulfur Proteins/*genetics ; Kinetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA-Binding Proteins/*genetics ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*enzymology ; },
abstract = {Mitochondrial energy metabolism and Krebs cycle activities are developmentally regulated in the life cycle of the protozoan parasite Trypanosoma brucei. Here we report cloning of a T. brucei aconitase gene that is closely related to mammalian iron-regulatory protein 1 (IRP-1) and plant aconitases. Kinetic analysis of purified recombinant TbACO expressed in Escherichia coli resulted in a K(m) (isocitrate) of 3 +/- 0.4 mM, similar to aconitases of other organisms. This was unexpected since an arginine conserved in the aconitase protein family and crucial for substrate positioning in the catalytic center and for activity of pig mitochondrial aconitase (Zheng, L., Kennedy, M. C., Beinert, H., and Zalkin, H. (1992) J. Biol. Chem. 267, 7895-7903) is substituted by leucine in the TbACO sequence. Expression of the 98-kDa TbACO was shown to be lowest in the slender bloodstream stage of the parasite, 8-fold elevated in the stumpy stage, and increased a further 4-fold in the procyclic stage. The differential expression of TbACO protein contrasted with only minor changes in TbACO mRNA, indicating translational or post-translational mechanisms of regulation. Whereas animal cells express two distinct compartmentalized aconitases, mitochondrial aconitase and cytoplasmic aconitase/IRP-1, TbACO accounts for total aconitase activity in trypanosomes. By cell fractionation and immunofluorescence microscopy, we show that native as well as a transfected epitope-tagged TbACO localizes in both the mitochondrion (30%) and in the cytoplasm (70%). Together with phylogenetic reconstructions of the aconitase family, this suggests that animal IRPs have evolved from a multicompartmentalized ancestral aconitase. The possible functions of a cytoplasmic aconitase in trypanosomes are discussed.},
}
@article {pmid10664124,
year = {2000},
author = {Nakazono, M and Imamura, T and Tsutsumi, N and Sasaki, T and Hirai, A},
title = {Characterization of two cDNA clones encoding isozymes of the F(1)F(0)-ATPase inhibitor protein of rice mitochondria.},
journal = {Planta},
volume = {210},
number = {2},
pages = {188-194},
doi = {10.1007/pl00008125},
pmid = {10664124},
issn = {0032-0935},
mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; DNA, Complementary/chemistry/*genetics ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins ; Isoenzymes/antagonists &amp; inhibitors ; Luminescent Proteins/genetics ; Microscopy, Confocal ; Mitochondria/*genetics ; Molecular Sequence Data ; Oryza/*genetics ; Phylogeny ; Protein Isoforms/genetics ; Proteins/*genetics ; Proton-Translocating ATPases/antagonists &amp; inhibitors ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; ATPase Inhibitory Protein ; },
abstract = {Two cDNA clones encoding F(1)F(0)-ATPase inhibitor proteins, which are loosely associated with the F(1) part of the mitochondrial F(1)F(0)-ATPase, were characterized from rice (Oryza sativa L. cv. Nipponbare). A Northern hybridization showed that the two genes (designated as IF(1)-1 and IF(1)-2) are transcribed in all the organs examined. However, the steady-state mRNA levels varied among organs. A comparison of the deduced amino acid sequences of the two IF(1) genes and the amino acid sequence of the mature IF(1) protein from potato revealed that IF(1)-1 and IF(1)-2 have N-terminal extensions with features that are characteristic of a mitochondrial targeting signal. To determine the subcellular localization of the gene products, the IF(1)-1 or IF(1)-2 proteins were fused in frame to the green fluorescent protein (GFP) or the fused GFP-beta-glucuronidase, and expressed transiently in onion or dayflower epidermal cells. Localized fluorescence was detected in mitochondria, confirming that the two IF(1) proteins are targeted to mitochondria.},
}
@article {pmid10712839,
year = {2000},
author = {Koulianos, S and Schmid-Hempel, P},
title = {Phylogenetic relationships among bumble bees (Bombus, latreille) inferred from mitochondrial cytochrome b and cytochrome oxidase I sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {14},
number = {3},
pages = {335-341},
doi = {10.1006/mpev.1999.0621},
pmid = {10712839},
issn = {1055-7903},
mesh = {Animals ; Bees/classification/*enzymology/*genetics ; Cytochrome b Group/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {We conducted a molecular study intending to derive an estimate of the relationships within the genus Bombus (bumble bees) by comparing the mitochondrial cytochrome b and cytochrome oxidase I (COI) genes from 19 species, spanning 10 of approximately 16 European subgenera and 3 subgenera from North and South America. Our trees differ from the most recent classifications of bumble bees. Although bootstrap values for deep branches are low, our sequences show significant data structure and low homoplasy, and all trees share some groups and patterns. In all cases, the subgenus Bombus s. str. clusters among the most derived bumble bees, contrary to other molecular studies. In all trees, B. funebris is the sister taxon of B. robustus, and in five of the six trees, B. wurflenii is the sister taxon to this clade. B. nevadensis is basal to the other species in the analysis of the cytochrome b gene, but appears to be among the most derived according to the analysis of the COI region. The species representing the subgenera Thoracobombus and Fervidobombus are consistently among the earliest diverged. Species that appear in very different positions in different trees are B. nevadensis, B. mesomelas, B. balteatus, and B. hyperboreus. All subgenera with two representatives in our analysis are apparently monophyletic except Fervidobombus, Melanobombus, and Pyrobombus. The groups formed by pocket makers and non-pocket makers within Bombus also appear to be paraphyletic, and therefore some subgenera may not accurately reflect phylogeny.},
}
@article {pmid10713448,
year = {2000},
author = {Kirby, RR},
title = {Cloning and primary structure of putative cytosolic and mitochondrial malate dehydrogenase from the mollusc Nucella lapillus (L.).},
journal = {Gene},
volume = {245},
number = {1},
pages = {81-88},
doi = {10.1016/s0378-1119(00)00036-6},
pmid = {10713448},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/chemistry/genetics ; Malate Dehydrogenase/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Snails/enzymology/*genetics ; },
abstract = {The evolutionary history of the malate dehydrogenase (MDH) gene family [NAD-dependent MDH; EC 1.1.1.37 and NAD(P)-dependent MDH; EC 1.1.1.82] has received much attention. MDHs have also featured extensively as electrophoretic markers in population genetics and evolutionary ecology, and in many cases, intraspecific variation in MDH has been correlated with environmental variables. However, while the amino acid residues essential for MDH function are known, no studies have examined intraspecific nucleotide variation despite evidence indicating that natural selection may be operating on this locus. This study presents two sets of degenerate oligonucleotide PCR primers to facilitate the cloning of cytosolic MDH (cMDH) and mitochondrial MDH (mMDH) from a broad range of animals (cMDH) and animals and plants (mMDH). These primers were used to obtain putative cMDH and mMDH cDNAs from the mollusc Nucella lapillus. The N. lapillus cMDH cDNA was found to encode a putative cMDH protein of 334aa and 36kDa, while the mMDH cDNA encoded a putative mature mMDH protein of 315aa and 33kDa. The putative amino acid sequences of the two compartmentalised N. lapillus MDHs are presented and compared to other known MDH sequences.},
}
@article {pmid10734603,
year = {1999},
author = {Cao, Y and Kim, KS and Ha, JH and Hasegawa, M},
title = {Model dependence of the phylogenetic inference: relationship among carnivores, Perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences.},
journal = {Genes &amp; genetic systems},
volume = {74},
number = {5},
pages = {211-217},
doi = {10.1266/ggs.74.211},
pmid = {10734603},
issn = {1341-7568},
mesh = {Animals ; Artiodactyla/*classification/genetics ; Carnivora/*classification/genetics ; Cetacea/*classification/genetics ; Genetic Heterogeneity ; Genome ; Mitochondria/*genetics ; Models, Genetic ; Perissodactyla/*classification/genetics ; *Phylogeny ; Proteins/genetics ; },
abstract = {Some previous analysis of mitochondrial proteins strongly support the Carnivora/Perissodactyla grouping excluding Cetartiodactyla (Artiodactyla + Cetacea) as an outgroup, but the support of the hypothesis remains equivocal from the analysis of several nuclear-encoded proteins. In order to evaluate the strength of the support by mitochondrial proteins, phylogenetic relationship among Carnivora, Perissodactyla, and Cetartiodactyla was estimated with the ML method by using the updated data set of the 12 mitochondrial proteins with several alternative models. The analyses demonstrate that the phylogenetic inference depends on the model used in the ML analysis; i.e., whether the site-heterogeneity is taken into account and whether the rate parameters are estimated for each individual proteins or for the concatenated sequences. Although the analysis of concatenated sequences strongly supports the Carnivora/Perissodactyla grouping, the total evaluation of the separate analyses of individual proteins, which approximates the data better than the concatenated analysis, gives only ambiguous results, and therefore it is concluded that more data are needed to resolve this trichotomy.},
}
@article {pmid10747106,
year = {2000},
author = {Wang, L and Yokoyama, K and Miyaji, M and Nishimura, K},
title = {Mitochondrial cytochrome b gene analysis of Aspergillus fumigatus and related species.},
journal = {Journal of clinical microbiology},
volume = {38},
number = {4},
pages = {1352-1358},
pmid = {10747106},
issn = {0095-1137},
mesh = {Amino Acid Sequence ; Aspergillosis/microbiology ; Aspergillus/*classification/enzymology/*genetics ; Aspergillus fumigatus/*classification/enzymology/genetics ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/genetics ; Genes, Fungal ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Nucleotide sequences of 426 bp from the mitochondrial (mt) cytochrome b genes of six anamorph species and two species of Neosartorya teleomophs of Aspergillus section Fumigati were determined. These sequences were used to build nucleotide- and amino acid-based trees for phylogenetic analysis. Thirteen strains of A. fumigatus including 10 clinical isolates of A. fumigatus, 1 type culture of A. fumigatus var. fumigatus, 1 type culture of A. fumigatus var. ellipticus, and 1 strain of A. fumigatus var. albus, had the same nucleotide sequences. One strain of A. fumisynnematus, two strains labeled A. neoellipticus, two strains of A. viridinutans, and one strain of A. duricaulis had distinct nucleotide and amino acid sequences. Two strains of A. brevipes were divided into two types. One produced a 1,500-bp fragment that included an intron. The nucleotide sequences of its two exons were similar to those of the A. fumigatus, and the derived amino acid sequence was the same as that for A. fumigatus. The other produced a 426-bp fragment and had the same nucleotide and amino acid sequences as A. unilateralis. Neosartorya fischeri var. fischeri and N. stramenia had nucleotide sequences that differed from that of A. fumigatus. These species possessed their own characteristic nucleotide sequences that differed from each other. In comparisons of homologous sequences from four other pathogenic species of Aspergillus, regions specific to section Fumigati were found. The mt cytochrome b gene analysis was valuable for the identification, classification, and phylogenetic analysis of isolates of section Fumigati.},
}
@article {pmid10748252,
year = {2000},
author = {Howitt, SM and Udvardi, MK},
title = {Structure, function and regulation of ammonium transporters in plants.},
journal = {Biochimica et biophysica acta},
volume = {1465},
number = {1-2},
pages = {152-170},
doi = {10.1016/s0005-2736(00)00136-x},
pmid = {10748252},
issn = {0006-3002},
mesh = {Acyltransferases/metabolism ; Amino Acid Sequence ; Biological Transport ; Carrier Proteins/chemistry/genetics/*metabolism ; *Cation Transport Proteins ; Cell Membrane/chemistry/metabolism ; Gene Expression Regulation, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*metabolism ; Proton-Motive Force ; Proton-Translocating ATPases/metabolism ; Quaternary Ammonium Compounds/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; },
abstract = {Ammonium is an important source of nitrogen for plants. It is taken up by plant cells via ammonium transporters in the plasma membrane and distributed to intracellular compartments such as chloroplasts, mitochondria and vacuoles probably via different transporters in each case. Ammonium is generally not used for long-distance transport of nitrogen within the plant. Instead, most of the ammonium transported into plant cells is assimilated locally via glutamine synthetases in the cytoplasm and plastids. Ammonium is also produced by plant cells during normal metabolism, and ammonium transporters enable it to be moved from intracellular sites of production to sites of consumption. Ammonium can be generated de novo from molecular nitrogen (N(2)) by nitrogen-fixing bacteria in some plant cells, such as rhizobia in legume root nodule cells, and at least one ammonium transporter is implicated in the transfer of ammonium from the bacteria to the plant cytoplasm. Plant physiologists have described many of these ammonium transport processes over the last few decades. However, the genes and proteins that underlie these processes have been isolated and studied only recently. In this review, we consider in detail the molecular structure, function and regulation of plant ammonium transporters. We also attempt to reconcile recent discoveries at the molecular level with our knowledge of ammonium transport at the whole plant level.},
}
@article {pmid10764530,
year = {2000},
author = {Misof, B and Anderson, CL and Hadrys, H},
title = {A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers.},
journal = {Molecular phylogenetics and evolution},
volume = {15},
number = {1},
pages = {5-14},
doi = {10.1006/mpev.1999.0724},
pmid = {10764530},
issn = {1055-7903},
mesh = {Animals ; DNA, Ribosomal/chemistry/genetics ; Genetic Markers ; Geography ; Insecta/classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups.},
}
@article {pmid10764533,
year = {2000},
author = {Vences, M and Kosuch, J and Lötters, S and Widmer, A and Jungfer, KH and Köhler, J and Veith, M},
title = {Phylogeny and classification of poison frogs (Amphibia: dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {15},
number = {1},
pages = {34-40},
doi = {10.1006/mpev.1999.0738},
pmid = {10764533},
issn = {1055-7903},
mesh = {Amphibians/classification/*genetics ; Animals ; DNA/chemistry/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; },
abstract = {An analysis of partial sequences of the 16S ribosomal rRNA gene (582 bp) of 20 poison frog species (Dendrobatidae) confirmed their phylogenetic relationships to bufonid and leptodactylid frogs. Representatives of the ranoid families and subfamilies Raninae, Mantellinae, Petropedetinae, Cacosterninae, Arthroleptidae, Astylosternidae, and Microhylidae did not cluster as sister group of the Dendrobatidae. Similar results were obtained in an analysis using a partial sequence of the 12S gene (350 bp) in a reduced set of taxa and in a combined analysis. Within the Dendrobatidae, our data supported monophyly of the genus Phyllobates but indicated paraphyly of Epipedobates and Colostethus. Minyobates clustered within Dendrobates, contradicting its previously assumed phylogenetic position. Phobobates species clustered as a monophyletic unit within Epipedobates. Allobates was positioned in a group containing two Colostethus species, indicating that lack of amplexus, presence of skin alkaloids, and aposematic coloration evolved independently in Allobates and the remaining aposematic dendrobatids.},
}
@article {pmid10765727,
year = {2000},
author = {Emel'ianov, VV},
title = {[Evolutionary relationship of Rickettsia and eukaryotic mitochondria].},
journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk},
volume = {},
number = {3},
pages = {3-7},
pmid = {10765727},
issn = {0869-6047},
mesh = {Animals ; Archaea/genetics ; Eukaryota/genetics ; Heat-Shock Proteins/genetics ; Mitochondria/*genetics ; Paramecium/genetics ; *Phylogeny ; Rickettsia/*genetics ; Rickettsia prowazekii/genetics ; },
abstract = {To clarify the evolutionary relationship of rickettsiae and mitochondria, the conserved flat heat-shock protein Hsp60 was phylogenetically studied in detail by using PHYLIP and PROTML packages. The ample data set (50 species) included as many as possible representatives from the Rickettsiaceae family, mitochondrial-type homologs from Archezoa and mitochondrial homologs from Protozoa. Rickettsia prowazekii (that is the genus Rickettsia) was shown to be the least diverging member within Rickettsia--a sister group to the monophyletic clade of mitochondria. These findings were also evidenced by the phylogenetic analysis of 16S rRNA. Rickettsia-like endosymbionts (the parasites Paramecium caudatum and the etiological agent of hepatopancreatitis in shrimps) included within the order Rickettsiales appear to have diverged prior to the Rickettsiaceae/mitochondria cluster. Thus, the Rickettsiales does not seem to be a monophyletic group. An idea concerning the nature of obligate intracellular parasitism of rickettsiae is proposed in the paper from the suggested profound similarity of Rickettsiae genus bacteria and mitochondria which could have a common evolutionary history.},
}
@article {pmid10779593,
year = {2000},
author = {Wu, Y and Egerton, G and Ball, A and Tanguay, RM and Bianco, AE},
title = {Characterization of the heat-shock protein 60 chaperonin from Onchocerca volvulus.},
journal = {Molecular and biochemical parasitology},
volume = {107},
number = {2},
pages = {155-168},
doi = {10.1016/s0166-6851(99)00227-3},
pmid = {10779593},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Antibodies, Helminth/blood ; Chaperonin 60/*chemistry/genetics/*immunology/metabolism ; Cloning, Molecular ; Cross Reactions ; DNA, Helminth/genetics ; Enzyme-Linked Immunosorbent Assay ; Humans ; Immunohistochemistry ; Mitochondria/metabolism ; Molecular Sequence Data ; Onchocerca volvulus/*chemistry/genetics/immunology/metabolism ; Onchocerciasis/immunology/parasitology ; Phylogeny ; Rabbits ; Recombinant Proteins/immunology ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {Chaperonin 60 (cpn60) belongs to the group of ubiquitous molecular chaperones that comprise the heat shock proteins, nucleoplasmins and chaperonins. Antibodies to recombinant CPN60 from humans was used to screen a cDNA library of Onchocerca volvulus and antigen-positive clones were selected. Sequencing of the DNA inserts confirmed their identity as cpn60 transcripts. These are distinct from a cpn60 sequence recorded previously from O. volvulus (GenBank accession number Y09416) that appears to be of endobacterial origin, rather than derived from the parasite itself. The full-length sequence of the cDNA (designated Ov-cpn60) codes for a protein of 64.3kDa (598 amino acid residues) and shares significant identity with homologous gene products from Caenorhabditis elegans (72%), humans (69%), yeast (53%) and Escherichia coli (50%). The endobacterial and parasite sequences are 41% conserved. Ov-CPN60 migrates with an apparent molecular mass of 65kDa on SDS-PAGE and is present in all life-cycle stages, as determined by immunoblotting with rabbit antibodies raised against the recombinant protein. Immunogold electron microscopy identified the protein within mitochondria, as expected, but also in extra-mitochondrial sites, including inclusion bodies of the glandular oesophagus (in infective larvae), the uterine wall, cytosol of developing spermatids, and the hypodermis and cuticle. Endobacteria were also labelled, indicating cross-reactivity between CPN60 from the parasite and its intracellular symbiont. In human infections, serum antibodies to Ov-CPN60 were present in only 11% of cases from Ecuador, but in 81-89% of subjects in three separate foci from West Africa. There was no relationship between antibody levels and age, sex, or infection intensity, and no consistent association between the serological response and immune status. An evaluation of antibody specificities in individual sera revealed a mixture of parasite-specific and host crossreactive anti-CPN60 antibodies, the ratio of which varied amongst geographic areas. It is concluded that antibody responses to Ov-CPN60 are unlikely to contribute either to host protection or pathology in onchocerciasis.},
}
@article {pmid10806421,
year = {2000},
author = {Kayingo, G and Potier, S and Hohmann, S and Prior, BA},
title = {Isolation and characterization of the TIM10 homologue from the yeast Pichia sorbitophila: a putative component of the mitochondrial protein import system.},
journal = {Yeast (Chichester, England)},
volume = {16},
number = {7},
pages = {589-596},
doi = {10.1002/(SICI)1097-0061(200005)16:7&lt;589::AID-YEA555&gt;3.0.CO;2-G},
pmid = {10806421},
issn = {0749-503X},
mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Western ; Cross Reactions ; Fungal Proteins/genetics/immunology/*isolation &amp; purification/*metabolism ; Genes, Fungal ; Genetic Complementation Test ; Membrane Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Phylogeny ; Pichia/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; },
abstract = {The Saccharomyces cerevisiae TIM10 gene encodes one of the few essential mitochondrial proteins that are required for the import of nuclear-encoded precursor proteins from the cytosol and their subsequent sorting into the different mitochondrial compartments. We have isolated and characterized a putative homologue of TIM10 from the halotolerant yeast Pichia sorbitophila. The Pichia TIM10 gene encodes a protein of 90 amino acids with 66% identity to S. cerevisiae Tim10p. It was capable of suppressing the temperature sensitivity of tim10-1 mutant in S. cerevisiae, suggesting that Pichia TIM10 is both a functional and structural homologue of S. cerevisiae TIM10. The putative Pichia TIM10 gene product contains all the four conserved cysteine residues and the two CX(3)C motifs typical of the Tim family proteins in the mitochondrial intermembrane space. Using anti-Tim10p serum, Western blots detected a protein of about 10 kDa, suggesting that the Pichia Tim10p is a mitochondrial protein. The results suggest that mitochondrial import and sorting systems might be also strongly conserved in other fungi. The coding sequence of the P. sorbitophila TIM10 has been deposited in the EMBL Nucleotide Sequence Database under Accession No. AJ243940.},
}
@article {pmid10824085,
year = {2000},
author = {Peeters, NM and Chapron, A and Giritch, A and Grandjean, O and Lancelin, D and Lhomme, T and Vivrel, A and Small, I},
title = {Duplication and quadruplication of Arabidopsis thaliana cysteinyl- and asparaginyl-tRNA synthetase genes of organellar origin.},
journal = {Journal of molecular evolution},
volume = {50},
number = {5},
pages = {413-423},
doi = {10.1007/s002390010044},
pmid = {10824085},
issn = {0022-2844},
mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Animals ; Arabidopsis/enzymology/*genetics ; *Aspartate-tRNA Ligase ; Base Sequence ; DNA Primers ; DNA, Complementary ; *Gene Duplication ; Humans ; Molecular Sequence Data ; Organelles/enzymology ; Phylogeny ; *RNA, Transfer, Amino Acyl ; Sequence Homology, Amino Acid ; },
abstract = {Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial). These case histories are the best examples to date of capture of organellar aminoacyl-tRNA synthetases by the cytosolic protein synthesis machinery.},
}
@article {pmid10826829,
year = {2000},
author = {Belloch, C and Querol, A and García, MD and Barrio, E},
title = {Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 1},
number = {},
pages = {405-416},
doi = {10.1099/00207713-50-1-405},
pmid = {10826829},
issn = {1466-5026},
mesh = {Electron Transport Complex IV/*genetics ; Genes, Fungal ; Kluyveromyces/*classification/enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; },
abstract = {A phylogenetic analysis of 17 species belonging to the genus Kluyveromyces and 12 reference and outgroup species was performed using mitochondrial cytochrome-c oxidase II gene sequences. The genus Kluyveromyces appears as a polyphyletic taxon formed by species included within the following four main groups. The Kluyveromyces phaffii group encompasses the species Kluyveromyces blattae, K. phaffii and Kluyveromyces yarrowii. The Kluyveromyces marxianus group is a monophyletic group consisting of the species Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, K. marxianus and Kluyveromyces wickerhamii. The monophyletic Kluyveromyces thermotolerans group is formed by K. thermotolerans, Kluyveromyces waltii and Saccharomyces kluyveri (which appears in the mitochondrial tree as the sister clade of the K. marxianus group). Finally, the Saccharomyces cerevisiae group contains the remaining Kluyveromyces species, as well as the reference Saccharomyces species (sensu lato and sensu stricto) and Candida glabrata (the phylogenetic relationships within this group are unclear according to the bootstrap test). The phylogenetic relationships obtained for this mitochondrial gene are, for the most part, congruent with previous trees based on nuclear rRNA sequences, except for the position of K. yarrowii and the close relationship between the K. marxianus and K. thermotolerans groups. These differences, as well as the existence of these groups, are discussed in the context of previous studies based on phenotypic, genetic and molecular data. Although additional studies are required to decipher the phylogenetic relationships between the genus Kluyveromyces and the closely related genera Saccharomyces, Torulaspora and Zygosaccharomyces, future changes to their taxonomic status should take account of the existence of these four groups of Kluyveromyces species.},
}
@article {pmid10837153,
year = {2000},
author = {Ståhls, G and Nyblom, K},
title = {Phylogenetic analysis of the genus Cheilosia (Diptera, Syrphidae) using mitochondrial COI sequence data.},
journal = {Molecular phylogenetics and evolution},
volume = {15},
number = {2},
pages = {235-241},
doi = {10.1006/mpev.1999.0748},
pmid = {10837153},
issn = {1055-7903},
mesh = {Animals ; Diptera/*classification/genetics ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology/*genetics ; *Phylogeny ; },
abstract = {The genus Cheilosia is one of the most diverse and speciose genera of Syrphidae (Diptera). The phylogenetic relationships of the hoverfly genus Cheilosia was investigated for the first time using molecular data. The mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) was chosen for sequencing; 1341 characters were obtained for 24 ingroup taxa and these were analyzed with parsimony. The monophyly of the genus Cheilosia was well supported. Current taxonomic division of Cheilosia into two subgenera (sg. Nigrocheilosia and sg. Neocheilosia) and most nonformalized species groups based on morphology were supported by the monophyletic groups identified in the molecular analysis. The phylogenetic informativeness of COI in resolving the subtribal relationships within the tribe Cheilosiini remains ambiguous.},
}
@article {pmid10838480,
year = {2000},
author = {Hansen, A and Finger, TE},
title = {Phyletic distribution of crypt-type olfactory receptor neurons in fishes.},
journal = {Brain, behavior and evolution},
volume = {55},
number = {2},
pages = {100-110},
doi = {10.1159/000006645},
pmid = {10838480},
issn = {0006-8977},
support = {P01DC00244/DC/NIDCD NIH HHS/United States ; R01DC03792/DC/NIDCD NIH HHS/United States ; },
mesh = {Animals ; Fishes/*anatomy &amp; histology ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Mitochondria/ultrastructure ; Olfactory Mucosa/*ultrastructure ; Olfactory Receptor Neurons/*ultrastructure ; Phylogeny ; },
abstract = {The olfactory epithelium of teleost fishes contains ciliated and microvillous olfactory receptor neurons intermingled with supporting cells. Recently the crypt cell, a third type of olfactory receptor neuron (ORN), was described for two ostariophysans. This type of ORN bears apical microvilli as well as occult cilia extending into a crypt at the apex of the cell. The present study used scanning and transmission electron-microscopic methods to examine how widespread this cell type is in other groups of fish. We investigated the olfactory epithelia of 18 species, freshwater and marine, including various actinopterygian fish as well as 2 species of lungfishes belonging to the sarcopterygians. Crypt cells were detected in 13 species of actinopterygian fish, but in none of the sarcopterygian lungfishes. Crypt cells are present in basic as well as in highly derived actinopterygians. We conclude that crypt cells are a common feature of actinopterygian fish.},
}
@article {pmid10849078,
year = {2000},
author = {Mirol, PM and Mascheretti, S and Searle, JB},
title = {Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, rodentia) with either great similarity to or high divergence from the true mitochondrial sequence.},
journal = {Heredity},
volume = {84 (Pt 5)},
number = {},
pages = {538-547},
doi = {10.1046/j.1365-2540.2000.00689.x},
pmid = {10849078},
issn = {0018-067X},
mesh = {Animals ; Cytochrome b Group/*genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genetic Variation ; Mitochondria/*enzymology/genetics ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; Pseudogenes/*genetics ; Rodentia/*genetics ; Sequence Analysis, DNA ; },
abstract = {A fragment of the mitochondrial cytochrome b gene was studied in 13 species of the South American fossorial rodent Ctenomys using PCR with 'universal' primers and DNA sequencing after cloning. Five different groups of sequences were found, one of which corresponds to the functional mitochondrial gene (mt). The other four groups (A, B, C and D) were believed to be nuclear pseudogenes. Sequences A-C were highly divergent from the mt sequences and included substitutions, deletions and insertions such that they could not possibly have coded a functional protein. They all shared a common insertion between positions 15055 and 15056 suggestive of a common origin, although the A, B and C sequences otherwise differed greatly from each other. The D sequences also could not have been functional on the basis of nucleotide sequence, but the differences with the mt sequences were far more subtle and in a more limited study the D sequences could easily have been classified as a true mtDNA sequence. It is suggested that there were two transfers of the cytochrome b gene from the mitochondrion to the nucleus; the first leading to sequences A-C and the second to the D sequence. Subsequent to transfer, a sequence of duplications within the nucleus appears to have generated the full range of pseudogenes that are observed. This study adds to other recent observations suggesting the frequent transfer of mtDNA sequences to the nucleus and reinforces the necessity of great care in interpreting PCR-generated sequences, particularly those produced with universal primers. There are now data from several species of mammals and birds relating to PCR-generated nuclear copies of cytochrome b, which we review.},
}
@article {pmid10852618,
year = {2000},
author = {Blusch, JH and Roos, C and Nitschko, H},
title = {A polymerase chain reaction-based protocol for the detection of transmission of pig endogenous retroviruses in pig to human xenotransplantation.},
journal = {Transplantation},
volume = {69},
number = {10},
pages = {2167-2172},
doi = {10.1097/00007890-200005270-00036},
pmid = {10852618},
issn = {0041-1337},
mesh = {Actins/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cytochrome b Group/chemistry/*genetics ; DNA Primers ; Endogenous Retroviruses/*isolation &amp; purification ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Papio ; Phylogeny ; Polymerase Chain Reaction/*methods ; Primates ; Sequence Alignment ; Sequence Homology, Amino Acid ; Swine/*virology ; *Terminal Repeat Sequences ; Transplantation Chimera ; *Transplantation, Heterologous ; },
abstract = {BACKGROUND: Xenotransplantation of pig organs and tissues to humans bears the risk of infection of immunosuppressed recipients by porcine endogenous retrovirus (PERV) released from the transplanted tissue. However, when diagnosing potential PERV transmission, it is essential to exclude microchimerism, i.e., persisting pig cells in analyzed bioptic material of xenotransplanted patients, which give rise to false positive PERV signals. Polymerase chain reaction (PCR) is so far the only suitable method to diagnose a cross-species transfer of PERV, but the exclusion of microchimerism might be a serious problem because most of the presently employed primer pairs detect PERV sequences with higher sensitivity than primers used for the detection of contaminating pig sequences.<br><br>METHODS: We designed and evaluated a novel and improved primer set for detection of pig sequences as well as complementing positive control primers on the basis of mitochondrial cytochrome B, an approved marker for phylogenetic studies. We further established primer pairs derived from the long terminal repeat/leader region of PERV isolated from a Duroc German Landrace cross-bred pig and tested their sensitivity in comparison with known PERV- and pig-specific PCR markers.<br><br>RESULTS: In standard PCR assays, the new cytochrome B-derived primers are at least 10 times more sensitive than the presently used PERV retroviral polymerase gene and mammalian beta-actin primers. When tested in a tissue culture infection model, PERV transmission to human 293 cells can be unambiguously demonstrated, even in the presence of up to 10% pig cells. One of the primer combinations derived from the PERV DuxDL3791 long terminal repeat/leader region amplifies with even lower sensitivity than primers detecting porcine beta-globin, thus permitting the exclusion of microchimerism also via chromosomal loci.<br><br>CONCLUSIONS: The availability of the new PCR markers allows the proposal of a rigorous setup for the routine detection of PERV transmission after xenotransplantation.},
}
@article {pmid10880490,
year = {2000},
author = {Taylor, JS and Breden, F},
title = {Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth.},
journal = {Genetics},
volume = {155},
number = {3},
pages = {1313-1320},
pmid = {10880490},
issn = {0016-6731},
mesh = {Animals ; Base Pair Mismatch/*genetics ; Base Sequence ; DNA, Mitochondrial/analysis/genetics ; Genetics, Population ; Minisatellite Repeats/*genetics ; Mitochondria/*genetics ; *Models, Genetic ; Molecular Sequence Data ; Mutation ; Phylogeny ; Poecilia/*genetics ; Sequence Analysis, DNA ; Trinidad and Tobago ; },
abstract = {The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the "raw material" for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the "imperfect" or "short direct" repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.},
}
@article {pmid10886388,
year = {2000},
author = {Carmona, JA and Domínguez, J and Doadrio, I},
title = {Congruence between allozyme and cytochrome b gene sequence data in assessing genetic differentiation within the Iberian endemic Chondrostoma lemmingii (Pisces: cyprinidae).},
journal = {Heredity},
volume = {84 (Pt 6)},
number = {},
pages = {721-732},
doi = {10.1046/j.1365-2540.2000.00720.x},
pmid = {10886388},
issn = {0018-067X},
mesh = {Animals ; Cyprinidae/*genetics ; Cytochrome b Group/*genetics ; Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; },
abstract = {To understand further the fragmentation of the hydrographical basins and the processes of divergence and speciation of freshwater fishes of the Iberian Peninsula, 10 populations of the Iberian endemic cyprinid Chondrostoma lemmingii were studied using 26 loci encoding 19 enzymes and the complete nucleotide sequence of the mitochondrial cytochrome b gene. Nuclear and mitochondrial DNA markers showed complete congruence in assessing the genetic differentiation among the samples analysed. This congruence was supported by a Mantel test in which a significant correlation (r=0.89) between Nei's genetic distances and sequence divergence (uncorrected p distances) was obtained. Diagnostic loci, Nei's genetic distances, and FST values, as well as the percentage of sequence divergence indicate that the Duero basin population accumulates the highest level of genetic differentiation. A moderate divergence was also observed among populations of the rest of the basins. Phenetic and phylogenetic relationships support the hypothesis that the differentiation process was not only due to hydrographical basin isolation but also due to an ancient endorrheism event, previous to hydrographical configuration, that could explain the marked differentiation of the Duero basin population.},
}
@article {pmid10899162,
year = {2000},
author = {Pérez-Martínez, X and Vazquez-Acevedo, M and Tolkunova, E and Funes, S and Claros, MG and Davidson, E and King, MP and González-Halphen, D},
title = {Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae.},
journal = {The Journal of biological chemistry},
volume = {275},
number = {39},
pages = {30144-30152},
doi = {10.1074/jbc.M003940200},
pmid = {10899162},
issn = {0021-9258},
support = {TW01176-01/TW/FIC NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/*genetics ; Chlorophyta/enzymology/*genetics ; Electron Transport Complex IV/classification/*genetics/isolation &amp; purification ; Eukaryota/enzymology/genetics ; Magnoliopsida/enzymology/genetics ; Membrane Proteins/classification/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Sorting Signals ; Protein Structure, Quaternary ; Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {The algae of the family Chlamydomonadaceae lack the gene cox3 that encodes subunit III of cytochrome c oxidase in their mitochondrial genomes. This observation has raised the question of whether this subunit is present in cytochrome c oxidase or whether the corresponding gene is located in the nucleus. Cytochrome c oxidase was isolated from the colorless chlamydomonad Polytomella spp., and the existence of subunit III was established by immunoblotting analysis with an antibody directed against Saccharomyces cerevisiae subunit III. Based partly upon the N-terminal sequence of this subunit, oligodeoxynucleotides were designed and used for polymerase chain reaction amplification, and the resulting product was used to screen a cDNA library of Chlamydomonas reinhardtii. The complete sequences of the cox3 cDNAs from Polytomella spp. and C. reinhardtii are reported. Evidence is provided that the genes for cox3 are encoded by nuclear DNA, and the predicted polypeptides exhibit diminished physical constraints for import as compared with mitochondrial-DNA encoded homologs. This indicates that transfer of this gene to the nucleus occurred before Polytomella diverged from the photosynthetic Chlamydomonas lineage and that this transfer may have occurred in all chlamydomonad algae.},
}
@article {pmid10908563,
year = {2000},
author = {McKenzie, M and Trounce, I},
title = {Expression of Rattus norvegicus mtDNA in Mus musculus cells results in multiple respiratory chain defects.},
journal = {The Journal of biological chemistry},
volume = {275},
number = {40},
pages = {31514-31519},
doi = {10.1074/jbc.M004070200},
pmid = {10908563},
issn = {0021-9258},
mesh = {Animals ; Blotting, Southern ; Cell Line ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*metabolism ; Electron Transport/*genetics/*physiology ; Genotype ; Humans ; Hybrid Cells ; Lactic Acid/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Oxidative Phosphorylation ; Phylogeny ; Protein Biosynthesis ; Rats ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; },
abstract = {The production of in vitro and in vivo models of mitochondrial DNA (mtDNA) defects is currently limited by a lack of characterized mouse cell mtDNA mutants that may be expected to model human mitochondrial diseases. Here we describe the creation of transmitochondrial mouse (Mus musculus) cells repopulated with mtDNA from different murid species (xenomitochondrial cybrids). The closely related Mus spretus mtDNA is readily maintained when introduced into M. musculus mtDNA-less (rho(0)) cells, and the resulting cybrids have normal oxidative phosphorylation (OXPHOS). When the more distantly related Rattus norvegicus mtDNA is transferred to the mouse nuclear background the mtDNA is replicated, transcribed, and translated efficiently. However, function of several OXPHOS complexes that depend on the coordinated assembly of nuclear and mtDNA-encoded proteins is impaired. Complex I activity in the Rattus xenocybrid was 46% of the control mean; complex III was 37%, and complex IV was 78%. These defects combined to restrict maximal respiration to 12-31% of the control and M. spretus xenocybrids, as measured polarographically using isolated cybrid mitochondria. These defects are distinct to those previously reported for human/primate xenocybrids. It should be possible to produce other mouse xenocybrid constructs with less severe OXPHOS phenotypes, to model human mtDNA diseases.},
}
@article {pmid10916154,
year = {2000},
author = {Bullerwell, CE and Burger, G and Lang, BF},
title = {A novel motif for identifying rps3 homologs in fungal mitochondrial genomes.},
journal = {Trends in biochemical sciences},
volume = {25},
number = {8},
pages = {363-365},
doi = {10.1016/s0968-0004(00)01612-1},
pmid = {10916154},
issn = {0968-0004},
mesh = {*Amino Acid Motifs ; Amino Acid Sequence ; Fungal Proteins/genetics ; *Membrane Proteins ; Mitochondria/*genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Mortierella/*genetics ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Analysis, Protein ; *Sequence Homology, Amino Acid ; },
}
@article {pmid10922475,
year = {2000},
author = {Zhang, F and Hogue, DL and Liu, L and Fisher, CL and Hui, D and Childs, S and Ling, V},
title = {M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein.},
journal = {FEBS letters},
volume = {478},
number = {1-2},
pages = {89-94},
doi = {10.1016/s0014-5793(00)01823-8},
pmid = {10922475},
issn = {0014-5793},
mesh = {ATP-Binding Cassette Transporters/chemistry/*genetics/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bone Marrow/metabolism ; Cell Line ; Chromosomes, Human, Pair 1/genetics ; Chromosomes, Human, Pair 15/genetics ; Cloning, Molecular ; Gene Expression Profiling ; Humans ; In Situ Hybridization, Fluorescence ; Intracellular Membranes/chemistry ; Mitochondria/*chemistry ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Protein Sorting Signals/genetics ; Pseudogenes/genetics ; RNA, Messenger/analysis/genetics ; Sequence Alignment ; Transfection ; },
abstract = {We have isolated a human cDNA encoding a novel ATP-binding cassette (ABC) protein whose gene was previously localized to chromosome 1q42 [Allikmets et al. (1995) Mamm. Genome 6, 111-117]. The gene transcript is expressed in all human tissues examined, with the highest levels in bone marrow. A non-expressed pseudogene also exists at chromosome 15q13-14. The new protein, which is most similar to the mitochondrial (M)-ABC1 protein, was also localized to mitochondria and therefore designated 'M-ABC2'. The N-terminus of M-ABC2 was shown to contain a mitochondrial-targeting signal sequence.},
}
@article {pmid10928858,
year = {2000},
author = {Barrett, TG and Scott-Brown, M and Seller, A and Bednarz, A and Poulton, K and Poulton, J},
title = {The mitochondrial genome in Wolfram syndrome.},
journal = {Journal of medical genetics},
volume = {37},
number = {6},
pages = {463-466},
doi = {10.1136/jmg.37.6.463},
pmid = {10928858},
issn = {1468-6244},
mesh = {Adult ; Cohort Studies ; DNA, Mitochondrial/*genetics ; Female ; Genome ; Haplotypes/genetics ; Humans ; Male ; Membrane Proteins/genetics ; Mitochondria/enzymology/*genetics ; Mutation/genetics ; Phylogeny ; United Kingdom ; Wolfram Syndrome/diagnosis/enzymology/*genetics ; },
}
@article {pmid10930580,
year = {2000},
author = {Shah, ZH and Hakkaart, GA and Arku, B and de Jong, L and van der Spek, H and Grivell, LA and Jacobs, HT},
title = {The human homologue of the yeast mitochondrial AAA metalloprotease Yme1p complements a yeast yme1 disruptant.},
journal = {FEBS letters},
volume = {478},
number = {3},
pages = {267-270},
doi = {10.1016/s0014-5793(00)01859-7},
pmid = {10930580},
issn = {0014-5793},
mesh = {ATP-Dependent Proteases ; ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Cell Line ; Chromosomes, Human, Pair 10/genetics ; Cloning, Molecular ; *Gene Deletion ; *Genetic Complementation Test ; Glycerol/metabolism ; Humans ; Metalloendopeptidases/chemistry/genetics/*metabolism ; Mitochondria/*enzymology/metabolism ; Mitochondrial Proteins ; Phylogeny ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/*genetics/growth &amp; development/metabolism ; *Saccharomyces cerevisiae Proteins ; },
abstract = {In yeast, three AAA superfamily metalloproteases (Yme1p, Afg3p and Rca1p) are localized to the mitochondrial inner membrane where they perform roles in the assembly and turnover of the respiratory chain complexes. We have investigated the function of the proposed human orthologue of yeast Yme1p, encoded by the YME1L gene on chromosome 10p. Transfection of both HEK-293EBNA and yeast cells with a green fluorescent protein-tagged YME1L cDNA confirmed mitochondrial targeting. When expressed in a yme1 disruptant yeast strain, YME1L restored growth on glycerol at 37 degrees C. We propose that YME1L plays a phylogenetically conserved role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies.},
}
@article {pmid10942615,
year = {2000},
author = {Pruess, KP and Adams, BJ and Parsons, TJ and Zhu, X and Powers, TO},
title = {Utility of the mitochondrial cytochrome oxidase II gene for resolving relationships among black flies (Diptera: simuliidae).},
journal = {Molecular phylogenetics and evolution},
volume = {16},
number = {2},
pages = {286-295},
doi = {10.1006/mpev.2000.0807},
pmid = {10942615},
issn = {1055-7903},
support = {AI29456/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Classification ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; },
abstract = {The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. Phylogenetic trees based on weighted parsimony (a priori and a posteriori), maximum likelihood, and neighbor-joining (log-determinant distances) differed topologically, with deeper nodes being the least well-supported. All analyses supported current classification into species groups but relationships among those groups were poorly resolved. The majority of phylogenetic signal came from closely related sister taxa. The CO-II gene may be useful for exploring relationships at or below the subgeneric level, but is of questionable value at higher taxonomic levels. The weighting method employed gave phylogenetic results similar to those reported by other authors for other insect CO-II data sets. A best estimate of phylogenetic relationships based on the CO-II gene is presented and discussed in relation to current black fly classification.},
}
@article {pmid10944470,
year = {2000},
author = {Jones, JM and Gould, SJ},
title = {Identification of PTE2, a human peroxisomal long-chain acyl-CoA thioesterase.},
journal = {Biochemical and biophysical research communications},
volume = {275},
number = {1},
pages = {233-240},
doi = {10.1006/bbrc.2000.3285},
pmid = {10944470},
issn = {0006-291X},
support = {DK45787/DK/NIDDK NIH HHS/United States ; HD10981/HD/NICHD NIH HHS/United States ; },
mesh = {Acyl Coenzyme A/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Databases, Factual ; Fluorescent Antibody Technique ; Humans ; Hydrogen-Ion Concentration ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Peroxisomes/*enzymology/metabolism ; Phylogeny ; Protein Sorting Signals ; Recombinant Proteins/metabolism ; Sequence Alignment ; Substrate Specificity ; Thiolester Hydrolases/chemistry/*genetics/*metabolism ; Transfection ; },
abstract = {Computer-based approaches identified PTE2 as a candidate human peroxisomal acyl-CoA thioesterase gene. The PTE2 gene product is highly similar to the rat cytosolic and mitochondrial thioesterases, CTE1 and MTE1, respectively, and terminates in a tripeptide sequence, serine-lysine-valine(COOH), that resembles the consensus sequence for type-1 peroxisomal targeting signals. PTE2 was targeted to peroxisomes and recombinant PTE2 showed intrinsic acyl-CoA thioesterase activity with a pH optimum of 8.5. A comparison of PTE2 and PTE1 thioesterase activities across multiple acyl-CoA substrates indicated that while PTE1 was most active on medium-chain acyl-CoAs, with little activity on long-chain acyl-CoAs, PTE2 displayed high activity on medium- and long-chain acyl-CoAs. The identification of PTE2 therefore offers an explanation for the observed long-chain acyl-CoA thioesterase activity of mammalian peroxisomes.},
}
@article {pmid10958850,
year = {2000},
author = {Schmitz, J and Ohme, M and Zischler, H},
title = {The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders.},
journal = {Molecular biology and evolution},
volume = {17},
number = {9},
pages = {1334-1343},
doi = {10.1093/oxfordjournals.molbev.a026417},
pmid = {10958850},
issn = {0737-4038},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Scandentia/classification/*genetics ; Sequence Analysis, DNA ; Tupaia/*genetics ; },
abstract = {The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the general organization of the mammalian mitochondrial genome. Thus, features such as start codon usage, incomplete stop codons, and overlapping coding regions, as well as the presence of tandem repeats in the control region, are within the range of mammalian mitochondrial (mt) DNA variation. To address the question of a possible close phylogenetic relationship between primates and Tupaia, the evolutionary affinities among primates, Tupaia and bats as representatives of the Archonta superorder, ferungulates, guinea pigs, armadillos, rats, mice, and hedgehogs were examined on the basis of the complete mitochondrial DNA sequences. The opossum sequence was used as an outgroup. The trees, estimated from 12 concatenated genes encoded on the mitochondrial H-strand, add further molecular evidence against an Archonta monophyly. With the new data described in this paper, most of both the mitochondrial and the nuclear data point away from Scandentia as the closest extant relatives to primates. Instead, the complete mitochondrial data support a clustering of Scandentia with Lagomorpha connecting to the branch leading to ferungulates. This closer phylogenetic relationship of Tupaia to rabbits than to primates first received support from several analyses of nuclear and partial mitochondrial DNA data sets. Given that short sequences are of limited use in determining deep mammalian relationships, the partial mitochondrial data available to date support this hypothesis only tentatively. Our complete mitochondrial genome data therefore add considerably more evidence in support of this hypothesis.},
}
@article {pmid10973051,
year = {2000},
author = {Malik, HS and Henikoff, S},
title = {Dual recognition-incision enzymes might be involved in mismatch repair and meiosis.},
journal = {Trends in biochemical sciences},
volume = {25},
number = {9},
pages = {414-418},
doi = {10.1016/s0968-0004(00)01623-6},
pmid = {10973051},
issn = {0968-0004},
support = {GM-29009/GM/NIGMS NIH HHS/United States ; },
mesh = {*Adenosine Triphosphatases ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics/metabolism/physiology ; *Base Pair Mismatch ; Cnidaria/genetics/metabolism ; DNA/biosynthesis ; *DNA Repair ; *DNA-Binding Proteins ; *Escherichia coli Proteins ; Mitochondria/metabolism ; Models, Genetic ; Molecular Sequence Data ; MutL Proteins ; MutS DNA Mismatch-Binding Protein ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; },
abstract = {Mismatch repair in many organisms depends on three proteins: the mismatch-recognition protein MutS, a nicking endonuclease MutH, and MutL, which acts as a scaffold between these. However, many genomes lack MutL but possess MutS. In one of these cases, in a coral mitochondrial genome, a gene is present that encodes a MutS protein fused to an HNH nicking endonuclease, potentially eliminating the requirement for MutL. Likewise, many prokaryotes could operate similarly, independently of MutL by encoding a fused MutS-Smr (MutS2) protein. Smr, which is proposed to be a nicking endonuclease, can also be found separately in many eukaryotes, where it might play a role in mismatch repair or meiotic chromosome crossing-over.},
}
@article {pmid10978543,
year = {2000},
author = {Gupta, RS},
title = {The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.},
journal = {FEMS microbiology reviews},
volume = {24},
number = {4},
pages = {367-402},
doi = {10.1111/j.1574-6976.2000.tb00547.x},
pmid = {10978543},
issn = {0168-6445},
mesh = {ATP-Dependent Proteases ; Adenosine Triphosphatases/genetics ; Alanine-tRNA Ligase/genetics ; Amino Acid Sequence ; Bacterial Proteins/*classification/genetics ; Carrier Proteins/genetics ; Chaperonin 60/genetics ; DNA Topoisomerases, Type II/genetics ; *Escherichia coli Proteins ; Eukaryotic Cells ; Gene Deletion ; HSP70 Heat-Shock Proteins/genetics ; Heat-Shock Proteins/genetics ; Ligases/genetics/metabolism ; *Membrane Transport Proteins ; Mitochondria ; Molecular Sequence Data ; Phosphoribosyl Pyrophosphate/metabolism ; Phylogeny ; Proteobacteria/chemistry/*classification/genetics ; Pyrophosphatases/genetics ; Ribosomal Proteins/genetics ; SEC Translocation Channels ; SecA Proteins ; Sequence Alignment ; Serine Endopeptidases/genetics ; Succinate-CoA Ligases/genetics ; Sulfurtransferases/genetics ; Terminology as Topic ; UDPglucose 4-Epimerase/genetics ; Valine-tRNA Ligase/genetics ; },
abstract = {The evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. Sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of proteobacteria. These signature sequences provide molecular means to define the proteobacterial phyla and their various subdivisions and to understand their evolutionary relationships to the other groups of eubacteria as well as the eukaryotes. Based on signature sequences that are present in different proteins it is now possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low-G+C Gram-positive-->high-G+C Gram-positive-->Deinococcus-Thermus (green nonsulfur bacteria)-->cyanobacteria-->Spirochetes-->Chlamydia-Cytophaga-Aquifex -green sulfur bacteria-->Proteobacteria-1 (epsilon and delta)-->Proteobacteria-2 (alpha)-->Proteobacteria-3 (beta)-->Proteobacteria-4 (gamma). An unexpected but important aspect of the relationship deduced here is that the main eubacterial phyla are related to each other linearly rather than in a tree-like manner, suggesting that the major evolutionary changes within Bacteria have taken place in a directional manner. The identified signatures permit placement of prokaryotes into different groups/divisions and could be used for determinative purposes. These signatures generally support the origin of mitochondria from an alpha-proteobacterium and provide evidence that the nuclear cytosolic homologs of many genes are also derived from proteobacteria.},
}
@article {pmid10981697,
year = {2000},
author = {Nakai, R and Sen, K and Kurosawa, S and Shibai, H},
title = {Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases.},
journal = {FEMS microbiology letters},
volume = {190},
number = {1},
pages = {99-102},
doi = {10.1111/j.1574-6968.2000.tb09269.x},
pmid = {10981697},
issn = {0378-1097},
mesh = {Agaricales/*enzymology/genetics/ultrastructure ; Amino Acid Sequence ; Cloning, Molecular ; DNA, Fungal/analysis/genetics ; DNA-Directed DNA Polymerase/chemistry/*genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; },
abstract = {Basidiomycetous fungus Flammulina velutipes R15 strain had two linear plasmids in its mitochondria designated pFV1 and pFV2. They were double-stranded DNAs, whose sizes were 8.3 and 8.9 kb, respectively. Sequencing analysis of 7364 bases of the pFV1 and 6861 bases of the pFV2 revealed that the both plasmids had one set of two open reading frames (ORFs) each of that encoded putative DNA and RNA polymerases similar to those of mitochondrial plasmids in other filamentous fungi. In phylogenetic analysis of deduced amino acid sequences of the ORFs and counterparts of other filamentous fungi, the pFV2 was expectedly clustered with plasmids of basidiomycetous fungi. whereas the pFV1 with kalilo plasmid of ascomycetous fungus Neurospora intermedia.},
}
@article {pmid10989156,
year = {2000},
author = {Bakatselou, C and Kidgell, C and Graham Clark, C},
title = {A mitochondrial-type hsp70 gene of Entamoeba histolytica.},
journal = {Molecular and biochemical parasitology},
volume = {110},
number = {1},
pages = {177-182},
doi = {10.1016/s0166-6851(00)00264-4},
pmid = {10989156},
issn = {0166-6851},
mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; Entamoeba histolytica/*genetics/growth &amp; development/metabolism ; HSP70 Heat-Shock Proteins/chemistry/*genetics/*metabolism ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; },
}
@article {pmid10996302,
year = {2000},
author = {Juhola, MK and Shah, ZH and Grivell, LA and Jacobs, HT},
title = {The mitochondrial inner membrane AAA metalloprotease family in metazoans.},
journal = {FEBS letters},
volume = {481},
number = {2},
pages = {91-95},
doi = {10.1016/s0014-5793(00)01989-x},
pmid = {10996302},
issn = {0014-5793},
mesh = {Animals ; Humans ; Intracellular Membranes/*enzymology ; Invertebrates ; Metalloendopeptidases/*genetics/*metabolism ; Mitochondria/*enzymology ; Multigene Family ; Phylogeny ; },
abstract = {Three metalloproteases belonging to the AAA superfamily (Yme1p, Afg3p and Rca1p) are involved in protein turnover and respiratory chain complex assembly in the yeast inner mitochondrial membrane. Analysis of the completed genome sequences of Caenorhabditis elegans and Drosophila melanogaster indicates that this gene family typically comprises 3-4 members in metazoans. Phylogenetic analysis reveals three main branches represented, respectively, by Saccharomyces cerevisiae YME1, human SPG7 (paraplegin) and S. cerevisiae AFG3 and RCA1. mt-AAA metalloproteases are weak candidates for several previously studied Drosophila mutants. A full elucidation of the cellular and physiological roles of mt-AAA metalloproteases in metazoans will require the creation of targeted mutations.},
}
@article {pmid11027335,
year = {2000},
author = {Telford, MJ and Herniou, EA and Russell, RB and Littlewood, DT},
title = {Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {97},
number = {21},
pages = {11359-11364},
pmid = {11027335},
issn = {0027-8424},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; DNA Primers ; *Genetic Code ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Platyhelminths/*genetics ; Species Specificity ; },
abstract = {Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate).},
}
@article {pmid11029671,
year = {2000},
author = {Lessinger, AC and Martins Junqueira, AC and Lemos, TA and Kemper, EL and da Silva, FR and Vettore, AL and Arruda, P and Azeredo-Espin, AM},
title = {The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae).},
journal = {Insect molecular biology},
volume = {9},
number = {5},
pages = {521-529},
doi = {10.1046/j.1365-2583.2000.00215.x},
pmid = {11029671},
issn = {0962-1075},
mesh = {Animals ; Base Composition ; Codon ; DNA, Mitochondrial/chemistry/*genetics ; Diptera/classification/*genetics ; *Genes, Insect ; *Genome ; Insect Proteins/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; },
abstract = {The complete sequence of the mitochondrial genome of the screwworm Cochliomyia hominivorax was determined. This genome is 16,022 bp in size and corresponds to a typical Brachycera mtDNA. A Serine start codon for COI and incomplete termination codons for COII, NADH 5 and NADH 4 genes were described. The nucleotide composition of C. hominivorax mtDNA is 77% AT-rich, reflected in the predominance of AT-rich codons in protein-coding genes. Non-optimal codon usage was commonly observed in C. hominivorax mitochondrial genes. Phylogenetic analysis distributed the Acalypterate species as a monophyletic group and assembled the C. hominivorax (Calyptratae) and the Acalyptratae in a typical Brachycera cluster. The identification of diagnostic restriction sites on the sequenced mitochondrial genome and the correlation with previous RFLP analysis are discussed.},
}
@article {pmid11034499,
year = {2000},
author = {Sauer, C and Stackebrandt, E and Gadau, J and Hölldobler, B and Gross, R},
title = {Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {50 Pt 5},
number = {},
pages = {1877-1886},
doi = {10.1099/00207713-50-5-1877},
pmid = {11034499},
issn = {1466-5026},
mesh = {Animals ; Ants/classification/enzymology/*microbiology ; Base Composition ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Digestive System/microbiology ; Electron Transport Complex IV/genetics ; Gammaproteobacteria/*classification/genetics/isolation &amp; purification ; Genes, rRNA ; In Situ Hybridization ; Introns ; Mitochondria/enzymology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; rRNA Operon ; },
abstract = {The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.},
}
@article {pmid11035803,
year = {2000},
author = {Marcotte, EM and Xenarios, I and van Der Bliek, AM and Eisenberg, D},
title = {Localizing proteins in the cell from their phylogenetic profiles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {97},
number = {22},
pages = {12115-12120},
pmid = {11035803},
issn = {0027-8424},
mesh = {Algorithms ; Animals ; Caenorhabditis elegans/genetics/metabolism ; Membrane Proteins/*metabolism ; *Phylogeny ; Protein Sorting Signals/*physiology ; Saccharomyces cerevisiae/genetics/metabolism ; Subcellular Fractions/*metabolism ; },
abstract = {We introduce a computational method for identifying subcellular locations of proteins from the phylogenetic distribution of the homologs of organellar proteins. This method is based on the observation that proteins localized to a given organelle by experiments tend to share a characteristic phylogenetic distribution of their homologs-a phylogenetic profile. Therefore any other protein can be localized by its phylogenetic profile. Application of this method to mitochondrial proteins reveals that nucleus-encoded proteins previously known to be destined for mitochondria fall into three groups: prokaryote-derived, eukaryote-derived, and organism-specific (i.e., found only in the organism under study). Prokaryote-derived mitochondrial proteins can be identified effectively by their phylogenetic profiles. In the yeast Saccharomyces cerevisiae, 361 nucleus-encoded mitochondrial proteins can be identified at 50% accuracy with 58% coverage. From these values and the proportion of conserved mitochondrial genes, it can be inferred that approximately 630 genes, or 10% of the nuclear genome, is devoted to mitochondrial function. In the worm Caenorhabditis elegans, we estimate that there are approximately 660 nucleus-encoded mitochondrial genes, or 4% of its genome, with approximately 400 of these genes contributed from the prokaryotic mitochondrial ancestor. The large fraction of organism-specific and eukaryote-derived genes suggests that mitochondria perform specialized roles absent from prokaryotic mitochondrial ancestors. We observe measurably distinct phylogenetic profiles among proteins from different subcellular compartments, allowing the general use of prokaryotic genomes in learning features of eukaryotic proteins.},
}
@article {pmid11080313,
year = {2000},
author = {Moran, JF and Iturbe-Ormaetxe, I and Matamoros, MA and Rubio, MC and Clemente, MR and Brewin, NJ and Becana, M},
title = {Glutathione and homoglutathione synthetases of legume nodules. Cloning, expression, and subcellular localization.},
journal = {Plant physiology},
volume = {124},
number = {3},
pages = {1381-1392},
pmid = {11080313},
issn = {0032-0889},
mesh = {Amino Acid Sequence ; Bacteroides/enzymology ; Blotting, Northern ; Cell Compartmentation ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/isolation &amp; purification ; Fabaceae/enzymology/*genetics/microbiology ; Glutathione Synthase/*genetics/metabolism ; Molecular Sequence Data ; *Nitrogen Fixation ; Peptide Synthases/*genetics/metabolism ; Phylogeny ; Plant Roots/enzymology/ultrastructure ; *Plants, Medicinal ; Plastids/enzymology ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Subcellular Fractions/*enzymology ; Symbiosis ; },
abstract = {The thiol tripeptides glutathione (GSH) and homoglutathione (hGSH) are very abundant in legume root nodules and their synthesis is catalyzed by the enzymes gamma-glutamylcysteine synthetase (gammaECS), GSH synthetase (GSHS), and hGSH synthetase (hGSHS). As an essential step to elucidate the role of thiols in N(2) fixation we have isolated cDNAs encoding the three enzymes and have quantified the transcripts in nodules. Assay of enzyme activities in highly purified nodule organelles revealed that gammaECS is localized in the plastids, hGSHS in the cytosol, and GSHS in the cytosol and mitochondria. These results are consistent with sequence analyses. Subcellular fractionation of nodules also showed that bacteroids contain high thiol concentrations and high specific gammaECS and GSHS activities. Results emphasize the role of nodule plastids in antioxidant protection and in control of thiol synthesis, and suggest that plastids may be important in the stress response of nodules. Overall, our results provide further evidence that thiol synthesis is critical for nodule functioning.},
}
@article {pmid11080589,
year = {2000},
author = {Choi, KR and Roh, K and Kim, J and Sim, W},
title = {Genomic cloning and characterization of mitochondrial elongation factor Tu (EF-Tu) gene (tufM) from maize (Zea mays L.).},
journal = {Gene},
volume = {257},
number = {2},
pages = {233-242},
doi = {10.1016/s0378-1119(00)00404-2},
pmid = {11080589},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Plant/chemistry/*genetics/isolation &amp; purification ; Genes, Plant/*genetics ; Mitochondria/*chemistry ; Molecular Sequence Data ; Peptide Elongation Factor Tu/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Zea mays/*genetics ; },
abstract = {We have cloned and characterized a mitochondrial elongation factor Tu (EF-Tu) gene (tufM) in maize (Zea mays L.). This maize tufM gene encoded a polypeptide of 452 amino acid residues, consisting of a putative transit peptide of 55 residues and a mature EF-Tu of 397 residues. The coding region was composed of 12 exons and 11 introns that ranged from 76 to 1673bp in length. The deduced amino acid sequence showed 85.9% and 61.2% identity with Arabidopsis mitochondrial EF-Tu and Arabidopsis chloroplast EF-Tu sequence respectively. The transcription initiation site was determined to be 165bp upstream of the AUG initiation codon by primer extension analysis. Southern blot analysis revealed that the cloned EF-Tu gene was encoded by the members of small gene family in maize. Although this gene does not resemble the Arabidopsis nuclear tufA gene, which encodes the plastid EF-Tu, and does not contain sequence elements found in all cyanobacterial and plastid tufA genes, the predicted amino acid sequence includes an N-terminal extension that resembles a mitochondrial targeting sequence, and shares three unique sequence elements with mitochondrial EF-Tu's from Arabidopsis thaliana, Saccharomyces cerevisiae, and Homo sapiens. Therefore, we concluded that this gene encodes the maize mitochondrial EF-Tu.},
}
@article {pmid11094747,
year = {2000},
author = {Filipenko, ML and Timofeeva, OA and Gusachenko, AM and Sergeev, MG and Vysotskaia, LV},
title = {[Reconstruction of phylogeny of locusts from the family Acrididae (Orthoptera) based on analysis of nucleotide sequences of 16S ribosome RNA gene in mitochondria].},
journal = {Genetika},
volume = {36},
number = {10},
pages = {1355-1361},
pmid = {11094747},
issn = {0016-6758},
mesh = {Animals ; Base Sequence ; Grasshoppers/classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {The sequences of two mitochondrial 16S RNA gene fragments (137- and 174-bp in size) were determined in nine grasshopper species belonging to three Acrididae subfamilies. Phylogenetic reconstruction was performed using the sequences of twelve grasshopper species and the cricket Acheta domesticus sequence as an outgroup (some data were purchased from the GeneBank Data Library (NCBI). In the phylogenetic tree, the Acridinae and Locustinae formed compact groups. Annexpected position of Celes scalozubovi (Locustinae) within the subfamily Acridinae indicated its vague phylogeny. The Catantopinae species lied close to the base of the Acridinae. Almost all branches of phylogenetic trees were strongly (55-100%) supported by bootstrap analysis.},
}
@article {pmid11101587,
year = {2000},
author = {Yokoyama, K and Biswas, SK and Miyaji, M and Nishimura, K},
title = {Identification and phylogenetic relationship of the most common pathogenic Candida species inferred from mitochondrial cytochrome b gene sequences.},
journal = {Journal of clinical microbiology},
volume = {38},
number = {12},
pages = {4503-4510},
pmid = {11101587},
issn = {0095-1137},
mesh = {Amino Acid Sequence ; Base Sequence ; Candida/*classification/enzymology/genetics ; Cytochrome b Group/*genetics ; DNA, Fungal/*chemistry ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We sequenced a 396-bp region of the mitochondrial cytochrome b gene of the most common clinically important Candida species: Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. lusitaniae. The recently described species of Candida, C. dubliniensis, associated with mucosal candidiasis in human immunodeficiency virus-infected individuals, was also included. Two to five strains of each species were examined. Some species represented intraspecies variation, which was not more than 1.8% (DNA). However, interspecies variations were more than 10 and 7%, respectively, for DNA and amino acid sequences. Multiple alignments of nucleotide and deduced amino acid sequences revealed species-specific nucleotides and amino acids. Nucleotide- and amino acid-based phylogenetic trees were constructed and are discussed. Using the database, it is possible to identify presumptive Candida species within a working day.},
}
@article {pmid11121736,
year = {2000},
author = {Schneider, A and Maréchal-Drouard, L},
title = {Mitochondrial tRNA import: are there distinct mechanisms?.},
journal = {Trends in cell biology},
volume = {10},
number = {12},
pages = {509-513},
doi = {10.1016/s0962-8924(00)01854-7},
pmid = {11121736},
issn = {0962-8924},
mesh = {Animals ; Biological Transport ; Cell Nucleus/genetics/metabolism ; Humans ; Mitochondria/*genetics/metabolism ; Models, Biological ; Nucleic Acid Conformation ; Phylogeny ; RNA/genetics/*metabolism ; RNA, Mitochondrial ; RNA, Transfer/genetics/*metabolism ; },
abstract = {Sequence information from an increasing number of complete mitochondrial genomes indicates that a large number of evolutionary distinct organisms import nucleus-encoded tRNAs. In the past five years, much research has been initiated on the features of imported tRNAs, the mechanism and the energetics of the process as well as on the components of the import machinery. In summary, these studies show that the import systems of different species exhibit some unique features, suggesting that more than one mechanism might exist to import tRNAs.},
}
@article {pmid11129049,
year = {2000},
author = {Takahara, M and Takahashi, H and Matsunaga, S and Miyagishima, S and Takano, H and Sakai, A and Kawano, S and Kuroiwa, T},
title = {A putative mitochondrial ftsZ gene is present in the unicellular primitive red alga Cyanidioschyzon merolae.},
journal = {Molecular &amp; general genetics : MGG},
volume = {264},
number = {4},
pages = {452-460},
doi = {10.1007/s004380000307},
pmid = {11129049},
issn = {0026-8925},
mesh = {Amino Acid Sequence ; Animals ; Antibodies/isolation &amp; purification ; Arabidopsis Proteins ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; DNA Primers/genetics ; Gene Expression ; *Genes, Plant ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plasmids/genetics ; Rhodophyta/*genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {Two ftsZ homologues were isolated from the unicellular primitive red alga Cyanidioschyzon merolae (CmftsZ1 and CmftsZ2). Phylogenetic analysis revealed that CmftsZ1 is most closely related to the ftsZ genes of alpha-Proteobacteria, suggesting that it is a mitochondrial-type ftsZ gene, whereas CmftsZ2 is most closely related to the ftsZ genes of cyanobacteria, suggesting that it is a plastid-type ftsZ gene. Southern analysis indicates that CmftsZ1 and CmftsZ2 are both single-copy genes located on chromosome XIV in the C. merolae genome. Northern analysis revealed that both CmftsZ1 and CmftsZ2 are transcribed, and accumulate specifically before cell and organelle division. The results of Western analysis suggest that CmFtsZ1 is localized in mitochondria.},
}
@article {pmid11137175,
year = {2000},
author = {Brown, JK},
title = {Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.},
journal = {Virus research},
volume = {71},
number = {1-2},
pages = {233-260},
doi = {10.1016/s0168-1702(00)00221-5},
pmid = {11137175},
issn = {0168-1702},
mesh = {Amino Acid Sequence ; Animals ; Capsid/genetics ; Geminiviridae/classification/*genetics ; Genes, Insect ; Genes, Viral ; Genetic Markers ; Genetic Variation ; Geography ; Hemiptera/*genetics/virology ; Insect Vectors/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Diseases/*virology ; Sequence Alignment ; Species Specificity ; Virus Replication/genetics ; },
abstract = {Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a basis in the most highly conserved viral ORFs, CP (V1) and a portion of replication-associated protein (REP) (L1/C1), and a key non-coding sequence that contain sufficient variability and/or virus-specific sequences, and are consequently of potential epidemiological relevance. Because B. tabaci occurs as a cryptic species, or species complex, that exhibits biotic polymorphism, yet morphological invariance, traditional morphologically based identification is impossible. An overriding complication to establishing molecular markers for identifying whitefly vector variants is that whitefly sequences in general, have not been available. However, recent work has shown that a partial mitochondria cytochrome oxidase I (mt COI) sequence separates vector variants with a basis in geographical origin, suggesting it is useful for further exploring variability and the phylogenetic history of whiteflies on a large scale. Here, the utility of whitefly mt COI nucleotides (nt) sequences is illustrated for inferring relationships between B. tabaci collected from major world regions. Used collectively, these approaches permit investigations of the patterns of distribution and dissemination of begomovirus-whitefly vector complexes for the first time. Ultimately, more immediate recognition of exotic viruses and whitefly vectors and early detection of upsurges in vector populations and of emerging viruses will be possible.},
}
@article {pmid11155936,
year = {2000},
author = {McDonnell, A and Love, S and Tait, A and Lichtenfels, JR and Matthews, JB},
title = {Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I and large ribosomal RNA sequences and nuclear internal transcribed spacer I sequences from species of Cyathostominae and Strongylinae (Nematoda, Order Strongylida), parasites of the horse.},
journal = {Parasitology},
volume = {121 Pt 6},
number = {},
pages = {649-659},
doi = {10.1017/s003118200000696x},
pmid = {11155936},
issn = {0031-1820},
mesh = {Animals ; DNA, Helminth/*chemistry ; DNA, Ribosomal Spacer/*chemistry ; Electron Transport Complex IV/*genetics ; Horse Diseases/*parasitology ; Horses ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*chemistry ; Strongylida/*classification/genetics ; Strongylida Infections/parasitology/*veterinary ; },
abstract = {Three nucleotide data sets, one nuclear (ITS-2) and two mitochondrial (COI and l-rRNA), have been investigated in order to determine relationships among species of Strongylinae and Cyathostominae, intestinal parasites of the horse. The data exhibited a strong mutational bias towards A and T and in the COI gene, silent sites appeared to saturate rapidly partly due to this substitution bias. Thus, the COI gene was found to be less phylogenetically informative than the l-rRNA and ITS-2 genes. Combined analysis of the l-rRNA and ITS-2 genes supported a monophyletic clade of the cyathostomes with Tridentoinfundibulum gobi, which had previously been classified as a nematode of' uncertain origin'. The Strongylinae grouped consistently outside the clade containing the cyathostomes and T. gobi. Molecular analysis failed to provide strong evidence for the separation of cyathostomes into classical genera, as previously defined by morphological classification.},
}
@article {pmid11161741,
year = {2001},
author = {Söller, R and Wohltmann, A and Witte, H and Blohm, D},
title = {Phylogenetic relationships within terrestrial mites (Acari: Prostigmata, Parasitengona) inferred from comparative DNA sequence analysis of the mitochondrial cytochrome oxidase subunit I gene.},
journal = {Molecular phylogenetics and evolution},
volume = {18},
number = {1},
pages = {47-53},
doi = {10.1006/mpev.2000.0855},
pmid = {11161741},
issn = {1055-7903},
mesh = {Animals ; Codon ; Electron Transport Complex IV/*genetics ; Likelihood Functions ; Mites/*classification/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Partial DNA and amino acid sequences translated from the mitochondrial cytochrome subunit I gene (408 bp) of 17 mite species have been used for analyzing the phylogenetic relationships within the terrestrial Parasitengona (Trombidia). Due to mutational saturation of the third codon position, only first and second codon positions and amino acid sequences were analyzed, applying neighbor-joining, maximum-parsimony, and maximum-likelihood tree-building methods. The reconstructed trees revealed similar topologies of taxa; however, the phylogenetic relationships could be convincingly resolved only within several trombidioid taxa. The proposed basic relationships within the Parasitengona, in particular those of Calyptostomatoidea, Smarididae, and Erythraeidae, were poorly supported in bootstrap tests. A comparison of the presented gene tree with a phylogenetic tree based upon traditional characters revealed only few contradictions in nodes only weakly supported by morphological data. The most astonishing result is the proposed early derivative position of Microtrombidiidae within the terrestrial Parasitengona.},
}
@article {pmid11169765,
year = {2001},
author = {Liu, L and Zhou, J and Pesacreta, TC},
title = {Maize myosins: diversity, localization, and function.},
journal = {Cell motility and the cytoskeleton},
volume = {48},
number = {2},
pages = {130-148},
doi = {10.1002/1097-0169(200102)48:2&lt;130::AID-CM1004&gt;3.0.CO;2-Y},
pmid = {11169765},
issn = {0886-1544},
mesh = {Amino Acid Sequence ; Blotting, Northern ; Blotting, Southern ; Cell Membrane/chemistry/physiology ; Cloning, Molecular ; Cytoskeleton/*chemistry/metabolism ; DNA Probes ; DNA, Plant/analysis ; DNA-Binding Proteins/genetics ; Gene Expression Regulation, Plant ; Gene Library ; Genetic Testing ; Genetic Variation ; Immunohistochemistry ; MADS Domain Proteins ; Molecular Sequence Data ; Myosins/*analysis/*genetics/metabolism ; Phylogeny ; Plant Proteins ; Plant Roots/chemistry/physiology ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; RNA, Plant/analysis ; Transcription Factors/genetics ; Zea mays/*genetics ; },
abstract = {This first analysis of monocotyledon myosin genes showed that at least five genes, one of which was probably spliced to yield two isoforms, were expressed in maize (Zea mays L.). The complete coding sequence of ZMM1 was determined, as were most of the sequences of two other myosin cDNAs (ZMM2 and ZMM3). ZMM1 and ZMM2 belonged to myosin class XI while ZMM3 was in class VIII. ZMM1 was abundantly expressed in leaves, roots, coleoptiles, and stems. ZMM3 showed a similar distribution but was expressed poorly in pollen. ZMM2 was predominantly expressed in seeds and may be part of a suite of cytoskeletal proteins in reproductive tissues. Phylogenetic analysis suggested that the origin of myosin classes VIII and XI predated that of angiosperms. Immunofluorescence studies using M11L1, a myosin XI antibody specific for the exposed loop 1 head region of myosin, indicated that myosin XI occurred in the cytoplasm of all root tip cells. The highest concentration of myosin XI was in the differentiating epidermal cells. In dividing cells, myosin XI was present near the cytokinetic apparatus at approximately the same concentration seen in other portions of the cytoplasm. Western blot analysis of subcellular fractions indicated that myosin XI was concentrated in mitochondria and low-density membranes.},
}
@article {pmid11195343,
year = {2000},
author = {Chiang, TY},
title = {Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France.},
journal = {Genome},
volume = {43},
number = {6},
pages = {1090-1094},
pmid = {11195343},
issn = {0831-2796},
mesh = {Chloroplasts/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; France ; Haplotypes ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; Rosales/*genetics ; },
abstract = {Dumolin-Lapégue et al. (Mol. Biol. Evol. 15: 1321-1331. 1998) suggested that recurrent inversions of a 4-bp sequence of the mtDNA nad4-1/2 locus due to intramolecular recombination were responsible for the disassociation of chloroplast and mitochondrial genomes of French oaks. Based on their PCR-RFLP (PCR-restriction fragment length polymorphism) data obtained from three noncoding spacers, a minimum spanning network representing the phylogeny of the cpDNA was reconstructed. The mapping of alleles b and c of the mtDNA nad4-1/2 locus on the cpDNA network revealed a nonrandom distribution, which contradicted the expected patterns when repeated, and ongoing inversions had been occurring. The fact that polymorphisms (a mixed c + d type) were mostly restricted to the interior nodes of the network, which represented ancient haplotypes and geographically coincided with probable glacial refugia in southern Europe, agreed with a migrant-pool model. Evidence of a widespread pattern of polymorphism distribution indicated that mtDNA haplotypes were likely to be more ancient than the cpDNA haplotypes. Lineage sorting, due to relative age of cpDNA vs. mtDNA, plus the specific migratory mode, which recruited colonists from a random sample of resource populations during glacial expansion (thereby extending the lineage sorting period, LSP), may have resulted in the disassociation of chloroplast and mitochondrial genomes in oaks.},
}
@article {pmid11198014,
year = {2000},
author = {van der Kuyl, AC and van Gennep, DR and Dekker, JT and Goudsmit, J},
title = {Routine DNA analysis based on 12S rRNA gene sequencing as a tool in the management of captive primates.},
journal = {Journal of medical primatology},
volume = {29},
number = {5},
pages = {309-317},
pmid = {11198014},
issn = {0047-2565},
mesh = {Animal Husbandry ; Animals ; Animals, Zoo ; Cercopithecidae/*genetics ; *Classification ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal ; Sequence Analysis, DNA ; },
abstract = {Automated DNA sequencing of a fragment of the relatively slowly evolving mitochondrial 12S rRNA gene was used to distinguish primate species, and the method was compared with species determination based upon classical taxonomy. DNA from blood from 53 monkeys housed at the Stichting AAP Shelter for Exotic Animals, all Old World monkeys, was amplified by polymerase chain reaction (PCR) with a primer set spanning approximately 390 nucleotides of the mitochondrial 12S rRNA gene. The products were directly sequenced and compared with our database of primate 12S sequences. Many individuals were found to harbor a 12S sequence identical to one of the reference sequences. For others, phylogenetic methods were used for species estimation, which was especially informative in Cercopithecus species.},
}
@article {pmid11203236,
year = {2000},
author = {Moreira, D and Rodríguez-Valera, F},
title = {A mitochondrial origin for eukaryotic C2H2 zinc finger regulators?.},
journal = {Trends in microbiology},
volume = {8},
number = {10},
pages = {448-450},
doi = {10.1016/s0966-842x(00)01850-3},
pmid = {11203236},
issn = {0966-842X},
mesh = {Bacteria/*genetics ; *Eukaryotic Cells ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Mitochondria/*genetics ; Phylogeny ; Proteins/chemistry/*genetics ; *Zinc Fingers ; },
}
@article {pmid11251792,
year = {2001},
author = {Hurwood, DA and Hughes, JM},
title = {Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia.},
journal = {Molecular ecology},
volume = {10},
number = {1},
pages = {113-125},
doi = {10.1046/j.1365-294x.2001.01175.x},
pmid = {11251792},
issn = {0962-1083},
mesh = {Animals ; Australia ; Base Sequence ; DNA, Mitochondrial/analysis/*genetics ; Decapoda/*genetics ; Electron Transport Complex IV/*genetics ; Gene Frequency ; *Genetic Variation ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {The freshwater shrimp, Caridina zebra, is endemic to montane rainforest streams of the Atherton Tableland, north-eastern Australia. As the confluences of many of the headwater streams are in unsuitable habitat, dispersal is expected to be highly restricted. Results from a previous allozyme survey for this species suggested that historical dispersal between separate river drainages had occurred due to rearrangements of the drainage lines at some stage in the recent past. The aim of this study was to use temporal information from the mitochondrial cytochrome oxidase subunit I (CO-I) gene to determine whether the observed genetic structure was a result of historical processes, or alternatively, due to low levels of terrestrial dispersal. The mitochondrial DNA (mtDNA) data were analysed using nested clade analysis, which can differentiate between historical fragmentation and range expansion vs. contemporary restricted gene flow. The results displayed three divergent clades that were likely to have arisen in allopatry. One widespread clade, with individuals in more than one river drainage, reflected a pattern of restricted gene flow. This suggests that this species is capable of terrestrial dispersal.},
}
@article {pmid11285367,
year = {2001},
author = {Vianna, CR and Hagen, T and Zhang, CY and Bachman, E and Boss, O and Gereben, B and Moriscot, AS and Lowell, BB and Bicudo, JE and Bianco, AC},
title = {Cloning and functional characterization of an uncoupling protein homolog in hummingbirds.},
journal = {Physiological genomics},
volume = {5},
number = {3},
pages = {137-145},
doi = {10.1152/physiolgenomics.2001.5.3.137},
pmid = {11285367},
issn = {1531-2267},
support = {R37 DK053477/DK/NIDDK NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Birds/*genetics/physiology ; Carrier Proteins/*genetics ; Cloning, Molecular ; Ion Channels ; Membrane Potentials ; Membrane Proteins/*genetics ; *Membrane Transport Proteins ; Mitochondria/physiology ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; RNA, Messenger/biosynthesis ; Saccharomyces cerevisiae/physiology ; Sequence Homology, Amino Acid ; Thermogenesis ; Tissue Distribution ; Uncoupling Protein 1 ; Uncoupling Protein 2 ; Uncoupling Protein 3 ; },
abstract = {The cDNA of an uncoupling protein (UCP) homolog has been cloned from the swallow-tailed hummingbird, Eupetomena macroura. The hummingbird uncoupling protein (HmUCP) cDNA was amplified from pectoral muscle (flight muscle) using RT-PCR and primers for conserved domains of various known UCP homologs. The rapid amplification of cDNA ends (RACE) method was used to complete the cloning of the 5' and 3' ends of the open reading frame. The HmUCP coding region contains 915 nucleotides, and the deduced protein sequence consists of 304 amino acids, being approximately 72, 70, and 55% identical to human UCP3, UCP2, and UCP1, respectively. The uncoupling activity of this novel protein was characterized in yeast. In this expression system, the 12CA5-tagged HmUCP fusion protein was detected by Western blot in the enriched mitochondrial fraction. Similarly to rat UCP1, HmUCP decreased the mitochondrial membrane potential as measured in whole yeast by uptake of the fluorescent potential-sensitive dye 3',3-dihexyloxacarbocyanine iodide. The HmUCP mRNA is primarily expressed in skeletal muscle, but high levels can also be detected in heart and liver, as assessed by Northern blot analysis. Lowering the room's temperature to 12-14 degrees C triggered the cycle torpor/rewarming, typical of hummingbirds. Both in the pectoral muscle and heart, HmUCP mRNA levels were 1.5- to 3.4-fold higher during torpor. In conclusion, this is the first report of an UCP homolog in birds. The data indicate that HmUCP has the potential to function as an UCP and could play a thermogenic role during rewarming.},
}
@article {pmid11319255,
year = {2001},
author = {Rotte, C and Stejskal, F and Zhu, G and Keithly, JS and Martin, W},
title = {Pyruvate : NADP+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: a biochemical relic linking pyruvate metabolism in mitochondriate and amitochondriate protists.},
journal = {Molecular biology and evolution},
volume = {18},
number = {5},
pages = {710-720},
doi = {10.1093/oxfordjournals.molbev.a003853},
pmid = {11319255},
issn = {0737-4038},
support = {AI 40320/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Apicomplexa/*parasitology ; Blotting, Northern ; Blotting, Southern ; Cryptosporidium parvum/*enzymology/genetics/metabolism ; Euglena gracilis/*enzymology/metabolism ; Ketone Oxidoreductases/*genetics/*metabolism ; Kinetics ; Mitochondria/drug effects/*genetics/*metabolism ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Oxygen/*pharmacology ; Phylogeny ; Protozoan Infections/parasitology ; Pyruvate Dehydrogenase Complex/*genetics/*metabolism ; Pyruvate Synthase ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Most eukaryotes perform the oxidative decarboxylation of pyruvate in mitochondria using pyruvate dehydrogenase (PDH). Eukaryotes that lack mitochondria also lack PDH, using instead the O(2)-sensitive enzyme pyruvate : ferredoxin oxidoreductase (PFO), which is localized either in the cytosol or in hydrogenosomes. The facultatively anaerobic mitochondria of the photosynthetic protist Euglena gracilis constitute a hitherto unique exception in that these mitochondria oxidize pyruvate with the O(2)-sensitive enzyme pyruvate : NADP oxidoreductase (PNO). Cloning and analysis of Euglena PNO revealed that the cDNA encodes a mitochondrial transit peptide followed by an N-terminal PFO domain that is fused to a C-terminal NADPH-cytochrome P450 reductase (CPR) domain. Two independent 5.8-kb full-size cDNAs for Euglena mitochondrial PNO were isolated; the gene was expressed in cultures supplied with 2% CO(2) in air and with 2% CO(2) in N(2). The apicomplexan Cryptosporidium parvum was also shown to encode and express the same PFO-CPR fusion, except that, unlike E. gracilis, no mitochondrial transit peptide for C. parvum PNO was found. Recombination-derived remnants of PNO are conserved in the genomes of Saccharomyces cerevisiae and Schizosaccharomyces pombe as proteins involved in sulfite reduction. Notably, Trypanosoma brucei was found to encode homologs of both PFO and all four PDH subunits. Gene organization and phylogeny revealed that eukaryotic nuclear genes for mitochondrial, hydrogenosomal, and cytosolic PFO trace to a single eubacterial acquisition. These findings suggest a common ancestry of PFO in amitochondriate protists with Euglena mitochondrial PNO and Cryptosporidium PNO. They are also consistent with the view that eukaryotic PFO domains are biochemical relics inherited from a facultatively anaerobic, eubacterial ancestor of mitochondria and hydrogenosomes.},
}
@article {pmid11319256,
year = {2001},
author = {von Nickisch-Rosenegk, M and Brown, WM and Boore, JL},
title = {Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans.},
journal = {Molecular biology and evolution},
volume = {18},
number = {5},
pages = {721-730},
doi = {10.1093/oxfordjournals.molbev.a003854},
pmid = {11319256},
issn = {0737-4038},
mesh = {Animals ; Cestoda ; Codon, Nonsense/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genetic Linkage ; Hymenolepis/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Platyhelminths/classification/genetics ; Polymerase Chain Reaction ; RNA, Transfer/genetics ; },
abstract = {Using "long-PCR," we amplified in overlapping fragments the complete mitochondrial genome of the tapeworm Hymenolepis diminuta (Platyhelminthes: Cestoda) and determined its 13,900-nt sequence. The gene content is the same as that typically found for animal mitochondrial DNA (mtDNA) except that atp8 appears to be lacking, a condition found previously for several other animals. Despite the small size of this mtDNA, there are two large noncoding regions, one of which contains 13 repeats of a 31-nt sequence and a potential stem-loop structure of 25 bp with an 11-member loop. Large potential secondary structures were identified also for the noncoding regions of two other cestode mtDNAS: Comparison of the mitochondrial gene arrangement of H. diminuta with those previously published supports a phylogenetic position of flatworms as members of the Eutrochozoa, rather than placing them basal to either a clade of protostomes or a clade of coelomates.},
}
@article {pmid11320888,
year = {2001},
author = {Gietl, C and Schmid, M},
title = {Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues.},
journal = {Die Naturwissenschaften},
volume = {88},
number = {2},
pages = {49-58},
doi = {10.1007/s001140000203},
pmid = {11320888},
issn = {0028-1042},
mesh = {Apoptosis/*physiology ; Cysteine Endopeptidases/genetics/metabolism ; Organelles/*physiology ; Phylogeny ; *Plant Cells ; *Plant Development ; Plants, Toxic ; Ricinus/cytology/growth &amp; development/ultrastructure ; Signal Transduction ; },
abstract = {This review describes aspects of programmed cell death (PCD). Present research maps the enzymes involved and explores the signal transduction pathways involved in their synthesis. A special organelle (the ricinosome) has been discovered in the senescing endosperm of germinating castor beans (Ricinus communis) that develops at the beginning of PCD and delivers large amounts of a papain-type cysteine endopeptidase (CysEP) in the final stages of cellular disintegration. Castor beans store oil and proteins in a living endosperm surrounding the cotyledons. These stores are mobilized during germination and transferred into the cotyledons. PCD is initiated after this transfer is complete. The CysEP is synthesized in the lumen of the endoplasmic reticulum (ER) where it is retained by its C-terminal KDEL peptide as a rather inactive pro-enzyme. Large number of ricinosomes bud from the ER at the same time as the nuclear DNA is characteristically fragmented during PCD. The mitochondria, glyoxysomes and ribosomes are degraded in autophagic vacuoles, while the endopeptidase is activated by removal of the propeptide and the KDEL tail and enters the cytosol. The endosperm dries and detaches from the cotyledons. A homologous KDEL-tailed cysteine endopeptidase has been found in several senescing tissues; it has been localized in ricinosomes of withering day-lily petals and dying seed coats. Three genes for a KDEL-tailed cysteine endopeptidase have been identified in Arabidopsis. One is expressed in senescing ovules, the second in the vascular vessels and the third in maturing siliques. These genes open the way to exploring PCD in plants.},
}
@article {pmid11342215,
year = {2001},
author = {Lorain, S and Lécluse, Y and Scamps, C and Mattéi, MG and Lipinski, M},
title = {Identification of human and mouse HIRA-interacting protein-5 (HIRIP5), two mammalian representatives in a family of phylogenetically conserved proteins with a role in the biogenesis of Fe/S proteins.},
journal = {Biochimica et biophysica acta},
volume = {1517},
number = {3},
pages = {376-383},
doi = {10.1016/s0167-4781(00)00300-6},
pmid = {11342215},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carrier Proteins/*genetics/*metabolism ; *Cell Cycle Proteins ; Chromosome Mapping ; Conserved Sequence ; DNA, Complementary/genetics ; HeLa Cells ; Histone Chaperones ; Humans ; In Situ Hybridization ; In Vitro Techniques ; Iron-Sulfur Proteins/*biosynthesis ; Mice ; Molecular Sequence Data ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/*metabolism ; Two-Hybrid System Techniques ; },
abstract = {The human HIRA protein is encoded from a region of chromosome 22q that is critical for the DiGeorge syndrome and the velocardiofacial syndrome. We have previously reported that it directly interacts with core histones, with a novel histone-binding protein, HIRIP3, and during mouse embryogenesis, with the developmentally regulated homeodomain protein Pax3, suggesting a promoter-targeted function at the chromatin level. We here report on HIRA-interacting protein 5 (HIRIP5), a small acidic protein that interacted with HIRA in a double-hybrid screen performed in yeast and in in vitro protein interaction experiments. HIRIP5 has highly conserved homologs in both prokaryotes and eukaryotes, including the NFU1 gene product which has been implicated in iron metabolism in mitochondria of the yeast Saccharomyces cerevisiae. By radioactive in situ hybridization, the HIRIP5 gene was mapped to the 2p13-p15 chromosomal region, separate from any region previously associated with DiGeorge syndrome.},
}
@article {pmid11345318,
year = {2000},
author = {Toda, S and Osakabe, M and Komazaki, S},
title = {Interspecific diversity of mitochondrial COI sequences in Japanese Panonychus species (Acari: Tetranychidae).},
journal = {Experimental &amp; applied acarology},
volume = {24},
number = {10-11},
pages = {821-829},
pmid = {11345318},
issn = {0168-8162},
mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Female ; Genetic Variation/*genetics ; Japan ; Mites/classification/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; },
abstract = {Sequences of a part of the mitochondrial cytochrome oxidase subunit I (COI) gene were analyzed in four Japanese Panonychus species to determine their phylogenetic relationships. Neighbor-Joining and maximum likelihood analysis resulted in a high bootstrap support of the relationships within the genus Panonychus. In contrast with a previous study based on ribosomal DNA data, the COI phylogeny suggested that P. mori was more distantly related to P. citri than to P. ulmi. This study shows for the first time that P. osmanthi is closely related to P. citri. Intraspecific variation analysis shows that the genetic distance between two local populations of P. mori is higher than between P. citri and P. osmanthi.},
}
@article {pmid11347902,
year = {2001},
author = {Legen, J and Miséra, S and Herrmann, RG and Meurer, J},
title = {Map positions of 69 Arabidopsis thaliana genes of all known nuclear encoded constituent polypeptides and various regulatory factors of the photosynthetic membrane: a case study.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {8},
number = {2},
pages = {53-60},
doi = {10.1093/dnares/8.2.53},
pmid = {11347902},
issn = {1340-2838},
mesh = {Arabidopsis/*genetics ; *Chromosome Mapping ; Chromosomes, Artificial, Bacterial/genetics ; Crosses, Genetic ; Gene Duplication ; *Genome, Plant ; Membrane Proteins/biosynthesis/genetics/*physiology ; Nuclear Proteins/biosynthesis/genetics/*physiology ; Photosynthetic Reaction Center Complex Proteins/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Thylakoids/chemistry/genetics/*physiology ; },
abstract = {Landsberg erecta x Columbia F8 recombinant inbred lines of Arabidopsis thaliana, arrayed BAC clones covering most of the genome, and databank sequence information were used to map the positions of 69 genes in the genome of A. thaliana. These genes encode all known constituents of the photosynthetic thylakoid membrane, some regulatory factors involved in its biogenesis, and the RNA polymerases of nuclear origin that operate in chloroplasts and mitochondria. Designations of novel genes are proposed. The data of these three approaches are generally consistent, although ambiguities have been noted for some genome segments and with gene duplications. For thylakoid multi-subunit structures, no positional clustering of genes has been found, not even for genes encoding different subunits of the same membrane complex. The genes of the lhc superfamily encoding antenna apoproteins and their relatives are a particularly intriguing example. The lack of positional clustering is consistent with phylogenetically independent gene translocations from the plastid (endosymbiont) to the nucleus. This raises the basic question of how independently translocated genes which acquired different promoter sequences and transit peptides were functionally integrated into common signal transduction chains.},
}
@article {pmid11352464,
year = {2001},
author = {Halperin, T and Zheng, B and Itzhaki, H and Clarke, AK and Adam, Z},
title = {Plant mitochondria contain proteolytic and regulatory subunits of the ATP-dependent Clp protease.},
journal = {Plant molecular biology},
volume = {45},
number = {4},
pages = {461-468},
pmid = {11352464},
issn = {0167-4412},
mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; *Bacterial Proteins ; Caseins/metabolism ; DNA, Complementary/chemistry/genetics ; Endopeptidase Clp ; Escherichia coli Proteins ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Mitochondria/*enzymology/metabolism ; Molecular Chaperones ; Molecular Sequence Data ; Phylogeny ; Protein Subunits ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Serine Endopeptidases/metabolism ; Tissue Distribution ; },
abstract = {The proteolytic machinery of plant organelles is largely unknown, although indications so far point to several proteases of bacterial origin. In this study an Arabidopsis thaliana cDNA was isolated that encodes a homologue of bacterial ClpX, a molecular chaperone and regulatory subunit of the ATP-dependent, serine-type Clp protease. Computer analysis of the predicted plant ClpX revealed a putative mitochondrial transit peptide at the N-terminus, as well as overall sequence similarity to other eukaryotic ClpX homologues. Specific polyclonal antibodies were made to the Arabidopsis ClpX protein and used to confirm its localization in plant mitochondria. In addition to ClpX, a ClpP protein located in mitochondria was also identified from the numerous ClpP isomers in Arabidopsis. Localization of this nuclear-encoded protein, termed ClpP2, was determined first by its close sequence similarity to mitochondrial ClpP human, and later experimentally using ClpP2-specific antibodies with isolated plant organellar fractions. In Arabidopsis, transcripts for both clpX and clpP2 genes were detected in various tissues and under different growth conditions, with no significant variation in mRNA level (i.e. 2-fold) for each gene between samples. Using beta-casein as a substrate, plant mitochondria were found to possess an ATP-stimulated, serine-type proteolytic activity that could be strongly inhibited by antibodies specific for ClpX or ClpP2, suggesting an active ClpXP protease. The recent discovery of homologous mitochondrial ClpX and ClpP proteins in mammals suggests that this type of protease may be common to multicellular eukaryotes.},
}
@article {pmid11402041,
year = {2001},
author = {Suzuki, T and Terasaki, M and Takemoto-Hori, C and Hanada, T and Ueda, T and Wada, A and Watanabe, K},
title = {Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28 S small subunit.},
journal = {The Journal of biological chemistry},
volume = {276},
number = {35},
pages = {33181-33195},
doi = {10.1074/jbc.M103236200},
pmid = {11402041},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Caenorhabditis elegans/genetics ; Cattle ; Chromatography, Liquid ; DNA, Complementary ; Drosophila melanogaster/genetics ; Humans ; Mammals ; Mass Spectrometry ; Mice ; Mitochondria, Liver/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Peptide Fragments/chemistry ; *Phylogeny ; Protein Structure, Secondary ; Proteome/*chemistry ; Recombinant Proteins/chemistry ; Ribosomal Proteins/*chemistry/genetics/isolation &amp; purification ; Ribosomes/*chemistry/genetics ; Saccharomyces cerevisiae/genetics ; },
abstract = {The mammalian mitochondrial ribosome (mitoribosome) has a highly protein-rich composition with a small sedimentation coefficient of 55 S, consisting of 39 S large and 28 S small subunits. In the previous study, we analyzed 39 S large subunit proteins from bovine mitoribosome (Suzuki, T., Terasaki, M., Takemoto-Hori, C., Hanada, T., Ueda, T., Wada, A., and Watanabe, K. (2001) J. Biol. Chem. 276, 21724-21736). The results suggested structural compensation for the rRNA deficit through proteins of increased molecular mass in the mitoribosome. We report here the identification of 28 S small subunit proteins. Each protein was separated by radical-free high-reducing two-dimensional polyacrylamide gel electrophoresis and analyzed by liquid chromatography/mass spectrometry/mass spectrometry using electrospray ionization/ion trap mass spectrometer to identify cDNA sequence by expressed sequence tag data base searches in silico. Twenty one proteins from the small subunit were identified, including 11 new proteins along with their complete cDNA sequences from human and mouse. In addition to these proteins, three new proteins were also identified in the 55 S mitoribosome. We have clearly identified a mitochondrial homologue of S12, which is a key regulatory protein of translation fidelity and a candidate for the autosomal dominant deafness gene, DFNA4. The apoptosis-related protein DAP3 was found to be a component of the small subunit, indicating a new function for the mitoribosome in programmed cell death. In summary, we have mapped a total of 55 proteins from the 55 S mitoribosome on the two-dimensional polyacrylamide gels.},
}
@article {pmid11413367,
year = {2001},
author = {Hayajneh, WA and Contopoulos-Ioannidis, DG and Lesperance, MM and Venegas, AM and Colberg-Poley, AM},
title = {The carboxyl terminus of the human cytomegalovirus UL37 immediate-early glycoprotein is conserved in primary strains and is important for transactivation.},
journal = {The Journal of general virology},
volume = {82},
number = {Pt 7},
pages = {1569-1579},
doi = {10.1099/0022-1317-82-7-1569},
pmid = {11413367},
issn = {0022-1317},
mesh = {Amino Acid Sequence ; Cell Line ; Chloramphenicol O-Acetyltransferase ; Cytomegalovirus/*genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Genetic Variation ; Glycoproteins/genetics/metabolism ; HSP70 Heat-Shock Proteins/genetics ; Humans ; Immediate-Early Proteins/*genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Phylogeny ; Promoter Regions, Genetic ; *Transcriptional Activation ; Transfection ; Viral Proteins/*genetics/metabolism ; },
abstract = {The human cytomegalovirus (HCMV) UL37 exon 3 (UL37x3) open reading frame (ORF) encodes the carboxyl termini of two immediate-early glycoproteins (gpUL37 and gpUL37(M)). UL37x3 homologous sequences are not required for mouse cytomegalovirus (MCMV) growth in vitro; yet, they are important for MCMV growth and pathogenesis in vivo. Similarly, UL37x3 sequences are dispensable for HCMV growth in culture, but their requirement for HCMV growth in vivo is not known. To determine this requirement, we directly sequenced the complete UL37x3 gene in multiple HCMV primary strains. A total of 63 of the 310 amino acids in the UL37x3 ORF differ non-conservatively in one or more HCMV primary strains. The HCMV UL37x3 genetic diversity is non-random: the N-glycosylation (46/186 aa) and basic (9/15 aa) domains have the highest proportion of non-conservative variant amino acids. Nonetheless, most (15/17 signals) of the N-glycosylation signals are retained in all HCMV primary strains. Moreover, new N-glycosylation signals are encoded by 5/20 primary strains. In sharp contrast, the UL37x3 transmembrane (TM) ORF completely lacks diversity in all 20 HCMV sequenced primary strains, and only 1 of 28 cytosolic tail residues differs non-conservatively. To test the functional significance of the conserved carboxyl terminus, gpUL37 mutants lacking the TM and/or cytosolic tail were tested for transactivating activity. The gpUL37 carboxyl-terminal mutants are partially defective in hsp70 promoter transactivation even though they trafficked similarly to the wild-type protein into the endoplasmic reticulum and to mitochondria. From these results, we conclude that N-glycosylated gpUL37, particularly its TM and cytosolic domains, is important for HCMV growth in humans.},
}
@article {pmid11425482,
year = {2001},
author = {Yokoyama, K and Wang, L and Miyaji, M and Nishimura, K},
title = {Identification, classification and phylogeny of the Aspergillus section Nigri inferred from mitochondrial cytochrome b gene.},
journal = {FEMS microbiology letters},
volume = {200},
number = {2},
pages = {241-246},
doi = {10.1111/j.1574-6968.2001.tb10722.x},
pmid = {11425482},
issn = {0378-1097},
mesh = {Aspergillus/*classification/genetics ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/analysis ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Sequence Homology, Nucleic Acid ; },
abstract = {The partial mitochondrial cytochrome b gene from 32 strains of 12 species belonging to Aspergillus section Nigri was amplified by the polymerase chain reaction and sequenced directly. Using 402 nucleotide characters, nucleotide-based and amino acid-based phylogenetic trees were inferred and the genetic divergence among the species was evaluated. Based on analyses of the 402-bp nucleotide and 133-amino acid sequences, strains were divided into 11 DNA types and five amino acid types. Aspergillus niger and Aspergillus awamori showed different amino acid sequences. A. niger clade included A. niger var. niger and Aspergillus ficuum. A. awamori clade included A. awamori, Aspergillus phoenicis, Aspergillus pulverulentus, Aspergillus tubingensis, Aspergillus foetidus, and two varieties of A. niger, var. nanus and var. intermedius. Two varieties of A. niger will be reclassified. One strain of A. phoenicis and one strain of Aspergillus carbonarius were reidentified.},
}
@article {pmid11437920,
year = {2001},
author = {Malloch, G and Fenton, B and Goodrich, MA},
title = {Phylogeny of raspberry beetles and other Byturidae (Coleoptera).},
journal = {Insect molecular biology},
volume = {10},
number = {3},
pages = {281-291},
doi = {10.1046/j.1365-2583.2001.00266.x},
pmid = {11437920},
issn = {0962-1075},
mesh = {Animals ; Base Sequence ; Coleoptera/classification/enzymology/*genetics ; DNA ; Electron Transport Complex IV/*genetics ; Fruit ; Genetic Variation ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Point Mutation ; Polymerase Chain Reaction/methods ; Repetitive Sequences, Nucleic Acid ; Ribosomes ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; },
abstract = {Nuclear ribosomal ITS2 and mitochondrial cytochrome oxidase DNA sequences were analysed from the Byturidae (Coleoptera), which includes the raspberry beetles. The secondary structure of ITS2 was plotted and interspecific changes analysed. Evidence for selection on simple sequence repeats within the ITS2 was found. Phylogenetic trees based on the mitochondrial and ribosomal sequences were compared. They were in parity, indicating they reflect the true evolutionary histories of these insects. There was no evidence for hybridization in the populations surveyed, but there was evidence that the American raspberry beetle, Byturus unicolor, is divided into at least three distinct groupings. Despite sharing a related host, the raspberry pests from America were not the most related to the European raspberry beetle. Instead, links between Byturus affinis from Japan and the American raspberry beetle suggest that this lineage originated in Asia and colonized the Western USA.},
}
@article {pmid11454296,
year = {2001},
author = {Piertney, SB and Summers, R and Marquiss, M},
title = {Microsatellite and mitochondrial DNA homogeneity among phenotypically diverse crossbill taxa in the UK.},
journal = {Proceedings. Biological sciences},
volume = {268},
number = {1475},
pages = {1511-1517},
doi = {10.1098/rspb.2001.1015},
pmid = {11454296},
issn = {0962-8452},
mesh = {Alleles ; Animals ; Base Sequence ; *DNA, Mitochondrial ; Gene Frequency ; Genetic Variation ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/classification/*genetics ; Species Specificity ; United Kingdom ; },
abstract = {Genetic differentiation within and between the three morphologically divergent crossbill species extant in the UK was assessed by comparison of allele frequencies at five unlinked microsatellite loci and DNA sequence variation across the mitochondrial control region. No significant differences in microsatellite allele frequency were found either between different populations of the same species or between the crossbill species themselves. A similar lack of genetic divergence was apparent from the mitochondrial sequence data. We resolved 33 different haplotypes, separated by low levels of sequence divergence (0-0.15%). Levels of divergence within and between species were not significantly different. Haplotypes formed a polyphyletic phylogeny, indicating that the crossbill species do not form genetically separate clades. Discordance between neutral DNA polymorphisms and adaptive morphological variation is discussed in relation to defining the systematic relationship between crossbill forms. If adaptive differences have arisen without a concomitant divergence in neutral DNA then attempting to define crossbill types from microsatellite and mitochondrial DNA without recourse to ecology and behaviour may be misleading.},
}
@article {pmid11454299,
year = {2001},
author = {Phillips, MJ and Lin, YH and Harrison, GL and Penny, D},
title = {Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials.},
journal = {Proceedings. Biological sciences},
volume = {268},
number = {1475},
pages = {1533-1538},
doi = {10.1098/rspb.2001.1677},
pmid = {11454299},
issn = {0962-8452},
mesh = {Animals ; Cytosine Nucleotides/analysis ; Genetic Heterogeneity ; Marsupialia/classification/*genetics ; Mitochondria, Liver/*genetics ; Phylogeny ; Pyrimidines/analysis ; RNA/analysis ; Thymine Nucleotides/analysis ; },
abstract = {Recent molecular analyses suggest that the position of bandicoots is the major difficulty in determining the root of the tree of extant marsupials. To resolve this, we analyse mitochondrial genome sequences of a bandicoot (Isoodon macrourus) and a brushtail possum (Trichosurus vulpecula) together with the previously available marsupial mitochondrial genomes, the Virginia opossum (Didelphis virginiana) and the wallaroo (Macropus robustus). Analyses of mitochondrial protein-coding and RNA genes strongly support the bandicoot as sister to the wallaroo and the brushtail possum. This result, combined with other recent molecular analyses, confirms the monophyly of Australidelphia (Australasian marsupials plus Dromiciops from South America). Further, RY coding was found to nullify AGCT coding nucleotide composition bias.},
}
@article {pmid11457448,
year = {2001},
author = {Emelyanov, VV},
title = {Evolutionary relationship of Rickettsiae and mitochondria.},
journal = {FEBS letters},
volume = {501},
number = {1},
pages = {11-18},
doi = {10.1016/s0014-5793(01)02618-7},
pmid = {11457448},
issn = {0014-5793},
mesh = {Energy Metabolism ; Genome ; Mitochondria/genetics/metabolism/*physiology ; *Models, Biological ; *Phylogeny ; Rickettsia/classification/genetics/*physiology ; Symbiosis ; },
abstract = {Phylogenetic data support an origin of mitochondria from the alpha-proteobacterial order Rickettsiales. This high-rank taxon comprises exceptionally obligate intracellular endosymbionts of eukaryotic cells, and includes family Rickettsiaceae and a group of microorganisms termed Rickettsia-like endosymbionts (RLEs). Most detailed phylogenetic analyses of small subunit rRNA and chaperonin 60 sequences consistently show the RLEs to have emerged before Rickettsiaceae and mitochondria sister clades. These data suggest that the origin of mitochondria and Rickettsiae has been preceded by the long-term mutualistic relationship of an intracellular bacterium with a pro-eukaryote, in which an invader has lost many dispensable genes, yet evolved carrier proteins to exchange respiration-derived ATP for host metabolites as envisaged in classic endosymbiont theory.},
}
@article {pmid11508688,
year = {2001},
author = {Emelyanov, VV},
title = {Rickettsiaceae, rickettsia-like endosymbionts, and the origin of mitochondria.},
journal = {Bioscience reports},
volume = {21},
number = {1},
pages = {1-17},
doi = {10.1023/a:1010409415723},
pmid = {11508688},
issn = {0144-8463},
mesh = {Animals ; Bacteria/cytology/genetics/metabolism ; Chaperonin 60/genetics/metabolism ; Energy Metabolism/genetics ; Eukaryotic Cells/*cytology/metabolism ; Humans ; Mitochondria/genetics/metabolism/*ultrastructure ; *Phylogeny ; Rickettsiaceae/*cytology/genetics/metabolism ; Symbiosis/*genetics ; },
abstract = {Accumulating evolutionary data point to a monophyletic origin of mitochondria from the order Rickettsiales. This large group of obligate intracellular alpha-Proteobacteria includes the family Rickettsiaceae and several rickettsia-like endosymbionts (RLEs). Detailed phylogenetic analysis of small subunit (SSU) rRNA and chaperonin 60 (Cpn60) sequences testify to polyphyly of the Rickettsiales, and consistently indicate a sisterhood of Rickettsiaceae and mitochondria that excludes RLEs. Thus RLEs are considered as the nearest extant relatives of an extinct last common ancestor of mitochondria and rickettsiae. Phylogenetic inferences prompt the following assumptions. (1) Mitochondrial origin has been predisposed by the long-term endosymbiotic relationship between rickettsia-like bacteria and proto-eukaryotes, in which many endosymbiont genes have been lost while some indispensable genes have been transferred to the host genome. (2) The obligate dependence of rickettsiae upon a eukaryotic host rests on the import of proteins encoded by these transferred genes. The nature of a proto-eukaryotic cell still remains elusive. The divergence of Rickettsiaceae and mitochondria based on Cpn60, and the evolutionary history of two aminoacyl-tRNA synthetases favor the hypothesis that it was a chimera created by fusion of an archaebacterium and a eubacterium not long before an endosymbiotic event. These and other, mostly biochemical data suggest that all the mitochondrion-related organelles, i.e., both aerobically and anaerobically respiring mitochondria and hydrogenosomes, have originated from the same RLE, while hydrogenosomal energy metabolism may have a separate origin resulting from a eubacterial fusion partner.},
}
@article {pmid11542018,
year = {1985},
author = {Villanueva, E and Luehrsen, KR and Gibson, J and Delihas, N and Fox, GE},
title = {Phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5S ribosomal RNA sequences.},
journal = {Journal of molecular evolution},
volume = {22},
number = {},
pages = {46-52},
pmid = {11542018},
issn = {0022-2844},
support = {NSG-7440/NS/NINDS NIH HHS/United States ; PCM 83-02127/PC/NCI NIH HHS/United States ; },
mesh = {Base Sequence ; Burkholderia cepacia/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Paracoccus denitrificans/*genetics ; Phylogeny ; RNA, Bacterial/analysis/genetics ; RNA, Plant/*analysis/genetics ; RNA, Ribosomal, 5S/*analysis/genetics ; Rhodobacter sphaeroides/genetics ; Rhodospirillaceae/*genetics ; Sequence Homology, Nucleic Acid ; Symbiosis/genetics ; Triticum/genetics ; },
abstract = {The complete nucleotide sequences of 5S ribosomal RNAs from Rhodocyclus gelatinosa, Rhodobacter sphaeroides, and Pseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains. Rhodobacter sphaeroides is specifically related to Paracoccus denitrificans and Rc. gelatinosa is related to Ps. cepacia. These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found in P. denitrificans are present also in the 5S RNA of Rb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of our obtaining these new sequences is that we are able to clarify the phylogenetic origins of the plant mitochondrion. In particular, we find a close phylogenetic relationship between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely, Rb. sphaeroides, P. denitrificans, and Rhodospirillum rubrum.},
}
@article {pmid11557797,
year = {2001},
author = {Tachezy, J and Sánchez, LB and Müller, M},
title = {Mitochondrial type iron-sulfur cluster assembly in the amitochondriate eukaryotes Trichomonas vaginalis and Giardia intestinalis, as indicated by the phylogeny of IscS.},
journal = {Molecular biology and evolution},
volume = {18},
number = {10},
pages = {1919-1928},
doi = {10.1093/oxfordjournals.molbev.a003732},
pmid = {11557797},
issn = {0737-4038},
support = {AI11942/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/*genetics/metabolism ; DNA, Protozoan/chemistry/genetics ; Giardia lamblia/enzymology/*genetics ; Iron-Sulfur Proteins/*biosynthesis ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; },
abstract = {Pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS) is an essential enzyme in the assembly of FeS clusters in bacteria as well as in the mitochondria of eukaryotes. Although FeS proteins are particularly important for the energy metabolism of amitochondrial anaerobic eukaryotes, there is no information about FeS cluster formation in these organisms. We identified and sequenced two IscS homologs of Trichomonas vaginalis (TviscS-1 and TviscS-2) and one of Giardia intestinalis (GiiscS). TviscS-1, TviscS-2, and GiiscS possess the typical conserved regions implicated in cysteine desulfurase activity. N-termini of TviscS-1 and TviscS-2 possess eight amino acid extensions, which resemble the N-terminal presequences that target proteins to hydrogenosomes in trichomonads. No presequence was evident in GiiscS from Giardia, an organism that apparently lacks hydrogenosmes or mitochondria. Phylogenetic analysis showed a close relationship among all eukaryotic IscS genes including those of amitochondriates. IscS of proteobacteria formed a sister group to the eukaryotic clade, suggesting that isc-related genes were present in the proteobacterial endosymbiotic ancestor of mitochondria and hydrogenosomes. NifS genes of nitrogen-fixing bacteria, which are IscS homologs required for specific formation of FeS clusters in nitrogenase, formed a more distant group. The phylogeny indicates the presence of a common mechanism for FeS cluster formation in mitochondriates as well as in amitochondriate eukaryotes. Furthermore, the analyses support a common origin of Trichomonas hydrogenosomes and mitochondria, as well as secondary loss of mitochondrion/hydrogenosome-like organelles in Giardia.},
}
@article {pmid11557802,
year = {2001},
author = {Horner, DS and Embley, TM},
title = {Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes.},
journal = {Molecular biology and evolution},
volume = {18},
number = {10},
pages = {1970-1975},
doi = {10.1093/oxfordjournals.molbev.a003737},
pmid = {11557802},
issn = {0737-4038},
mesh = {Amino Acid Sequence ; Animals ; Chaperonin 60/*genetics ; Diplomonadida/classification/genetics ; Eukaryotic Cells/classification/*metabolism ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; },
}
@article {pmid11577165,
year = {2001},
author = {Sakamoto, J and Shibata, T and Mine, T and Miyahara, R and Torigoe, T and Noguchi, S and Matsushita, K and Sone, N},
title = {Cytochrome c oxidase contains an extra charged amino acid cluster in a new type of respiratory chain in the amino-acid-producing Gram-positive bacterium Corynebacterium glutamicum.},
journal = {Microbiology (Reading, England)},
volume = {147},
number = {Pt 10},
pages = {2865-2871},
doi = {10.1099/00221287-147-10-2865},
pmid = {11577165},
issn = {1350-0872},
mesh = {Amino Acid Sequence ; *Cloning, Molecular ; Corynebacterium/*enzymology/genetics/physiology ; Electron Transport Complex IV/*chemistry/genetics/*metabolism ; *Genes, Bacterial ; Glutamates/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {The membranes from Corynebacterium glutamicum cells contain a hydrophobic di-haem C protein as the cytochrome c subunit of the new type of cytochrome bc complex (complex III in the respiratory chain) encoded by the qcrCAB operon [Sone, N., Nagata, K., Kojima, H., Tajima, J., Kodera, Y., Kanamaru, T., Noguchi, S. &amp; Sakamoto, J. (2001). Biochim Biophys Acta 1503, 279-290]. To characterize complex IV, cytochrome c oxidase and its structural genes were isolated. The oxidase is of the cytochrome aa(3) type, but mass spectrometry indicated that the haem is haem As, which contains a geranylgeranyl side-chain instead of a farnesyl group. The enzyme is a SoxM-type haem-copper oxidase composed of three subunits. Edman degradation and mass spectrometry suggested that the N-terminal signal sequence of subunit II is cleaved and that the new N-terminal cysteine residue is diacylglycerated, while neither subunit I nor subunit III is significantly modified. The genes for subunits II (ctaC) and III (ctaE) are located upstream of the qcrCAB operon, while that for subunit I (ctaD) is located separately. The oxidase showed low enzyme activity with extrinsic substrates such as cytochromes c from horse heart or yeast, and has the Cu(A)-binding motif in its subunit II. A prominent structural feature is the insertion of an extra charged amino acid cluster between the beta2 and beta4 strands in the substrate-binding domain of subunit II. The beta2-beta4 loop of this oxidase is about 30 residues longer than that of major cytochrome c oxidases from mitochondria and proteobacteria, and is rich in both acidic and basic residues. These findings suggest that the extra charged cluster may play a role in the interaction of the oxidase with the cytochrome c subunit of the new type of bc complex.},
}
@article {pmid11594626,
year = {2001},
author = {James, SA and Collins, MD and Roberts, IN},
title = {Phylogenetic analysis of the psychrophobic yeast Arxiozyma telluris and the reinstatement of Candida pintolopesii (van Uden) Meyer et Yarrow and Candida slooffii van Uden et do Carmo Sousa.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {51},
number = {Pt 5},
pages = {1917-1925},
doi = {10.1099/00207713-51-5-1917},
pmid = {11594626},
issn = {1466-5026},
mesh = {Candida/*classification/*genetics ; DNA, Ribosomal/analysis ; Electron Transport Complex IV/genetics ; Genes, rRNA ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Saccharomycetales/*classification/*genetics ; Sequence Analysis, DNA ; },
abstract = {A phylogenetic analysis was conducted upon ten strains of the psychrophobic yeast species Arxiozyma telluris using nuclear rDNA (18S and 26S) and mitochondrial cytochrome-c oxidase subunit II (COX2) gene sequences. Strains examined included those described originally as Candida slooffii, Torulopsis bovina (= Candida bovina) and Torulopsis pintolopesii (= Candida pintolopesii), which are all currently accepted as synonyms of Arxiozyma telluris. Comparative 18S rDNA sequence analysis showed that these strains formed a genealogically highly related group, which was phylogenetically distinct from any other ascomycetous species studied. The results showed that A. telluris, as currently described, appears to be composed of a complex of closely related but nevertheless separate taxa. rDNA and COX2 gene sequence data revealed that CBS 1787T, the type strain of C. pintolopesii, the currently recognized asexual form (anamorph) of A. telluris, along with strains CBS 2676 and CBS 2985 formed a distinct taxon that is phylogenetically separate from A. telluris. Similarly, the sequence data also showed that C. slooffii is a distinct taxon and support the reinstatement of this species. However, with regard to the relationship between the type strains of A. telluris (CBS 2685T) and C bovina (CBS 2760T), discrepancies were observed between the rDNA and COX2 sequence datasets, and these results are discussed in more detail.},
}
@article {pmid11598119,
year = {2001},
author = {Perez-Jannotti, RM and Klein, SM and Bogenhagen, DF},
title = {Two forms of mitochondrial DNA ligase III are produced in Xenopus laevis oocytes.},
journal = {The Journal of biological chemistry},
volume = {276},
number = {52},
pages = {48978-48987},
doi = {10.1074/jbc.M107177200},
pmid = {11598119},
issn = {0021-9258},
support = {R01GM29681/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Cell Fractionation ; Cloning, Molecular ; Cross-Linking Reagents/chemistry ; DNA Ligase ATP ; DNA Ligases/chemistry/classification/*genetics/metabolism ; Female ; Genes, Reporter ; HeLa Cells ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Male ; Mitochondria/*enzymology/physiology ; Molecular Sequence Data ; Molecular Weight ; Oocytes/chemistry/*enzymology ; Ovary/enzymology ; Phylogeny ; Poly-ADP-Ribose Binding Proteins ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Testis/enzymology ; Tissue Distribution ; Xenopus Proteins ; Xenopus laevis/genetics/*metabolism ; },
abstract = {Full-length cDNAs for DNA ligase IV and the alpha and beta isoforms of DNA ligase III were cloned from Xenopus laevis to permit study of the genes encoding mitochondrial DNA ligase. DNA ligase III alpha and III beta share a common NH(2) terminus that encodes a mitochondrial localization signal capable of targeting green fluorescent protein to mitochondria while the NH(2) terminus of DNA ligase IV does not. Reverse transcriptase-polymerase chain reaction analyses with adult frog tissues demonstrate that while DNA ligase III alpha and DNA ligase IV are ubiquitously expressed, DNA ligase III beta expression is restricted to testis and ovary. Mitochondrial lysates from X. laevis oocytes contain both DNA ligase III alpha and III beta but no detectable DNA ligase IV. Gel filtration, sedimentation, native gel electrophoresis, and in vitro cross-linking experiments demonstrate that mtDNA ligase III alpha exists as a high molecular weight complex. We discuss the possibility that DNA ligase III alpha exists in mitochondria in association with novel mitochondrial protein partners or as a homodimer.},
}
@article {pmid11599560,
year = {2001},
author = {Hill, JE and Hemmingsen, SM},
title = {Arabidopsis thaliana type I and II chaperonins.},
journal = {Cell stress &amp; chaperones},
volume = {6},
number = {3},
pages = {190-200},
pmid = {11599560},
issn = {1355-8145},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/physiology ; Arabidopsis Proteins/chemistry/*genetics/metabolism ; Chaperonins/chemistry/classification/*genetics/metabolism ; Chloroplasts/genetics/metabolism ; Databases, Genetic ; Humans ; Mitochondria/genetics/metabolism ; Molecular Chaperones/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; },
abstract = {An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein sequences and indicate that the CPN family is more diverse than previously described. In addition to surprising sequence diversity within CPN subclasses, the genomic data also suggest the existence of previously undescribed family members, including a 10-kDa chloroplast cochaperonin. Consideration of the sequence data described in this review prompts questions about the complexities of plant CPN systems and the evolutionary relationships and functions of the component proteins, most of which have not been studied experimentally.},
}
@article {pmid11605957,
year = {2001},
author = {Rubio, MC and Ramos, J and Webb, KJ and Minchin, FR and González, E and Arrese-Igor, C and Becana, M},
title = {Expression studies of superoxide dismutases in nodules and leaves of transgenic alfalfa reveal abundance of iron-containing isozymes, posttranslational regulation, and compensation of isozyme activities.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {14},
number = {10},
pages = {1178-1188},
doi = {10.1094/MPMI.2001.14.10.1178},
pmid = {11605957},
issn = {0894-0282},
mesh = {Amino Acid Sequence ; Antioxidants/metabolism ; Base Sequence ; Catalase/metabolism ; Chloroplasts/metabolism ; DNA, Complementary/chemistry/genetics ; Gene Expression Regulation, Enzymologic ; Isoenzymes ; Medicago sativa/*enzymology/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Peroxidases/metabolism ; Phylogeny ; Plant Leaves/*enzymology/genetics ; Plant Roots/*enzymology/genetics/microbiology ; Plants, Genetically Modified ; Protein Processing, Post-Translational ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA ; Superoxide Dismutase/*genetics/metabolism ; Symbiosis ; Transcription, Genetic ; },
abstract = {The composition of antioxidant enzymes, especially superoxide dismutase (SOD), was studied in one nontransgenic and three transgenic lines of nodulated alfalfa plants. Transgenic lines overproduced MnSOD in the mitochondria of nodules and leaves (line 1-10), MnSOD in the chloroplasts (line 4-6), and FeSOD in the chloroplasts (line 10-7). In nodules of line 10-7, the absence of transgene-encoded FeSOD activity was due to a lack of mRNA, whereas in nodules of line 4-6 the absence of transgene-encoded MnSOD activity was due to enzyme inactivation or degradation. Transgenic alfalfa showed a novel compensatory effect in the activities of MnSOD (mitochondrial) and FeSOD (plastidic) in the leaves, which was not caused by changes in the mRNA levels. These findings imply that SOD activity in plant tissues and organelles is regulated, at least partially, at the posttranslational level. All four lines had low CuZnSOD activities and an abundant FeSOD isozyme, especially in nodules, indicating that FeSOD performs important antioxidant functions other than the scavenging of superoxide radicals generated in photosynthesis. This was confirmed by the detection of FeSOD cDNAs and proteins in nodules of other legumes such as cowpea, pea, and soybean. The cDNA encoding alfalfa nodule FeSOD was characterized and the deduced protein found to contain a plastid transit peptide. A comparison of sequences and other properties reveals that there are two types of FeSODs in nodules.},
}
@article {pmid11693658,
year = {2001},
author = {Qian, Q and Keeling, PJ},
title = {Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer.},
journal = {Protist},
volume = {152},
number = {3},
pages = {193-201},
doi = {10.1078/1434-4610-00059},
pmid = {11693658},
issn = {1434-4610},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Protozoan ; Eukaryota/classification/*enzymology/genetics ; Eukaryotic Cells ; Gene Transfer Techniques ; Genes, Protozoan ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Lateral gene transfer refers to the movement of genetic information from one genome to another, and the integration of that foreign DNA into its new genetic environment. There are currently only a few well-supported cases of prokaryote-to-eukaryote transfer known that do not involve mitochondria or plastids, but it is not clear whether this reflects a lack of such transfer events, or poor sampling of diverse eukaryotes. One gene where this process is apparently active is glyceraldehyde-3-phosphate dehydrogenase (GAPDH), where lateral transfer has been implicated in the origin of euglenoid and kinetoplastid genes. We have characterised GAPDH genes from diplonemids, heterotrophic flagellates that are closely related to kinetoplastids and euglenoids. Two distinct classes of diplonemid GAPDH genes were found in diplonemids, however, neither class is closely related to any other euglenozoan GAPDH. One diplonemid GAPDH is related to the cytosolic gapC of eukaryotes, although not to either euglenoids or kinetoplastids, and the second is related to cyanobacterial and proteobacterial gap3. The bacterial gap3 gene in diplonemids provides one of the most well-supported examples of lateral gene transfer from a bacterium to a eukaryote characterised to date, and may indicate that diplonemids have acquired a novel biochemical capacity through lateral transfer.},
}
@article {pmid11695830,
year = {2001},
author = {Schulte, U},
title = {Biogenesis of respiratory complex I.},
journal = {Journal of bioenergetics and biomembranes},
volume = {33},
number = {3},
pages = {205-212},
pmid = {11695830},
issn = {0145-479X},
mesh = {Acyl Carrier Protein/chemistry/genetics ; Electron Transport Complex I ; Genes, Fungal ; Mitochondria/enzymology ; Models, Molecular ; Mutation ; NADH, NADPH Oxidoreductases/*biosynthesis/chemistry/genetics ; Neurospora crassa/enzymology/genetics ; Oxidation-Reduction ; Phylogeny ; Protein Subunits ; },
abstract = {Proteins specifically involved in the biogenesis of respiratory complex I in eukaryotes have been characterized. The complex I intermediate associated proteins CIA30 and CIA84 are tightly bound to an assembly intermediate of the membrane arm. Like chaperones, they are involved in multiple rounds of membrane arm assembly without being part of the mature structure. Two biosynthetic subunits of eukaryotic complex I have been characterized. The acyl carrier subunit is needed for proper assembly of the peripheral arm as well as the membrane arm of complex I. It may interact with enzymes of a mitochondrial fatty acid synthetase. The 39/40-kDa subunit appears to be an isomerase with a tightly bound NADPH. It is related to a protein family of reductases/isomerases. Both subunits have been discussed to be involved in the synthesis of a postulated, novel, high-potential redox group.},
}
@article {pmid11696185,
year = {2001},
author = {Papenbrock, J and Mishra, S and Mock, HP and Kruse, E and Schmidt, EK and Petersmann, A and Braun, HP and Grimm, B},
title = {Impaired expression of the plastidic ferrochelatase by antisense RNA synthesis leads to a necrotic phenotype of transformed tobacco plants.},
journal = {The Plant journal : for cell and molecular biology},
volume = {28},
number = {1},
pages = {41-50},
doi = {10.1046/j.1365-313x.2001.01126.x},
pmid = {11696185},
issn = {0960-7412},
mesh = {Cloning, Molecular ; Ferrochelatase/*biosynthesis/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Heme/metabolism ; Isoenzymes/biosynthesis/genetics/metabolism ; Light ; Mitochondria/enzymology ; Necrosis ; Phenotype ; Phylogeny ; Plants, Genetically Modified ; Plastids/*enzymology/genetics/metabolism/radiation effects ; Protoporphyrins/metabolism ; RNA, Antisense/biosynthesis/genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Nicotiana/*cytology/*enzymology/genetics/metabolism ; },
abstract = {Protoporphyrin IX is the last common intermediate of tetrapyrrole biosynthesis. The chelation of a Mg2+ ion by magnesium chelatase and of a ferrous ion by ferrochelatase directs protoporphyrin IX towards the formation of chlorophyll and heme, respectively. A full length cDNA clone encoding a ferrochelatase was identified from a Nicotiana tabacum cDNA library. The encoded protein consists of 497 amino acid residues with a molecular weight of 55.4 kDa. In vitro import of the protein into chloroplasts and its location in stroma and thylakoids confirm its close relationship to the previously described Arabidopsis thaliana plastid-located ferrochelatase (FeChII). A 1700-bp tobacco FeCh cDNA sequence was expressed in Nicotiana tabacum cv. Samsun NN under the control of the CaMV 35S promoter in antisense orientation allowing investigation into the consequences of selective reduction of the plastidic ferrochelatase activity for protoporphyrin IX channeling in chloroplasts and for interactions between plastidic and mitochondrial heme synthesis. Leaves of several transformants showed a reduced chlorophyll content and, during development, a light intensity-dependent formation of necrotic leaf lesions. In comparison with wild-type plants the total ferrochelatase activity was decreased in transgenic lines leading to an accumulation of photosensitizing protoporphyrin IX. Ferrochelatase activity was reduced only in plastids but not in mitochondria of transgenic plants. By means of the specifically diminished ferrochelatase activity consequences of the selective inhibition of protoheme formation for the intracellular supply of heme can be investigated in the future.},
}
@article {pmid11718729,
year = {2001},
author = {Sweetlove, LJ and Mowday, B and Hebestreit, HF and Leaver, CJ and Millar, AH},
title = {Nucleoside diphosphate kinase III is localized to the inter-membrane space in plant mitochondria.},
journal = {FEBS letters},
volume = {508},
number = {2},
pages = {272-276},
doi = {10.1016/s0014-5793(01)03069-1},
pmid = {11718729},
issn = {0014-5793},
mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*enzymology ; Electrophoresis, Gel, Two-Dimensional ; Mass Spectrometry ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Nucleoside-Diphosphate Kinase/*analysis/chemistry/metabolism ; Peptide Mapping ; Phylogeny ; Sequence Homology, Amino Acid ; Solanum tuberosum/cytology/*enzymology ; },
abstract = {Three types of nucleoside diphosphate kinases (NDPKs) are found in plants but the intra-cellular compartmentation of these proteins is not certain, especially the location of the recently identified type III proteins. Through the fractionation of plant mitochondria from potato and Arabidopsis, display of protein profiles by 2D gel electrophoresis, and identification by mass spectrometry, we present the first direct evidence that type III proteins are localized in the inter-membrane space of plant mitochondria. The possible metabolic functions of NDPK III are discussed in light of its sub-cellular localization.},
}
@article {pmid11722843,
year = {2001},
author = {Kobayashi, Y and Dokiya, Y and Sugiura, M and Niwa, Y and Sugita, M},
title = {Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris.},
journal = {Gene},
volume = {279},
number = {1},
pages = {33-40},
doi = {10.1016/s0378-1119(01)00729-6},
pmid = {11722843},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Bacteriophage T7/enzymology ; Biological Transport ; Blotting, Northern ; Cell Nucleus/genetics ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; DNA, Plant/chemistry/genetics/isolation &amp; purification ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Exons ; Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; Green Fluorescent Proteins ; Introns ; Luminescent Proteins/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; Nicotiana/enzymology/*genetics ; },
abstract = {We have isolated and sequenced a nuclear gene and cDNA encoding bacteriophage T7-type single subunit RNA polymerase, NsRpoT-A, from Nicotiana sylvestris. NsRpoT-A consists of 19 exons and 18 introns; the first intron is 17 kb, the longest yet identified in a plant gene. Genomic Southern analysis indicated that N. sylvestris contains a small family of NsRpoT genes. Quantitative RT-PCR revealed that steady-state mRNA levels are highest in the leaves and lowest in the cotyledons. Phylogenetic analysis of NsRpoT-A and the RpoT proteins of other plant species suggested that NsRpoT-A is a mitochondrial protein. The TargetP program predicted localization of the NsRpoT-A gene product to the mitochondria. Using a transient expression assay and protoplasts from N. sylvestris mesophyll cells, we clearly demonstrated that the N-terminal sequence of NsRpoT-A targets the protein to the mitochondria. We therefore named this protein NsRpoTm.},
}
@article {pmid11724862,
year = {2001},
author = {Wang, L and Yokoyama, K and Miyaji, M and Nishimura, K},
title = {Identification, classification, and phylogeny of the pathogenic species Exophiala jeanselmei and related species by mitochondrial cytochrome b gene analysis.},
journal = {Journal of clinical microbiology},
volume = {39},
number = {12},
pages = {4462-4467},
pmid = {11724862},
issn = {0095-1137},
mesh = {Cytochrome b Group/*genetics/metabolism ; DNA, Bacterial/analysis ; Exophiala/*classification/enzymology/genetics/pathogenicity ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mycoses/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {We analyzed a 402-bp sequence of the mitochondrial cytochrome b gene of 34 strains of Exophiala jeanselmei and 16 strains representing 12 related species. The strains of E. jeanselmei were classified into 20 DNA types and 17 amino acid types. The differences between these strains were found in 1 to 60 nucleotides and 1 to 17 amino acids. On the basis of the identities and similarities of nucleotide and amino acid sequences, some strains were reidentified: i.e., two strains of E. jeanselmei var. hetermorpha and one strain of E. castellanii as E. dermatitidis (including the type strain), three strains of E. jeanselmei as E. jeanselmei var. lecanii-corni (including the type strain), three strains of E. jeanselmei as E. bergeri (including the type strain), seven strains of E. jeanselmei as E. pisciphila (including the type strain), seven strains of E. jeanselmei as E. jeanselmei var. jeanselmei (including the type strain), one strain of E. jeanselmei as Fonsecaea pedrosoi (including the type strain), and one strain of E. jeanselmei as E. spinifera (including the type strain). Some E. jeanselmei strains showed distinct nucleotide and amino acid sequences. The amino-acid-based UPGMA (unweighted pair group method with the arithmetic mean) tree exhibited nearly the same topology as those of the DNA-based trees obtained by neighbor joining, maximum parsimony, and maximum likelihood methods.},
}
@article {pmid11736810,
year = {2001},
author = {Nishibori, M and Hayashi, T and Tsudzuki, M and Yamamoto, Y and Yasue, H},
title = {Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species.},
journal = {Animal genetics},
volume = {32},
number = {6},
pages = {380-385},
doi = {10.1046/j.1365-2052.2001.00795.x},
pmid = {11736810},
issn = {0268-9146},
mesh = {Animals ; Base Sequence ; Coturnix/classification/*genetics ; DNA, Mitochondrial/genetics ; Genome ; Male ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {The Japanese quail (Coturnix japonica; JQ) is one of the domesticated fowl species of Japan. To provide DNA sequence information for examination of its phylogenetic position in the order Galliformes, the complete sequence of the JQ mitochondria was determined. Sequence analysis revealed that the JQ mitochondrial genome is a circular DNA of 16 697 basepairs (bp), which is smaller than the chicken mitochondrial DNA of 16 775 bp, but the genomic structure of JQ mitochondria was the same as that of the chicken. The sequence homologies of all mitochondrial genes including those for 12S and 16S ribosomal RNA (rRNA), between Japanese quail and chicken ranged from 78.0 to 89.9%. Because the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes had been reported in five species [Phasianus colchicus (ring-neck pheasant: RP), Gallus gallus domesticus (chicken: CH), Perdix perdix (grey partridge: GP), Bambusicola thoracia (Chinese bamboo partridge: CP), and Aythya americana (redhead: RH)], the concatenated nucleotide sequences (2184 bp) and amino acid sequences of these two genes were used in a phylogenetic analysis of JQ against these five species using a maximum likelihood (ML) method. Using the first and second bases of the codons, and the third base of the codons indicated a phylogenic tree of [RH, (RP, GP), (JQ, (CH, CP))]. A phylogenic tree of [RH, JQ, (RP, GP), (CH, CP)] was determined using amino acid sequences. Because the local bootstrap values for the JQ branch in these trees are not high, additional sequence is necessary for construction of a reliable tree.},
}
@article {pmid11738829,
year = {2001},
author = {Iwabe, N and Miyata, T},
title = {Overlapping genes in parasitic protist Giardia lamblia.},
journal = {Gene},
volume = {280},
number = {1-2},
pages = {163-167},
doi = {10.1016/s0378-1119(01)00767-3},
pmid = {11738829},
issn = {0378-1119},
mesh = {Animals ; DNA, Complementary/chemistry/genetics ; Databases, Genetic ; Genes, Overlapping/*genetics ; Giardia lamblia/*genetics ; Kinesins/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Protein Isoforms/genetics ; Sequence Analysis, DNA ; },
abstract = {The parasitic protist Giardia lamblia lacks mitochondria and peroxisomes, as well as many typical membrane-bound organella characteristics of higher eukaryotic cells, together with extremely economized usage of DNA sequence, as demonstrated by the lack of introns. We describe here the presence of overlapping genes in G. lamblia, in which a part of the protein coding sequence of one mRNA exists in a region corresponding to the 3'-noncoding region of another mRNA transcribed from a gene on the opposite strand. Recently we isolated 13 kinesin-related cDNAs from G. lamblia. Nine of these cDNAs contain long 3'-noncoding sequences in which long open reading frames (ORFs) exist (in the remaining four cDNAs, the lengths of the 3'-noncoding sequences are very short). The predicted amino acid sequences of these ORFs were subjected to a search for homologies with sequences in databases. The amino acid sequences of the six ORFs exhibited significant sequence similarities with known sequences. These lines of evidence suggest the frequent occurrence of gene overlap in Giardial genome.},
}
@article {pmid11741306,
year = {2001},
author = {Kobayashi, Y and Dokiya, Y and Sugita, M},
title = {Dual targeting of phage-type RNA polymerase to both mitochondria and plastids is due to alternative translation initiation in single transcripts.},
journal = {Biochemical and biophysical research communications},
volume = {289},
number = {5},
pages = {1106-1113},
doi = {10.1006/bbrc.2001.6130},
pmid = {11741306},
issn = {0006-291X},
mesh = {Alternative Splicing ; Amino Acid Sequence ; Bacteriophage T7/enzymology/genetics ; Base Sequence ; DNA, Complementary/genetics ; DNA, Plant/genetics ; DNA-Directed RNA Polymerases/*genetics/*metabolism ; Exons ; Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Peptide Chain Initiation, Translational ; Phylogeny ; *Plant Proteins ; Plastids/*enzymology ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*enzymology/*genetics ; Viral Proteins ; },
abstract = {We isolated and sequenced a nuclear gene and cDNA encoding a bacteriophage T7-type RNA polymerase, NsRpoT-B, from Nicotiana sylvestris. The gene, NsRpoT-B, consists of 19 exons and 18 introns and encodes a polypeptide of 1020 amino acid residues. The predicted NsRpoT-B protein shows 71% amino acid identity with NsRpoT-A which is a mitochondrial protein. Quantitative RT-PCR revealed that steady-state NsRpoT-B mRNA accumulation is highest in the mature leaves and lowest in the cotyledons. Transient expression assays in protoplasts from N. sylvestris leaves demonstrated that the putative N-terminal transit peptide of NsRpoT-B encodes dual targeting signals directing the protein into mitochondria and plastids. This strongly suggests that NsRpoT-B functions as an RNA polymerase transcribing genes from two different plant organelle genomes. NsRpoT-B transcripts have two potential translation initiation codons. An in vitro translation assay indicated that a chimeric mRNA encoding the N-terminal NsRpoT-B fused to an sGFP produced two polypeptides translated from the first and second initiation codons. This implies that the dual targeting of NsRpoT-B protein is regulated, in part, at the level of translation. We have designated this protein NsRpoTpm.},
}
@article {pmid11752383,
year = {2001},
author = {Skinner, DJ and Baker, SC and Meister, RJ and Broadhvest, J and Schneitz, K and Gasser, CS},
title = {The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein.},
journal = {The Plant cell},
volume = {13},
number = {12},
pages = {2719-2730},
pmid = {11752383},
issn = {1040-4651},
mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development ; Arabidopsis Proteins/classification/*genetics/metabolism ; Chromosome Mapping ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Mitochondria/*metabolism ; *Mitochondrial Proteins ; Molecular Sequence Data ; Mutagenesis ; Phenotype ; Phylogeny ; Plant Stems/genetics/growth &amp; development ; Plant Structures/genetics/growth &amp; development ; *Recombinant Proteins ; Ribosomal Proteins/classification/*genetics/metabolism ; Sequence Homology, Amino Acid ; },
abstract = {The HUELLENLOS (HLL) gene participates in patterning and growth of the Arabidopsis ovule. We have isolated the HLL gene and shown that it encodes a protein homologous to the L14 proteins of eubacterial ribosomes. The Arabidopsis genome also includes a highly similar gene, HUELLENLOS PARALOG (HLP), and genes for both cytosolic (L23) and chloroplast ribosome L14 proteins. Phylogenetic analysis shows that HLL and HLP differ significantly from these other two classes of such proteins. HLL and HLP fusions to green fluorescent protein were localized to mitochondria. Ectopic expression of HLP complemented the hll mutant, indicating that HLP and HLL share redundant functions. We conclude that HLL and HLP encode L14 subunits of mitochondrial ribosomes. HLL mRNA was at significantly higher levels than HLP mRNA in pistils, with the opposite pattern in leaves. This differential expression can explain the confinement of effects of hll mutations to gynoecia and ovules. Our elucidation of the nature of HLL shows that metabolic defects can have specific effects on developmental patterning.},
}
@article {pmid11752472,
year = {2001},
author = {Ravanel, S and Cherest, H and Jabrin, S and Grunwald, D and Surdin-Kerjan, Y and Douce, R and Rébeillé, F},
title = {Tetrahydrofolate biosynthesis in plants: molecular and functional characterization of dihydrofolate synthetase and three isoforms of folylpolyglutamate synthetase in Arabidopsis thaliana.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {98},
number = {26},
pages = {15360-15365},
pmid = {11752472},
issn = {0027-8424},
mesh = {Arabidopsis/enzymology/genetics/*metabolism ; DNA, Complementary ; Genetic Complementation Test ; Isoenzymes/*metabolism ; Molecular Sequence Data ; Peptide Synthases/genetics/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Subcellular Fractions/enzymology ; Tetrahydrofolates/*biosynthesis ; },
abstract = {Tetrahydrofolate coenzymes involved in one-carbon (C1) metabolism are polyglutamylated. In organisms that synthesize tetrahydrofolate de novo, dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS) catalyze the attachment of glutamate residues to the folate molecule. In this study we isolated cDNAs coding a DHFS and three isoforms of FPGS from Arabidopsis thaliana. The function of each enzyme was demonstrated by complementation of yeast mutants deficient in DHFS or FPGS activity, and by measuring in vitro glutamate incorporation into dihydrofolate or tetrahydrofolate. DHFS is present exclusively in the mitochondria, making this compartment the sole site of synthesis of dihydrofolate in the plant cell. In contrast, FPGS is present as distinct isoforms in the mitochondria, the cytosol, and the chloroplast. Each isoform is encoded by a separate gene, a situation that is unique among eukaryotes. The compartmentation of FPGS isoforms is in agreement with the predominance of gamma-glutamyl-conjugated tetrahydrofolate derivatives and the presence of serine hydroxymethyltransferase and C1-tetrahydrofolate interconverting enzymes in the cytosol, the mitochondria, and the plastids. Thus, the combination of FPGS with these folate-mediated reactions can supply each compartment with the polyglutamylated folate coenzymes required for the reactions of C1 metabolism. Also, the multicompartmentation of FPGS in the plant cell suggests that the transported forms of folate are unconjugated.},
}
@article {pmid11764895,
year = {2001},
author = {Wang, L and Yokoyama, K and Takahasi, H and Kase, N and Hanya, Y and Yashiro, K and Miyaji, M and Nishimura, K},
title = {Identification of species in Aspergillus section Flavi based on sequencing of the mitochondrial cytochrome b gene.},
journal = {International journal of food microbiology},
volume = {71},
number = {1},
pages = {75-86},
doi = {10.1016/s0168-1605(01)00597-9},
pmid = {11764895},
issn = {0168-1605},
mesh = {Amino Acid Sequence ; Aspergillus/*classification/*genetics/ultrastructure ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/genetics ; Microscopy, Electron, Scanning ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; },
abstract = {The partial sequences of the mitochondrial (mt) cytochrome b gene (402 bp) were determined for species of Aspergillus section Flavi. On the basis of identities of DNA sequences, 77 strains were divided into seven DNA types, from D-1 to D-7. The type strains of A. sojae, A. parasiticus, A. flavus and A. oryzae together, A. tamarii, and A. nomius were placed in DNA types D-1. D-2, D-4, D-5 and D-7, respectively. These species could be differentiated from each other. Furthermore, two other DNA types, D-3 and D-6 were found. DNA type D-3 was closely related to A. parasiticus (D-2) and included one strain that deposited as A. flatus var. flavus and produced aflatoxins B and G. DNA types D-6 included one strain named A. flavus and closely related to A. tamarii. The observations of conidial wall texture by SEM (Scanning Electron Microscopy) supported the relationships derived from the cytochrome b gene. The production of aflatoxins was also examined. Using the DNA sequence of cytochrome b gene, several strains were reidentified. The derived amino acids sequences were all the same in the studied strains. The mt cytochrome b gene is useful and reliable in distinguishing and identifying the species in Aspergillus section Flavi.},
}
@article {pmid11766842,
year = {2000},
author = {Pimentel-Smith, GE and Shi, L and Drummond, P and Tu, Z and Smith, EJ},
title = {Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides.},
journal = {Genetica},
volume = {110},
number = {3},
pages = {219-226},
doi = {10.1023/a:1012772831699},
pmid = {11766842},
issn = {0016-6707},
mesh = {APOBEC-1 Deaminase ; Animals ; Chickens/genetics ; Collagen Type X/genetics ; Columbidae/genetics ; Coturnix/genetics ; Cytidine Deaminase/genetics ; DNA Primers/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Sequence Tagged Sites ; Species Specificity ; Turkeys/genetics ; },
abstract = {Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey.},
}
@article {pmid11780787,
year = {2001},
author = {Fujita, K and Horie, T and Isono, K},
title = {Cross-genomic analysis of the translational systems of various organisms.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {27},
number = {3},
pages = {163-169},
doi = {10.1038/sj.jim.7000093},
pmid = {11780787},
issn = {1367-5435},
mesh = {Bacteria/*genetics ; Base Sequence ; Escherichia coli/genetics ; Genomics ; Mitochondria/*metabolism ; Phylogeny ; *Protein Biosynthesis ; Ribosomal Proteins/*genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; },
abstract = {We have characterized the genes encoding ribosomal proteins (r-proteins) as well as other translation-related factors of 15 eubacteria and four archaebacteria, and the genes for the mitochondrial r-proteins of Saccharomyces cerevisiae by using the complete genomic nucleotide sequence data of these organisms. In eubacteria, including two species of Mycoplasma, the operon structure of the r-protein genes is well conserved, while their relative orientation and chromosomal location are quite divergent. The operon structure of the r-protein genes in archaebacteria, on the other hand, is quite different from eubacteria and also among themselves. In addition, many archaebacterial r-proteins show similarity to rat cytoplasmic r-proteins. Nonetheless, characteristic features of several genes encoding proteins of functional importance are well conserved throughout the bacterial species including archaebacteria, as well as in S. cerevisiae. We searched for the genes encoding mitochondrial r-proteins in yeast by combining informatics and genetic experiments. Furthermore, we characterized some of the r-proteins genes by exchanging portions between Escherichia coli and S. cerevisiae and performed functional analysis of some of the genes from different evolutionary points of view. Our work may be extended towards phylogenetic analysis of organisms producing secondary metabolites of various sorts.},
}
@article {pmid11797917,
year = {2001},
author = {Hine, PM and Cochennec-Laureau, N and Berthe, FC},
title = {Bonamia exitiosus n. sp. (Haplosporidia) infecting flat oysters Ostrea chilensis in New Zealand.},
journal = {Diseases of aquatic organisms},
volume = {47},
number = {1},
pages = {63-72},
doi = {10.3354/dao047063},
pmid = {11797917},
issn = {0177-5103},
mesh = {Animals ; Base Sequence ; DNA, Ribosomal/*analysis/chemistry ; Eukaryota/*classification/genetics/*ultrastructure ; Host-Parasite Interactions ; Molecular Sequence Data ; New Zealand ; Ostreidae/*parasitology ; Phylogeny ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sequence Alignment/veterinary ; Sequence Analysis, DNA ; },
abstract = {Bonamia sp. is a pathogenic parasite that occurs in the haemocytes of dredge oysters Ostrea chilensis Philippi in New Zealand. Ultrastructurally it resembles other haplosporidians in the possession of haplosporosomes, haplosporogenesis, persistence of mitotic microtubules during interphase and of the nuclear envelope during mitosis, and occurrence of a diplokaryotic or multi-nucleate plasmodial stage. Another stage containing a large vacuole derived from enlargement of 1 or more mitochondria has not previously been described from other haplosporidians. It most closely resembles B. ostreae Pichot et al., 1979, which parasitises and is pathogenic in haemocytes of European flat oysters, O. edulis. However, B. ostreae is smaller and denser, and has fewer lipoid bodies and haplosporosomes. We have nearly completely sequenced the small ribosomal gene of the organism from O. chilensis. Initial comparisons of these sequences with those of other protozoans showed similarities to B. ostreae. Polymorphism within Bonamia sp. was confirmed by restriction fragment length polymorphism analysis. On the basis of ultrastructural and molecular considerations it is proposed that this organism be named Bonamia exitiosus sp. nov.},
}
@article {pmid11801744,
year = {2002},
author = {Lavrov, DV and Boore, JL and Brown, WM},
title = {Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss.},
journal = {Molecular biology and evolution},
volume = {19},
number = {2},
pages = {163-169},
doi = {10.1093/oxfordjournals.molbev.a004068},
pmid = {11801744},
issn = {0737-4038},
mesh = {Animals ; Arthropods/classification/*genetics ; Base Sequence ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; *Gene Duplication ; Gene Order/genetics ; Gene Rearrangement/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; Translocation, Genetic ; },
abstract = {We determined the complete mitochondrial DNA (mtDNA) sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified, in both genomes, all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from others found in arthropod mtDNAs in the location of at least four genes or gene blocks. This novel gene arrangement is unusual for animal mtDNA in that genes with identical transcriptional polarities are clustered in the genome, and the two clusters are separated by two noncoding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.},
}
@article {pmid11803022,
year = {2002},
author = {Kita, K and Hirawake, H and Miyadera, H and Amino, H and Takeo, S},
title = {Role of complex II in anaerobic respiration of the parasite mitochondria from Ascaris suum and Plasmodium falciparum.},
journal = {Biochimica et biophysica acta},
volume = {1553},
number = {1-2},
pages = {123-139},
doi = {10.1016/s0005-2728(01)00237-7},
pmid = {11803022},
issn = {0006-3002},
mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Ascaris suum/*enzymology ; Electron Transport Complex II ; Energy Metabolism ; Fumarates/metabolism ; Life Cycle Stages ; Mitochondria/metabolism ; Models, Chemical ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*metabolism ; Oxidoreductases/chemistry/*metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phylogeny ; Plasmodium falciparum/*enzymology ; Sequence Alignment ; Succinate Dehydrogenase/chemistry/*metabolism ; Succinic Acid/metabolism ; },
abstract = {Parasites have developed a variety of physiological functions necessary for existence within the specialized environment of the host. Regarding energy metabolism, which is an essential factor for survival, parasites adapt to low oxygen tension in host mammals using metabolic systems that are very different from that of the host. The majority of parasites do not use the oxygen available within the host, but employ systems other than oxidative phosphorylation for ATP synthesis. In addition, all parasites have a life cycle. In many cases, the parasite employs aerobic metabolism during their free-living stage outside the host. In such systems, parasite mitochondria play diverse roles. In particular, marked changes in the morphology and components of the mitochondria during the life cycle are very interesting elements of biological processes such as developmental control and environmental adaptation. Recent research has shown that the mitochondrial complex II plays an important role in the anaerobic energy metabolism of parasites inhabiting hosts, by acting as quinol-fumarate reductase.},
}
@article {pmid11811990,
year = {2002},
author = {Fuku, N and Oshida, Y and Takeyasu, T and Guo, LJ and Kurata, M and Yamada, Y and Sato, Y and Tanaka, M},
title = {Mitochondrial ATPase subunit 6 and cytochrome B gene polymorphisms in young obese adults.},
journal = {Biochemical and biophysical research communications},
volume = {290},
number = {4},
pages = {1199-1205},
doi = {10.1006/bbrc.2002.6330},
pmid = {11811990},
issn = {0006-291X},
mesh = {Adenosine Triphosphatases/*genetics ; Adult ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Humans ; Japan ; Mitochondria/enzymology ; Mitochondrial Proton-Translocating ATPases ; Models, Genetic ; Mutation ; Obesity/*genetics/metabolism ; Phylogeny ; *Polymorphism, Genetic ; },
abstract = {We hypothesized that the mutational strand asymmetry is more strongly exerted upon the mitochondrial cytochrome b (Cytb) gene, which is distant from the origin of the light-strand replication (Ori(L)), than upon the ATPase subunit 6 (ATP6) gene, which is close to the Ori(L). To test this hypothesis, we determined the sequences of these two genes in 96 Japanese young obese adults. The frequency of G-->A transitions was significantly higher than that of C-->T transitions in the Cytb gene, whereas the frequencies of G-->A and C-->T transitions were not significantly different in the ATP6 gene. The marked mutational strand asymmetry in the Cytb gene can be explained by the deamination of C to uracil in the long single-stranded state of the heavy strand during replication. The ratio of the nonsynonymous substitutions at the second codon positions to those at the first codon positions was significantly lower in the Cytb gene than in the ATP6 gene. The physicochemical differences between the standard and the replaced amino acid residues were significantly smaller in the Cytb gene than in ATP6 one. The present study indicates that amino acid sequences are less variable for Cytb than for ATP6 in spite of the strong mutational strand asymmetry for the Cytb gene.},
}
@article {pmid11818061,
year = {2002},
author = {Andersson, JO and Roger, AJ},
title = {A cyanobacterial gene in nonphotosynthetic protists--an early chloroplast acquisition in eukaryotes?.},
journal = {Current biology : CB},
volume = {12},
number = {2},
pages = {115-119},
doi = {10.1016/s0960-9822(01)00649-2},
pmid = {11818061},
issn = {0960-9822},
mesh = {Arabidopsis/classification/genetics ; Chloroplasts/*metabolism ; Cyanobacteria/classification/*genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; },
abstract = {Since the incorporation of mitochondria and chloroplasts (plastids) into the eukaryotic cell by endosymbiosis, genes have been transferred from the organellar genomes to the nucleus of the host, via an ongoing process known as endosymbiotic gene transfer. Accordingly, in photosynthetic eukaryotes, nuclear genes with cyanobacterial affinity are believed to have originated from endosymbiotic gene transfer from chloroplasts. Analysis of the Arabidopsis thaliana genome has shown that a significant fraction (2%-9%) of the nuclear genes have such an endosymbiotic origin. Recently, it was argued that 6-phosphogluconate dehydrogenase (gnd)-the second enzyme in the oxidative pentose phosphate pathway-was one such example. Here we show that gnd genes with cyanobacterial affinity also are present in several nonphotosynthetic protistan lineages, such as Heterolobosea, Apicomplexa, and parasitic Heterokonta. Current data cannot definitively resolve whether these groups acquired the gnd gene by primary and/or secondary endosymbiosis or via an independent lateral gene transfer event. Nevertheless, our data suggest that chloroplasts were introduced into eukaryotes much earlier than previously thought and that several major groups of heterotrophic eukaryotes have secondarily lost photosynthetic plastids.},
}
@article {pmid11828469,
year = {2001},
author = {Ludwig, B and Bender, E and Arnold, S and Hüttemann, M and Lee, I and Kadenbach, B},
title = {Cytochrome C oxidase and the regulation of oxidative phosphorylation.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {2},
number = {6},
pages = {392-403},
doi = {10.1002/1439-7633(20010601)2:6&lt;392::AID-CBIC392&gt;3.0.CO;2-N},
pmid = {11828469},
issn = {1439-4227},
mesh = {Adenosine Triphosphate/metabolism ; Animals ; Bacterial Proteins/chemistry/*metabolism ; Diiodothyronines/metabolism ; Electron Transport Complex IV/chemistry/classification/*metabolism ; Heart/physiology ; Humans ; Membrane Potentials/physiology ; Mitochondria/enzymology/*metabolism ; Models, Molecular ; *Oxidative Phosphorylation ; Oxygen/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Protein Subunits ; Reactive Oxygen Species/metabolism ; },
abstract = {Life of higher organisms is essentially dependent on the efficient synthesis of ATP by oxidative phosphorylation in mitochondria. An important and as yet unsolved question of energy metabolism is how are the variable rates of ATP synthesis at maximal work load during exercise or mental work and at rest or during sleep regulated. This article reviews our present knowledge on the structure of bacterial and eukaryotic cytochrome c oxidases and correlates it with recent results on the regulatory functions of nuclear-coded subunits of the eukaryotic enzyme, which are absent from the bacterial enzyme. A new molecular hypothesis on the physiological regulation of oxidative phosphorylation is proposed, assuming a hormonally controlled dynamic equilibrium in vivo between two states of energy metabolism, a relaxed state with low ROS (reactive oxygen species) formation, and an excited state with elevated formation of ROS, which are known to accelerate aging and to cause degenerative diseases and cancer. The hypothesis is based on the allosteric ATP inhibition of cytochrome c oxidase at high intramitochondrial ATP/ADP ratios ("second mechanism of respiratory control"), which is switched on by cAMP-dependent phosphorylation and switched off by calcium-induced dephosphorylation of the enzyme.},
}
@article {pmid11846101,
year = {2001},
author = {Lee, YH and Kim, KH},
title = {The ultrastructure of spermatozoa of the slender catfish Silurus microdorsalis (Teleostei, Siluriformes, Siluridae) with phylogenetic considerations.},
journal = {Journal of submicroscopic cytology and pathology},
volume = {33},
number = {3},
pages = {329-336},
pmid = {11846101},
issn = {1122-9497},
mesh = {Animals ; Catfishes/*physiology ; Male ; Organelles/ultrastructure ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; },
abstract = {The spermatozoa of the slender catfish Silurus microdorsalis examined using transmission and scanning electron microscopy are characterized by a tubular structure and the absence of axonemal fins. Their characteristics can be considered to represent a valid symplesiomorphy uniting the Siluridae and taxon-specific for this family. The tubules of Silurus spermatozoon are not observed in the other siluroids. Unusual tubules occur in Citharinus spermatozoa of Characiformes. In addition, there is a considerable similarity in the absence of axonemal fins between Siluridae and Characiformes. Thus the two shared characteristics provide strong evidence that there exists a phylogenetic link between Characiformes and Siluriformes. Silurus appears to be plesiomorphic in having lost the axonemal fins while retaining the tubules in midpiece. The spermatozoa of S. microdorsalis are similar to those of other siluroids having a spherical head with a deep nuclear fossa, a short midpiece and an elongated tail. However, there are some differences between Silurus and other siluroids in the orientation of the centrioles, the number of the mitochondria and the axonemal fins, and minor differences between S. microdorsalis and S. asotus, in particular the orientation of the centriolar complex, and the arrangement of the tubules and the mitochondria in the midpiece. The deep nuclear fossa represents a synapomorphy uniting the Siluriformes, while the shallow nuclear fossa and the absence of axonemal fins are shared by two orders, Characiformes and Cypriniformes.},
}
@article {pmid11847105,
year = {2002},
author = {van der Giezen, M and Slotboom, DJ and Horner, DS and Dyal, PL and Harding, M and Xue, GP and Embley, TM and Kunji, ER},
title = {Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles.},
journal = {The EMBO journal},
volume = {21},
number = {4},
pages = {572-579},
pmid = {11847105},
issn = {0261-4189},
support = {1U01 AI 48594-01/AI/NIAID NIH HHS/United States ; },
mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers ; Genetic Complementation Test ; Humans ; Hydrogen/*metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; },
abstract = {Mitochondria are one of the hallmarks of eukaryotic cells, exporting ATP in exchange for cytosolic ADP using ADP/ATP carriers (AAC) located in the inner mitochondrial membrane. In contrast, several evolutionarily important anaerobic eukaryotes lack mitochondria but contain hydrogenosomes, peculiar organelles of controversial ancestry that also supply ATP but, like some fermentative bacteria, make molecular hydrogen in the process. We have now identified genes from two species of the hydrogenosome-containing fungus Neocallimastix that have three-fold sequence repeats and signature motifs that, along with phylogenetic analysis, identify them as AACs. When expressed in a mitochondrial AAC- deficient yeast strain, the hydrogenosomal protein was correctly targeted to the yeast mitochondria inner membrane and yielded mitochondria able to perform ADP/ATP exchange. Characteristic inhibitors of mitochondrial AACs blocked adenine nucleotide exchange by the Neocallimastix protein. Thus, our data demonstrate that fungal hydrogenosomes and yeast mitochondria use the same pathway for ADP/ATP exchange. These experiments provide some of the strongest evidence yet that yeast mitochondria and Neocallimastix hydrogenosomes are but two manifestations of the same fundamental organelle.},
}
@article {pmid11851985,
year = {2001},
author = {Bandelt, HJ and Alves-Silva, J and Guimarães, PE and Santos, MS and Brehm, A and Pereira, L and Coppa, A and Larruga, JM and Rengo, C and Scozzari, R and Torroni, A and Prata, MJ and Amorim, A and Prado, VF and Pena, SD},
title = {Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade.},
journal = {Annals of human genetics},
volume = {65},
number = {Pt 6},
pages = {549-563},
doi = {10.1017/S0003480001008892},
pmid = {11851985},
issn = {0003-4800},
mesh = {Africa/ethnology ; Brazil ; Caribbean Region ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Emigration and Immigration/history ; *Haplotypes ; History, Ancient ; *Phylogeny ; Time ; },
abstract = {The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (-3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (+/-14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.},
}
@article {pmid11880223,
year = {2002},
author = {Arisue, N and Sánchez, LB and Weiss, LM and Müller, M and Hashimoto, T},
title = {Mitochondrial-type hsp70 genes of the amitochondriate protists, Giardia intestinalis, Entamoeba histolytica and two microsporidians.},
journal = {Parasitology international},
volume = {51},
number = {1},
pages = {9-16},
pmid = {11880223},
issn = {1383-5769},
support = {R01 AI011942/AI/NIAID NIH HHS/United States ; R01 AI031788/AI/NIAID NIH HHS/United States ; AI 11942/AI/NIAID NIH HHS/United States ; AI 31788/AI/NIAID NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Encephalitozoon/genetics ; Entamoeba histolytica/*genetics ; Giardia lamblia/*genetics ; HSP70 Heat-Shock Proteins/chemistry/*genetics ; Microsporidia/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/genetics ; Sequence Analysis, DNA ; },
abstract = {Genes encoding putative mitochondrial-type heat shock protein 70 (mit-hsp70) were isolated and sequenced from amitochondriate protists, Giardia intestinalis, Entamoeba histolytica, and two microsporidians, Encephalitozoon hellem and Glugea plecoglossi. The deduced mit-hsp70 sequences were analyzed by sequence alignments and phylogenetic reconstructions. The mit-hsp70 sequence of these four amitochondriate protists were divergent from other mit-hsp70 sequences of mitochondriate eukaryotes. However, all of these sequences were clearly located within a eukaryotic mitochondrial clade in the tree including various type hsp70 sequences, supporting the emerging notion that none of these amitochondriate lineages are primitively amitochodrial, but lost their mitochondria secondarily in their evolutionary past.},
}
@article {pmid11903896,
year = {2001},
author = {Sota, T and Ishikawa, R and Ujiie, M and Kusumoto, F and Vogler, AP},
title = {Extensive trans-species mitochondrial polymorphisms in the carabid beetles Carabus subgenus Ohomopterus caused by repeated introgressive hybridization.},
journal = {Molecular ecology},
volume = {10},
number = {12},
pages = {2833-2847},
doi = {10.1046/j.1365-294x.2001.t01-1-01404.x},
pmid = {11903896},
issn = {0962-1083},
mesh = {Animals ; Base Sequence ; Coleoptera/anatomy &amp; histology/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Ecology ; Female ; Hybridization, Genetic/genetics ; Japan ; Male ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sequence Homology, Nucleic Acid ; },
abstract = {To study the potential importance of introgressive hybridization to the evolutionary diversification of a carabid beetle lineage, we studied intraspecific and trans-species polymorphisms in the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequence (1083 bp) in four species of the subgenus Ohomopterus (genus Carabus) in central and eastern Honshu, Japan. Of the four species, C. insulicola is parapatric with the other three, and can hybridize naturally with at least two. This species possesses two haplotypes of remote lineages. We classified ND5 haplotypes using polymerase chain reaction-restriction fragment length polymorphism with TaqI endonuclease for 524 specimens, and sequenced 143 samples. Analysis revealed that each species was polyphyletic in its mitochondrial DNA phylogeny, representing a marked case of trans-species polymorphism. Recent one-way introgression of mitochondria from C. arrowianus nakamurai to C. insulicola, and from C. insulicola to C. esakii, was inferred from the frequency of identical sequences between these species and from direct evidence of hybridization in their contact zones. Other intraspecific polymorphisms in the four species may be due to undetected introgressive hybridization (e.g. C. insulicola to C. maiyasanus) or from stochastic lineage sorting of ancestral polymorphisms. This beetle group has a genital lock-and-key system, with species-specific or subspecies-specific genital morphology that may act as a barrier to hybridization. However, our results demonstrate that introgressive hybridization has occurred multiple times, at least for mitochondria, despite differences among, and stability within, morphological characters that distinguish local populations. Thus, hybridization and introgression could have been key processes in the evolutionary diversification of Ohomopterus.},
}
@article {pmid11906012,
year = {2001},
author = {Furuta, T and Kikuchi, T and Miyadera, H and Yoshikawa, Y},
title = {Pneumocystis carinii infection in red-bellied tamarins and cynomolgus monkeys, and the characterization of the mitochondrial large subunit ribosomal RNA gene of Pneumocystis carinii.},
journal = {The Journal of eukaryotic microbiology},
volume = {Suppl},
number = {},
pages = {107S-108S},
doi = {10.1111/j.1550-7408.2001.tb00472.x},
pmid = {11906012},
issn = {1066-5234},
mesh = {Animals ; Cats ; DNA, Fungal/analysis/isolation &amp; purification ; Dogs ; Genes, rRNA/*genetics ; Humans ; Lung/microbiology ; *Macaca fascicularis ; Mice ; Mitochondria/*genetics ; Monkey Diseases/epidemiology/*microbiology ; Phylogeny ; Pneumocystis/genetics/isolation &amp; purification ; Pneumonia, Pneumocystis/epidemiology/microbiology/*veterinary ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; Rats ; *Saguinus ; },
}
@article {pmid11912229,
year = {2002},
author = {Weber, A and Flügge, UI},
title = {Interaction of cytosolic and plastidic nitrogen metabolism in plants.},
journal = {Journal of experimental botany},
volume = {53},
number = {370},
pages = {865-874},
doi = {10.1093/jexbot/53.370.865},
pmid = {11912229},
issn = {0022-0957},
mesh = {Amino Acid Oxidoreductases/metabolism ; Ammonia/*metabolism ; Biological Transport ; Cycadopsida/metabolism ; Cytosol/*metabolism ; Dicarboxylic Acid Transporters/genetics/metabolism ; Gene Expression Regulation, Plant ; Glucose-6-Phosphate/metabolism ; Glutamate-Ammonia Ligase/metabolism ; Glutamic Acid/metabolism ; Glutamine/metabolism ; Ketoglutaric Acids/metabolism ; Models, Biological ; Nitrogen/*metabolism ; Phylogeny ; Plants/classification/*metabolism ; Plastids/*metabolism ; },
abstract = {In angiosperms, the assimilation of ammonia resulting from nitrate reduction and from photorespiration depends on the operation of the plastidic GS/GOGAT cycle. The precursor for ammonia assimilation, 2-oxoglutarate, is synthesized in the mitochondria and in the cytosol. It is imported into the plastid by a 2-oxoglutarate/malate translocator (DiT1). In turn, the product of ammonia assimilation, glutamate, is exported from the plastids by a glutamate/malate translocator (DiT2). These transport processes link plastidic and cytosolic nitrogen metabolism and are essential for plant metabolism. DiT1 was purified to homogeneity from spinach chloroplast envelope membranes and identified as a protein with an apparent molecular mass of 45 kDa. Peptide sequences were obtained from the protein and the corresponding cDNA was cloned. The function of the DiT1 protein and its substrate specificity were confirmed by expression of the cDNA in yeast cells and functional reconstitution of the recombinant protein into liposomes. Recent advances in the molecular cloning of DiT2 and in the analysis of the in vivo function of DiT1 by antisense repression in transgenic tobacco plants will be discussed. In non-green tissues, the reducing equivalents required for glutamate formation by NADH-GOGAT are supplied by the oxidative pentose phosphate pathway. Glucose 6-phosphate, the immediate precursor of the oxidative pentose phosphate pathway is generated in the cytosol and imported into the plastids by the plastidic glucose 6-phosphate/phosphate translocator.},
}
@article {pmid11912232,
year = {2002},
author = {Suárez, MF and Avila, C and Gallardo, F and Cantón, FR and García-Gutiérrez, A and Claros, MG and Cánovas, FM},
title = {Molecular and enzymatic analysis of ammonium assimilation in woody plants.},
journal = {Journal of experimental botany},
volume = {53},
number = {370},
pages = {891-904},
doi = {10.1093/jexbot/53.370.891},
pmid = {11912232},
issn = {0022-0957},
mesh = {Amino Acid Oxidoreductases/genetics/metabolism ; Carbon/metabolism ; Cycadopsida/enzymology/genetics ; Enzymes/*genetics/metabolism ; Gene Expression Regulation, Plant ; Glutamate-Ammonia Ligase/genetics/metabolism ; Isocitrate Dehydrogenase/genetics/metabolism ; Magnoliopsida/enzymology/genetics ; Mitochondria/enzymology ; Nitrogen/*metabolism ; Phylogeny ; Plants, Genetically Modified ; Quaternary Ammonium Compounds/*metabolism ; Trees/enzymology/*genetics ; },
abstract = {Ammonium is assimilated into amino acids through the sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) enzymes. This metabolic pathway is driven by energy, reducing power and requires the net supply of 2-oxoglutarate that can be provided by the reaction catalysed by isocitrate dehydrogenase (IDH). Most studies on the biochemistry and molecular biology of N-assimilating enzymes have been carried out on annual plant species and the available information on woody models is far more limited. This is in spite of their economic and ecological importance and the fact that nitrogen is a common limiting factor for tree growth. GS, GOGAT and IDH enzymes have been purified from several woody species and their kinetic and molecular properties determined. A number of cDNA clones have also been isolated and characterized. Although the enzymes are remarkably well conserved along the evolutionary scale, major differences have been found in their compartmentation within the cell between angiosperms and conifers, suggesting possible adaptations to specific functional roles. The analysis of the gene expression patterns in a variety of biological situations such as changes in N nutrition, development, biotic or abiotic stresses and senescence, suggest that cytosolic GS plays a central and pivotal role in ammonium assimilation and metabolism in woody plants. The modification of N assimilation efficiency has been recently approached in trees by overexpression of a cytosolic pine GS in poplar. The results obtained, suggest that an increase in cytosolic GS might lead to a global effect on the synthesis of nitrogenous compounds in the leaves, with enhanced vegetative growth of transgenic trees. All these data suggest that manipulation of cytosolic GS may have consequences for plant growth and biomass production.},
}
@article {pmid11940519,
year = {2002},
author = {Brett, CL and Wei, Y and Donowitz, M and Rao, R},
title = {Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria.},
journal = {American journal of physiology. Cell physiology},
volume = {282},
number = {5},
pages = {C1031-41},
doi = {10.1152/ajpcell.00420.2001},
pmid = {11940519},
issn = {0363-6143},
support = {P01-DK-44484/DK/NIDDK NIH HHS/United States ; R01-DK-26523/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Biomarkers ; CHO Cells ; Cell Fractionation ; Cell Line ; Cell Membrane/*metabolism ; Cricetinae ; Endosomes/*metabolism ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins ; Humans ; Luminescent Proteins/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Opossums ; Phylogeny ; Protein Isoforms ; Receptors, Transferrin/metabolism ; Recombinant Fusion Proteins/metabolism ; Sodium-Hydrogen Exchangers/*metabolism ; },
abstract = {Since the discovery of the first intracellular Na(+)/H(+) exchanger in yeast, Nhx1, multiple homologs have been cloned and characterized in plants. Together, studies in these organisms demonstrate that Nhx1 is located in the prevacuolar/vacuolar compartment of cells where it sequesters Na(+) into the vacuole, regulates intravesicular pH, and contributes to vacuolar biogenesis. In contrast, the human homolog of Nhx1, Na(+)/H(+) exchanger isoform 6 (NHE6), has been reported to localize to mitochondria when transiently expressed as a fusion with green fluorescent protein. This result warrants reevaluation because it conflicts with predictions from phylogenetic analyses. Here we demonstrate that when epitope-tagged NHE6 is transiently expressed in cultured mammalian cells, it does not colocalize with mitochondrial markers. It also does not colocalize with markers of the lysosome, late endosome, trans-Golgi network, or Golgi cisternae. Rather, NHE6 is distributed in recycling compartments and transiently appears on the plasma membrane. These results suggest that, like its homologs in yeast and plants, NHE6 is an endosomal Na(+)/H(+) exchanger that may regulate intravesicular pH and volume and contribute to lysosomal biogenesis.},
}
@article {pmid11950885,
year = {2002},
author = {Rojo, M and Legros, F and Chateau, D and Lombès, A},
title = {Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo.},
journal = {Journal of cell science},
volume = {115},
number = {Pt 8},
pages = {1663-1674},
doi = {10.1242/jcs.115.8.1663},
pmid = {11950885},
issn = {0021-9533},
mesh = {Actins/metabolism ; Animals ; Cell Fractionation ; Cytoskeleton/metabolism ; *Drosophila Proteins ; GTP Phosphohydrolases/*genetics ; HeLa Cells ; Humans ; Immunohistochemistry ; Membrane Proteins/chemistry/classification/*genetics/*metabolism ; Membrane Transport Proteins ; Microtubules/metabolism ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Proteins/chemistry/classification/genetics/*metabolism ; Phylogeny ; *Protein Structure, Tertiary ; },
abstract = {Two human Fzo-homologs, mitofusins Mfn1 and Mfn2, are shown by RT-PCR and western blot to be ubiquitous mitochondrial proteins. Protease digestion experiments reveal that Mfn2 is an outer membrane protein with N-terminal and C-terminal domains exposed towards the cytosol. The transmembrane and C-terminal domains of Mfn2 (Mfn2-TMCT) are targeted to mitochondria and deletion of these domains leads to the cytosolic localization of truncated Mfn2 (Mfn2-NT). Mfn2 is targeted to the endoplasmic reticulum or to mitochondria when the C-terminal domain is replaced by short stretches of neutral/hydrophobic (Mfn2-IYFFT) or polar/basic (Mfn2-RRD) amino acids. The coiled-coil domains of Mfn2, upstream and downstream of the transmembrane domain, are also important for mitochondrial targeting: Mfn2-mutants deleted of any of its coiled-coil domains are only partially targeted to mitochondria and significant protein amounts remain cytosolic. We show that these coiled-coil domains interact with each other: mistargeted Mfn2-NT or Mfn2-IYFFT localize to mitochondria if co-expressed with Mfn2-TMCT. This relocalization is abolished when the coiled-coil domain is deleted in any of the co-transfected molecules. We also found that Mfn2 can cluster active mitochondria in the perinuclear region independently of the cytoskeleton, bring mitochondrial membranes into close contact and modify mitochondrial structure, without disturbing the integrity of the inner and outer membrane.},
}
@article {pmid11972043,
year = {2002},
author = {Vermel, M and Guermann, B and Delage, L and Grienenberger, JM and Maréchal-Drouard, L and Gualberto, JM},
title = {A family of RRM-type RNA-binding proteins specific to plant mitochondria.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {99},
number = {9},
pages = {5866-5871},
pmid = {11972043},
issn = {0027-8424},
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis ; Blotting, Northern ; Cold Temperature ; DNA, Complementary/metabolism ; DNA, Single-Stranded ; Detergents/pharmacology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acids/metabolism ; Octoxynol/pharmacology ; Phylogeny ; Plant Proteins/*metabolism ; Plants/metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA/*metabolism ; *RNA-Binding Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Ribonucleoside Diphosphate Reductase ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Solanum tuberosum/genetics ; Temperature ; Nicotiana/genetics ; Tumor Suppressor Proteins/metabolism ; },
abstract = {Expression of higher plant mitochondrial (mt) genes is regulated at the transcriptional, posttranscriptional, and translational levels, but the vast majority of the mtDNA and RNA-binding proteins involved remain to be identified. Plant mt single-stranded nucleic acid-binding proteins were purified by affinity chromatography, and corresponding genes have been identified. A majority of these proteins belong to a family of RNA-binding proteins characterized by the presence of an N-terminal RNA-recognition motif (RRM) sequence. They diverge in their C-terminal sequences, suggesting that they can be involved in different plant mt regulation processes. Mitochondrial localization of the proteins was confirmed both in vitro and in vivo and by immunolocalization. Binding experiments showed that several proteins have a preference for poly(U)-rich sequences. This mt protein family contains the ubiquitous RRM motif and has no known mt counterpart in non-plant species. Phylogenetic and functional analysis suggest a common ancestor with RNA-binding glycine-rich proteins (GRP), a family of developmentally regulated proteins of unknown function. As with several plant, cyanobacteria, and animal proteins that have similar structures, the expression of one of the Arabidopsis thaliana mt RNA-binding protein genes is induced by low temperatures.},
}
@article {pmid11992819,
year = {2002},
author = {Balmer, Y and Buchanan, BB},
title = {Yet another plant thioredoxin.},
journal = {Trends in plant science},
volume = {7},
number = {5},
pages = {191-193},
doi = {10.1016/s1360-1385(02)02263-x},
pmid = {11992819},
issn = {1360-1385},
mesh = {Animals ; Bacteria/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/*genetics/metabolism ; Signal Transduction ; Thioredoxins/*genetics/metabolism ; Yeasts/genetics/metabolism ; },
abstract = {Thioredoxins are widely distributed proteins that function in a broad spectrum of cellular reactions. Plant cells have well characterized chloroplast and cytosolic thioredoxin systems, but, unlike animals and yeast, a mitochondrial counterpart has not been clearly defined. Recently, a complete thioredoxin system has been described in plant mitochondria, opening a new door for the study of thioredoxins as well as mitochondria.},
}
@article {pmid11999848,
year = {2002},
author = {Skibbe, DS and Liu, F and Wen, TJ and Yandeau, MD and Cui, X and Cao, J and Simmons, CR and Schnable, PS},
title = {Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis.},
journal = {Plant molecular biology},
volume = {48},
number = {5-6},
pages = {751-764},
pmid = {11999848},
issn = {0167-4412},
mesh = {Aldehyde Dehydrogenase/*genetics/metabolism ; Arabidopsis/enzymology/*genetics ; Cloning, Molecular ; Escherichia coli/genetics ; Exons ; Genes/genetics ; Genetic Complementation Test ; Introns ; Isoenzymes/genetics/metabolism ; Mutation ; Phylogeny ; Species Specificity ; Zea mays/enzymology/*genetics ; },
abstract = {Cytoplasmic male sterility is a maternally transmitted inability to produce viable pollen. Male sterility occurs in Texas (T) cytoplasm maize as a consequence of the premature degeneration of the tapetal cell layer during microspore development. This sterility can be overcome by the combined action of two nuclear restorer genes, rf1 and rf2a. The rf2a gene encodes a mitochondrial aldehyde dehydrogenase (ALDH) that is capable of oxidizing a variety of aldehydes. Six additional ALDH genes were cloned from maize and Arabidopsis. In vivo complementation assays and in vitro enzyme analyses demonstrated that all six genes encode functional ALDHs. Some of these ALDHs are predicted to accumulate in the mitochondria, others in the cytosol. The intron/exon boundaries of these genes are highly conserved across maize and Arabidopsis and between mitochondrial and cytosolic ALDHs. Although animal, fungal, and plant genomes each encode both mitochondrial and cytosolic ALDHs, it appears that either the gene duplications that generated the mitochondrial and the cytosolic ALDHs occurred independently within each lineage or that homogenizing gene conversion-like events have occurred independently within each lineage. All studied plant genomes contain two confirmed or predicted mitochondrial ALDHs. It appears that these mitochondrial ALDH genes arose via independent duplications after the divergence of monocots and dicots or that independent gene conversion-like events have homogenized the mitochondrial ALDH genes in the monocot and dicot lineages. A computation approach was used to identify amino acid residues likely to be responsible for functional differences between mitochondrial and cytosolic ALDHs.},
}
@article {pmid12022276,
year = {2002},
author = {Brugerolle, G and Bricheux, G and Philippe, H and Coffea, G},
title = {Collodictyon triciliatum and Diphylleia rotans (=Aulacomonas submarina) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups.},
journal = {Protist},
volume = {153},
number = {1},
pages = {59-70},
doi = {10.1078/1434-4610-00083},
pmid = {12022276},
issn = {1434-4610},
mesh = {Animals ; Cell Division/physiology ; Cell Nucleus/metabolism/ultrastructure ; DNA, Ribosomal/analysis ; Eukaryota/*classification/genetics/physiology/ultrastructure ; Flagella/ultrastructure ; Golgi Apparatus/ultrastructure ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Mitosis ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Comparative electron microscopic studies of Collodictyon triciliatum and Diphylleia rotans (=Aulacomonas submarina) showed that they share a distinctive flagellar transitional zone and a very similar flagellar apparatus. In both species, the basic couple of basal bodies and flagella #1 and #2 are connected to the dorsal and ventral roots, respectively. Collodictyon triciliatum has two additional basal bodies and flagella, #3 and #4, situated on each side of the basic couple, each of which also bears a dorsal root. The horseshoe-shaped arrangement of dictyosomes, mitochondria with tubular cristae and the deep ventral groove are very similar to those of Diphylleia rotans. These two genera have very specific features and are placed in a new family, Collodictyonidae, distinct from other eukaryotic groups. Electron microscopic observation of mitotic telophase in Diphylleia rotans revealed two chromosomal masses, surrounded by the nuclear envelope, within the dividing parental nucleus, as in the telophase stage of the heliozoan Actinophrys and the helioflagellate Dimorpha. Spindle microtubules arise from several MTOCs outside the nucleus, and several microtubules penetrate within the dividing nucleus, via pores at the poles. This semi-open type of orthomitosis is reminiscent of that of actinophryids. The SSU rDNA sequence of Diphylleia rotans was compared with that of all the eukaryotic groups that have a slow-evolving rDNA. Diphylleia did not strongly assemble with any group and emerged in a very poorly resolved part of the eukaryotic phylogenetic tree.},
}
@article {pmid12022280,
year = {2002},
author = {Vickerman, K and Le Ray, D and Hoef-Emden, K and De Jonckheere, J},
title = {The soil flagellate Proleptomonas faecicola: cell organisation and phylogeny suggest that the only described free-living trypanosomatid is not a kinetoplastid but has cercomonad affinities.},
journal = {Protist},
volume = {153},
number = {1},
pages = {9-24},
doi = {10.1078/1434-4610-00079},
pmid = {12022280},
issn = {1434-4610},
mesh = {Animals ; Eukaryota/*classification/ultrastructure ; Flagella/classification/*physiology/ultrastructure ; Kinetoplastida/classification ; Life Cycle Stages ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Soil ; },
abstract = {The only putative free-living trypanosomatid is Proleptomonas faecicola described first by Woodcock in 1916 as a coprophilic flagellate with striking Leptomonas-like flagellar movement but lacking a kinetoplast. P faecicola was later identified by Sandon in 1927 as a widespread non-phagotrophic inhabitant of soils. No division stages were seen by either observer. An organism conforming to Woodcock's light microscope description has been isolated from tapwater and cultivated axenically in various serum-containing media. Division has been shown to occur in an aflagellate stage enclosed in a thin cyst wall. Electron microscopy of the flagellate stage reveals that, in addition to the long locomotory flagellum, a second non-motile flagellum is present attached to the body along its entire length. The flagellate's ultrastructure lacks all the major features of the Trypanosomatidae. The several mitochondria of Proleptomonas have tubular cristae and lie between intracytoplasmic microtubules originating as a loose cone associated with the flagellar basal bodies. This cytoskeleton is much reduced in the division cyst. A comparable Proleptomonas-like flagellate with similar division cysts has been observed in soil samples from farmland. Phylogenetic analysis based on SSU rRNA gene sequences suggests that the cultured organism identified here as Proleptomonas is unrelated to the Kinetoplastida and has affinities with the Phylum Cercozoa Cavalier-Smith, even though in morphology, life cycle and mode of feeding it bears little resemblance to any member of that diverse grouping.},
}
@article {pmid12032073,
year = {2002},
author = {Wang, HW and Sharp, TV and Koumi, A and Koentges, G and Boshoff, C},
title = {Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcoma-associated herpesvirus which resembles a spliced variant of human survivin.},
journal = {The EMBO journal},
volume = {21},
number = {11},
pages = {2602-2615},
pmid = {12032073},
issn = {0261-4189},
mesh = {*Alternative Splicing ; Amino Acid Sequence ; Apoptosis ; Blotting, Northern ; Caspase 3 ; Caspases/metabolism ; Cell Line ; Chromosomal Proteins, Non-Histone/*chemistry ; Cloning, Molecular ; DNA, Complementary/metabolism ; Endoplasmic Reticulum/metabolism ; Glutathione Transferase/metabolism ; Glycoproteins/*metabolism ; Herpesvirus 8, Human/*genetics/*metabolism ; Humans ; Inhibitor of Apoptosis Proteins ; Microscopy, Fluorescence ; *Microtubule-Associated Proteins ; Mitochondria/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasm Proteins ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Sequence Homology, Amino Acid ; Software ; Subcellular Fractions/metabolism ; Survivin ; Transfection ; },
abstract = {We have investigated the expression and function of a novel protein encoded by open reading frame (ORF) K7 of Kaposi's sarcoma-associated herpesvirus (KSHV). Computational analyses revealed that K7 is structurally related to survivin-DeltaEx3, a splice variant of human survivin that protects cells from apoptosis by an undefined mechanism. Both K7 and survivin-DeltaEx3 contain a mitochondrial-targeting sequence, an N-terminal region of a BIR (baculovirus IAP repeat) domain and a putative BH2 (Bcl-2 homology)-like domain. These suggested that K7 is a new viral anti-apoptotic protein and survivin-DeltaEx3 is its likely cellular homologue. We show that K7 is a glycoprotein, which can inhibit apoptosis and anchor to intracellular membranes where Bcl-2 resides. K7 does not associate with Bax, but does bind to Bcl-2 via its putative BH2 domain. In addition, K7 binds to active caspase-3 via its BIR domain and thus inhibits the activity of caspase-3. The BH2 domain of K7 is crucial for the inhibition of caspase-3 activity and is therefore essential for its anti-apoptotic function. Furthermore, K7 bridges Bcl-2 and activated caspase-3 into a protein complex. K7 therefore appears to be an adaptor protein and part of an anti-apoptotic complex that presents effector caspases to Bcl-2, enabling Bcl-2 to inhibit caspase activity. These data also suggest that survivin-DeltaEx3 might function by a similar mechanism to that of K7. We denote K7 as vIAP (viral inhibitor-of-apoptosis protein).},
}
@article {pmid12045142,
year = {2002},
author = {Woischnik, M and Moraes, CT},
title = {Pattern of organization of human mitochondrial pseudogenes in the nuclear genome.},
journal = {Genome research},
volume = {12},
number = {6},
pages = {885-893},
pmid = {12045142},
issn = {1088-9051},
support = {R01 GM055766/GM/NIGMS NIH HHS/United States ; GM 55766/GM/NIGMS NIH HHS/United States ; },
mesh = {Biological Transport/genetics ; Cell Nucleus/*genetics ; Chromosome Mapping/methods ; DNA, Mitochondrial/genetics/metabolism ; Databases, Genetic ; Gene Order ; *Genome, Human ; Humans ; Mitochondria/*genetics ; Phylogeny ; Pseudogenes/*genetics ; Recombination, Genetic/genetics ; },
abstract = {Mitochondrial pseudogenes in the human nuclear genome have been previously described, mostly as a source of artifacts during the analysis of the mitochondrial genome. With the availability of the complete human genome sequence, we performed a comprehensive analysis of mtDNA insertions into the nucleus. We found 612 independent integrations that are evenly distributed among all chromosomes as well as within each individual chromosome. The identified pseudogenes account for a content of at least 0.016% of the human nuclear DNA. Up to 30% of a chromosome's mtDNA pseudogene content is composed of fragments that encompass two or more adjacent mitochondrial genes, and we found no correlation between the abundance of mitochondrial transcripts and the multiplicity of integrations. These observations indicate that the migrations of mitochondrial DNA sequences to the nucleus were predominantly DNA mediated. Phylogenetic analysis of the mtDNA pseudogenes and mtDNA sequences of primates indicate a continuous transfer into the nucleus. Because of the limited window of opportunity for mtDNA transfer to the germline, sperm mtDNA, which is released from degenerating mitochondria after fertilization, could be an important source of nuclear mtDNA pseudogenes.},
}
@article {pmid12062804,
year = {2002},
author = {Richter, U and Kiessling, J and Hedtke, B and Decker, E and Reski, R and Börner, T and Weihe, A},
title = {Two RpoT genes of Physcomitrella patens encode phage-type RNA polymerases with dual targeting to mitochondria and plastids.},
journal = {Gene},
volume = {290},
number = {1-2},
pages = {95-105},
doi = {10.1016/s0378-1119(02)00583-8},
pmid = {12062804},
issn = {0378-1119},
mesh = {Amino Acid Sequence ; Bryopsida/enzymology/*genetics ; Cloning, Molecular ; DNA, Plant/chemistry/genetics/isolation &amp; purification ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Exons ; Genes, Plant/drug effects ; Green Fluorescent Proteins ; Introns ; Isoenzymes/genetics ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Plastids/*enzymology ; Protein Biosynthesis ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; },
abstract = {Angiosperms possess a small family of phage-type RNA polymerase genes that arose by gene duplication from an ancestral gene encoding the mitochondrial RNA polymerase. We have isolated and sequenced the genes and cDNAs encoding two phage-type RNA polymerases, PpRpoT1 and PpRpoT2, from the moss Physcomitrella patens. PpRpoT1 comprises 19 exons and 18 introns, PpRpoT2 contains two additional introns. The N-terminal transit peptides of both polymerases are shown to confer dual-targeting of green fluorescent protein fusions to mitochondria and plastids. In vitro translation of the cDNAs revealed initiation of translation at two in-frame AUG start codons. Translation from the first methionine gives rise to a plastid-targeted polymerase, whereas initiation from the second methionine results in exclusively mitochondrial-targeted protein. Thus, dual-targeting of Physcomitrella RpoT is caused by and might be regulated by multiple translational starts. In phylogenetic analyses, the Physcomitrella RpoT polymerases form a sister group to all other phage-type polymerases of land plants. The two genes result from a gene duplication event that occurred independently from the one which led to the organellar polymerases with mitochondrial or plastid targeting properties in angiosperms. Yet, according to their conserved exon-intron structures they are representatives of the molecular evolutionary line leading to the RpoT genes of higher land plants.},
}
@article {pmid12067335,
year = {2002},
author = {Voncken, F and Boxma, B and Tjaden, J and Akhmanova, A and Huynen, M and Verbeek, F and Tielens, AG and Haferkamp, I and Neuhaus, HE and Vogels, G and Veenhuis, M and Hackstein, JH},
title = {Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp.},
journal = {Molecular microbiology},
volume = {44},
number = {6},
pages = {1441-1454},
doi = {10.1046/j.1365-2958.2002.02959.x},
pmid = {12067335},
issn = {0950-382X},
mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Blotting, Western ; Escherichia coli/genetics ; Hydrogen/*metabolism ; Immunohistochemistry ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/classification/genetics/*metabolism ; Molecular Sequence Data ; Neocallimastix/classification/*enzymology/genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Trichomonas/genetics ; },
abstract = {A mitochondrial-type ADP/ATP carrier (AAC) has been identified in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2. Biochemical and immunocytochemical studies revealed that this ADP/ATP carrier is an integral component of hydrogenosomal membranes. Expression of the corresponding cDNA in Escherichia coli confers the ability on the bacterial host to incorporate ADP at significantly higher rates than ATP--similar to isolated mitochondria of yeast and animals. Phylogenetic analysis of this AAC gene (hdgaac) confirmed with high statistical support that the hydrogenosomal ADP/ATP carrier of Neocallimastix sp. L2 belongs to the family of veritable mitochondrial-type AACs. Hydrogenosome-bearing anaerobic ciliates possess clearly distinct mitochondrial-type AACs, whereas the potential hydrogenosomal carrier Hmp31 of the anaerobic flagellate Trichomonas vaginalis and its homologue from Trichomonas gallinae do not belong to this family of proteins. Also, phylogenetic analysis of genes encoding mitochondrial-type chaperonin 60 proteins (HSP 60) supports the conclusion that the hydrogenosomes of anaerobic chytrids and anaerobic ciliates had independent origins, although both of them arose from mitochondria.},
}
@article {pmid12076630,
year = {2002},
author = {Alvarez-Pellitero, P and Sitjà-Bobadilla, A},
title = {Cryptosporidium molnari n. sp. (Apicomplexa: Cryptosporidiidae) infecting two marine fish species, Sparus aurata L. and Dicentrarchus labrax L.},
journal = {International journal for parasitology},
volume = {32},
number = {8},
pages = {1007-1021},
doi = {10.1016/s0020-7519(02)00058-9},
pmid = {12076630},
issn = {0020-7519},
mesh = {Animals ; Bass/*parasitology ; Cryptosporidiidae/*classification/growth &amp; development/*isolation &amp; purification/ultrastructure ; Cryptosporidiosis/diagnosis/epidemiology/*parasitology/pathology ; Fish Diseases/diagnosis/epidemiology/parasitology/pathology ; Host-Parasite Interactions ; Oceans and Seas ; Phylogeny ; Prevalence ; Sea Bream/*parasitology ; Spain ; Stomach/parasitology ; },
abstract = {Cryptosporidium molnari n. sp. is described from two teleost fish, the gilthead sea bream (Sparus aurata L.) and the European sea bass (Dicentrarchus labrax L.). The parasite was found mainly in the stomach epithelium and seldom in the intestine. Oocysts were almost spherical, with four naked sporozoites and a prominent residuum, and measured 3.23-5.45 x 3.02-5.04 (mean 4.72 x 4.47) microm in the type host, gilthead sea bream (shape index 1-1.17, mean 1.05). Sporulation was endogenous, as fully sporulated oocysts were found within the fish, both in the stomach epithelium and lumen, and in faeces. Oocysts and other stages of C. molnari fit most of the diagnostic features of the genus Cryptosporidium, but differ from hitherto described species, including piscine ones. All stages were located within a host contributed parasitophorous vacuole lined by a double host microvillar membrane. Merogonial and gamogonial stages appeared in the typical extracytoplasmic position, whereas oogonial and sporogonial stages were located deeply within the epithelium. Ultrastructural features, including the characteristic contact zone of the parasite with the host epithelial surface, were mostly coincident with those of other Cryptosporidium spp. Mitochondria were found in dividing meronts, merozoites, microgamonts and sporozoites. Pathological effects were more evident in gilthead sea bream, which also exhibited a clearly higher prevalence (24.4 versus 4.64% in sea bass). External clinical signs, consisting of whitish faeces, abdominal swelling and ascites, were rarely observed, in contrast with important histopathological damage. The wide zones of epithelium invaded by oogonial and sporogonial stages appeared necrotic, with abundant cell debris, and sloughing of epithelial cells, which detached to the lumen. No inflammation reaction was observed and the cellular reaction was limited to the cells involved in the engulfing of intraepithelial stages and debris, probably macrophages.},
}
@article {pmid12079646,
year = {2002},
author = {Shimodaira, H},
title = {An approximately unbiased test of phylogenetic tree selection.},
journal = {Systematic biology},
volume = {51},
number = {3},
pages = {492-508},
doi = {10.1080/10635150290069913},
pmid = {12079646},
issn = {1063-5157},
mesh = {Animals ; Mitochondria/metabolism ; Models, Statistical ; *Phylogeny ; },
abstract = {An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.},
}
@article {pmid12087190,
year = {2002},
author = {Takumi, S and Tomioka, M and Eto, K and Naydenov, N and Nakamura, C},
title = {Characterization of two non-homoeologous nuclear genes encoding mitochondrial alternative oxidase in common wheat.},
journal = {Genes &amp; genetic systems},
volume = {77},
number = {2},
pages = {81-88},
doi = {10.1266/ggs.77.81},
pmid = {12087190},
issn = {1341-7568},
mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics ; Chromosomes, Plant ; Cold Temperature ; DNA, Plant/genetics ; Enzyme Inhibitors/pharmacology ; Exons ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant/drug effects ; *Genes, Plant ; Genome, Plant ; Introns ; Mitochondria/*enzymology/genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Ploidies ; Potassium Cyanide/pharmacology ; Sequence Homology, Amino Acid ; Transcription, Genetic/drug effects/physiology ; Triticum/drug effects/*enzymology/genetics ; Alternative Oxidase ; },
abstract = {Mitochondrial alternative oxidase (AOX) is the terminal oxidase responsible for cyanide-insensitive and salicylhydroxamic acid-sensitive respiration. We have isolated two non-homoeologous genes (Waox1a and Waox1c) encoding AOX proteins from common wheat (Triticum aestivum L.). These two genes were orthologous to rice AOX1a and AOX1c, and their exon/intron structure was conserved, as it is in most other plant AOX genes. Southern blot analysis indicated that both Waox1a and Waox1c were located in at least three homoeologous loci and that additional AOX genes with lower homology were present in the genome of common wheat. The Waox1a and Waox1c loci were respectively assigned to the homoeologous group 2 and 6 chromosomes. The steady-state level of Waox1a and Waox1c transcripts increased under cold stress, while only that of Waox1a was increased by cyanide treatment.},
}
@article {pmid12099794,
year = {2002},
author = {Wilkinson, M and A Sheps, J and Oommen, OV and Cohen, BL},
title = {Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences.},
journal = {Molecular phylogenetics and evolution},
volume = {23},
number = {3},
pages = {401-407},
doi = {10.1016/s1055-7903(02)00031-3},
pmid = {12099794},
issn = {1055-7903},
mesh = {Amphibians/*physiology ; Animals ; India ; Mitochondria/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; *RNA, Ribosomal ; *RNA, Ribosomal, 16S ; },
abstract = {India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia.},
}
@article {pmid12099801,
year = {2002},
author = {Irestedt, M and Fjeldså, J and Johansson, US and Ericson, PG},
title = {Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes).},
journal = {Molecular phylogenetics and evolution},
volume = {23},
number = {3},
pages = {499-512},
doi = {10.1016/s1055-7903(02)00034-9},
pmid = {12099801},
issn = {1055-7903},
mesh = {Animals ; Birds/*classification/*physiology ; Cytochrome b Group/genetics ; Genes, myc ; Homeodomain Proteins/genetics ; Introns ; Mitochondria/genetics ; Myoglobin/genetics ; Nuclear Proteins/genetics ; *Phylogeny ; },
abstract = {Based on their highly specialized "tracheophone" syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos), and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1, and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. The results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, but several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic and that Sclerurus is the sister taxon to an ovenbird-woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent.},
}
@article {pmid12113307,
year = {2002},
author = {Hine, PM and Wakefield, S and Diggles, BK and Webb, VL and Maas, EW},
title = {Ultrastructure of a haplosporidian containing Rickettsiae, associated with mortalities among cultured paua Haliotis iris.},
journal = {Diseases of aquatic organisms},
volume = {49},
number = {3},
pages = {207-219},
doi = {10.3354/dao049207},
pmid = {12113307},
issn = {0177-5103},
mesh = {Alphaproteobacteria/genetics/*isolation &amp; purification/ultrastructure ; Animals ; Apicomplexa/classification/genetics/microbiology/*ultrastructure ; Aquaculture ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry ; Gene Amplification ; Mollusca/microbiology/*parasitology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Uninucleate and multinucleate stages of a protozoan parasite are described from cultured abalone Haliotis iris Martyn, 1784 in New Zealand. The parasite is identified as a haplosporidian by the occurrence of multinucleate plasmodia, mitochondria with tubular cristae, lipid droplets, anastomosing endoplasmic reticulum (aER), multivesicular bodies (MVBs), haplosporogenesis by the production of haplosporosome-like bodies from nuclear membrane-bound Golgi, and their maturation to haplosporosomes. Coated pits occurred in the plasma membrane and coated vesicles were scattered in the cytoplasm, particularly in association with the Golgi face away from the nucleus, and aER. It is concluded that the outward face of the Golgi may be the trans face, and that aER is the trans-Golgi network. Coated pits and bristle-coated vesicles are reported from a haplosporidian for the first time. The vesicles in the MVBs resembled the cores and inner membranes of haplosporosomes, without the outer layer. The possible inter-relationships of these features are discussed. The abalone parasite differs from previously described haplosporidians in the apparent absence of a persistent mitotic spindle, and the presence of intracytoplasmic coccoid to rod-shaped bacteria resembling Rickettsiales-like prokaryotes. Phylogenetic analysis of the 16S rRNA gene sequence of the Rickettsiales-like prokaryotes indicated that these organisms belong to the Rickettsia cluster. The prokaryotes have a high (7%) sequence divergence from known Rickettsieae, with Rickettsia sp. and R. massiliae being the closest relatives. The lack of non-molecular evidence prevents us from proposing a new rickettsial genus at this time.},
}
@article {pmid12114550,
year = {2002},
author = {Considine, MJ and Holtzapffel, RC and Day, DA and Whelan, J and Millar, AH},
title = {Molecular distinction between alternative oxidase from monocots and dicots.},
journal = {Plant physiology},
volume = {129},
number = {3},
pages = {949-953},
doi = {10.1104/pp.004150},
pmid = {12114550},
issn = {0032-0889},
mesh = {Arabidopsis/enzymology/*genetics ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Isoenzymes/genetics ; Magnoliopsida/classification/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Mitochondrial Proteins ; Multigene Family/genetics ; Oryza/enzymology/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins ; Review Literature as Topic ; Alternative Oxidase ; },
}
@article {pmid12115897,
year = {2002},
author = {Wilson, JM and Laurent, P},
title = {Fish gill morphology: inside out.},
journal = {The Journal of experimental zoology},
volume = {293},
number = {3},
pages = {192-213},
doi = {10.1002/jez.10124},
pmid = {12115897},
issn = {0022-104X},
mesh = {Adaptation, Physiological ; Animals ; Fishes/*anatomy &amp; histology ; Gills/*anatomy &amp; histology/blood supply/ultrastructure ; Mitochondria/physiology ; *Phylogeny ; Regional Blood Flow ; },
abstract = {In this short review of fish gill morphology we cover some basic gross anatomy as well as in some more detail the microscopic anatomy of the branchial epithelia from representatives of the major extant groups of fishes (Agnathans, Elasmobranchs, and Teleosts). The agnathan hagfishes have primitive gill pouches, while the lampreys have arch-like gills similar to the higher fishes. In the lampreys and elasmobranchs, the gill filaments are supported by a complete interbranchial septum and water exits via external branchial slits or pores. In contrast, the teleost interbranchial septum is much reduced, leaving the ends of the filaments unattached, and the multiple gill openings are replaced by the single caudal opening of the operculum. The basic functional unit of the gill is the filament, which supports rows of plate-like lamellae. The lamellae are designed for gas exchange with a large surface area and a thin epithelium surrounding a well-vascularized core of pillar cell capillaries. The lamellae are positioned for the blood flow to be counter-current to the water flow over the gills. Despite marked differences in the gross anatomy of the gill among the various groups, the cellular constituents of the epithelium are remarkably similar. The lamellar gas-exchange surface is covered by squamous pavement cells, while large, mitochondria-rich, ionocytes and mucocytes are found in greatest frequency in the filament epithelium. Demands for ionoregulation can often upset this balance. There has been much study of the structure and function of the branchial mitochondria-rich cells. These cells are generally characterized by a high mitochondrial density and an amplification of the basolateral membrane through folding or the presence of an intracellular tubular system. Morphological subtypes of MRCs as well as some methods of MRC detection are discussed.},
}
@article {pmid12120991,
year = {2002},
author = {Zhu, G and Keithly, JS},
title = {Alpha-proteobacterial relationship of apicomplexan lactate and malate dehydrogenases.},
journal = {The Journal of eukaryotic microbiology},
volume = {49},
number = {3},
pages = {255-261},
doi = {10.1111/j.1550-7408.2002.tb00532.x},
pmid = {12120991},
issn = {1066-5234},
support = {AI40320/AI/NIAID NIH HHS/United States ; AI44594/AI/NIAID NIH HHS/United States ; },
mesh = {Alphaproteobacteria/enzymology/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cryptosporidium parvum/*enzymology/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Gammaproteobacteria/genetics ; L-Lactate Dehydrogenase/chemistry/*genetics ; Malate Dehydrogenase/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; },
abstract = {We have cloned and sequenced a lactate dehydrogenase (LDH) gene from Cryptosporidium parvum (CpLDH1). With this addition, and that of four recently deposited alpha-proteobacterial malate dehydrogenase (MDH) genes, the phylogenetic relationships among apicomplexan LDH and bacterial MDH were re-examined. Consistent with previous studies, our maximum likelihood (ML) analysis using the quartet-puzzling method divided 105 LDH/MDH enzymes into five clades, and confirmed that mitochondrial MDH is a sister clade to those of y-proteobacteria, rather than to alpha-proteobacteria. In addition, a Cryptosporidium parvum MDH (CpMDH1) was identified from the ongoing Cryptosporidium genome project that appears to belong to a distinct clade (III) comprised of 22 sequences from one archaebacterium, numerous eubacteria, and several apicomplexans. Using the ML puzzling test and bootstrapping analysis with protein distance and parsimony methods, the resulting trees not only robustly confirmed the alpha-proteobacterial relationship of apicomplexan LDH/MDH, but also supported a monophyletic relationship of CpLDH1 with CpMDHI. These data suggest that, unlike most other eukaryotes, the Apicomplexa may be one of the few lineages retaining an alpha-proteobacterial-type MDH that could have been acquired from an ancestral alpha-proteobacterium through primary endosymbiosis giving rise to the mitochondria, or through an unknown lateral gene transfer (LGT) event.},
}
@article {pmid12125065,
year = {2002},
author = {Giugliano, LG and Teixeira, RD and Colli, GR and Báo, SN},
title = {Ultrastructure of spermatozoa of the lizard Ameiva ameiva, with considerations on polymorphism within the family Teiidae (Squamata).},
journal = {Journal of morphology},
volume = {253},
number = {3},
pages = {264-271},
doi = {10.1002/jmor.10002},
pmid = {12125065},
issn = {0362-2525},
mesh = {Acrosome/ultrastructure ; Animals ; Lizards/*anatomy &amp; histology/genetics ; Male ; Phylogeny ; *Polymorphism, Genetic ; Species Specificity ; Spermatozoa/*ultrastructure ; },
abstract = {A detailed description of sperm ultrastructure of the lizard Ameiva ameiva (Teiidae) is provided. Mature spermatozoa are characterized by: a depressed acrosome at the anterior portion; a unilateral ridge at the anterolateral portion; an acrosome vesicle divided into cortex and medulla; medulla divided into two regions with different electron-densities; paracrystalline subacrosomal material with radial organization in transverse section; a pointed prenuclear perforatorium; a stopper-like perforatorium base plate that appears embedded in the subacrosomal material; the presence of an epinuclear lucent zone surrounded by its own membrane; a large nuclear rostrum; round nuclear shoulders; a nuclear space at the nucleus tip; a bilateral stratified laminar structure; a central dense body within the proximal centriole; a short midpiece; an axonemal midpiece axial component; peripheral fibers 3 and 8 grossly enlarged at the anterior portion of axoneme; columnar mitochondria with linear cristae; solid dense bodies arranged as rings or spirals; a triangular-shaped annulus in transverse section; a fibrous sheath into the midpiece; a thin zone of cytoplasm at the anterior portion of the principal piece; and a slight decrease in diameter of the principal piece immediately after the annulus. Comparisons with Cnemidophorus sexlineatus and Micrablepharus maximiliani failed to identify unique sperm ultrastructure traits of Teiidae or Teiioidea (Teiidae + Gymnophthalmidae). High levels of polymorphism between Ameiva and Cnemidophorus, two closely related genera of the family Teiidae, were detected, suggesting that extensive sampling within squamate families is essential if sperm ultrastructure data are to be used in phylogenetic analyses at this taxonomic level.},
}
@article {pmid12125756,
year = {2002},
author = {Moriya, M and Nakayama, T and Inouye, I},
title = {A new class of the stramenopiles, Placididea Classis nova: description of Placidia cafeteriopsis gen. et sp. nov.},
journal = {Protist},
volume = {153},
number = {2},
pages = {143-156},
doi = {10.1078/1434-4610-00093},
pmid = {12125756},
issn = {1434-4610},
mesh = {Animals ; DNA, Ribosomal/*genetics ; Eukaryota/*classification/cytology/*genetics/ultrastructure ; Eukaryotic Cells/*classification/cytology/*metabolism/ultrastructure ; Flagella/ultrastructure ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Homology, Nucleic Acid ; },
abstract = {A marine flagellate resembling Cafeteria roenbergensis (bicosoecids, stramenopiles) in cell shape and behavior of the cell while attached to substratum was collected from the coast of Japan. The flagellate was examined by light and electron microscopy, and the 18S rDNA was sequenced to elucidate its taxonomic and phylogenetic position. Ultrastructural features suggested that the flagellate is not a bicosoecid, but a relative of the recently described stramenopile, Wobblia lunata. 18S rDNA phylogenetic trees also revealed that the flagellate forms a monophyletic clade with W. lunata and that it is distantly related to Cafeteria and other bicosoecids. The flagellate differs from W. lunata due to its lack of wobbling motion as well as intracellular features such as the number of mitochondria, flagellar apparatus architecture, the presence of a paranuclear body and cytoplasmic microtubules. The similarity of 18S rDNA sequences was 81% between the flagellate and W. lunata. This new flagellate was described as Placidia cafeteriopsis gen. et sp. nov. Because the phylogenetic lineage comprised of W. lunata and P. cafeteriopsis was one of the major, deep-branching clades of the stramenopiles, the class Placididea (= Placidiophyceae) classis nova was proposed.},
}
@article {pmid12138089,
year = {2002},
author = {Besteiro, S and Biran, M and Biteau, N and Coustou, V and Baltz, T and Canioni, P and Bringaud, F},
title = {Succinate secreted by Trypanosoma brucei is produced by a novel and unique glycosomal enzyme, NADH-dependent fumarate reductase.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {41},
pages = {38001-38012},
doi = {10.1074/jbc.M201759200},
pmid = {12138089},
issn = {0021-9258},
mesh = {Animals ; Biomarkers ; Cell Line ; Citric Acid Cycle ; Crithidia fasciculata/metabolism ; Digitonin/pharmacology ; Glucose/metabolism ; Leishmania/metabolism ; Magnetic Resonance Spectroscopy ; Microbodies/*enzymology ; Mitochondria/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/metabolism ; Oxidoreductases/classification/genetics/*metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phenotype ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Rats ; Succinic Acid/*metabolism ; Trypanosoma brucei brucei/cytology/drug effects/genetics/*metabolism ; },
abstract = {In all trypanosomatids, including Trypanosoma brucei, glycolysis takes place in peroxisome-like organelles called glycosomes. These are closed compartments wherein the energy and redox (NAD(+)/NADH) balances need to be maintained. We have characterized a T. brucei gene called FRDg encoding a protein 35% identical to Saccharomyces cerevisiae fumarate reductases. Microsequencing of FRDg purified from glycosome preparations, immunofluorescence, and Western blot analyses clearly identified this enzyme as a glycosomal protein that is only expressed in the procyclic form of T. brucei but is present in all the other trypanosomatids studied, i.e. Trypanosoma congolense, Crithidia fasciculata and Leishmania amazonensis. The specific inactivation of FRDg gene expression by RNA interference showed that FRDg is responsible for the NADH-dependent fumarate reductase activity detected in glycosomal fractions and that at least 60% of the succinate secreted by the T. brucei procyclic form (in the presence of d-glucose as the sole carbon source) is produced in the glycosome by FRDg. We conclude that FRDg plays a key role in the energy metabolism by participating in the maintenance of the glycosomal NAD(+)/NADH balance. We have also detected a significant pyruvate kinase activity in the cytosol of the T. brucei procyclic cells that was not observed previously. Consequently, we propose a revised model of glucose metabolism in procyclic trypanosomes that may also be valid for all other trypanosomatids except the T. brucei bloodstream form. Interestingly, H. Gest has hypothesized previously (Gest, H. (1980) FEMS Microbiol. Lett. 7, 73-77) that a soluble NADH-dependent fumarate reductase has been present in primitive organisms and evolved into the present day fumarate reductases, which are quinol-dependent. FRDg may have the characteristics of such an ancestral enzyme and is the only NADH-dependent fumarate reductase characterized to date.},
}
@article {pmid12140266,
year = {2002},
author = {Espinoza, NR and Noor, MA},
title = {Population genetics of a polyploid: is there hybridization between lineages of Hyla versicolor?.},
journal = {The Journal of heredity},
volume = {93},
number = {2},
pages = {81-85},
doi = {10.1093/jhered/93.2.81},
pmid = {12140266},
issn = {0022-1503},
support = {GM58060/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Gene Frequency ; Genetic Markers ; *Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polyploidy ; Ranidae/*genetics ; },
abstract = {Several studies have demonstrated that polyploid species can form recurrently from their progenitors, but few studies have evaluated gene flow between the resultant polyploid lineages. Here we examine the possibility of hybridization between lineages of the tetraploid common gray treefrog (Hyla versicolor). We utilize a polymerase chain reaction (PCR) cloning approach to estimate the genotypes of tetraploid individuals and measure genetic differentiation between (1) sympatric populations of two lineages and (2) allopatric populations of a single lineage. We find that allele frequencies in sympatric populations of two lineages do not differ, suggesting that frogs of these two lineages hybridize in areas where they co-occur.},
}
@article {pmid12144677,
year = {2002},
author = {Castilla, JC and Collins, AG and Meyer, CP and Guiñez, R and Lindberg, DR},
title = {Recent introduction of the dominant tunicate, Pyura praeputialis (Urochordata, Pyuridae) to Antofagasta, Chile.},
journal = {Molecular ecology},
volume = {11},
number = {8},
pages = {1579-1584},
doi = {10.1046/j.1365-294x.2002.01524.x},
pmid = {12144677},
issn = {0962-1083},
mesh = {Animals ; Australia ; Chile ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; South Africa ; Urochordata/classification/*genetics/*physiology ; },
abstract = {The large sessile tunicate Pyura stolonifera (Pleurogona: Stolibranchiata: Pyuridae), has been regarded as a complex taxon with disjointed distributions, including Australia (Pyura stolonifera praeputialis), South Africa (Pyura stolonifera stolonifera) and South America (Chile, Antofagasta: Pyura sp., the 'piure de Antofagasta'), and has been cited under at least five taxonomic combinations. The 'piure de Antofagasta' is a competitively dominant species in rocky intertidal habitats and shows a limited geographical range (60-70 km) exclusively inside the Bay of Antofagasta. Using cytochrome oxidase I (COI) mitochondrial sequence data from Pyura specimens of the three taxa we tested whether the Chilean taxon represents: (i) a Gondwana relict; (ii) a more recently divergent species; or (iii) a recently introduced species. The results suggest that the Chilean taxon is a recent introduction to Chile from Australian populations and that Pyura stolonifera praeputialis, from Australia, and the 'piure de Antofagasta' are geographical populations of a single species: Pyura praeputialis; whereas the South African taxon represents a second species: Pyura stolonifera.},
}
@article {pmid12150917,
year = {2002},
author = {Klingbeil, MM and Motyka, SA and Englund, PT},
title = {Multiple mitochondrial DNA polymerases in Trypanosoma brucei.},
journal = {Molecular cell},
volume = {10},
number = {1},
pages = {175-186},
doi = {10.1016/s1097-2765(02)00571-3},
pmid = {12150917},
issn = {1097-2765},
support = {5F32AI09789/AI/NIAID NIH HHS/United States ; GM27608/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; DNA, Kinetoplast ; DNA-Directed DNA Polymerase/chemistry/classification/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; RNA, Double-Stranded/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*enzymology/genetics ; },
abstract = {Kinetoplast DNA (kDNA), the unusual mitochondrial DNA of Trypanosoma brucei, is a network containing thousands of catenated circles. Database searching for a kDNA replicative polymerase (pol) revealed no mitochondrial pol gamma homolog. Instead, we identified four proteins (TbPOLIA, IB, IC, and ID) related to bacterial pol I. Remarkably, all four localized to the mitochondrion. TbPOLIB and TbPOLIC localized beside the kDNA where replication occurs, and their knockdown by RNA interference caused kDNA network shrinkage. Furthermore, silencing of TbPOLIC caused loss of both minicircles and maxicircles and accumulation of minicircle replication intermediates, consistent with a role in replication. While typical mitochondria contain one DNA polymerase, pol gamma, trypanosome mitochondria contain five such enzymes, including the previously characterized pol beta.},
}
@article {pmid12182806,
year = {2002},
author = {Teixeira, RD and Scheltinga, DM and Trauth, SE and Colli, GR and Báo, SN},
title = {A comparative ultrastructural study of spermatozoa of the teiid lizards Cnemidophorus gularis gularis, Cnemidophorus ocellifer, and Kentropyx altamazonica (Reptilia, Squamata, Teiidae).},
journal = {Tissue &amp; cell},
volume = {34},
number = {3},
pages = {135-142},
doi = {10.1016/s0040-8166(02)00021-6},
pmid = {12182806},
issn = {0040-8166},
mesh = {Animals ; Cell Size ; Lizards/*anatomy &amp; histology/genetics ; Male ; Microscopy, Electron ; *Phylogeny ; Spermatozoa/*ultrastructure ; },
abstract = {The ultrastructure of the spermatozoa of Cnemidophorus gularis gularis, Cnemidophorus ocellifer, and Kentropyx altamazonica is described for the first time. Mature spermatozoa of Cnemidophorus spp. and K. altamazonica differ in the occurrence of a perforatorial base plate, the enlargement of axonemal fibers 3 and 8, and shape of mitochondria. The comparisons of the ultrastructure sperm of Cnemidophorus spp. and K. altamazonica with Ameiva ameiva [J. Morphol. (2002) in press] suggest that Ameiva and Cnemidophorus are more similar to each other than either is to Kentropyx. Statistical analyses reveal that sperm of all three species studied are significantly different in the following dimensions: head, acrosome, distal centriole length, and nuclear shoulders width. There was no variable statistically different between the Cnemidophorus spp. only. The length of the tail, midpiece, entire sperm, and nuclear rostrum are significantly different between K. altamazonica and Cnemidophorus spp. Our results indicate that sperm ultrastructure presents intra and intergeneric variability.},
}
@article {pmid12191769,
year = {2002},
author = {Gakh, O and Cavadini, P and Isaya, G},
title = {Mitochondrial processing peptidases.},
journal = {Biochimica et biophysica acta},
volume = {1592},
number = {1},
pages = {63-77},
doi = {10.1016/s0167-4889(02)00265-3},
pmid = {12191769},
issn = {0006-3002},
support = {AG15709/AG/NIA NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Escherichia coli ; Humans ; Intracellular Membranes/*enzymology ; Metalloendopeptidases/chemistry/genetics/*metabolism ; Mitochondria/*enzymology ; Mitochondrial Proteins/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Precursors/*metabolism ; Saccharomyces cerevisiae ; Sequence Alignment ; Structure-Activity Relationship ; Substrate Specificity ; Mitochondrial Processing Peptidase ; },
abstract = {Three peptidases are responsible for the proteolytic processing of both nuclearly and mitochondrially encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. Mitochondrial processing peptidase (MPP) cleaves the vast majority of mitochondrial proteins, while inner membrane peptidase (IMP) and mitochondrial intermediate peptidase (MIP) process specific subsets of precursor polypeptides. All three enzymes are structurally and functionally conserved across species, and their human homologues begin to be recognized as potential players in mitochondrial disease.},
}
@article {pmid12200038,
year = {2002},
author = {Rose, G and Passarino, G and Franceschi, C and De Benedictis, G},
title = {The variability of the mitochondrial genome in human aging: a key for life and death?.},
journal = {The international journal of biochemistry &amp; cell biology},
volume = {34},
number = {11},
pages = {1449-1460},
doi = {10.1016/s1357-2725(02)00042-0},
pmid = {12200038},
issn = {1357-2725},
mesh = {Aging/*physiology ; Apoptosis/physiology ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; Humans ; Mitochondria/*genetics/metabolism ; Models, Biological ; Oxidative Phosphorylation ; Phylogeny ; },
abstract = {The impressive performance of the research in mitochondrial genetics and human aging in the last decade outlines a new scenery in which the inherited variation of the mitochondrial genome (mtDNA) may play a role in rate and quality of aging. This variation in humans was initially looked at as nearly neutral, and useful just for the reconstruction of human population history. However, recent data suggest that different mtDNA molecules are qualitatively different from each other. The aim of this paper is to discuss current ideas on the relationships among mitochondrial function, mtDNA inherited variation, and aging. The main processes where the mitochondrion is involved and the importance these processes have on aging and death of individuals will be described. A possible connection between programmed death phenomena (mitoptosis, apoptosis, phenoptosis) and rate and quality of aging will be discussed. Finally, the possible role played in these processes by the mtDNA germline variation will be explored.},
}
@article {pmid12207015,
year = {2002},
author = {Roje, S and Janave, MT and Ziemak, MJ and Hanson, AD},
title = {Cloning and characterization of mitochondrial 5-formyltetrahydrofolate cycloligase from higher plants.},
journal = {The Journal of biological chemistry},
volume = {277},
number = {45},
pages = {42748-42754},
doi = {10.1074/jbc.M205632200},
pmid = {12207015},
issn = {0021-9258},
mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/*enzymology ; Base Sequence ; Carbon-Nitrogen Ligases/*genetics/metabolism ; Cloning, Molecular ; DNA Primers ; DNA, Complementary/genetics ; Escherichia coli/enzymology/genetics ; Humans ; Solanum lycopersicum/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; },
abstract = {5-Formyltetrahydrofolate cycloligase (5-FCL) catalyzes the conversion of 5-formyltetrahydrofolate (5-CHO-H(4)PteGlu(n)) to 5,10-methenyltetrahydrofolate and is considered to be the main means whereby 5-CHO-H(4)PteGlu(n) is metabolized in mammals, yeast, and bacteria. 5-CHO-H(4)PteGlu(n) is known to occur in plants and to be highly abundant in leaf mitochondria. Genomics-based approaches identified Arabidopsis and tomato cDNAs encoding proteins homologous to 5-FCLs of other organisms but containing N-terminal extensions with the features of mitochondrial targeting peptides. These homologs were shown to have 5-FCL activity by characterizing recombinant enzymes produced in Escherichia coli and by functional complementation of a yeast fau1 mutation with the Arabidopsis 5-FCL cDNA. The recombinant Arabidopsis enzyme is active as a monomer, prefers the penta- to the monoglutamyl form of 5-CHO-H(4)PteGlu(n), and has kinetic properties broadly similar to those of 5-FCLs from other organisms. Enzyme assays and immunoblot analyses indicated that 5-FCL is located predominantly if not exclusively in plant mitochondria and that the mature, active enzyme lacks the putative targeting sequence. Serine hydroxymethyltransferase (SHMT) from plant mitochondria was shown to be inhibited by 5-CHO-H(4)PteGlu(n) as are SHMTs from other organisms. Since mitochondrial SHMT is crucial to photorespiration, 5-FCL may help prevent 5-CHO-H(4)PteGlu(n) from reaching levels that would inhibit this process. Consistent with this possibility, 5-FCL activity was far higher in leaf mitochondria than root mitochondria.},
}
@article {pmid12228005,
year = {2002},
author = {Savolainen, V and Chase, MW and Salamin, N and Soltis, DE and Soltis, PS and López, AJ and Fédrigo, O and Naylor, GJ},
title = {Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion.},
journal = {Systematic biology},
volume = {51},
number = {4},
pages = {638-647},
doi = {10.1080/10635150290102348},
pmid = {12228005},
issn = {1063-5157},
mesh = {Animals ; Codon ; *Genome ; Mitochondria/*genetics ; *Phylogeny ; Plants/genetics ; Plastids/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; },
}
@article {pmid12230538,
year = {2002},
author = {Martin, J and Guryev, V and Blinov, A},
title = {Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow.},
journal = {Insect molecular biology},
volume = {11},
number = {5},
pages = {387-397},
doi = {10.1046/j.1365-2583.2002.00348.x},
pmid = {12230538},
issn = {0962-1075},
mesh = {Animals ; Base Sequence ; Chironomidae/classification/enzymology/*genetics ; Cytochrome b Group/*genetics ; DNA, Complementary ; *DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Globins/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; },
abstract = {Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My.},
}
@article {pmid12233780,
year = {2000},
author = {Olson, MS and McCauley, DE},
title = {Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes in Silene vulgaris.},
journal = {Proceedings. Biological sciences},
volume = {267},
number = {1454},
pages = {1801-1808},
pmid = {12233780},
issn = {0962-8452},
mesh = {DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; *Linkage Disequilibrium ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Silene/*genetics/physiology ; },
abstract = {Both the chloroplast and mitochondrial genomes are used extensively in studies of plant population genetics and systematics. In the majority of angiosperms, the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) are each primarily transmitted maternally, but rare biparental transmission is possible. The extent to which the cpDNA and mtDNA are in linkage disequilibrium is argued to be dependent on the fidelity of co-transmission and the population structure. This study reports complete linkage disequilibrium between cpDNA and mtDNA haplotypes in 86 individuals from 17 populations of Silene vulgaris, a gynodioecious plant species. Phylogenetic analysis of cpDNA and mtDNA haplotypes within 14 individuals supports a hypothesis that the evolutionary histories of the chloroplasts and mitochondria are congruent within S. vulgaris, as might be expected if this association persists for long periods. This provides the first documentation of the evolutionary consequences of long-term associations between chloroplast and mitochondrial genomes within a species. Factors that contribute to the phylogenetic and linkage associations, as well as the potential for intergenomic hitchhiking resulting from selection on genes in one organellar genome are discussed.},
}
@article {pmid12244696,
year = {2002},
author = {Kuznetsova, MV and Kholodova, MV and Lushchekina, AA},
title = {[Phylogenetic analysis of sequences of the 12S and 16S rRNA mitochondrial genes in the family Bovidae: new evidence].},
journal = {Genetika},
volume = {38},
number = {8},
pages = {1115-1124},
pmid = {12244696},
issn = {0016-6758},
mesh = {Animals ; Mitochondria/genetics ; Models, Biological ; Molecular Sequence Data ; *Phylogeny ; *RNA, Ribosomal ; *RNA, Ribosomal, 16S ; Ruminants/classification/*genetics ; },
abstract = {The phylogeny of the family Bovidae has been inferred from our data on the 12S and 16S rRNA gene sequences and from the results of other authors. A considerable (2,460 bp) length of the analyzed fragments of these conserved genes and the use of different methods of cladogram construction allowed us to verify the systematic position of the genera Saiga, Pantholops, Procarpa, and Oreamnos. Saigas were shown to be phylogenetically far closer to gazelles than black-tailed gazelles and pygmy antelopes. In general, the genetic analysis data are in agreement with the results of morphological studies.},
}
@article {pmid12270262,
year = {2002},
author = {Garda, AA and Colli, GR and Aguiar-Júnior, O and Recco-Pimentel, SM and Báo, SN},
title = {The ultrastructure of the spermatozoa of Epipedobates flavopictus (Amphibia, Anura, Dendrobatidae), with comments on its evolutionary significance.},
journal = {Tissue &amp; cell},
volume = {34},
number = {5},
pages = {356-364},
doi = {10.1016/s0040816602000368},
pmid = {12270262},
issn = {0040-8166},
mesh = {Acrosome/physiology/ultrastructure ; Animals ; Anura/*anatomy &amp; histology/*classification/physiology ; Cell Nucleus/physiology/ultrastructure ; Centrioles/physiology/ultrastructure ; Fertilization/*physiology ; Flagella/physiology/ultrastructure ; Intracellular Membranes/physiology/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Spermatozoa/physiology/*ultrastructure ; Testis/physiology/*ultrastructure ; },
abstract = {We describe, for the first time, the spermatozoon ultrastructure of a dendrobatid frog, Epipedobates flavopictus. Mature spermatozoa of E. flavopictus are filiform, with a moderately curved head and a proportionally short tail. The acrosomal vesicle is a conical structure that covers the nucleus for a considerable distance. A homogeneous subacrosomal cone lies between the acrosome vesicle and the nucleus. The nucleus contains a nuclear space at its anterior end, and electron-lucent spaces and inclusions. No perforatorium is present. In the midpiece, the proximal centriole is housed inside a deep nuclear fossa. Mitochondria are scattered around the posterior end of the nucleus and inside the undulating membrane in the anterior portion of the tail. In transverse section the tail is formed by an U-shaped axial fiber connected to the axoneme through an axial sheath, which supports the undulating membrane. The juxta-axonemal fiber is absent. The spermatozoon of E. flavopictus has several characteristics not observed before in any anurans, such as a curved axial fiber, absence of a juxta-axonemal fiber, and presence of mitochondria in the typical undulating membrane. Our results endorse the view that, in anurans, the conical perforatorium and subacrosomal cone are homologous and that Dendrobatidae should be grouped within Bufonoidea rather than Ranoidea.},
}
@article {pmid12359132,
year = {2002},
author = {Nguyen, TV and Andresen, BS and Corydon, TJ and Ghisla, S and Abd-El Razik, N and Mohsen, AW and Cederbaum, SD and Roe, DS and Roe, CR and Lench, NJ and Vockley, J},
title = {Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans.},
journal = {Molecular genetics and metabolism},
volume = {77},
number = {1-2},
pages = {68-79},
doi = {10.1016/s1096-7192(02)00152-x},
pmid = {12359132},
issn = {1096-7192},
mesh = {Amino Acid Metabolism, Inborn Errors/enzymology/genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Base Sequence ; DNA, Complementary/genetics ; Escherichia coli/genetics ; Exons ; Humans ; In Vitro Techniques ; Introns ; Kinetics ; Models, Molecular ; Oxidoreductases/*deficiency/*genetics/metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phylogeny ; Point Mutation ; Protein Conformation ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Valine/metabolism ; },
abstract = {The acyl-CoA dehydrogenases (ACDs) are a family of related enzymes that catalyze the alpha,beta-dehydrogenation of acyl-CoA esters. Two homologues active in branched chain amino acid metabolism have previously been identified. We have used expression in Escherichia coli to produce a previously uncharacterized ACD-like sequence (ACAD8) and define its substrate specificity. Purified recombinant enzyme had a k(cat)/K(m) of 0.8, 0.23, and 0.04 (microM(-1)s(-1)) with isobutyryl-CoA, (S) 2-methylbutyryl-CoA, and n-propionyl-CoA, respectively, as substrates. Thus, this enzyme is an isobutyryl-CoA dehydrogenase. A single patient has previously been described whose fibroblasts exhibit a specific deficit in the oxidation of valine. Amplified ACAD8 cDNA made from patient fibroblast mRNA was homozygous for a single nucleotide change (905G>A) in the ACAD8 coding region compared to the sequence from control cells. This encodes an Arg302Gln substitution in the full-length protein (position 280 in the mature protein), a position predicted by molecular modeling to be important in subunit interactions. The mutant enzyme was stable but inactive when expressed in E. coli. It was also stable and appropriately targeted to mitochondria, but inactive when expressed in mammalian cells. These data confirm further the presence of a separated ACD in humans specific to valine catabolism (isobutyryl-CoA dehydrogenase, IBDH), along with the first enzymatic and molecular confirmation of a deficiency of this enzyme in a patient.},
}
@article {pmid12369098,
year = {2002},
author = {Catanesi, CI and Vidal-Rioja, L and Crisci, JV and Zambelli, A},
title = {Phylogenetic relationships among Robertsonian karyomorphs of Graomys griseoflavus (Rodentia, Muridae) by mitochondrial cytochrome b DNA sequencing.},
journal = {Hereditas},
volume = {136},
number = {2},
pages = {130-136},
doi = {10.1034/j.1601-5223.2002.1360207.x},
pmid = {12369098},
issn = {0018-0661},
mesh = {Animals ; Argentina ; Cytochrome b Group/*genetics ; *DNA, Mitochondrial ; Karyotyping ; Mitochondria/*genetics ; Muridae/classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; },
abstract = {Graomys griseoflavus (Waterhouse 1837) is a phyllotine murid rodent with a Robertsonian autosomal polymorphism, having been described 2n = 42, 41, 38, 37, 36, 35 and 34 karyomorphs, and proposed a chromosomal divergence pathway accounted by four sequential Robertsonian fusions. Sequences of a fragment (422 bp long) of the cytochrome b (cyt b) mitochondrial gene and its 5' flanking region (tRNA Glu) were obtained for 19 Graomys griseoflavus from different karyomorphs to infer phylogenetic relationships by using maximum parsimony. Outgroups considered for this analysis were the phyllotine rodents Phyllotis xanthopygus and Eligmodontia typus cyt b sequences. Three trees were produced showing the 2n = 38-34 karyomorphs grouped in a single clade while the 2n = 42-41 animals formed a different one. This is in agreement with a hypothesis of a single origin for 2n = 38-34 Robertsonian karyomorphs from the ancestral 2n = 42.},
}
@article {pmid12393015,
year = {2002},
author = {Rutherford, S and Moore, I},
title = {The Arabidopsis Rab GTPase family: another enigma variation.},
journal = {Current opinion in plant biology},
volume = {5},
number = {6},
pages = {518-528},
doi = {10.1016/s1369-5266(02)00307-2},
pmid = {12393015},
issn = {1369-5266},
mesh = {Arabidopsis/*enzymology/genetics ; Chloroplasts/metabolism ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Mitochondria/metabolism ; Multigene Family/*genetics/physiology ; Phylogeny ; rab GTP-Binding Proteins/*genetics/physiology ; },
abstract = {The Arabidopsis genome sequence reveals that gene families such as the Rab GTPase family, which encodes key determinants of vesicle-targeting specificity, are considerably more diverse in plants and mammals than in yeast. In mammals, this diversity appears to reflect the complexity of membrane trafficking. Phylogenetic analyses indicate that, despite its large size, the Arabidopsis Rab family lacks most of the Rab subclasses found in mammals. The Arabidopsis Rab family has, however, undergone a distinct 'adaptive radiation' that has given rise to proteins that may perform plant-specific functions.},
}
@article {pmid12399392,
year = {2002},
author = {Steinborn, R and Schinogl, P and Wells, DN and Bergthaler, A and Müller, M and Brem, G},
title = {Coexistence of Bos taurus and B. indicus mitochondrial DNAs in nuclear transfer-derived somatic cattle clones.},
journal = {Genetics},
volume = {162},
number = {2},
pages = {823-829},
pmid = {12399392},
issn = {0016-6731},
mesh = {Animals ; Cattle ; Cell Nucleus/*genetics ; *Cloning, Organism ; *DNA, Mitochondrial ; Gene Dosage ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; },
abstract = {We investigated the mitochondrial DNA (mtDNA) composition in one of the largest adult somatic mammalian clones (n = 20) reported so far. The healthy cloned cattle were derived from nuclear transfer of an identical nuclear genetic background (mural granulosa donor cells including surrounding cytoplasm) into enucleated oocytes with either Bos indicus or B. taurus mtDNA. Here we report the first cases of coexisting mtDNAs of two closely related subspecies following nuclear transfer. Heteroplasmy (0.6-2.8%) was found in 4 out of 11 cross-subspecies cloned cattle. Quantitation was performed using "amplification refractory mutation system (ARMS) allele-specific real-time PCR." We determined that the ratio of donor cell to recipient cytoplast mtDNA copy number was 0.9% before nuclear transfer. Therefore, we concluded that the percentage of donor cell mtDNA in the heteroplasmic intersubspecific cloned animals is in accordance with neutral transmission of donor mtDNA. We determined an amino acid sequence divergence of up to 1.3% for the two subspecies-specific mtDNA haplotypes. In addition, intrasubspecific B. indicus heteroplasmy of approximately 1% (but up to 7.3 and 12.7% in muscle and follicular cells of one animal) was detected in 7 out of the 9 B. indicus intrasubspecific cloned cattle.},
}
@article {pmid12399993,
year = {2002},
author = {Orth, A and Auffray, JC and Bonhomme, F},
title = {Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus.},
journal = {Heredity},
volume = {89},
number = {5},
pages = {353-357},
doi = {10.1038/sj.hdy.6800147},
pmid = {12399993},
issn = {0018-067X},
mesh = {Animals ; Animals, Wild ; Base Sequence ; Chromosomes/chemistry/*genetics ; DNA, Mitochondrial/*analysis ; *Genetic Variation ; Haplotypes ; Mediterranean Region ; Mice/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; },
abstract = {A survey of 77 individuals covering the range of Mus macedonicus from Georgia in the East to Greece and Bulgaria in the West and Israel in the South has shown the existence of two deeply divergent mitochondrial clades. The southern clade was until now undetected and characterises mice from Israel. Nuclear genes also show some amount of regional differentiation tending to separate the southern M. macedonicus from the northern ones. These results point towards the fact that the eastern Mediterranean short-tailed mouse, which was seen as a fairly homogeneous monotypic species, has in fact a more complex phylogeographic history than has been suspected, and that it warrants the existence of two subspecies. The reasons for this non-uniformity probably ought to be looked for in the history of faunal movements linked to glacial periods, underlining the possible existence of at least two refugia south of the Caucasus.},
}
@article {pmid12399995,
year = {2002},
author = {Klossa-Kilia, E and Prassa, M and Papasotiropoulos, V and Alahiotis, S and Kilias, G},
title = {Mitochondrial DNA diversity in Atherina boyeri populations as determined by RFLP analysis of three mtDNA segments.},
journal = {Heredity},
volume = {89},
number = {5},
pages = {363-370},
doi = {10.1038/sj.hdy.6800144},
pmid = {12399995},
issn = {0018-067X},
mesh = {Animals ; DNA, Mitochondrial/*genetics ; Fishes/*genetics ; *Genetic Variation ; Greece ; Haplotypes ; Mitochondria, Muscle/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Restriction Mapping ; },
abstract = {The genetic differentiation and the phylogenetic relationships of eight Atherina boyeri Greek populations have been investigated at the mtDNA level. The populations studied are from two different lakes, a lagoon, the interface zone between the lagoon and the sea, and four marine sites. RFLP analysis of three mtDNA segments (12s rRNA, 16s rRNA and D-loop) amplified by PCR was used. Six, seven and eight restriction enzymes were found to have at least one recognition site at 12s rRNA, 16s rRNA and D-loop respectively. Twenty-one different haplotypes were detected among the populations studied. Several restriction patterns were revealed. These patterns can be used for the discrimination of the populations living in the sea ('marine' type populations) from the others inhabiting the lagoon and the lakes ('lagoon' type populations). The estimated net nucleotide sequence divergence between the populations examined ranged from 0 to 10.385%, while the Nst value of 0.92 indicates the existence of high interpopulation genetic differentiation. This high degree of differentiation detected between the 'lagoon' and 'marine' type populations makes the classification of these two types of populations as a single taxon questionable.},
}
@article {pmid12403467,
year = {2002},
author = {Dai, L and Zimmerly, S},
title = {The dispersal of five group II introns among natural populations of Escherichia coli.},
journal = {RNA (New York, N.Y.)},
volume = {8},
number = {10},
pages = {1294-1307},
pmid = {12403467},
issn = {1355-8382},
mesh = {Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA Transposable Elements ; Escherichia coli/*genetics ; Genetics, Population ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry ; Retroelements ; Sequence Analysis, DNA ; },
abstract = {Group II introns are self-splicing RNAs that also act as retroelements in bacteria, mitochondria, and chloroplasts. Group II introns were identified in Escherichia coli in 1994, but have not been characterized since, and, instead, other bacterial group II introns have been studied for splicing and mobility properties. Despite their apparent intractability, at least five distinct group II introns exist naturally in E. coli strains. To illuminate their function and learn how the introns have dispersed in their natural host, we have investigated their distribution in the ECOR reference collection. Two introns were cloned and sequenced to complete their partial sequences. Unexpectedly, southern blots showed all ECOR strains to contain fragments and/or full-length copies of group II introns, with some strains containing up to 15 intron copies. One intron, E.c.14, has two natural homing sites in IS629 and IS911 elements, and the intron can be present in one, both, or neither homing site in a given strain. Nearly all strains that contain full-length introns also contain unfilled homing sites, suggesting either that mobility is highly inefficient or that most full-length copies are nonfunctional. The data indicate independent mobility of the introns, as well as mobility via the host DNA elements, and overall, the pattern of intron distribution resembles that of IS elements.},
}
@article {pmid12414306,
year = {2002},
author = {Braband, A and Richter, S and Hiesel, R and Scholtz, G},
title = {Phylogenetic relationships within the Phyllopoda (Crustacea, Branchiopoda) based on mitochondrial and nuclear markers.},
journal = {Molecular phylogenetics and evolution},
volume = {25},
number = {2},
pages = {229-244},
doi = {10.1016/s1055-7903(02)00253-1},
pmid = {12414306},
issn = {1055-7903},
mesh = {Animals ; Cell Nucleus/*genetics ; Crustacea/*genetics ; DNA, Ribosomal ; Genetic Markers ; Likelihood Functions ; Mitochondria/*genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; },
abstract = {For several decades the relationships within the Branchiopoda (Anostraca + Phyllopoda) have been a matter of controversy. Interpretations of plesiomorphic or apomorphic character states are a difficult venture, in particular in the Phyllopoda. We explore the relationships within the Phyllopoda at the level of nucleotid comparisons of the two genes 12S rDNA (mitochondrial) and EF1alpha (nuclear), and at a higher molecular level based on introns found in the gene EF1alpha. Within the Phyllopoda our explorations show further evidence for a non-monophyletic Conchostraca (Spinicaudata + Cyclestherida + Laevicaudata). The monotypic Cyclestherida is more closely related to the Cladocera, both together forming the Cladoceromorpha. The Spinicaudata (Leptestheriidae, Limnadiidae, and Cyzicidae) is well supported. Spinicaudata and Cladoceromorpha form a monophylum. The position of the Laevicaudata remains unclear but we find neither support for a sister group relationship to the Spinicaudata nor for a close relationship of Laevicaudata and Cladocera. Within the Cladocera, we favour the Gymnomera concept with the monotypic Haplopoda being the sister group to the monophyletic Onychopoda. The Ctenopoda seems to be the sister group to the Gymnomera, which contradicts the common view of a more basal position of the Ctenopoda.},
}
@article {pmid12414316,
year = {2002},
author = {Wilcox, TP and Zwickl, DJ and Heath, TA and Hillis, DM},
title = {Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.},
journal = {Molecular phylogenetics and evolution},
volume = {25},
number = {2},
pages = {361-371},
doi = {10.1016/s1055-7903(02)00244-0},
pmid = {12414316},
issn = {1055-7903},
mesh = {Animals ; Bayes Theorem ; Boidae/*genetics ; Data Interpretation, Statistical ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxoc