@article {pmid17233593,
year = {2007},
author = {Michell, RH},
title = {Evolution of the diverse biological roles of inositols.},
journal = {Biochemical Society symposium},
volume = {},
number = {74},
pages = {223-246},
doi = {10.1042/BSS0740223},
pmid = {17233593},
issn = {0067-8694},
mesh = {*Biological Evolution ; Models, Biological ; Phosphatidylinositols/chemistry/*metabolism ; },
abstract = {Several of the nine hexahydroxycylohexanes (inositols) have functions in Biology, with myo-inositol (Ins) in most of the starring roles; and Ins polyphosphates are amongst the most abundant organic phosphate constituents on Earth. Many Archaea make Ins and use it as a component of diphytanyl membrane phospholipids and the thermoprotective solute di-L-Ins-1,1'-phosphate. Few bacteria make Ins or use it, other than as a carbon source. Those that do include hyperthermophilic Thermotogales (which also employ di-L-Ins-1,1'-phosphate) and actinomycetes such as Mycobacterium spp. (which use mycothiol, an inositol-containing thiol, as an intracellular redox reagent and have characteristic phosphatidylinositol-linked surface oligosaccharides). Bacteria acquired their Ins3P synthases by lateral gene transfer from Archaea. Many eukaryotes, including stressed plants, insects, deep-sea animals and kidney tubule cells, adapt to environmental variation by making or accumulating diverse inositol derivatives as 'compatible' solutes. Eukaryotes use phosphatidylinositol derivatives for numerous roles in cell signalling and regulation and in protein anchoring at the cell surface. Remarkably, the diradylglycerol cores of archaeal and eukaryote/bacterial glycerophospholipids have mirror image configurations: sn-2,3 and sn-1,2 respectively. Multicellular animals and amoebozoans exhibit the greatest variety of functions for PtdIns derivatives, including the use of PtdIns(3,4,5)P3 as a signal. Evolutionarily, it seems likely that (i) early archaeons first made myo-inositol approx. 3500 Ma (million years) ago; (ii) archeons brought inositol derivatives into early eukaryotes (approx. 2000 Ma?); (iii) soon thereafter, eukaryotes established ubiquitous functions for phosphoinositides in membrane trafficking and Ins polyphosphate synthesis; and (iv) since approx. 1000 Ma, further waves of functional diversification in amoebozoans and metazoans have introduced Ins(1,4,5)P3 receptor Ca2+ channels and the messenger role of PtdIns(3,4,5)P3.},
}

*Biological Evolution
Models, Biological
Phosphatidylinositols/chemistry/*metabolism

@article {pmid17275131,
year = {2007},
author = {Ma, J and Wing, RA and Bennetzen, JL and Jackson, SA},
title = {Plant centromere organization: a dynamic structure with conserved functions.},
journal = {Trends in genetics : TIG},
volume = {23},
number = {3},
pages = {134-139},
doi = {10.1016/j.tig.2007.01.004},
pmid = {17275131},
issn = {0168-9525},
mesh = {Centromere/*chemistry/metabolism ; Chromatin/chemistry ; Chromosomes, Plant/*chemistry/metabolism ; DNA, Plant/metabolism ; DNA, Satellite/metabolism ; Epigenesis, Genetic ; *Evolution, Molecular ; Gene Rearrangement ; Models, Genetic ; Oryza/genetics ; Plants/*genetics ; *Recombination, Genetic ; },
abstract = {Although the structural features of centromeres from most multicellular eukaryotes remain to be characterized, recent analyses of the complete sequences of two centromeric regions of rice, together with data from Arabidopsis thaliana and maize, have illuminated the considerable size variation and sequence divergence of plant centromeres. Despite the severe suppression of meiotic chromosomal exchange in centromeric and pericentromeric regions of rice, the centromere core shows high rates of unequal homologous recombination in the absence of chromosomal exchange, resulting in frequent and extensive DNA rearrangement. Not only is the sequence of centromeric tandem and non-tandem repeats highly variable but also the copy number, spacing, order and orientation, providing ample natural variation as the basis for selection of superior centromere performance. This review article focuses on the structural and evolutionary dynamics of plant centromere organization and the potential molecular mechanisms responsible for the rapid changes of centromeric components.},
}

Centromere/*chemistry/metabolism
Chromatin/chemistry
Chromosomes, Plant/*chemistry/metabolism
DNA, Plant/metabolism
DNA, Satellite/metabolism
Epigenesis, Genetic
*Evolution, Molecular
Gene Rearrangement
Models, Genetic
Oryza/genetics
Plants/*genetics
*Recombination, Genetic

@article {pmid17275133,
year = {2007},
author = {Ruiz-Trillo, I and Burger, G and Holland, PW and King, N and Lang, BF and Roger, AJ and Gray, MW},
title = {The origins of multicellularity: a multi-taxon genome initiative.},
journal = {Trends in genetics : TIG},
volume = {23},
number = {3},
pages = {113-118},
doi = {10.1016/j.tig.2007.01.005},
pmid = {17275133},
issn = {0168-9525},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Classification ; *Evolution, Molecular ; Fungi/classification/genetics ; Genome ; *Genome, Fungal ; *Genomics ; Models, Genetic ; *Phylogeny ; Selection, Genetic ; },
abstract = {The emergence of multicellular organisms from single-celled ancestors -- which occurred several times, independently in different branches of the eukaryotic tree -- is one of the most profound evolutionary transitions in the history of life. These events not only radically changed the course of life on Earth but also created new challenges, including the need for cooperation and communication between cells, and the division of labor among different cell types. However, the genetic changes that accompanied the several origins of multicellularity remain elusive. Recently, the National Human Genome Research Institute (NHGRI) endorsed a multi-taxon genome-sequencing initiative that aims to gain insights into how multicellularity first evolved. This initiative (which we have termed UNICORN) will generate extensive genomic data from some of the closest extant unicellular relatives of both animals and fungi. Here, we introduce this initiative and the biological questions that underpin it, summarize the rationale guiding the choice of organisms and discuss the anticipated benefits to the broader scientific community.},
}

Animals
Classification
*Evolution, Molecular
Fungi/classification/genetics
Genome
*Genome, Fungal
*Genomics
Models, Genetic
*Phylogeny
Selection, Genetic

@article {pmid17295128,
year = {2007},
author = {Yan, H and Jiang, J},
title = {Rice as a model for centromere and heterochromatin research.},
journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology},
volume = {15},
number = {1},
pages = {77-84},
pmid = {17295128},
issn = {0967-3849},
mesh = {Centromere/*genetics ; Epigenesis, Genetic ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Heterochromatin/*metabolism/ultrastructure ; Histones/metabolism ; *Models, Genetic ; Oryza/*genetics/metabolism ; Transcription, Genetic ; },
abstract = {Rice (Oryza sativa) has become an important model plant species in numerous research projects involving genome, molecular and evolutionary biology. In this review we describe the reasons why rice provides an excellent model system for centromere and heterochromatin research. In most multicellular eukaryotes, centromeres and heterochromatic domains contain long arrays of repetitive DNA elements that are recalcitrant to DNA sequencing. In contrast, three rice centromeres and the majority of the cytologically defined heterochromatin in the rice genome have been sequenced to high quality, providing an unparalleled resource compared to other model multicellular eukaryotes. Most importantly, active genes have been discovered in the functional domains of several rice centromeres. The centromeric genes and sequence resources provide an unprecedented opportunity to study function and evolution of centromeres and centromere-associated genes.},
}

Centromere/*genetics
Epigenesis, Genetic
Evolution, Molecular
*Gene Expression Regulation, Plant
Heterochromatin/*metabolism/ultrastructure
Histones/metabolism
*Models, Genetic
Oryza/*genetics/metabolism
Transcription, Genetic

@article {pmid17296731,
year = {2007},
author = {Sakwe, AM and Nguyen, T and Athanasopoulos, V and Shire, K and Frappier, L},
title = {Identification and characterization of a novel component of the human minichromosome maintenance complex.},
journal = {Molecular and cellular biology},
volume = {27},
number = {8},
pages = {3044-3055},
pmid = {17296731},
issn = {0270-7306},
support = {84306/CAPMC/CIHR/Canada ; },
mesh = {Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Cycle Proteins/genetics/metabolism ; Chromatin/metabolism ; DNA Helicases/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Down-Regulation/genetics ; G1 Phase ; Gene Silencing ; HeLa Cells ; Humans ; Immunoprecipitation ; Minichromosome Maintenance Complex Component 4 ; Minichromosome Maintenance Complex Component 6 ; Minichromosome Maintenance Complex Component 7 ; Molecular Sequence Data ; Multiprotein Complexes/*chemistry/*metabolism ; Nuclear Proteins/chemistry/genetics/*metabolism ; Protein Binding ; Protein Transport ; Recombinant Proteins/metabolism ; Replication Origin ; Sequence Analysis, Protein ; },
abstract = {Minichromosome maintenance (MCM) complex replicative helicase complexes play essential roles in DNA replication in all eukaryotes. Using a tandem affinity purification-tagging approach in human cells, we discovered a form of the MCM complex that contains a previously unstudied protein, MCM binding protein (MCM-BP). MCM-BP is conserved in multicellular eukaryotes and shares limited homology with MCM proteins. MCM-BP formed a complex with MCM3 to MCM7, which excluded MCM2; and, conversely, hexameric complexes of MCM2 to MCM7 lacked MCM-BP, indicating that MCM-BP can replace MCM2 in the MCM complex. MCM-BP-containing complexes exhibited increased stability under experimental conditions relative to those containing MCM2. MCM-BP also formed a complex with the MCM4/6/7 core helicase in vitro, but, unlike MCM2, did not inhibit this helicase activity. A proportion of MCM-BP bound to cellular chromatin in a cell cycle-dependent manner typical of MCM proteins, and, like other MCM subunits, preferentially associated with a cellular origin in G(1) but not in S phase. In addition, down-regulation of MCM-BP decreased the association of MCM4 with chromatin, and the chromatin association of MCM-BP was at least partially dependent on MCM4 and cdc6. The results indicate that multicellular eukaryotes contain two types of hexameric MCM complexes with unique properties and functions.},
}

Adaptor Proteins, Signal Transducing
Amino Acid Sequence
Carrier Proteins/chemistry/genetics/*metabolism
Cell Cycle Proteins/genetics/metabolism
Chromatin/metabolism
DNA Helicases/metabolism
DNA-Binding Proteins/genetics/metabolism
Down-Regulation/genetics
G1 Phase
Gene Silencing
HeLa Cells
Humans
Immunoprecipitation
Minichromosome Maintenance Complex Component 4
Minichromosome Maintenance Complex Component 6
Minichromosome Maintenance Complex Component 7
Molecular Sequence Data
Multiprotein Complexes/*chemistry/*metabolism
Nuclear Proteins/chemistry/genetics/*metabolism
Protein Binding
Protein Transport
Recombinant Proteins/metabolism
Replication Origin
Sequence Analysis, Protein

@article {pmid17299594,
year = {2007},
author = {Janhunen, P and Kaartokallio, H and Oksanen, I and Lehto, K and Lehto, H},
title = {Biological feedbacks as cause and demise of the Neoproterozoic icehouse: astrobiological prospects for faster evolution and importance of cold conditions.},
journal = {PloS one},
volume = {2},
number = {2},
pages = {e214},
pmid = {17299594},
issn = {1932-6203},
mesh = {Biodiversity ; Carbon Dioxide/chemistry/metabolism ; Carbon Isotopes/*analysis ; *Cold Climate ; *Earth, Planet ; Eukaryota/growth & development/metabolism/*physiology ; *Evolution, Planetary ; Exobiology ; *Feedback, Physiological ; Greenhouse Effect ; *Ice Cover ; Marine Biology ; Origin of Life ; Oxygen/chemistry/metabolism ; Photosynthesis ; Phytoplankton/*physiology ; Seawater/chemistry ; Solar System ; Solubility ; },
abstract = {Several severe glaciations occurred during the Neoproterozoic eon, and especially near its end in the Cryogenian period (630-850 Ma). While the glacial periods themselves were probably related to the continental positions being appropriate for glaciation, the general coldness of the Neoproterozoic and Cryogenian as a whole lacks specific explanation. The Cryogenian was immediately followed by the Ediacaran biota and Cambrian Metazoan, thus understanding the climate-biosphere interactions around the Cryogenian period is central to understanding the development of complex multicellular life in general. Here we present a feedback mechanism between growth of eukaryotic algal phytoplankton and climate which explains how the Earth system gradually entered the Cryogenian icehouse from the warm Mesoproterozoic greenhouse. The more abrupt termination of the Cryogenian is explained by the increase in gaseous carbon release caused by the more complex planktonic and benthic foodwebs and enhanced by a diversification of metazoan zooplankton and benthic animals. The increased ecosystem complexity caused a decrease in organic carbon burial rate, breaking the algal-climatic feedback loop of the earlier Neoproterozoic eon. Prior to the Neoproterozoic eon, eukaryotic evolution took place in a slow timescale regulated by interior cooling of the Earth and solar brightening. Evolution could have proceeded faster had these geophysical processes been faster. Thus, complex life could theoretically also be found around stars that are more massive than the Sun and have main sequence life shorter than 10 Ga. We also suggest that snow and glaciers are, in a statistical sense, important markers for conditions that may possibly promote the development of complex life on extrasolar planets.},
}

Biodiversity
Carbon Dioxide/chemistry/metabolism
Carbon Isotopes/*analysis
*Cold Climate
*Earth, Planet
Eukaryota/growth & development/metabolism/*physiology
*Evolution, Planetary
Exobiology
*Feedback, Physiological
Greenhouse Effect
*Ice Cover
Marine Biology
Origin of Life
Oxygen/chemistry/metabolism
Photosynthesis
Phytoplankton/*physiology
Seawater/chemistry
Solar System
Solubility

@article {pmid17313526,
year = {2007},
author = {Kooijman, SA and Troost, TA},
title = {Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {82},
number = {1},
pages = {113-142},
doi = {10.1111/j.1469-185X.2006.00006.x},
pmid = {17313526},
issn = {1464-7931},
mesh = {Animals ; *Biological Evolution ; Biomass ; Body Temperature Regulation ; *Cell Physiological Phenomena ; Energy Metabolism/*physiology ; Homeostasis/physiology ; Humans ; Kinetics ; *Models, Biological ; Thermodynamics ; },
abstract = {The Dynamic Energy Budget (DEB) theory quantifies the metabolic organisation of organisms on the basis of mechanistically inspired assumptions. We here sketch a scenario for how its various modules, such as maintenance, storage dynamics, development, differentiation and life stages could have evolved since the beginning of life. We argue that the combination of homeostasis and maintenance induced the development of reserves and that subsequent increases in the maintenance costs came with increases of the reserve capacity. Life evolved from a multiple reserves - single structure system (prokaryotes, many protoctists) to systems with multiple reserves and two structures (plants) or single reserve and single structure (animals). This had profound consequences for the possible effects of temperature on rates. We present an alternative explanation for what became known as the down-regulation of maintenance at high growth rates in microorganisms; the density of the limiting reserve increases with the growth rate, and reserves do not require maintenance while structure-specific maintenance costs are independent of the growth rate. This is also the mechanism behind the variation of the respiration rate with body size among species. The DEB theory specifies reserve dynamics on the basis of the requirements of weak homeostasis and partitionability. We here present a new and simple mechanism for this dynamics which accounts for the rejection of mobilised reserve by busy maintenance/growth machinery. This module, like quite a few other modules of DEB theory, uses the theory of Synthesising Units; we review recent progress in this field. The plasticity of membranes that evolved in early eukaryotes is a major step forward in metabolic evolution; we discuss quantitative aspects of the efficiency of phagocytosis relative to the excretion of digestive enzymes to illustrate its importance. Some processes of adaptation and gene expression can be understood in terms of allocation linked to the relative workload of metabolic modules in (unicellular) prokaryotes and organs in (multicellular) eukaryotes. We argue that the evolution of demand systems can only be understood in the light of that of supply systems. We illustrate some important points with data from the literature.},
}

Animals
*Biological Evolution
Biomass
Body Temperature Regulation
*Cell Physiological Phenomena
Energy Metabolism/*physiology
Homeostasis/physiology
Humans
Kinetics
*Models, Biological
Thermodynamics

@article {pmid17367545,
year = {2007},
author = {Eisenhaber, B and Chumak, N and Eisenhaber, F and Hauser, MT},
title = {The ring between ring fingers (RBR) protein family.},
journal = {Genome biology},
volume = {8},
number = {3},
pages = {209},
pmid = {17367545},
issn = {1474-760X},
support = {P 17888/FWF_/Austrian Science Fund FWF/Austria ; },
mesh = {Amino Acid Motifs ; Evolution, Molecular ; Gene Expression Regulation ; *Proteins/chemistry/genetics/metabolism/physiology ; Tissue Distribution ; *Zinc Fingers ; },
abstract = {Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the amino-terminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The three-dimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni- and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation.},
}

Amino Acid Motifs
Evolution, Molecular
Gene Expression Regulation
*Proteins/chemistry/genetics/metabolism/physiology
Tissue Distribution
*Zinc Fingers

@article {pmid17369437,
year = {2007},
author = {Sanderfoot, A},
title = {Increases in the number of SNARE genes parallels the rise of multicellularity among the green plants.},
journal = {Plant physiology},
volume = {144},
number = {1},
pages = {6-17},
pmid = {17369437},
issn = {0032-0889},
mesh = {Cluster Analysis ; *Evolution, Molecular ; Expressed Sequence Tags ; Gene Duplication ; *Genome, Plant ; Multigene Family ; Phylogeny ; Plant Cells ; Plants/*genetics ; SNARE Proteins/chemistry/*genetics/physiology ; Vacuoles/genetics ; },
abstract = {The green plant lineage is the second major multicellular expansion among the eukaryotes, arising from unicellular ancestors to produce the incredible diversity of morphologies and habitats observed today. In the unicellular ancestors, secretion of material through the endomembrane system was the major mechanism for interacting and shaping the external environment. In a multicellular organism, the external environment can be made of other cells, some of which may have vastly different developmental fates, or be part of different tissues or organs. In this context, a given cell must find ways to organize its secretory pathway at a level beyond that of the unicellular ancestor. Recently, sequence information from many green plants have become available, allowing an examination of the genomes for the machinery involved in the secretory pathway. In this work, the SNARE proteins of several green plants have been identified. While little increase in gene number was seen in the SNAREs of the early secretory system, many new SNARE genes and gene families have appeared in the multicellular green plants with respect to the unicellular plants, suggesting that this increase in the number of SNARE genes may have some relation to the rise of multicellularity in green plants.},
}

Cluster Analysis
*Evolution, Molecular
Expressed Sequence Tags
Gene Duplication
*Genome, Plant
Multigene Family
Phylogeny
Plant Cells
Plants/*genetics
SNARE Proteins/chemistry/*genetics/physiology
Vacuoles/genetics

@article {pmid17390287,
year = {2007},
author = {Doolen, JF and Geddes, GC and Blackstone, NW},
title = {Multicellular redox regulation in an early-evolving animal treated with glutathione.},
journal = {Physiological and biochemical zoology : PBZ},
volume = {80},
number = {3},
pages = {317-325},
doi = {10.1086/512587},
pmid = {17390287},
issn = {1522-2152},
mesh = {Animals ; Biological Evolution ; Glutathione/*pharmacology ; Oxidation-Reduction/drug effects ; Reactive Oxygen Species/metabolism ; Scyphozoa/*drug effects/*physiology ; },
abstract = {Redox signaling has emerged as a unifying theme in many seemingly disparate disciplines. Such signaling has been widely studied in bacteria and eukaryotic organelles and is often mediated by reactive oxygen species (ROS). In this context, reduced glutathione (GSH) acts as an important intracellular antioxidant, diminishing ROS and potentially affecting redox signaling. Complementing this cell-level perspective, colonial hydroids can be a useful model for understanding organism-level redox signaling. These simple, early-evolving animals consist of feeding polyps connected by tubelike stolons. Colonies treated exogenously with GSH or reduced glutathione ethyl ester (GEE) were expected to show a morphological change to sheetlike growth typical of low levels of ROS. Contrary to expectations, diminished stolon branching and polyp initiation was observed. Such runnerlike growth is associated with higher levels of ROS, and surprisingly, such higher levels were found in GSH- and GEE-treated colonies. Further investigations show that GSH triggered a feeding response in hydroid polyps, increasing oxygen uptake but at the same time relaxing mitochondrion-rich contractile regions at the base of polyps. Diminished gastrovascular flow and increased emissions of mitochondrial ROS also correlated with the observed runnerlike growth. In contrast to cell-level, "bottom-up" views of redox signaling, here the phenotype may arise from a "top-down" interaction of mitochondrion-rich regions and organism-level physiology. Such multicellular redox regulation may commonly occur in other animals as well.},
}

Animals
Biological Evolution
Glutathione/*pharmacology
Oxidation-Reduction/drug effects
Reactive Oxygen Species/metabolism
Scyphozoa/*drug effects/*physiology

@article {pmid17400358,
year = {2007},
author = {Bedard, K and Lardy, B and Krause, KH},
title = {NOX family NADPH oxidases: not just in mammals.},
journal = {Biochimie},
volume = {89},
number = {9},
pages = {1107-1112},
doi = {10.1016/j.biochi.2007.01.012},
pmid = {17400358},
issn = {0300-9084},
mesh = {Animals ; Evolution, Molecular ; Fungi/enzymology/genetics ; Mammals/genetics/*metabolism ; Models, Biological ; NADPH Oxidases/genetics/*metabolism ; Phylogeny ; Plants/enzymology/genetics ; Reactive Oxygen Species/metabolism ; },
abstract = {NOX family NADPH oxidases are enzymes whose biological function is electron transport and the generation of reactive oxygen species (ROS). NOX enzymes in mammalian organisms have received most attention. However, NOX enzymes are widely distributed in different kingdoms of life. While they are not found in prokaryotes and most unicellular eukaryotes, they are present in fungi, plants, and animals. The identity of the ancestral NOX is not known, but most likely it: (i) possessed the basic NOX structure consisting of 6 transmembrane domains (containing two assymmetrical hemes) and a long cytoplasmic C-terminal (containing the FAD and NADPH binding sites); and (ii) emerged before the divergence of life into fungi, plants, and animals. During evolution, acquisition of a Ca(2+)-binding EF hand domain by an ancestral NOX, led to NOX5-like isoforms. DUOX isoforms presumably developed from a NOX5-like isoform through the additional acquisition of a peroxidase homology domain. The expression pattern of NOX enzymes is specific to each kingdom of life. Fungi express only ancestral-type isoforms, and plants only NOX5-like isoforms. NOX expression patterns in animals are complex and ancestral NOXes, NOX5-like isoforms and DUOXes are generally found. But there are exceptions; for example rodents lack NOX5 and Caenorhabditis elegans expresses only DUOXes. Biological functions of NOX enzymes include, among others, host defense, post-translational modification of proteins, and regulation cell growth and differentiation. In summary, the invention of NOX enzymes early in the development of life was a success story: there is no evidence of multicellular life without NOX enzymes.},
}

Animals
Evolution, Molecular
Fungi/enzymology/genetics
Mammals/genetics/*metabolism
Models, Biological
NADPH Oxidases/genetics/*metabolism
Phylogeny
Plants/enzymology/genetics
Reactive Oxygen Species/metabolism

@article {pmid17442504,
year = {2007},
author = {Chen, CC and Li, WH and Sung, HM},
title = {Patterns of internal gene duplication in the course of metazoan evolution.},
journal = {Gene},
volume = {396},
number = {1},
pages = {59-65},
doi = {10.1016/j.gene.2007.02.021},
pmid = {17442504},
issn = {0378-1119},
support = {GM 30998/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Caenorhabditis elegans ; Carrier Proteins/chemistry ; Drosophila melanogaster ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; *Gene Duplication ; Genome ; Humans ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Software ; Transcription Factors/chemistry ; },
abstract = {Internal duplication can enhance the function of a gene or provide raw material for the emergence of a new function in a gene. Therefore, it is interesting to see whether the frequency of internal duplication has increased during metazoan evolution. The growing number of sequenced eukaryotic genomes provides an excellent opportunity to study the change in the pattern of internal duplication in the course of metazoan evolution. We studied repeated segments in proteins in the proteomes of 11 eukaryotes. We found that the frequency of internal duplication in Caenorhabditis elegans and Drosophila melanogaster (two protostomes) is higher than that in fungi but lower than that in chordates. Moreover, the frequencies of internal duplication for the chordates studied are largely similar. We classified orthologous proteins of chordates into three antiquity groups and found that more recently derived proteins in the metazoan lineage have higher repetitiveness than older ones. Our analysis suggests that lineage-specific internal duplication in protein evolution increases with organismal complexity before the emergence of chordates but not so afterward. Proteins with repeated regions might have been preferred before the protostome-chordate split. This finding supports the suggestion that exon-shuffling occurred more frequently after the first multicellular organism appeared and might have contributed to the metazoan radiation.},
}

Animals
Caenorhabditis elegans
Carrier Proteins/chemistry
Drosophila melanogaster
Eukaryotic Cells/*metabolism
*Evolution, Molecular
*Gene Duplication
Genome
Humans
Protein Structure, Tertiary
Repetitive Sequences, Amino Acid
Software
Transcription Factors/chemistry

@article {pmid17494762,
year = {2007},
author = {Moran, NA},
title = {Symbiosis as an adaptive process and source of phenotypic complexity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {104 Suppl 1},
number = {Suppl 1},
pages = {8627-8633},
pmid = {17494762},
issn = {0027-8424},
mesh = {Adaptation, Biological/*physiology ; Animals ; Bacteria/genetics/virology ; Bacteriophages/genetics/physiology ; Biological Evolution ; Eukaryotic Cells/physiology ; Gene Transfer, Horizontal ; Genetic Vectors ; Genome/genetics ; Insecta/genetics/physiology ; *Phenotype ; Symbiosis/genetics/*physiology ; },
abstract = {Genomics has revealed that inheritance systems of separate species are often not well segregated: genes and capabilities that evolve in one lineage are often stably acquired by another lineage. Although direct gene transfer between species has occurred at some level in all major groups, it appears to be far more frequent in prokaryotes than in multicellular eukaryotes. An alternative to incorporating novel genes into a recipient genome is acquiring a stable, possibly heritable, symbiotic association and thus enjoying benefits of complementary metabolic capabilities. These kinds of symbioses have arisen frequently in animals; for example, many insect groups have diversified on the basis of symbiotic associations acquired early in their evolutionary histories. The resulting associations are highly complex, often involving specialized cell types and organs, developmental mechanisms that ensure transfer of symbionts between generations, and mechanisms for controlling symbiont proliferation and location. The genomes of long-term obligate symbionts often undergo irreversible gene loss and deterioration even as hosts evolve dependence on them. In some cases, animal genomes may have acquired genes from symbionts, mirroring the gene uptake from mitochondrial and plastid genomes. Multiple symbionts often coexist in the same host, resulting in coadaptation among several phylogenetically distant genomes.},
}

Adaptation, Biological/*physiology
Animals
Bacteria/genetics/virology
Bacteriophages/genetics/physiology
Biological Evolution
Eukaryotic Cells/physiology
Gene Transfer, Horizontal
Genetic Vectors
Genome/genetics
Insecta/genetics/physiology
*Phenotype
Symbiosis/genetics/*physiology

@article {pmid17495008,
year = {2007},
author = {Carmel, L and Wolf, YI and Rogozin, IB and Koonin, EV},
title = {Three distinct modes of intron dynamics in the evolution of eukaryotes.},
journal = {Genome research},
volume = {17},
number = {7},
pages = {1034-1044},
pmid = {17495008},
issn = {1088-9051},
mesh = {Algorithms ; Animals ; Decision Trees ; *Evolution, Molecular ; Introns/*genetics ; *Models, Genetic ; Multigene Family ; Probability ; Time ; },
abstract = {Several contrasting scenarios have been proposed for the origin and evolution of spliceosomal introns, a hallmark of eukaryotic genes. A comprehensive probabilistic model to obtain a definitive reconstruction of intron evolution was developed and applied to 391 sets of conserved genes from 19 eukaryotic species. It is inferred that a relatively high intron density was reached early, i.e., the last common ancestor of eukaryotes contained >2.15 introns/kilobase, and the last common ancestor of multicellular life forms harbored approximately 3.4 introns/kilobase, a greater intron density than in most of the extant fungi and in some animals. The rates of intron gain and intron loss appear to have been dropping during the last approximately 1.3 billion years, with the decline in the gain rate being much steeper. Eukaryotic lineages exhibit three distinct modes of evolution of the intron-exon structure. The primary, balanced mode, apparently, operates in all lineages. In this mode, intron gain and loss are strongly and positively correlated, in contrast to previous reports on inverse correlation between these processes. The second mode involves an elevated rate of intron loss and is prevalent in several lineages, such as fungi and insects. The third mode, characterized by elevated rate of intron gain, is seen only in deep branches of the tree, indicating that bursts of intron invasion occurred at key points in eukaryotic evolution, such as the origin of animals. Intron dynamics could depend on multiple mechanisms, and in the balanced mode, gain and loss of introns might share common mechanistic features.},
}

Algorithms
Animals
Decision Trees
*Evolution, Molecular
Introns/*genetics
*Models, Genetic
Multigene Family
Probability
Time

@article {pmid17501745,
year = {2007},
author = {Derelle, R and Lopez, P and Le Guyader, H and Manuel, M},
title = {Homeodomain proteins belong to the ancestral molecular toolkit of eukaryotes.},
journal = {Evolution & development},
volume = {9},
number = {3},
pages = {212-219},
doi = {10.1111/j.1525-142X.2007.00153.x},
pmid = {17501745},
issn = {1520-541X},
mesh = {Animals ; Eukaryota/physiology ; *Evolution, Molecular ; Fungi/physiology ; Homeodomain Proteins/*metabolism ; Plants/metabolism ; },
abstract = {Multicellular organization arose several times by convergence during the evolution of eukaryotes (e.g., in terrestrial plants, several lineages of "algae," fungi, and metazoans). To reconstruct the evolutionary transitions between unicellularity and multicellularity, we need a proper understanding of the origin and diversification of regulatory molecules governing the construction of a multicellular organism in these various lineages. Homeodomain (HD) proteins offer a paradigm for studying such issues, because in multicellular eukaryotes, like animals, fungi and plants, these transcription factors are extensively used in fundamental developmental processes and are highly diversified. A number of large eukaryote lineages are exclusively unicellular, however, and it remains unclear to what extent this condition reflects their primitive lack of "good building blocks" such as the HD proteins. Taking advantage from the recent burst of sequence data from a wide variety of eukaryote taxa, we show here that HD-containing transcription factors were already existing and diversified (in at least two main classes) in the last common eukaryote ancestor. Although the family was retained and independently expanded in the multicellular taxa, it was lost in several lineages of unicellular parasites or intracellular symbionts. Our findings are consistent with the idea that the common ancestor of eukaryotes was complex in molecular terms, and already possessed many of the regulatory molecules, which later favored the multiple convergent acquisition of multicellularity.},
}

Animals
Eukaryota/physiology
*Evolution, Molecular
Fungi/physiology
Homeodomain Proteins/*metabolism
Plants/metabolism

@article {pmid17534075,
year = {2007},
author = {Maizels, R},
title = {Regulation of the immune system in metazoan parasite infections.},
journal = {Novartis Foundation symposium},
volume = {281},
number = {},
pages = {192-204; discussion 204-9},
doi = {10.1002/9780470062128.ch16},
pmid = {17534075},
issn = {1528-2511},
mesh = {Animals ; *Biological Evolution ; Host-Parasite Interactions ; Humans ; Immunity, Innate/*genetics/immunology ; Interleukin-10/immunology ; Parasites/*immunology ; Parasitic Diseases/genetics/*immunology ; *Polymorphism, Genetic ; T-Lymphocytes, Regulatory/*immunology ; },
abstract = {Eukaryotic, multicellular parasites such as the helminth worms have a major impact on the mammalian immune system in two contexts. First, they have evolved sophisticated strategies for long-term immune evasion including recruiting natural suppressive mechanisms such as the regulatory T cell (Tregs). Tregs play a role not only in repressing immunity to parasites, but also in dampening bystander responses such as those to allergens. To achieve these effects, they produce a range of immunomodulators some of which are evolutionary homologues of immune system cytokines, while others are novel proteins capable of interfering with immune cell signalling and differentiation. The second context in which metazoa may have influenced their host is at the level of genetic polymorphism in immune response genes. Alleles at loci originally associated with predisposition to asthma have more recently been found to confer heightened resistance to helminth parasites. This may suggest a mechanistic link between more vigorous type 2 responses in both allergy and infection. On a broader perspective, one may speculate that alleles advantageous in the historical environment of prevalent infection, now display a deleterious phenotype in our more 'hygienic' societies.},
}

Animals
*Biological Evolution
Host-Parasite Interactions
Humans
Immunity, Innate/*genetics/immunology
Interleukin-10/immunology
Parasites/*immunology
Parasitic Diseases/genetics/*immunology
*Polymorphism, Genetic
T-Lymphocytes, Regulatory/*immunology

@article {pmid17538623,
year = {2007},
author = {Molnár, A and Schwach, F and Studholme, DJ and Thuenemann, EC and Baulcombe, DC},
title = {miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii.},
journal = {Nature},
volume = {447},
number = {7148},
pages = {1126-1129},
doi = {10.1038/nature05903},
pmid = {17538623},
issn = {1476-4687},
mesh = {Animals ; Base Sequence ; Chlamydomonas reinhardtii/*cytology/*genetics ; Evolution, Molecular ; *Gene Expression Regulation ; MicroRNAs/genetics/*metabolism ; RNA, Algal/genetics/*metabolism ; RNA, Protozoan/genetics/*metabolism ; },
abstract = {MicroRNAs (miRNAs) in eukaryotes guide post-transcriptional regulation by means of targeted RNA degradation and translational arrest. They are released by a Dicer nuclease as a 21-24-nucleotide RNA duplex from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region. One of the two strands is then recruited by an Argonaute nuclease that is the effector protein of the silencing mechanism. Short interfering RNAs (siRNAs), which are similar to miRNAs, are also produced by Dicer but the precursors are perfectly double-stranded RNA. These siRNAs guide post-transcriptional regulation, as with miRNAs, and epigenetic genome modification. Diverse eukaryotes including fungi, plants, protozoans and metazoans produce siRNAs but, until now, miRNAs have not been described in unicellular organisms and it has been suggested that they evolved together with multicellularity in separate plant and animal lineages. Here we show that the unicellular alga Chlamydomonas reinhardtii contains miRNAs, putative evolutionary precursors of miRNAs and species of siRNAs resembling those in higher plants. The common features of miRNAs and siRNAs in an alga and in higher plants indicate that complex RNA-silencing systems evolved before multicellularity and were a feature of primitive eukaryotic cells.},
}

Animals
Base Sequence
Chlamydomonas reinhardtii/*cytology/*genetics
Evolution, Molecular
*Gene Expression Regulation
MicroRNAs/genetics/*metabolism
RNA, Algal/genetics/*metabolism
RNA, Protozoan/genetics/*metabolism

@article {pmid17583495,
year = {2007},
author = {Cahill, MA},
title = {Progesterone receptor membrane component 1: an integrative review.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {105},
number = {1-5},
pages = {16-36},
doi = {10.1016/j.jsbmb.2007.02.002},
pmid = {17583495},
issn = {0960-0760},
mesh = {Animals ; Cloning, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/*physiology ; Protein Binding ; Protein Conformation ; Receptors, Progesterone/chemistry/genetics/*physiology ; Subcellular Fractions/metabolism ; },
abstract = {Progesterone receptor membrane component 1 (PGRMC1) contains a cytochrome b5 domain fold and belongs to the so-called membrane-associated progesterone receptor (MAPR) protein family that is widespread in eukaryotes. PGRMC1 and the related PGRMC2 mammalian family member diverged sometime after the evolution of segmented metazoan body plan and the appearance of vertebrates. Therefore PGRMC1 might be expected to be involved in some ancient eukaryotic processes, as well as more modern functions related to multicellularity and tissue interactions. Perhaps this explains the perplexing diversity of contexts where PGRMC1 has been observed, apparently being involved in different cellular processes at various sub-cellular locations. This review attempts to collate and interpret these observations. Ironically, despite being the archetypal member of the MAPR family, it has yet to be demonstrated that PGRMC1 exhibits specific progesterone binding. Potential roles of heme and steroid/sterol ligands are reviewed, as well as the implications of apparent target sequences within PGRMC1 for binding by SH2- and SH3-domain proteins as well as kinases. These motifs are modelled using the cytochrome b5 domain NMR structure of the Arabidopsis protein 1J03, implicating a possible function for PGRMC1 as an adaptor protein involved in regulating protein interactions and intracellular signal transduction and/or membrane trafficking. This interpretation is supported by the apparent presence of immunoreceptor tyrosine-based activation motif/ITAM sequences that are involved in endocytosis and vesicle targeting, and the colocalisation of PGRMC1 with caveolin and at the cytoplasmic membrane. Evidence for roles in disease, especially cancer, is also discussed.},
}

Animals
Cloning, Molecular
Humans
Membrane Proteins/chemistry/genetics/*physiology
Protein Binding
Protein Conformation
Receptors, Progesterone/chemistry/genetics/*physiology
Subcellular Fractions/metabolism

@article {pmid17588271,
year = {2007},
author = {Itoh, M and Nacher, JC and Kuma, K and Goto, S and Kanehisa, M},
title = {Evolutionary history and functional implications of protein domains and their combinations in eukaryotes.},
journal = {Genome biology},
volume = {8},
number = {6},
pages = {R121},
pmid = {17588271},
issn = {1474-760X},
mesh = {Animals ; Eukaryotic Cells/chemistry/metabolism ; *Evolution, Molecular ; Humans ; Phylogeny ; Prokaryotic Cells/chemistry/metabolism ; Protein Structure, Tertiary ; Proteins/*chemistry/*genetics ; Proteome ; },
abstract = {BACKGROUND: In higher multicellular eukaryotes, complex protein domain combinations contribute to various cellular functions such as regulation of intercellular or intracellular signaling and interactions. To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes.

RESULTS: We observed a large number of group-specific domain combinations in animals, especially in vertebrates. Examples include animal-specific combinations in tyrosine phosphorylation systems and vertebrate-specific combinations in complement and coagulation cascades. These systems apparently underwent extensive evolution in the ancestors of these groups. In extant animals, especially in vertebrates, animal-specific domains have greater connectivity than do other domains on average, and contribute to the varying number of combinations in each animal subgroup. In other groups, the connectivities of older domains were greater on average. To observe the global behavior of domain combinations during evolution, we traced the changes in domain combinations among animals and fungi in a network analysis. Our results indicate that there is a correlation between the differences in domain combinations among different phylogenetic groups and different global behaviors.

CONCLUSION: Rapid emergence of animal-specific domains was observed in animals, contributing to specific domain combinations and functional diversification, but no such trends were observed in other clades of eukaryotes. We therefore suggest that the strategy for achieving complex multicellular systems in animals differs from that of other eukaryotes.},
}

Animals
Eukaryotic Cells/chemistry/metabolism
*Evolution, Molecular
Humans
Phylogeny
Prokaryotic Cells/chemistry/metabolism
Protein Structure, Tertiary
Proteins/*chemistry/*genetics
Proteome

@article {pmid17608793,
year = {2007},
author = {Brüssow, H},
title = {Bacteria between protists and phages: from antipredation strategies to the evolution of pathogenicity.},
journal = {Molecular microbiology},
volume = {65},
number = {3},
pages = {583-589},
doi = {10.1111/j.1365-2958.2007.05826.x},
pmid = {17608793},
issn = {0950-382X},
mesh = {Bacteria/*pathogenicity ; Bacteriophages/*physiology ; *Biological Evolution ; },
abstract = {Bacteriophages and protists are major causes of bacterial mortality. Genomics suggests that phages evolved well before eukaryotic protists. Bacteria were thus initially only confronted with phage predators. When protists evolved, bacteria were caught between two types of predators. One successful antigrazing strategy of bacteria was the elaboration of toxins that would kill the grazer. The released cell content would feed bystander bacteria. I suggest here that, to fight grazing protists, bacteria teamed up with those phage predators that concluded at least a temporary truce with them in the form of lysogeny. Lysogeny was perhaps initially a resource management strategy of phages that could not maintain infection chains. Subsequently, lysogeny might have evolved into a bacterium-prophage coalition attacking protists, which became a food source for them. When protists evolved into multicellular animals, the lysogenic bacteria tracked their evolving food source. This hypothesis could explain why a frequent scheme of bacterial pathogenicity is the survival in phagocytes, why a significant fraction of bacterial pathogens have prophage-encoded virulence genes, and why some virulence factors of animal pathogens are active against unicellular eukaryotes. Bacterial pathogenicity might thus be one playing option of the stone-scissor-paper game played between phages-bacteria-protists, with humans getting into the crossfire.},
}

Bacteria/*pathogenicity
Bacteriophages/*physiology
*Biological Evolution

@article {pmid17627470,
year = {2007},
author = {Webster, KA},
title = {Hypoxia: life on the edge.},
journal = {Antioxidants & redox signaling},
volume = {9},
number = {9},
pages = {1303-1307},
doi = {10.1089/ars.2007.1730},
pmid = {17627470},
issn = {1523-0864},
support = {HL072924/HL/NHLBI NIH HHS/United States ; HL44578/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Biological Evolution ; Cell Death ; Homeostasis ; Humans ; Hyperoxia/physiopathology ; Hypoxia/*physiopathology ; Reactive Oxygen Species ; },
abstract = {Hypoxia and its corollaries pose both negative and positive pressures to multicellular eukaryotes. Evolutionarily, life developed under hypoxia, and the building blocks were established under conditions close to anaerobiosis; therefore, reason exists to expect that certain biologic processes may perform preferentially under hypoxia. Evolving evidence suggests that by providing an environment of reduced oxidative stress, hypoxia may help preserve the biologic functions of some cells and prevent senescence. Hypoxia provides essential signals for development, trimming redundant tissue by inducing apoptosis and driving the growth and development of oxygen and nutrient delivery systems, as well as those for waste management. The pathologic consequences of hypoxia and ischemia, including acidosis and oxidative stress associated with hypoxia-reoxygenation, form the basis of most of the major diseases confronting humans, including heart disease, cancer, and age-related degenerative conditions. The 11 articles in the forum touch on multiple aspects of hypoxia, in particular, signaling responses, adaptations, and diseases that result from imbalance and fluctuations of supply and demand. Although we have developed elaborate processes to combat hypoxia and oxidative damage, it is clear that oxygen and our environment still control us, perhaps even more than they did our unicellular ancestors 2 billion years ago.},
}

Animals
Biological Evolution
Cell Death
Homeostasis
Humans
Hyperoxia/physiopathology
Hypoxia/*physiopathology
Reactive Oxygen Species

@article {pmid17637734,
year = {2007},
author = {Baer, CF and Miyamoto, MM and Denver, DR},
title = {Mutation rate variation in multicellular eukaryotes: causes and consequences.},
journal = {Nature reviews. Genetics},
volume = {8},
number = {8},
pages = {619-631},
doi = {10.1038/nrg2158},
pmid = {17637734},
issn = {1471-0056},
mesh = {Animals ; DNA Repair ; DNA Replication ; Eukaryotic Cells ; Evolution, Molecular ; Female ; Genetic Variation ; Genome ; Humans ; Male ; *Models, Genetic ; Mutagens/toxicity ; *Mutation ; Pedigree ; },
abstract = {A basic knowledge about mutation rates is central to our understanding of a myriad of evolutionary phenomena, including the maintenance of sex and rates of molecular evolution. Although there is substantial evidence that mutation rates vary among taxa, relatively little is known about the factors that underlie this variation at an empirical level, particularly in multicellular eukaryotes. Here we integrate several disparate lines of theoretical and empirical inquiry into a unified framework to guide future studies that are aimed at understanding why and how mutation rates evolve in multicellular species.},
}

Animals
DNA Repair
DNA Replication
Eukaryotic Cells
Evolution, Molecular
Female
Genetic Variation
Genome
Humans
Male
*Models, Genetic
Mutagens/toxicity
*Mutation
Pedigree

@article {pmid17687670,
year = {2007},
author = {Heidenreich, E},
title = {Adaptive mutation in Saccharomyces cerevisiae.},
journal = {Critical reviews in biochemistry and molecular biology},
volume = {42},
number = {4},
pages = {285-311},
doi = {10.1080/10409230701507773},
pmid = {17687670},
issn = {1040-9238},
mesh = {*Adaptation, Biological/genetics ; DNA Repair ; *Mutation ; Saccharomyces cerevisiae/*genetics ; },
abstract = {Adaptive mutation is a generic term for processes that allow individual cells of nonproliferating cell populations to acquire advantageous mutations and thereby to overcome the strong selective pressure of proliferation-limiting environmental conditions. Prerequisites for an occurrence of adaptive mutation are that the selective conditions are nonlethal and that a restart of proliferation may be accomplished by some genetic change in principle. The importance of adaptive mutation is derived from the assumption that it may, on the one hand, result in an accelerated evolution of microorganisms and, on the other, in multicellular organisms may contribute to a breakout of somatic cells from negative growth regulation, i.e., to cancerogenesis. Most information on adaptive mutation in eukaryotes has been gained with the budding yeast Saccharomyces cerevisiae. This review focuses comprehensively on adaptive mutation in this organism and summarizes our current understanding of this issue.},
}

*Adaptation, Biological/genetics
DNA Repair
*Mutation
Saccharomyces cerevisiae/*genetics

@article {pmid17698402,
year = {2007},
author = {Stiller, JW},
title = {Plastid endosymbiosis, genome evolution and the origin of green plants.},
journal = {Trends in plant science},
volume = {12},
number = {9},
pages = {391-396},
doi = {10.1016/j.tplants.2007.08.002},
pmid = {17698402},
issn = {1360-1385},
mesh = {*Evolution, Molecular ; *Genome, Plant ; Plants/*genetics ; Plastids/*genetics ; Symbiosis/*genetics ; },
abstract = {Evolutionary relationships among complex, multicellular eukaryotes are generally interpreted within the framework of molecular sequence-based phylogenies that suggest green plants and animals are only distantly related on the eukaryotic tree. However, important anomalies have been reported in phylogenomic analyses, including several that relate specifically to green plant evolution. In addition, plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups. This article explores the impacts of plastid endosymbioses on nuclear genomes, how they can explain incongruent phylogenetic signals in molecular data sets and reconcile conflicts among different sources of comparative data. Specifically, I argue that the large influx of plastid DNA into plant and algal nuclear genomes has resulted in tree-building artifacts that obscure a relatively close evolutionary relationship between green plants and animals.},
}

*Evolution, Molecular
*Genome, Plant
Plants/*genetics
Plastids/*genetics
Symbiosis/*genetics

@article {pmid17714660,
year = {2007},
author = {West, SA and Griffin, AS and Gardner, A},
title = {Evolutionary explanations for cooperation.},
journal = {Current biology : CB},
volume = {17},
number = {16},
pages = {R661-72},
doi = {10.1016/j.cub.2007.06.004},
pmid = {17714660},
issn = {0960-9822},
mesh = {Animals ; *Biological Evolution ; Cell Communication ; *Cooperative Behavior ; Eukaryotic Cells/metabolism ; *Genes ; Humans ; },
abstract = {Natural selection favours genes that increase an organism's ability to survive and reproduce. This would appear to lead to a world dominated by selfish behaviour. However, cooperation can be found at all levels of biological organisation: genes cooperate in genomes, organelles cooperate to form eukaryotic cells, cells cooperate to make multicellular organisms, bacterial parasites cooperate to overcome host defences, animals breed cooperatively, and humans and insects cooperate to build societies. Over the last 40 years, biologists have developed a theoretical framework that can explain cooperation at all these levels. Here, we summarise this theory, illustrate how it may be applied to real organisms and discuss future directions.},
}

Animals
*Biological Evolution
Cell Communication
*Cooperative Behavior
Eukaryotic Cells/metabolism
*Genes
Humans

@article {pmid17715154,
year = {2007},
author = {Dacks, JB and Field, MC},
title = {Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode.},
journal = {Journal of cell science},
volume = {120},
number = {Pt 17},
pages = {2977-2985},
doi = {10.1242/jcs.013250},
pmid = {17715154},
issn = {0021-9533},
support = {//Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Biological Evolution ; Biological Transport/physiology ; Eukaryotic Cells/cytology/*metabolism ; Genomics ; Humans ; Intracellular Membranes/*metabolism ; Phylogeny ; },
abstract = {The emergence of an endomembrane system was a crucial stage in the prokaryote-to-eukaryote evolutionary transition. Recent genomic and molecular evolutionary analyses have provided insight into how this critical system arrived at its modern configuration. The apparent relative absence of prokaryotic antecedents for the endomembrane machinery contrasts with the situation for mitochondria, plastids and the nucleus. Overall, the evidence suggests an autogenous origin for the eukaryotic membrane-trafficking machinery. The emerging picture is that early eukaryotic ancestors had a complex endomembrane system, which implies that this cellular system evolved relatively rapidly after the proto-eukaryote diverged away from the other prokaryotic lines. Many of the components of the trafficking system are the result of gene duplications that have produced proteins that have similar functions but differ in their subcellular location. A proto-eukaryote possessing a very simple trafficking system could thus have evolved to near modern complexity in the last common eukaryotic ancestor (LCEA) via paralogous gene family expansion of the proteins encoding organelle identity. The descendents of this common ancestor have undergone further modification of the trafficking machinery; unicellular simplicity and multicellular complexity are the prevailing trend, but there are some remarkable counter-examples.},
}

Animals
*Biological Evolution
Biological Transport/physiology
Eukaryotic Cells/cytology/*metabolism
Genomics
Humans
Intracellular Membranes/*metabolism
Phylogeny

@article {pmid17849148,
year = {2008},
author = {Hovav, R and Udall, JA and Hovav, E and Rapp, R and Flagel, L and Wendel, JF},
title = {A majority of cotton genes are expressed in single-celled fiber.},
journal = {Planta},
volume = {227},
number = {2},
pages = {319-329},
pmid = {17849148},
issn = {0032-0935},
mesh = {Cell Differentiation ; *Cotton Fiber ; Flowers ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; Gossypium/*genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Plant Proteins/genetics ; },
abstract = {Multicellular eukaryotes contain a diversity of cell types, presumably differing from one another in the suite of genes expressed during development. At present, little is known about the proportion of the genome transcribed in most cell types, nor the degree to which global patterns of expression change during cellular differentiation. To address these questions in a model plant system, we studied the unique and highly exaggerated single-celled, epidermal seed trichomes ("cotton") of cultivated cotton (Gossypium hirsutum). By taking advantage of advances in expression profiling and microarray technology, we evaluated the transcriptome of cotton fibers across a developmental time-course, from a few days post-anthesis through primary and secondary wall synthesis stages. Comparisons of gene expression in populations of developing cotton fiber cells to genetically complex reference samples derived from 6 different cotton organs demonstrated that a remarkably high proportion of the cotton genome is transcribed, with 75-94% of the total genome transcribed at each stage. Compared to the reference samples, more than half of all genes were up-regulated during at least one stage of fiber development. These genes were clustered into seven groups of expression profiles that provided new insight into biological processes governing fiber development. Genes implicated in vesicle coating and trafficking were found to be overexpressed throughout all stages of fiber development studied, indicating their important role in maintaining rapid growth of this unique plant cell.},
}

Cell Differentiation
*Cotton Fiber
Flowers
*Gene Expression Profiling
*Gene Expression Regulation, Plant
Genes, Plant/*genetics
Gossypium/*genetics/*metabolism
Oligonucleotide Array Sequence Analysis
Plant Proteins/genetics

@article {pmid17916237,
year = {2007},
author = {Irimia, M and Rukov, JL and Penny, D and Roy, SW},
title = {Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing.},
journal = {BMC evolutionary biology},
volume = {7},
number = {},
pages = {188},
pmid = {17916237},
issn = {1471-2148},
mesh = {*Alternative Splicing ; Animals ; Databases, Genetic ; *Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; *Genes ; Humans ; Introns ; Phylogeny ; Plants/genetics ; Spliceosomes ; },
abstract = {BACKGROUND: Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independently in the different eukaryotic groups or was inherited from their last common ancestor, and may therefore predate multicellularity, is still unknown. To better understand the origin and evolution of alternative splicing and its usage in diverse organisms, we studied alternative splicing in 12 eukaryotic species, comparing rates of alternative splicing across genes of different functional classes, cellular locations, intron/exon structures and evolutionary origins.

RESULTS: For each species, we find that genes from most functional categories are alternatively spliced. Ancient genes (shared between animals, fungi and plants) show high levels of alternative splicing. Genes with products expressed in the nucleus or plasma membrane are generally more alternatively spliced while those expressed in extracellular location show less alternative splicing. We find a clear correspondence between incidence of alternative splicing and intron number per gene both within and between genomes. In general, we find several similarities in patterns of alternative splicing across these diverse eukaryotes.

CONCLUSION: Along with previous studies indicating intron-rich genes with weak intron boundary consensus and complex spliceosomes in ancestral organisms, our results suggest that at least a simple form of alternative splicing may already have been present in the unicellular ancestor of plants, fungi and animals. A role for alternative splicing in the evolution of multicellularity then would largely have arisen by co-opting the preexisting process.},
}

*Alternative Splicing
Animals
Databases, Genetic
*Eukaryotic Cells
*Evolution, Molecular
Fungi/genetics
*Genes
Humans
Introns
Phylogeny
Plants/genetics
Spliceosomes

@article {pmid17935625,
year = {2007},
author = {Carmel, L and Rogozin, IB and Wolf, YI and Koonin, EV},
title = {Patterns of intron gain and conservation in eukaryotic genes.},
journal = {BMC evolutionary biology},
volume = {7},
number = {},
pages = {192},
pmid = {17935625},
issn = {1471-2148},
abstract = {BACKGROUND: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions.

RESULTS: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only approximately 8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs.

CONCLUSION: We obtained robust estimates of the contribution of parallel gain to the observed sharing of intron positions between eukaryotic species separated by different evolutionary distances. The results indicate that, although the contribution of parallel gains varies across the phylogenetic tree, the high level of intron position sharing is due, primarily, to evolutionary conservation. Accordingly, numerous introns appear to persist in the same position over hundreds of millions of years of evolution. This is compatible with recent observations of a negative correlation between the rate of intron gain and coding sequence evolution rate of a gene, suggesting that at least some of the introns are functionally relevant.},
}

@article {pmid17943195,
year = {2007},
author = {Chapman, EJ and Carrington, JC},
title = {Specialization and evolution of endogenous small RNA pathways.},
journal = {Nature reviews. Genetics},
volume = {8},
number = {11},
pages = {884-896},
doi = {10.1038/nrg2179},
pmid = {17943195},
issn = {1471-0064},
mesh = {Animals ; *Evolution, Molecular ; Humans ; MicroRNAs/*physiology ; Plants/genetics ; RNA Interference/physiology ; RNA, Small Interfering/*physiology ; Signal Transduction/*genetics ; },
abstract = {The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.},
}

Animals
*Evolution, Molecular
Humans
MicroRNAs/*physiology
Plants/genetics
RNA Interference/physiology
RNA, Small Interfering/*physiology
Signal Transduction/*genetics

@article {pmid17973655,
year = {2008},
author = {Pereira-Leal, JB},
title = {The Ypt/Rab family and the evolution of trafficking in fungi.},
journal = {Traffic (Copenhagen, Denmark)},
volume = {9},
number = {1},
pages = {27-38},
doi = {10.1111/j.1600-0854.2007.00667.x},
pmid = {17973655},
issn = {1398-9219},
mesh = {Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Fungi/classification/*metabolism ; Genome, Fungal ; Phylogeny ; Protein Transport ; rab GTP-Binding Proteins/genetics/*metabolism ; },
abstract = {The evolution of the eukaryotic endomembrane system and the transport pathways of their vesicular intermediates are poorly understood. A common set of organelles and pathways seems to be present in all free-living eukaryotes, but different branches of the tree of life have a variety of diverse, specialized organelles. Rab/Ypt proteins are small guanosine triphosphatases with tissue-specific and organelle-specific localization that emerged as markers for organelle diversity. Here, I characterize the Rab/Ypt family in the kingdom Fungi, a sister kingdom of Animals. I identify and annotate these proteins in 26 genomes representing near one billion years of evolution, multiple lifestyles and cellular types. Surprisingly, the minimal set of Rab/Ypt present in fungi is similar to, perhaps smaller than, the predicted eukaryotic ancestral set. This suggests that the saprophytic fungal lifestyle, multicellularity as well as the highly polarized secretion associated with hyphal growth did not require any major innovation in the molecular machinery that regulates protein trafficking. The Rab/Ypt and other protein traffic-related families are kept small, not paralleling increases in genome size, in contrast to the expansion of such components observed in other branches of the tree of life, such as the animal and plant kingdoms. This analysis suggests that multicellularity and cellular diversity in fungi followed different routes from those followed by plants and metazoa.},
}

Evolution, Molecular
Fungal Proteins/genetics/*metabolism
Fungi/classification/*metabolism
Genome, Fungal
Phylogeny
Protein Transport
rab GTP-Binding Proteins/genetics/*metabolism

@article {pmid17976716,
year = {2008},
author = {Kim, Y and Powell, EN and Wade, TL and Presley, BJ},
title = {Relationship of parasites and pathologies to contaminant body burden in sentinel bivalves: NOAA Status and Trends 'Mussel Watch' Program.},
journal = {Marine environmental research},
volume = {65},
number = {2},
pages = {101-127},
doi = {10.1016/j.marenvres.2007.09.003},
pmid = {17976716},
issn = {0141-1136},
mesh = {Analysis of Variance ; Animals ; Bivalvia/*drug effects/*parasitology ; Databases, Factual ; *Environmental Monitoring ; Hydrocarbons/*toxicity ; Parasites/*drug effects/isolation & purification/pathogenicity ; Principal Component Analysis ; Sentinel Surveillance ; Water Pollutants, Chemical/*toxicity ; },
abstract = {The 1995-1998 database from NOAA's National Status and Trends 'Mussel Watch' Program was used to compare the distributional patterns of parasites and pathologies with contaminant body burdens. Principal components analysis (PCA) resolved five groups of contaminants in both mussels and oysters: one dominated by polycyclic aromatic hydrocarbons (PAHs), one dominated by pesticides, and three dominated by metals. Metals produced a much more complex picture of spatial trends in body burden than did either the pesticides or PAHs. Contrasted to the relative simplicity of the contaminant groupings, PCA exposed a suite of parasite/pathology groups with few similarities between the sentinel bivalve taxa. Thus, the relationship between parasites/pathologies and contaminants differs significantly between taxa despite the similarity in contaminant pattern. Moreover, the combined effects of many contaminants and parasites may be important, leading to complex biological-contaminant interactions with synergies both of biological and chemical origin. Overall, correlations between parasites/pathologies and contaminants were more frequent with metals, frequent with pesticides, and less frequent with PAHs in mussels. In oysters, correlations with pesticides and metals were about equally frequent, but correlations with PAHs were still rare. In mytilids, correlations with metals predominated. Negative and positive correlations with metals occurred with about the same frequency in both taxa. The majority of correlations with pesticides were negative in oysters; not so for mytilids. Of the many significant correlations involving parasites, few involved single-celled eukaryotes or prokaryotes. The vast majority involved multi-cellular eukaryotes and nearly all of them either cestodes, trematode sporocysts, or trematode metacercariae. The few correlations for single-celled parasites all involved proliferating protozoa or protozoa reaching high body burdens through transmission. The tendency for the larger or more numerous parasites to be involved suggests that unequal sequestration of contaminates between host and parasite tissue is a potential mediator. An alternative is that contaminants differentially affect parasites and their hosts by varying host susceptibility or parasite survival.},
}

Analysis of Variance
Animals
Bivalvia/*drug effects/*parasitology
Databases, Factual
*Environmental Monitoring
Hydrocarbons/*toxicity
Parasites/*drug effects/isolation & purification/pathogenicity
Principal Component Analysis
Sentinel Surveillance
Water Pollutants, Chemical/*toxicity

@article {pmid17977455,
year = {2007},
author = {Javaux, EJ},
title = {The early eukaryotic fossil record.},
journal = {Advances in experimental medicine and biology},
volume = {607},
number = {},
pages = {1-19},
doi = {10.1007/978-0-387-74021-8_1},
pmid = {17977455},
issn = {0065-2598},
mesh = {Eukaryotic Cells/classification/*cytology/ultrastructure ; *Evolution, Molecular ; *Fossils ; Time Factors ; },
abstract = {The Precambrian era records the evolution of the domain Eucarya. Although the taxonomy of fossils is often impossible to resolve beyond the level of domain, their morphology and chemistry indicate the evolution of major biological innovations. The late Archean record for eukaryotes is limited to trace amounts of biomarkers. Morphological evidence appears in late Paleoproterozoic and early Mesoproterozoic (1800-1300 Ma) rocks. The moderate diversity of preservable eukaryotic organisms includes cell walls without surface ornament (but with complex ultrastructure), with regularly distributed surface ornamentation, and with irregularly or regularly arranged processes. Collectively, these fossils suggest that eukaryotes with flexible membranes and cytoskeletons existed in mid-Proterozoic oceans. The late Mesoproterozoic-early Neoproterozoic (1300-750 Ma) is a time of diversification and evolution when direct evidence for important biological innovations occurs in the fossil record such as multicellularity, sex, photosynthesis, biomineralization, predation, and heterotrophy. Members of extant clades can be recognized and include bangiophyte red algae, xanthophyte algae, cladophorale green algae, euglyphid, lobose, and filose amoebae and possible fungi. In the late Neoproterozoic, besides more diversification of ornamented fossils, florideophyte red algae and brown algae diversify, and animals take the stage. The record of biological innovations documented by the fossils shows that eukaryotes had evolved most cytological and molecular complexities very early in the Proterozoic but environmental conditions delayed their diversification within clades until oxygen level and predation pressure increased significantly.},
}

Eukaryotic Cells/classification/*cytology/ultrastructure
*Evolution, Molecular
*Fossils
Time Factors

@article {pmid17977460,
year = {2007},
author = {Gurkan, C and Koulov, AV and Balch, WE},
title = {An evolutionary perspective on eukaryotic membrane trafficking.},
journal = {Advances in experimental medicine and biology},
volume = {607},
number = {},
pages = {73-83},
doi = {10.1007/978-0-387-74021-8_6},
pmid = {17977460},
issn = {0065-2598},
support = {GM33301/GM/NIGMS NIH HHS/United States ; GM42336/GM/NIGMS NIH HHS/United States ; },
mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Biological Transport ; Cell Membrane/*metabolism ; Conserved Sequence ; Eukaryotic Cells/*cytology/*metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; Humans ; Intracellular Membranes/*metabolism ; Membrane Fusion ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Transport ; SNARE Proteins/metabolism ; Sequence Homology, Amino Acid ; rab GTP-Binding Proteins/chemistry/genetics/metabolism ; },
abstract = {The eukaryotic cell is defined by a complex set of sub-cellular compartments that include endomembrane systems making up the exocytic and endocytic trafficking pathways. Current evidence suggests that both the function and communication between these compartments are regulated by distinct families of proteins that direct membrane fission, targeting and fusion. These families include coat protein complexes (CPCs) involved in vesicle formation/fission, Rab GTPases involved in vesicle targeting, and soluble N-ethyl-maleimide-sensitive factor attachment protein receptors (SNAREs) involved in vesicle fusion. The origins of these gene families and their individual contributions to the evolutionary specialization of the membrane architectures of lower and higher eukaryotes are now better understood with the advent of powerful phylogenetic, structural and systems biology tools. Herein, we provide a perspective that suggests that while the core CPC and SNARE machineries have diversified modestly in the course of eukaryotic evolution, the Rab GTPase family expanded substantially to emerge as a key driving force in endomembrane specialization. The Rab GTPases appear to have provided the foundation for the intricate membrane architectures ranging from those requisite for the distinct amoebic life cycle stage of uni-cellular organisms such as the parasitic protozoa to the highly specialized tissue and cell type-specific endomembranes of multi-cellular eukaryotes. We propose that Rab-centric interaction networks orchestrate the divergent activities of fission and fusion through their capacity to control the sequential assembly of protein complexes that mediate endomembrane structure and communication.},
}

Amino Acid Motifs
Amino Acid Sequence
Animals
Biological Transport
Cell Membrane/*metabolism
Conserved Sequence
Eukaryotic Cells/*cytology/*metabolism
*Evolution, Molecular
Gene Expression Profiling
Humans
Intracellular Membranes/*metabolism
Membrane Fusion
Models, Biological
Models, Molecular
Molecular Sequence Data
Protein Conformation
Protein Transport
SNARE Proteins/metabolism
Sequence Homology, Amino Acid
rab GTP-Binding Proteins/chemistry/genetics/metabolism

@article {pmid17977464,
year = {2007},
author = {Bornens, M and Azimzadeh, J},
title = {Origin and evolution of the centrosome.},
journal = {Advances in experimental medicine and biology},
volume = {607},
number = {},
pages = {119-129},
doi = {10.1007/978-0-387-74021-8_10},
pmid = {17977464},
issn = {0065-2598},
mesh = {Animals ; Cell Nucleus/metabolism ; Centrosome/*metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Humans ; Models, Biological ; Phylogeny ; },
abstract = {In this brief account we specifically address the question of how the plasma membrane-associated basal body/axoneme of the unicellular ancestor of eukaryotes has evolved into the centrosome organelle through the several attempts to multicellularity. We propose that the connection between the flagellar apparatus and the nucleus has been a critical feature for leading to the centriole-based centrosome of metazoa, the Spindle Pole Body of fungi, or to the absence of any centrosome in seed plants. We further suggest that the evolution of this connection could be reflected in the evolution of the centrin proteins. We then review evidence showing that the evolution of the centrosome-based tubulin network has been correlated with the evolution of the cortical actin-based cleavage apparatus. Finally we argue that this coevolution had a major impact on the cell individuation process and on the evolution of multicellular organisms. We conclude that only the metazoan lineage evolved multicellularity without loosing the ancestral association of three basic cellular functions of the basal body/axoneme or the derived centrosome organelle, namely sensation, motion and division.},
}

Animals
Cell Nucleus/metabolism
Centrosome/*metabolism
Eukaryotic Cells/metabolism
*Evolution, Molecular
Humans
Models, Biological
Phylogeny

@article {pmid18005684,
year = {2007},
author = {Miller, SI and Hoffman, LR and Sanowar, S},
title = {Did bacterial sensing of host environments evolve from sensing within microbial communities?.},
journal = {Cell host & microbe},
volume = {1},
number = {2},
pages = {85-87},
doi = {10.1016/j.chom.2007.04.002},
pmid = {18005684},
issn = {1934-6069},
mesh = {Bacteria/pathogenicity ; *Bacterial Physiological Phenomena ; Biological Evolution ; *Environment ; Heme/physiology ; Staphylococcus aureus/pathogenicity ; Virulence ; },
abstract = {Bacteria sense and respond to their environment, enabling adaptation to diverse niches, including multicellular eukaryotes. In this issue of Cell Host & Microbe, Torres et al. describe how the bacterium Staphylococcus aureus responds to heme as a molecular marker of the mammalian host environment. It is likely that mechanisms for sensing such markers evolved from systems that recognized cues present in microbial communities before the emergence of eukaryotes.},
}

Bacteria/pathogenicity
*Bacterial Physiological Phenomena
Biological Evolution
*Environment
Heme/physiology
Staphylococcus aureus/pathogenicity
Virulence

@article {pmid18024428,
year = {2008},
author = {Ben-Dov, C and Hartmann, B and Lundgren, J and Valcárcel, J},
title = {Genome-wide analysis of alternative pre-mRNA splicing.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {3},
pages = {1229-1233},
doi = {10.1074/jbc.R700033200},
pmid = {18024428},
issn = {0021-9258},
mesh = {Alternative Splicing/*genetics ; Animals ; Disease ; Genome, Human/*genetics ; Humans ; RNA Precursors/*genetics ; },
abstract = {Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.},
}

Alternative Splicing/*genetics
Animals
Disease
Genome, Human/*genetics
Humans
RNA Precursors/*genetics

@article {pmid18027391,
year = {2007},
author = {Bhattacharya, D and Archibald, JM and Weber, AP and Reyes-Prieto, A},
title = {How do endosymbionts become organelles? Understanding early events in plastid evolution.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {29},
number = {12},
pages = {1239-1246},
doi = {10.1002/bies.20671},
pmid = {18027391},
issn = {0265-9247},
mesh = {*Biological Evolution ; Models, Biological ; Plant Proteins/chemistry ; Plastids/*physiology ; Protein Transport ; *Symbiosis ; },
abstract = {What factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? This question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, Chlorella cells in ciliates, Buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and the mitochondrion. Emerging data on (1) the discovery of non-canonical plastid protein targeting, (2) the recent origin of a cyanobacterial-derived organelle in the filose amoeba Paulinella chromatophora, and (3) the extraordinarily reduced genomes of psyllid bacterial endosymbionts begin to blur the distinction between endosymbiont and organelle. Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution.},
}

*Biological Evolution
Models, Biological
Plant Proteins/chemistry
Plastids/*physiology
Protein Transport
*Symbiosis

@article {pmid18031303,
year = {2008},
author = {Herron, MD and Michod, RE},
title = {Evolution of complexity in the volvocine algae: transitions in individuality through Darwin's eye.},
journal = {Evolution; international journal of organic evolution},
volume = {62},
number = {2},
pages = {436-451},
doi = {10.1111/j.1558-5646.2007.00304.x},
pmid = {18031303},
issn = {0014-3820},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Cell Differentiation ; Cell Division ; Chlamydomonas/*genetics ; Codon ; Eukaryota/*genetics/metabolism ; *Evolution, Molecular ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Monte Carlo Method ; Phylogeny ; Volvox/*genetics ; },
abstract = {The transition from unicellular to differentiated multicellular organisms constitutes an increase in the level complexity, because previously existing individuals are combined to form a new, higher-level individual. The volvocine algae represent a unique opportunity to study this transition because they diverged relatively recently from unicellular relatives and because extant species display a range of intermediate grades between unicellular and multicellular, with functional specialization of cells. Following the approach Darwin used to understand "organs of extreme perfection" such as the vertebrate eye, this jump in complexity can be reduced to a series of small steps that cumulatively describe a gradual transition between the two levels. We use phylogenetic reconstructions of ancestral character states to trace the evolution of steps involved in this transition in volvocine algae. The history of these characters includes several well-supported instances of multiple origins and reversals. The inferred changes can be understood as components of cooperation-conflict-conflict mediation cycles as predicted by multilevel selection theory. One such cycle may have taken place early in volvocine evolution, leading to the highly integrated colonies seen in extant volvocine algae. A second cycle, in which the defection of somatic cells must be prevented, may still be in progress.},
}

Animals
Bayes Theorem
*Biological Evolution
Cell Differentiation
Cell Division
Chlamydomonas/*genetics
Codon
Eukaryota/*genetics/metabolism
*Evolution, Molecular
Models, Biological
Models, Genetic
Models, Theoretical
Monte Carlo Method
Phylogeny
Volvox/*genetics

@article {pmid18058146,
year = {2007},
author = {Zhu, S},
title = {Evidence for myxobacterial origin of eukaryotic defensins.},
journal = {Immunogenetics},
volume = {59},
number = {12},
pages = {949-954},
pmid = {18058146},
issn = {0093-7711},
mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; Cysteine/chemistry ; Defensins/*chemistry/*genetics ; Eukaryotic Cells/*physiology ; Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Myxococcales/*chemistry/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; },
abstract = {Antimicrobial defensins with the cysteine-stabilized alpha-helical and beta-sheet (CS alpha beta) motif are a large family of ancient, evolutionarily related innate immunity effectors of multicellular organisms. Although the widespread distribution in plants, fungi, and invertebrates suggests their uniqueness to Eukarya, it is unknown whether these eukaryotic defensins originated before or posterior to the emergence of eukaryotes. In this study, we provide evidence in support of the existence of defensin-like peptides (DLPs) in myxobacteria based on structural bioinformatics analysis, which recognized two bacterial peptides with a conserved cysteine-stabilized alpha-helical motif, a nested structural unit of the CS alpha beta motif. Similarity in sequence and structure to fungal DLPs together with restricted distribution to the myxobacteria as well as central role of the myxobacteria in the origin of eukaryotes suggest that the bacterial DLPs represent the ancestor of the eukaryotic defensins and could mediate immune defense of early eukaryotes after gene transfer to the proto-eukaryotic genome. Our work thus offers a basis for further investigation of prokaryotic origin of eukaryotic immune effector molecules.},
}

Amino Acid Sequence
Animals
Computational Biology
Cysteine/chemistry
Defensins/*chemistry/*genetics
Eukaryotic Cells/*physiology
Evolution, Molecular
Models, Molecular
Molecular Sequence Data
Myxococcales/*chemistry/metabolism
Protein Structure, Tertiary
Sequence Homology, Amino Acid

@article {pmid18070109,
year = {2008},
author = {Liu, Q},
title = {Identification of rice TUBBY-like genes and their evolution.},
journal = {The FEBS journal},
volume = {275},
number = {1},
pages = {163-171},
doi = {10.1111/j.1742-4658.2007.06186.x},
pmid = {18070109},
issn = {1742-464X},
mesh = {*Evolution, Molecular ; *Genes, Plant ; Genetic Variation ; Oryza/*genetics ; Phylogeny ; },
abstract = {The identification of TUBBY-like genes in organisms ranging from single-celled to multicellular eukaryotes has allowed the phylogenetic history of this gene family to be traced back to the early evolutionary stages of eukaryote development. Rice TUBBY-like genes were located on chromosomes 1, 2, 3, 4, 5, 7, 8, 11 and 12 without any obvious clustering. On a genomic scale, it was revealed that the rice TUBBY-like gene family probably evolved mainly through segmental duplication produced by polyploidy. The altered selective constraints (or site-specific rate changes), related to functional divergence during protein evolution between plant and animal TUBBY-like genes, were statistically significant. Based on posterior probability analysis, five amino acid sites (103, 312, 315, 317 and 319) are thought to be responsible for functional divergence.},
}

*Evolution, Molecular
*Genes, Plant
Genetic Variation
Oryza/*genetics
Phylogeny

@article {pmid18073380,
year = {2008},
author = {Nikoh, N and Tanaka, K and Shibata, F and Kondo, N and Hizume, M and Shimada, M and Fukatsu, T},
title = {Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes.},
journal = {Genome research},
volume = {18},
number = {2},
pages = {272-280},
pmid = {18073380},
issn = {1088-9051},
mesh = {Animals ; Base Sequence ; Blotting, Southern ; Chromosome Mapping ; Chromosomes/*genetics ; Coleoptera/genetics/*microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; In Situ Hybridization, Fluorescence ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Pseudogenes/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics ; },
abstract = {Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we thoroughly investigated the bacterial genes derived from a Wolbachia endosymbiont on the nuclear genome of the beetle Callosobruchus chinensis. Exhaustive PCR detection and Southern blot analysis suggested that approximately 30% of Wolbachia genes, in terms of the gene repertoire of wMel, are present on the insect nuclear genome. Fluorescent in situ hybridization located the transferred genes on the proximal region of the basal short arm of the X chromosome. Molecular evolutionary and other lines of evidence indicated that the transferred genes are probably derived from a single lateral transfer event. The transferred genes were, for the length examined, structurally disrupted, freed from functional constraints, and transcriptionally inactive. Hence, most, if not all, of the transferred genes have been pseudogenized. Notwithstanding this, the transferred genes were ubiquitously detected from Japanese and Taiwanese populations of C. chinensis, while the number of the transferred genes detected differed between the populations. The transferred genes were not detected from congenic beetle species, indicating that the transfer event occurred after speciation of C. chinensis, which was estimated to be one or several million years ago. These features of the laterally transferred endosymbiont genes are compared with the evolutionary patterns of mitochondrial and plastid genome fragments acquired by nuclear genomes through recent endosymbiotic gene transfers.},
}

Animals
Base Sequence
Blotting, Southern
Chromosome Mapping
Chromosomes/*genetics
Coleoptera/genetics/*microbiology
*Evolution, Molecular
Gene Transfer, Horizontal/*genetics
Genome/*genetics
In Situ Hybridization, Fluorescence
Likelihood Functions
Models, Genetic
Molecular Sequence Data
Phylogeny
Polymerase Chain Reaction
Polymorphism, Genetic
Pseudogenes/genetics
Reverse Transcriptase Polymerase Chain Reaction
Sequence Analysis, DNA
*Symbiosis
Wolbachia/*genetics

@article {pmid18157077,
year = {2007},
author = {Sanchez, S and Hourdez, S and Lallier, FH},
title = {[Chemoautotrophic endosymbioses: contemporary models for symbiogenesis?].},
journal = {Journal de la Societe de biologie},
volume = {201},
number = {3},
pages = {247-257},
doi = {10.1051/jbio:2007036},
pmid = {18157077},
issn = {1295-0661},
mesh = {Animals ; Biological Evolution ; Cyanobacteria/physiology ; Earth, Planet ; Eukaryotic Cells/physiology ; Geography ; Models, Biological ; Photosynthesis ; Symbiosis/*physiology ; Time ; },
abstract = {Oxygen appears to be one of the key factors in understanding the evolution of life on Earth. Almost absent during more than 2 billion years, its subsequent increase is correlated with the emergence of oxygenic photosynthesis by Cyanobacteria, followed by aerobic Prokaryotes and eventually Eukaryotes, all primitively aerobic, and more recently, the development of complex multicellular organisms. However, in some reduced environments, still present at the surface of the Earth and even more so in ocean depths (hydrothermal vents, cold seeps, massive organic falls,...), anaerobic or micro-aerobic Prokaryotes continue to grow, including some chemoautotrophic bacteria deriving energy from sulfide oxidation for instance. A few Metazoa have managed to collaborate with such chemoautotroph Prokaryotes, the most abundant species forming endosymbiotic associations. The most studied of these endosymbioses (the mussels Bathymodiolus, the vestimentiferan tubeworm Riftia pachyptila, or the clams Calyptogena) have revealed important differences in the degree of interdependence between host and symbionts, and in the mode of symbiont transmission. The evolutive process of these symbioses is reminiscent of the primary endosymbioses which have given rise to the organelles of heterotrophic Eukaryotes (mitochondria) and phototrophic Eukaryotes (chloroplasts). The study of these modern days biological models could shed light on symbiogenesis itself and also potentially reveal thiotrophic Eukaryotes as a new lineage.},
}

Animals
Biological Evolution
Cyanobacteria/physiology
Earth, Planet
Eukaryotic Cells/physiology
Geography
Models, Biological
Photosynthesis
Symbiosis/*physiology
Time

@article {pmid18162580,
year = {2008},
author = {Yi, S and Sahni, N and Daniels, KJ and Pujol, C and Srikantha, T and Soll, DR},
title = {The same receptor, G protein, and mitogen-activated protein kinase pathway activate different downstream regulators in the alternative white and opaque pheromone responses of Candida albicans.},
journal = {Molecular biology of the cell},
volume = {19},
number = {3},
pages = {957-970},
pmid = {18162580},
issn = {1939-4586},
support = {AI-2392/AI/NIAID NIH HHS/United States ; },
mesh = {Biofilms/drug effects ; Biomarkers/metabolism ; Candida albicans/*cytology/*enzymology/genetics/physiology ; Fungal Proteins/genetics/metabolism ; GTP-Binding Proteins/*metabolism ; Gene Expression Regulation, Fungal/drug effects ; Genes, Switch ; Mitogen-Activated Protein Kinases/*metabolism ; Models, Biological ; Mutation/genetics ; Phenotype ; Pheromones/*pharmacology ; Receptors, Pheromone/*metabolism ; Transcription Factors/genetics/metabolism ; },
abstract = {Candida albicans must undergo a switch from white to opaque to mate. Opaque cells then release mating type-specific pheromones that induce mating responses in opaque cells. Uniquely in C. albicans, the same pheromones induce mating-incompetent white cells to become cohesive, form an adhesive basal layer of cells on a surface, and then generate a thicker biofilm that, in vitro, facilitates mating between minority opaque cells. Through mutant analysis, it is demonstrated that the pathways regulating the white and opaque cell responses to the same pheromone share the same upstream components, including receptors, heterotrimeric G protein, and mitogen-activated protein kinase cascade, but they use different downstream transcription factors that regulate the expression of genes specific to the alternative responses. This configuration, although common in higher, multicellular systems, is not common in fungi, and it has not been reported in Saccharomyces cerevisiae. The implications in the evolution of multicellularity in higher eukaryotes are discussed.},
}

Biofilms/drug effects
Biomarkers/metabolism
Candida albicans/*cytology/*enzymology/genetics/physiology
Fungal Proteins/genetics/metabolism
GTP-Binding Proteins/*metabolism
Gene Expression Regulation, Fungal/drug effects
Genes, Switch
Mitogen-Activated Protein Kinases/*metabolism
Models, Biological
Mutation/genetics
Phenotype
Pheromones/*pharmacology
Receptors, Pheromone/*metabolism
Transcription Factors/genetics/metabolism

@article {pmid18181960,
year = {2008},
author = {Charrier, B and Coelho, SM and Le Bail, A and Tonon, T and Michel, G and Potin, P and Kloareg, B and Boyen, C and Peters, AF and Cock, JM},
title = {Development and physiology of the brown alga Ectocarpus siliculosus: two centuries of research.},
journal = {The New phytologist},
volume = {177},
number = {2},
pages = {319-332},
doi = {10.1111/j.1469-8137.2007.02304.x},
pmid = {18181960},
issn = {0028-646X},
mesh = {Biological Evolution ; Ecology ; Ecosystem ; Genome, Plant ; Phaeophyceae/classification/genetics/*growth & development/*physiology ; },
abstract = {Brown algae share several important features with land plants, such as their photoautotrophic nature and their cellulose-containing wall, but the two groups are distantly related from an evolutionary point of view. The heterokont phylum, to which the brown algae belong, is a eukaryotic crown group that is phylogenetically distinct not only from the green lineage, but also from the red algae and the opisthokont phylum (fungi and animals). As a result of this independent evolutionary history, the brown algae exhibit many novel features and, moreover, have evolved complex multicellular development independently of the other major groups already mentioned. In 2004, a consortium of laboratories, including the Station Biologique in Roscoff and Genoscope, initiated a project to sequence the genome of Ectocarpus siliculosus, a small filamentous brown alga that is found in temperate, coastal environments throughout the globe. The E. siliculosus genome, which is currently being annotated, is expected to be the first completely characterized genome of a multicellular alga. In this review we look back over two centuries of work on this brown alga and highlight the advances that have led to the choice of E. siliculosus as a genomic and genetic model organism for the brown algae.},
}

Biological Evolution
Ecology
Ecosystem
Genome, Plant
Phaeophyceae/classification/genetics/*growth & development/*physiology

@article {pmid18184723,
year = {2008},
author = {Ruiz-Trillo, I and Roger, AJ and Burger, G and Gray, MW and Lang, BF},
title = {A phylogenomic investigation into the origin of metazoa.},
journal = {Molecular biology and evolution},
volume = {25},
number = {4},
pages = {664-672},
doi = {10.1093/molbev/msn006},
pmid = {18184723},
issn = {1537-1719},
mesh = {Animals ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genome ; Mitochondrial Proteins/chemistry/genetics ; *Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry ; },
abstract = {The evolution of multicellular animals (Metazoa) from their unicellular ancestors was a key transition that was accompanied by the emergence and diversification of gene families associated with multicellularity. To clarify the timing and order of specific events in this transition, we conducted expressed sequence tag surveys on 4 putative protistan relatives of Metazoa including the choanoflagellate Monosiga ovata, the ichthyosporeans Sphaeroforma arctica and Amoebidium parasiticum, and the amoeba Capsaspora owczarzaki, and 2 members of Amoebozoa, Acanthamoeba castellanii and Mastigamoeba balamuthi. We find that homologs of genes involved in metazoan multicellularity exist in several of these unicellular organisms, including 1 encoding a membrane-associated guanylate kinase with an inverted arrangement of protein-protein interaction domains (MAGI) in Capsaspora. In Metazoa, MAGI regulates tight junctions involved in cell-cell communication. By phylogenomic analyses of genes encoded in nuclear and mitochondrial genomes, we show that the choanoflagellates are the closest relatives of the Metazoa, followed by the Capsaspora and Ichthyosporea lineages, although the branching order between the latter 2 groups remains unclear. Understanding the function of "metazoan-specific" proteins we have identified in these protists will clarify the evolutionary steps that led to the emergence of the Metazoa.},
}

Animals
Eukaryota/classification/*genetics
*Evolution, Molecular
*Genome
Mitochondrial Proteins/chemistry/genetics
*Phylogeny
Protein Structure, Tertiary
Protozoan Proteins/chemistry

@article {pmid18202389,
year = {2008},
author = {Anderson, JA and Song, YS and Langley, CH},
title = {Molecular population genetics of Drosophila subtelomeric DNA.},
journal = {Genetics},
volume = {178},
number = {1},
pages = {477-487},
pmid = {18202389},
issn = {0016-6731},
support = {K99 GM080099/GM/NIGMS NIH HHS/United States ; R01 HG002942/HG/NHGRI NIH HHS/United States ; R01-HG002942/HG/NHGRI NIH HHS/United States ; 1K99-GM080099/GM/NIGMS NIH HHS/United States ; },
mesh = {Africa ; Animals ; Chromosomes/genetics ; Crossing Over, Genetic ; DNA/*genetics ; Drosophila melanogaster/classification/*genetics ; Molecular Sequence Data ; North America ; Polymorphism, Single Nucleotide/genetics ; Population Dynamics ; Telomere/*genetics ; },
abstract = {DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (approximately 80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.},
}

Africa
Animals
Chromosomes/genetics
Crossing Over, Genetic
DNA/*genetics
Drosophila melanogaster/classification/*genetics
Molecular Sequence Data
North America
Polymorphism, Single Nucleotide/genetics
Population Dynamics
Telomere/*genetics

@article {pmid18205615,
year = {2007},
author = {Aleshin, VV and Konstantinova, AV and Mikhailov, KV and Nikitin, MA and Petrov, NB},
title = {Do we need many genes for phylogenetic inference?.},
journal = {Biochemistry. Biokhimiia},
volume = {72},
number = {12},
pages = {1313-1323},
doi = {10.1134/s000629790712005x},
pmid = {18205615},
issn = {0006-2979},
mesh = {Animals ; Base Sequence ; Databases, Genetic ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Expressed Sequence Tags ; Genes/*genetics ; Humans ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Ribosomal Proteins/genetics ; },
abstract = {Fifty-six nuclear protein coding genes from Taxonomically Broad EST Database and other databases were selected for phylogenomic-based examination of alternative phylogenetic hypotheses concerning intergroup relationship between multicellular animals (Metazoa) and other representatives of Opisthokonta. The results of this work support sister group relationship between Metazoa and Choanoflagellata. Both of these groups form the taxon Holozoa along with the monophyletic Ichthyosporea or Mesomycetozoea (a group that includes Amoebidium parasiticum, Sphaeroforma arctica, and Capsaspora owczarzaki). These phylogenetic hypotheses receive high statistical support both when utilizing whole alignment and when only 5000 randomly selected alignment positions are used. The presented results suggest subdivision of Fungi into Eumycota and lower fungi, Chytridiomycota. The latter form a monophyletic group that comprises Chytridiales+Spizellomycetales+Blastocladiales (Batrachochytrium, Spizellomyces, Allomyces, Blastocladiella), contrary to the earlier reports based on the analysis of 18S rRNA and a limited set of protein coding genes. The phylogenetic distribution of genes coding for a ubiquitin-fused ribosomal protein S30 implies at least three independent cases of gene fusion: in the ancestors of Holozoa, in heterotrophic Heterokonta (Oomycetes and Blastocystis) and in the ancestors of Cryptophyta and Glaucophyta. Ubiquitin-like sequences fused with ribosomal protein S30 outside of Holozoa are not FUBI orthologs. Two independent events of FUBI replacement by the ubiquitin sequence were detected in the lineage of C. owczarzaki and in the monophyletic group of nematode worms Tylenchomorpha+Cephalobidae. Bursaphelenchus xylophilus (Aphelenchoidoidea) retains a state typical of the rest of the Metazoa. The data emphasize the fact that the reliability of phylogenetic reconstructions depends on the number of analyzed genes to a lesser extent than on our ability to recognize reconstruction artifacts.},
}

Animals
Base Sequence
Databases, Genetic
Eukaryotic Cells/metabolism
Evolution, Molecular
Expressed Sequence Tags
Genes/*genetics
Humans
Models, Genetic
*Phylogeny
RNA, Ribosomal, 18S/genetics
Ribosomal Proteins/genetics

@article {pmid18236175,
year = {2008},
author = {Rangan, L and Vogel, C and Srivastava, A},
title = {Analysis of context sequence surrounding translation initiation site from complete genome of model plants.},
journal = {Molecular biotechnology},
volume = {39},
number = {3},
pages = {207-213},
pmid = {18236175},
issn = {1073-6085},
mesh = {Arabidopsis/*genetics ; *Genome, Plant ; Humans ; Models, Genetic ; Oryza/*genetics ; *Protein Biosynthesis ; },
abstract = {Regions flanking the translation initiation site (TIS) are thought to play a crucial role in translation efficiency of mRNAs, but their exact sequence and evolution in eukaryotes are still a matter of debate. We investigated the context sequences in 20 nucleotides around the TIS in multi-cellular eukaryotes, with a focus on two model plants and a comparison to human. We identified consensus sequences aaaaaaa(A/G)(A/C)aAUGGcgaataata and ggcggc(g/c)(A/G)(A/C)(G/C)AUGGCggcggcgg for Arabidopsis thaliana and Oryza sativa, respectively. We observe strongly conserved G at position +4 and A or C at position -2; however, the exact nucleotide frequencies vary between the three organisms even at these conserved positions. The frequency of pyrimidines, which are considered sub optimum at position -3, is higher in both plants than in human. Arabidopsis is GC-depleted (AU-enriched) compared to both rice and human, and the enrichment is slightly stronger upstream than downstream of AUG. While both plants are similar though not identical in their variation of nucleotide frequencies, rice and human are more similar to each other than Arabidopsis and human. All three organisms display clear periodicity in A + G and C + U content when analyzing normalized frequencies. These findings suggest that, besides few highly conserved positions, overall structure of the context sequence plays a larger role in TIS recognition than the actual nucleotide frequencies.},
}

Arabidopsis/*genetics
*Genome, Plant
Humans
Models, Genetic
Oryza/*genetics
*Protein Biosynthesis

@article {pmid18272966,
year = {2008},
author = {Santorelli, LA and Thompson, CR and Villegas, E and Svetz, J and Dinh, C and Parikh, A and Sucgang, R and Kuspa, A and Strassmann, JE and Queller, DC and Shaulsky, G},
title = {Facultative cheater mutants reveal the genetic complexity of cooperation in social amoebae.},
journal = {Nature},
volume = {451},
number = {7182},
pages = {1107-1110},
doi = {10.1038/nature06558},
pmid = {18272966},
issn = {1476-4687},
support = {G0400103/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Amoeba/genetics/physiology ; Animals ; Cell Aggregation ; Chimera/genetics/physiology ; *Cooperative Behavior ; Dictyostelium/cytology/*genetics/*physiology ; Genes, Protozoan/genetics ; Genome/genetics ; Genomics ; Mutation/*genetics ; Myxococcus xanthus/genetics/physiology ; Phenotype ; *Social Behavior ; Spores, Protozoan/genetics/physiology ; },
abstract = {Cooperation is central to many major transitions in evolution, including the emergence of eukaryotic cells, multicellularity and eusociality. Cooperation can be destroyed by the spread of cheater mutants that do not cooperate but gain the benefits of cooperation from others. However, cooperation can be preserved if cheaters are facultative, cheating others but cooperating among themselves. Several cheater mutants have been studied before, but no study has attempted a genome-scale investigation of the genetic opportunities for cheating. Here we describe such a screen in a social amoeba and show that cheating is multifaceted by revealing cheater mutations in well over 100 genes of diverse types. Many of these mutants cheat facultatively, producing more than their fair share of spores in chimaeras, but cooperating normally when clonal. These findings indicate that phenotypically stable cooperative systems may nevertheless harbour genetic conflicts. The opportunities for evolutionary moves and countermoves in such conflicts may select for the involvement of multiple pathways and numerous genes.},
}

Amoeba/genetics/physiology
Animals
Cell Aggregation
Chimera/genetics/physiology
*Cooperative Behavior
Dictyostelium/cytology/*genetics/*physiology
Genes, Protozoan/genetics
Genome/genetics
Genomics
Mutation/*genetics
Myxococcus xanthus/genetics/physiology
Phenotype
*Social Behavior
Spores, Protozoan/genetics/physiology

@article {pmid18273011,
year = {2008},
author = {King, N and Westbrook, MJ and Young, SL and Kuo, A and Abedin, M and Chapman, J and Fairclough, S and Hellsten, U and Isogai, Y and Letunic, I and Marr, M and Pincus, D and Putnam, N and Rokas, A and Wright, KJ and Zuzow, R and Dirks, W and Good, M and Goodstein, D and Lemons, D and Li, W and Lyons, JB and Morris, A and Nichols, S and Richter, DJ and Salamov, A and Sequencing, JG and Bork, P and Lim, WA and Manning, G and Miller, WT and McGinnis, W and Shapiro, H and Tjian, R and Grigoriev, IV and Rokhsar, D},
title = {The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.},
journal = {Nature},
volume = {451},
number = {7180},
pages = {783-788},
pmid = {18273011},
issn = {1476-4687},
support = {R01 CA058530/CA/NCI NIH HHS/United States ; R01 GM077197/GM/NIGMS NIH HHS/United States ; R01 HG004164/HG/NHGRI NIH HHS/United States ; R37 HD028315/HD/NICHD NIH HHS/United States ; },
mesh = {Animals ; Cell Adhesion ; Conserved Sequence ; Eukaryotic Cells/classification/cytology/*metabolism ; Evolution, Molecular ; Extracellular Matrix/metabolism ; Gene Expression Regulation ; Genetic Speciation ; Genome/*genetics ; Hedgehog Proteins/chemistry/genetics ; Humans ; Introns/genetics ; Phosphotyrosine/metabolism ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Receptors, Notch/chemistry/genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; },
abstract = {Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.},
}

Animals
Cell Adhesion
Conserved Sequence
Eukaryotic Cells/classification/cytology/*metabolism
Evolution, Molecular
Extracellular Matrix/metabolism
Gene Expression Regulation
Genetic Speciation
Genome/*genetics
Hedgehog Proteins/chemistry/genetics
Humans
Introns/genetics
Phosphotyrosine/metabolism
*Phylogeny
Protein Structure, Tertiary/genetics
Receptors, Notch/chemistry/genetics
Signal Transduction/genetics
Transcription Factors/genetics/metabolism
Transcription, Genetic

@article {pmid18275891,
year = {2008},
author = {Yan, D and Olkkonen, VM},
title = {Characteristics of oxysterol binding proteins.},
journal = {International review of cytology},
volume = {265},
number = {},
pages = {253-285},
doi = {10.1016/S0074-7696(07)65007-4},
pmid = {18275891},
issn = {0074-7696},
mesh = {Animals ; Biological Transport ; Cell Membrane/chemistry/*metabolism ; Golgi Apparatus ; Humans ; Lipid Metabolism/*physiology ; Receptors, Steroid/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; Signal Transduction/*physiology ; Sterols/chemistry/*metabolism ; Oxysterol Binding Proteins ; },
abstract = {Protein families characterized by a ligand binding domain related to that of oxysterol binding protein (OSBP) have been identified in eukaryotic species from yeast to humans. These proteins, designated OSBP-related (ORP) or OSBP-like (OSBPL) proteins, have been implicated in various cellular functions. However, the detailed mechanisms of their action have remained elusive. Data from our and other laboratories suggest that binding of sterol ligands may be a unifying theme. Work with Saccharomyces cerevisiae ORPs suggests a function of these proteins in the nonvesicular intracellular transport of sterols, in secretory vesicle transport from the Golgi complex, and in the establishment of cell polarity. Mammals have more ORP genes, and differential splicing substantially increases the complexity of the encoded protein family. Functional studies on mammalian ORPs point in different directions: integration of sterol and sphingomyelin metabolism, sterol transport, regulation of neutral lipid metabolism, control of the microtubule-dependent motility of endosomes/lysosomes, and regulation of signaling cascades. We envision that during evolution, the functions of ORPs have diverged from an ancestral one in sterol transport, to meet the increasing demand of the regulatory potential in multicellular organisms. Our working hypothesis is that mammalian ORPs mainly act as sterol sensors that relay information to a spectrum of different cellular processes.},
}

Animals
Biological Transport
Cell Membrane/chemistry/*metabolism
Golgi Apparatus
Humans
Lipid Metabolism/*physiology
Receptors, Steroid/chemistry/*metabolism
Saccharomyces cerevisiae/metabolism
Signal Transduction/*physiology
Sterols/chemistry/*metabolism
Oxysterol Binding Proteins

@article {pmid18276888,
year = {2008},
author = {Abedin, M and King, N},
title = {The premetazoan ancestry of cadherins.},
journal = {Science (New York, N.Y.)},
volume = {319},
number = {5865},
pages = {946-948},
doi = {10.1126/science.1151084},
pmid = {18276888},
issn = {1095-9203},
mesh = {Actin Cytoskeleton/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cadherins/*chemistry/*genetics/physiology ; Cell Adhesion ; Ciona intestinalis/chemistry ; Cnidaria/chemistry ; Drosophila melanogaster/chemistry ; Eukaryota/*chemistry ; Eukaryotic Cells/*chemistry/physiology ; Mice ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Signal Transduction ; Tyrosine/metabolism ; src Homology Domains ; },
abstract = {Cadherin-mediated cell adhesion and signaling is essential for metazoan development and yet is absent from all other multicellular organisms. We found cadherin genes at numbers similar to those observed in complex metazoans in one of the closest single-celled relatives of metazoans, the choanoflagellate Monosiga brevicollis. Because the evolution of metazoans from a single-celled ancestor required novel cell adhesion and signaling mechanisms, the discovery of diverse cadherins in choanoflagellates suggests that cadherins may have contributed to metazoan origins.},
}

Actin Cytoskeleton/metabolism
Amino Acid Sequence
Animals
Base Sequence
*Biological Evolution
Cadherins/*chemistry/*genetics/physiology
Cell Adhesion
Ciona intestinalis/chemistry
Cnidaria/chemistry
Drosophila melanogaster/chemistry
Eukaryota/*chemistry
Eukaryotic Cells/*chemistry/physiology
Mice
Molecular Sequence Data
Protein Structure, Tertiary
Repetitive Sequences, Amino Acid
Signal Transduction
Tyrosine/metabolism
src Homology Domains

@article {pmid18285453,
year = {2008},
author = {Déry, U and Coulombe, Y and Rodrigue, A and Stasiak, A and Richard, S and Masson, JY},
title = {A glycine-arginine domain in control of the human MRE11 DNA repair protein.},
journal = {Molecular and cellular biology},
volume = {28},
number = {9},
pages = {3058-3069},
pmid = {18285453},
issn = {1098-5549},
mesh = {Acid Anhydride Hydrolases ; Amino Acid Motifs ; Animals ; Arginine/*metabolism ; Cell Cycle Proteins/metabolism ; Cell Line ; *DNA Breaks, Double-Stranded ; *DNA Repair ; DNA Repair Enzymes/metabolism ; DNA-Binding Proteins/genetics/metabolism/*physiology ; Glycine/*metabolism ; Histones/metabolism ; Humans ; MRE11 Homologue Protein ; Methylation ; Nuclear Proteins/metabolism ; Protein Binding ; Protein-Arginine N-Methyltransferases/metabolism ; Rad51 Recombinase/metabolism ; Recombinant Proteins/metabolism ; Repressor Proteins/metabolism ; },
abstract = {Human MRE11 is a key enzyme in DNA double-strand break repair and genome stability. Human MRE11 bears a glycine-arginine-rich (GAR) motif that is conserved among multicellular eukaryotic species. We investigated how this motif influences MRE11 function. Human MRE11 alone or a complex of MRE11, RAD50, and NBS1 (MRN) was methylated in insect cells, suggesting that this modification is conserved during evolution. We demonstrate that PRMT1 interacts with MRE11 but not with the MRN complex, suggesting that MRE11 arginine methylation occurs prior to the binding of NBS1 and RAD50. Moreover, the first six methylated arginines are essential for the regulation of MRE11 DNA binding and nuclease activity. The inhibition of arginine methylation leads to a reduction in MRE11 and RAD51 focus formation on a unique double-strand break in vivo. Furthermore, the MRE11-methylated GAR domain is sufficient for its targeting to DNA damage foci and colocalization with gamma-H2AX. These studies highlight an important role for the GAR domain in regulating MRE11 function at the biochemical and cellular levels during DNA double-strand break repair.},
}

Acid Anhydride Hydrolases
Amino Acid Motifs
Animals
Arginine/*metabolism
Cell Cycle Proteins/metabolism
Cell Line
*DNA Breaks, Double-Stranded
*DNA Repair
DNA Repair Enzymes/metabolism
DNA-Binding Proteins/genetics/metabolism/*physiology
Glycine/*metabolism
Histones/metabolism
Humans
MRE11 Homologue Protein
Methylation
Nuclear Proteins/metabolism
Protein Binding
Protein-Arginine N-Methyltransferases/metabolism
Rad51 Recombinase/metabolism
Recombinant Proteins/metabolism
Repressor Proteins/metabolism

@article {pmid18315817,
year = {2008},
author = {Nielsen, C},
title = {Six major steps in animal evolution: are we derived sponge larvae?.},
journal = {Evolution & development},
volume = {10},
number = {2},
pages = {241-257},
doi = {10.1111/j.1525-142X.2008.00231.x},
pmid = {18315817},
issn = {1525-142X},
mesh = {Animals ; *Biological Evolution ; Cnidaria/growth & development ; Ctenophora/growth & development ; Digestive System/growth & development ; Epithelium/growth & development ; Eukaryota/cytology ; Female ; Gastrulation ; Invertebrates/growth & development ; Larva/growth & development ; Male ; Mesoderm/growth & development ; Models, Biological ; Nervous System/growth & development ; Phylogeny ; Porifera/cytology/embryology/genetics/*growth & development ; },
abstract = {A review of the old and new literature on animal morphology/embryology and molecular studies has led me to the following scenario for the early evolution of the metazoans. The metazoan ancestor, "choanoblastaea," was a pelagic sphere consisting of choanocytes. The evolution of multicellularity enabled division of labor between cells, and an "advanced choanoblastaea" consisted of choanocytes and nonfeeding cells. Polarity became established, and an adult, sessile stage developed. Choanocytes of the upper side became arranged in a groove with the cilia pumping water along the groove. Cells overarched the groove so that a choanocyte chamber was formed, establishing the body plan of an adult sponge; the pelagic larval stage was retained but became lecithotrophic. The sponges radiated into monophyletic Silicea, Calcarea, and Homoscleromorpha. Homoscleromorph larvae show cell layers resembling true, sealed epithelia. A homoscleromorph-like larva developed an archenteron, and the sealed epithelium made extracellular digestion possible in this isolated space. This larva became sexually mature, and the adult sponge-stage was abandoned in an extreme progenesis. This eumetazoan ancestor, "gastraea," corresponds to Haeckel's gastraea. Trichoplax represents this stage, but with the blastopore spread out so that the endoderm has become the underside of the creeping animal. Another lineage developed a nervous system; this "neurogastraea" is the ancestor of the Neuralia. Cnidarians have retained this organization, whereas the Triploblastica (Ctenophora+Bilateria), have developed the mesoderm. The bilaterians developed bilaterality in a primitive form in the Acoelomorpha and in an advanced form with tubular gut and long Hox cluster in the Eubilateria (Protostomia+Deuterostomia). It is indicated that the major evolutionary steps are the result of suites of existing genes becoming co-opted into new networks that specify new structures. The evolution of the eumetazoan ancestor from a progenetic homoscleromorph larva implies that we, as well as all the other eumetazoans, are derived sponge larvae.},
}

Animals
*Biological Evolution
Cnidaria/growth & development
Ctenophora/growth & development
Digestive System/growth & development
Epithelium/growth & development
Eukaryota/cytology
Female
Gastrulation
Invertebrates/growth & development
Larva/growth & development
Male
Mesoderm/growth & development
Models, Biological
Nervous System/growth & development
Phylogeny
Porifera/cytology/embryology/genetics/*growth & development

@article {pmid18318857,
year = {2008},
author = {Leander, BS},
title = {A hierarchical view of convergent evolution in microbial eukaryotes.},
journal = {The Journal of eukaryotic microbiology},
volume = {55},
number = {2},
pages = {59-68},
doi = {10.1111/j.1550-7408.2008.00308.x},
pmid = {18318857},
issn = {1066-5234},
mesh = {Animals ; *Biological Evolution ; *Eukaryota ; *Eukaryotic Cells ; *Phylogeny ; },
abstract = {Distinguishing convergent evolution from other causes of similarity in organisms is necessary for reconstructing phylogenetic relationships, inferring patterns of character evolution, and investigating the forces of natural selection. In contrast to animals and land plants, the pervasiveness and adaptive significance of convergent evolution in microbes has yet to be systematically explored or articulated. Convergent evolution in microbial eukaryotes, for instance, often involves very distantly related lineages with relatively limited repertoires of morphological features. These large phylogenetic distances weaken the role of ancestral developmental programs on the subsequent evolution of morphological characters, making convergent evolution between very distantly related lineages fundamentally different from convergent evolution between closely related lineages. This suggests that examples of convergence at different levels in the phylogenetic hierarchy offer different clues about the causes and processes of macroevolutionary diversification. Accordingly (and despite opinions to the contrary), I recognize three broad and overlapping categories of phenotypic convergence-"parallel", "proximate" and "ultimate"-that represent either (1) subcellular analogues, (2) subcellular analogues to multicellular systems (and vice versa), or (3) multicellular analogues. Microbial eukaryotes living in planktonic environments, interstitial environments, and the intestinal environments of metazoan hosts provide compelling examples of ultimate convergence. After describing selected examples in microbial eukaryotes, I suggest some future directions needed to more fully understand the hierarchical structure of convergent evolution and the overall history of life.},
}

Animals
*Biological Evolution
*Eukaryota
*Eukaryotic Cells
*Phylogeny

@article {pmid18321378,
year = {2008},
author = {McGuire, AM and Pearson, MD and Neafsey, DE and Galagan, JE},
title = {Cross-kingdom patterns of alternative splicing and splice recognition.},
journal = {Genome biology},
volume = {9},
number = {3},
pages = {R50},
pmid = {18321378},
issn = {1474-760X},
support = {HHSN26620040001C//PHS HHS/United States ; },
mesh = {*Alternative Splicing ; Animals ; Base Sequence ; *Evolution, Molecular ; Exons ; Expressed Sequence Tags ; Genome ; *Introns ; Phylogeny ; *RNA Splice Sites ; *Transcription, Genetic ; },
abstract = {BACKGROUND: Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of splice site recognition inconsistently identifies intron-exon boundaries, and cassette exons (CEs) are often caused by variable recognition of splice junctions by the exon definition (ED) mechanism. We have performed a comprehensive survey of alternative splicing across 42 eukaryotes to gain insight into how spliceosomal introns are recognized.

RESULTS: All eukaryotes we studied exhibit RIs, which appear more frequently than previously thought. CEs are also present in all kingdoms and most of the organisms in our analysis. We observe that the ratio of CEs to RIs varies substantially among kingdoms, while the ratio of competing 3' acceptor and competing 5' donor sites remains nearly constant. In addition, we find the ratio of CEs to RIs in each organism correlates with the length of its introns. In all 14 fungi we examined, as well as in most of the 9 protists, RIs far outnumber CEs. This differs from the trend seen in 13 multicellular animals, where CEs occur much more frequently than RIs. The six plants we analyzed exhibit intermediate proportions of CEs and RIs.

CONCLUSION: Our results suggest that most extant eukaryotes are capable of recognizing splice sites via both ID and ED, although ED is most common in multicellular animals and ID predominates in fungi and most protists.},
}

*Alternative Splicing
Animals
Base Sequence
*Evolution, Molecular
Exons
Expressed Sequence Tags
Genome
*Introns
Phylogeny
*RNA Splice Sites
*Transcription, Genetic

@article {pmid18390552,
year = {2008},
author = {Li, W and Young, SL and King, N and Miller, WT},
title = {Signaling properties of a non-metazoan Src kinase and the evolutionary history of Src negative regulation.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {22},
pages = {15491-15501},
pmid = {18390552},
issn = {0021-9258},
support = {R01 CA058530/CA/NCI NIH HHS/United States ; CA 58530/CA/NCI NIH HHS/United States ; },
mesh = {Amino Acid Sequence ; Animals ; CSK Tyrosine-Protein Kinase ; Eukaryota/*enzymology/genetics ; *Evolution, Molecular ; Mammals/genetics/metabolism ; Molecular Sequence Data ; Protein-Tyrosine Kinases/genetics/metabolism ; Protozoan Proteins/genetics/*metabolism ; Signal Transduction/*physiology ; src Homology Domains/physiology ; src-Family Kinases/genetics/*metabolism ; },
abstract = {Choanoflagellates, unicellular organisms that are closely related to metazoans, possess cell adhesion and signaling proteins previously thought to be unique to animals, suggesting that these components may have played roles in the evolution of metazoan multicellularity. We have cloned, expressed, and purified the nonreceptor tyrosine kinase MbSrc1 from the choanoflagellate Monosiga brevicollis. The kinase has the same domain arrangement as mammalian Src kinases, and we find that the individual Src homology 3 (SH3), SH2, and catalytic domains have similar functions to their mammalian counterparts. In contrast to mammalian c-Src, the SH2 and catalytic domains of MbSrc1 do not appear to be functionally coupled. We cloned and expressed the M. brevicollis homolog of c-Src C-terminal kinase (MbCsk) and showed that it phosphorylates the C terminus of MbSrc1, yet this phosphorylation does not inhibit MbSrc to the same degree seen in the mammalian Src/Csk pair. Thus, Src autoinhibition likely evolved more recently within the metazoan lineage, and it may have played a role in the establishment of intercellular signaling in metazoans.},
}

Amino Acid Sequence
Animals
CSK Tyrosine-Protein Kinase
Eukaryota/*enzymology/genetics
*Evolution, Molecular
Mammals/genetics/metabolism
Molecular Sequence Data
Protein-Tyrosine Kinases/genetics/metabolism
Protozoan Proteins/genetics/*metabolism
Signal Transduction/*physiology
src Homology Domains/physiology
src-Family Kinases/genetics/*metabolism

@article {pmid18461162,
year = {2008},
author = {Shalchian-Tabrizi, K and Minge, MA and Espelund, M and Orr, R and Ruden, T and Jakobsen, KS and Cavalier-Smith, T},
title = {Multigene phylogeny of choanozoa and the origin of animals.},
journal = {PloS one},
volume = {3},
number = {5},
pages = {e2098},
pmid = {18461162},
issn = {1932-6203},
mesh = {Animals ; Cell Adhesion ; Dinoflagellida/classification/genetics/physiology ; Eukaryota/*classification/*genetics/physiology ; Evolution, Molecular ; Genetic Variation ; Humans ; *Origin of Life ; *Phylogeny ; Protein-Tyrosine Kinases/metabolism ; Signal Transduction ; Species Specificity ; },
abstract = {Animals are evolutionarily related to fungi and to the predominantly unicellular protozoan phylum Choanozoa, together known as opisthokonts. To establish the sequence of events when animals evolved from unicellular ancestors, and understand those key evolutionary transitions, we need to establish which choanozoans are most closely related to animals and also the evolutionary position of each choanozoan group within the opisthokont phylogenetic tree. Here we focus on Ministeria vibrans, a minute bacteria-eating cell with slender radiating tentacles. Single-gene trees suggested that it is either the closest unicellular relative of animals or else sister to choanoflagellates, traditionally considered likely animal ancestors. Sequencing thousands of Ministeria protein genes now reveals about 14 with domains of key significance for animal cell biology, including several previously unknown from deeply diverging Choanozoa, e.g. domains involved in hedgehog, Notch and tyrosine kinase signaling or cell adhesion (cadherin). Phylogenetic trees using 78 proteins show that Ministeria is not sister to animals or choanoflagellates (themselves sisters to animals), but to Capsaspora, another protozoan with thread-like (filose) tentacles. The Ministeria/Capsaspora clade (new class Filasterea) is sister to animals and choanoflagellates, these three groups forming a novel clade (filozoa) whose ancestor presumably evolved filose tentacles well before they aggregated as a periciliary collar in the choanoflagellate/sponge common ancestor. Our trees show ichthyosporean choanozoans as sisters to filozoa; a fusion between ubiquitin and ribosomal small subunit S30 protein genes unifies all holozoa (filozoa plus Ichthyosporea), being absent in earlier branching eukaryotes. Thus, several successive evolutionary innovations occurred among their unicellular closest relatives prior to the origin of the multicellular body-plan of animals.},
}

Animals
Cell Adhesion
Dinoflagellida/classification/genetics/physiology
Eukaryota/*classification/*genetics/physiology
Evolution, Molecular
Genetic Variation
Humans
*Origin of Life
*Phylogeny
Protein-Tyrosine Kinases/metabolism
Signal Transduction
Species Specificity

@article {pmid18493051,
year = {2008},
author = {Wheeler, GL and Miranda-Saavedra, D and Barton, GJ},
title = {Genome analysis of the unicellular green alga Chlamydomonas reinhardtii Indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families.},
journal = {Genetics},
volume = {179},
number = {1},
pages = {193-197},
pmid = {18493051},
issn = {0016-6731},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Algal Proteins/*genetics ; Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*genetics ; Conserved Sequence/genetics ; *Evolution, Molecular ; Genomics ; Molecular Sequence Data ; Multigene Family/*genetics ; *Protein Structure, Tertiary ; Protein-Tyrosine Kinases/genetics ; Signal Transduction/*genetics ; Species Specificity ; },
abstract = {The evolution of specific cell signaling and adhesion domains may have played an important role in the transition to a multicellular existence in the metazoans. Genomic analysis indicates that several signaling domains predominately found in animals are also present in the unicellular green alga, Chlamydomonas reinhardtii. A large group of proteins is present, containing scavenger receptor cysteine-rich (SRCR) and C-type lectin domains, which function in ligand binding and play key roles in the innate immune system of animals. Chlamydomonas also contains a large family of putative tyrosine kinases, suggesting an important role for phosphotyrosine signaling in the green algae. These important signaling domains may therefore be widespread among eukaryotes and most probably evolved in ancestral eukaryotes before the divergence of the Opisthokonts (the animal and fungal lineage).},
}

Algal Proteins/*genetics
Amino Acid Sequence
Animals
Chlamydomonas reinhardtii/*genetics
Conserved Sequence/genetics
*Evolution, Molecular
Genomics
Molecular Sequence Data
Multigene Family/*genetics
*Protein Structure, Tertiary
Protein-Tyrosine Kinases/genetics
Signal Transduction/*genetics
Species Specificity

@article {pmid18511852,
year = {2008},
author = {Cooper, EL},
title = {From Darwin and Metchnikoff to Burnet and beyond.},
journal = {Contributions to microbiology},
volume = {15},
number = {},
pages = {1-11},
doi = {10.1159/000135680},
pmid = {18511852},
issn = {1420-9519},
mesh = {Animals ; Biological Evolution ; Cnidaria/genetics/*immunology/physiology ; Eukaryota/genetics/*immunology/physiology ; Immunity, Innate ; *Phagocytosis ; Porifera/genetics/*immunology/physiology ; Signal Transduction ; Toll-Like Receptors/genetics/immunology ; },
abstract = {Phagocytosis in unicellular animals represents the most ancient and ubiquitous form of defense against foreign material. Unicellular invertebrates can phagocytose for food and defense. Multicellular invertebrates and vertebrates possess phagocytic cells and have evolved more complex functions attributed to immunodefense cells that specialized into cellular and humoral immune responses. Thus all animals possess: innate, natural, nonspecific (no memory) nonanticipatory, nonclonal, germline (hard wired) host defense functions. In addition, all vertebrates possess: adaptive, induced, specific (memory), anticipatory, clonal, somatic (flexible) immune responses. A similar situation exists with respect to components of the signaling system, immunity and development. With multicellularity, clearly numerous immune response characteristics are not possible in unicellular forms or even those that straddle the divide between unicellularity and multicellularity, beginning with colonial/social protozoans. Still, it is instructive to elucidate a hierarchy of animals based upon immunologic characteristics and how they parallel other physiological traits. Evidence is presented that the most primitive of invertebrates prior to the evolution of multicellular organisms possess varying degrees of complexity at the molecular level of those hallmarks that now characterize the immune system.},
}

Animals
Biological Evolution
Cnidaria/genetics/*immunology/physiology
Eukaryota/genetics/*immunology/physiology
Immunity, Innate
*Phagocytosis
Porifera/genetics/*immunology/physiology
Signal Transduction
Toll-Like Receptors/genetics/immunology

@article {pmid18541214,
year = {2008},
author = {Gottwein, E and Cullen, BR},
title = {Viral and cellular microRNAs as determinants of viral pathogenesis and immunity.},
journal = {Cell host & microbe},
volume = {3},
number = {6},
pages = {375-387},
pmid = {18541214},
issn = {1934-6069},
support = {R56 AI067968/AI/NIAID NIH HHS/United States ; GM071408/GM/NIGMS NIH HHS/United States ; R01 AI067968/AI/NIAID NIH HHS/United States ; AI067968/AI/NIAID NIH HHS/United States ; R01 GM071408/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; Evolution, Molecular ; Gene Expression/drug effects ; Gene Expression Regulation, Viral/drug effects ; *Host-Pathogen Interactions ; Humans ; MicroRNAs/*genetics/metabolism/pharmacology ; RNA, Viral/genetics/metabolism ; Sequence Alignment ; Virus Diseases/genetics/*immunology ; *Virus Physiological Phenomena ; Viruses/genetics/immunology/*pathogenicity ; },
abstract = {MicroRNAs (miRNAs) have recently emerged as key posttranscriptional regulators of gene expression in multicellular eukaryotes. It is increasingly clear that miRNAs of both viral and cellular origin can positively or negatively influence viral replication. Viral miRNAs can directly alter host physiology, including components of the immune system, and host miRNAs can directly alter the virus life cycle. Here, we discuss what is known about how viral and cellular miRNAs influence viral replication and pathogenic potential through their regulation of viral mRNAs or by reshaping cellular gene expression.},
}

Animals
Base Sequence
Evolution, Molecular
Gene Expression/drug effects
Gene Expression Regulation, Viral/drug effects
*Host-Pathogen Interactions
Humans
MicroRNAs/*genetics/metabolism/pharmacology
RNA, Viral/genetics/metabolism
Sequence Alignment
Virus Diseases/genetics/*immunology
*Virus Physiological Phenomena
Viruses/genetics/immunology/*pathogenicity

@article {pmid18593478,
year = {2008},
author = {Veerappan, CS and Avramova, Z and Moriyama, EN},
title = {Evolution of SET-domain protein families in the unicellular and multicellular Ascomycota fungi.},
journal = {BMC evolutionary biology},
volume = {8},
number = {},
pages = {190},
pmid = {18593478},
issn = {1471-2148},
mesh = {Animals ; Ascomycota/*genetics ; Conserved Sequence ; *Evolution, Molecular ; Genes, Fungal/*genetics ; Genome, Fungal ; Methyltransferases/genetics ; Multigene Family/*genetics ; Phylogeny ; Protein Structure, Tertiary ; },
abstract = {BACKGROUND: The evolution of multicellularity is accompanied by the occurrence of differentiated tissues, of organismal developmental programs, and of mechanisms keeping the balance between proliferation and differentiation. Initially, the SET-domain proteins were associated exclusively with regulation of developmental genes in metazoa. However, finding of SET-domain genes in the unicellular yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that SET-domain proteins regulate a much broader variety of biological programs. Intuitively, it is expected that the numbers, types, and biochemical specificity of SET-domain proteins of multicellular versus unicellular forms would reflect the differences in their biology. However, comparisons across the unicellular and multicellular domains of life are complicated by the lack of knowledge of the ancestral SET-domain genes. Even within the crown group, different biological systems might use the epigenetic 'code' differently, adapting it to organism-specific needs. Simplifying the model, we undertook a systematic phylogenetic analysis of one monophyletic fungal group (Ascomycetes) containing unicellular yeasts, Saccharomycotina (hemiascomycetes), and a filamentous fungal group, Pezizomycotina (euascomycetes).

RESULTS: Systematic analysis of the SET-domain genes across an entire eukaryotic phylum has outlined clear distinctions in the SET-domain gene collections in the unicellular and in the multicellular (filamentous) relatives; diversification of SET-domain gene families has increased further with the expansion and elaboration of multicellularity in animal and plant systems. We found several ascomycota-specific SET-domain gene groups; each was unique to either Saccharomycotina or Pezizomycotina fungi. Our analysis revealed that the numbers and types of SET-domain genes in the Saccharomycotina did not reflect the habitats, pathogenicity, mechanisms of sexuality, or the ability to undergo morphogenic transformations. However, novel genes have appeared for functions associated with the transition to multicellularity. Descendents of most of the SET-domain gene families found in the filamentous fungi could be traced in the genomes of extant animals and plants, albeit as more complex structural forms.

CONCLUSION: SET-domain genes found in the filamentous species but absent from the unicellular sister group reflect two alternative evolutionary events: deletion from the yeast genomes or appearance of novel structures in filamentous fungal groups. There were no Ascomycota-specific SET-domain gene families (i.e., absent from animal and plant genomes); however, plants and animals share SET-domain gene subfamilies that do not exist in the fungi. Phylogenetic and gene-structure analyses defined several animal and plant SET-domain genes as sister groups while those of fungal origin were basal to them. Plants and animals also share SET-domain subfamilies that do not exist in fungi.},
}

Animals
Ascomycota/*genetics
Conserved Sequence
*Evolution, Molecular
Genes, Fungal/*genetics
Genome, Fungal
Methyltransferases/genetics
Multigene Family/*genetics
Phylogeny
Protein Structure, Tertiary

@article {pmid18599463,
year = {2008},
author = {Pincus, D and Letunic, I and Bork, P and Lim, WA},
title = {Evolution of the phospho-tyrosine signaling machinery in premetazoan lineages.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {28},
pages = {9680-9684},
pmid = {18599463},
issn = {1091-6490},
mesh = {Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Genome/genetics ; Phylogeny ; Protein Tyrosine Phosphatases/*genetics ; Protein-Tyrosine Kinases/*genetics ; Signal Transduction/*genetics ; src Homology Domains ; },
abstract = {Multicellular animals use a three-part molecular toolkit to mediate phospho-tyrosine signaling: Tyrosine kinases (TyrK), protein tyrosine phosphatases (PTP), and Src Homology 2 (SH2) domains function, respectively, as "writers," "erasers," and "readers" of phospho-tyrosine modifications. How did this system of three components evolve, given their interdependent function? Here, we examine the usage of these components in 41 eukaryotic genomes, including the newly sequenced genome of the choanoflagellate, Monosiga brevicollis, the closest known unicellular relative to metazoans. This analysis indicates that SH2 and PTP domains likely evolved earliest-a handful of these domains are found in premetazoan eukaryotes lacking tyrosine kinases, most likely to deal with limited tyrosine phosphorylation cross-catalyzed by promiscuous Ser/Thr kinases. Modern TyrK proteins, however, are only observed in two lineages, metazoans and choanoflagellates. These two lineages show a dramatic coexpansion of all three domain families. Concurrent expansion of the three domain families is consistent with a stepwise evolutionary model in which preexisting SH2 and PTP domains were of limited utility until the appearance of the TyrK domain in the last common ancestor of metazoans and choanoflagellates. The emergence of the full three-component signaling system, with its dramatically increased encoding potential, may have contributed to the advent of metazoan multicellularity.},
}

Animals
Eukaryota/genetics
*Evolution, Molecular
Genome/genetics
Phylogeny
Protein Tyrosine Phosphatases/*genetics
Protein-Tyrosine Kinases/*genetics
Signal Transduction/*genetics
src Homology Domains

@article {pmid18613816,
year = {2008},
author = {Franklin-Tong, VE and Gourlay, CW},
title = {A role for actin in regulating apoptosis/programmed cell death: evidence spanning yeast, plants and animals.},
journal = {The Biochemical journal},
volume = {413},
number = {3},
pages = {389-404},
doi = {10.1042/BJ20080320},
pmid = {18613816},
issn = {1470-8728},
support = {G0600085/MRC_/Medical Research Council/United Kingdom ; 78573/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Actins/genetics/metabolism/*physiology ; Animals ; Apoptosis/genetics/*physiology ; Mitochondria/metabolism ; Models, Biological ; Plants/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; Yeasts/genetics/*metabolism ; },
abstract = {Achieving an understanding of how apoptosis/PCD (programmed cell death) is integrated within cellular responses to environmental and intracellular signals is a daunting task. From the sensation of a stimulus to the point of no return, a programme of cell death must engage specific pro-death components, whose effects can in turn be enhanced or repressed by downstream regulatory factors. In recent years, considerable progress has been made in our understanding of how components involved in these processes function. We now know that some of the factors involved in PCD networks have ancient origins that pre-date multicellularity and, indeed, eukaryotes themselves. A subject attracting much attention is the role that the actin cytoskeleton, itself a cellular component with ancient origins, plays in cell death regulation. Actin, a key cellular component, has an established role as a cellular sensor, with reorganization and alterations in actin dynamics being a well known consequence of signalling. A range of studies have revealed that actin also plays a key role in apoptosis/PCD regulation. Evidence implicating actin as a regulator of eukaryotic cell death has emerged from studies from the Animal, Plant and Fungal Kingdoms. Here we review recent data that provide evidence for an active, functional role for actin in determining whether PCD is triggered and executed, and discuss these findings within the context of regulation of actin dynamics.},
}

Actins/genetics/metabolism/*physiology
Animals
Apoptosis/genetics/*physiology
Mitochondria/metabolism
Models, Biological
Plants/genetics/*metabolism
Reactive Oxygen Species/metabolism
Yeasts/genetics/*metabolism

@article {pmid18621719,
year = {2008},
author = {Manning, G and Young, SL and Miller, WT and Zhai, Y},
title = {The protist, Monosiga brevicollis, has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {28},
pages = {9674-9679},
pmid = {18621719},
issn = {1091-6490},
support = {P30 CA014195/CA/NCI NIH HHS/United States ; R01 CA058530/CA/NCI NIH HHS/United States ; R01 HG004164/HG/NHGRI NIH HHS/United States ; 1 R01 HG004164-01/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; Eukaryota/*enzymology/genetics ; Evolution, Molecular ; Genome, Protozoan ; Genomics ; Phylogeny ; Protein-Tyrosine Kinases/*genetics ; *Signal Transduction ; },
abstract = {Tyrosine kinase signaling has long been considered a hallmark of intercellular communication, unique to multicellular animals. Our genomic analysis of the unicellular choanoflagellate Monosiga brevicollis discovers a remarkable count of 128 tyrosine kinases, 38 tyrosine phosphatases, and 123 phosphotyrosine (pTyr)-binding SH2 proteins, all higher counts than seen in any metazoan. This elaborate signaling network shows little orthology to metazoan counterparts yet displays many innovations reminiscent of metazoans. These include extracellular domains structurally related to those of metazoan receptor kinases, alternative methods for membrane anchoring and phosphotyrosine interaction in cytoplasmic kinases, and domain combinations that link kinases to small GTPase signaling and transcription. These proteins also display a wealth of combinations of known signaling domains. This uniquely divergent and elaborate signaling network illuminates the early evolution of pTyr signaling, explores innovative ways to traverse the cellular signaling circuitry, and shows extensive convergent evolution, highlighting pervasive constraints on pTyr signaling.},
}

Animals
Eukaryota/*enzymology/genetics
Evolution, Molecular
Genome, Protozoan
Genomics
Phylogeny
Protein-Tyrosine Kinases/*genetics
*Signal Transduction

@article {pmid18621745,
year = {2008},
author = {Kloepper, TH and Kienle, CN and Fasshauer, D},
title = {SNAREing the basis of multicellularity: consequences of protein family expansion during evolution.},
journal = {Molecular biology and evolution},
volume = {25},
number = {9},
pages = {2055-2068},
doi = {10.1093/molbev/msn151},
pmid = {18621745},
issn = {1537-1719},
mesh = {Animals ; Endosomes/metabolism ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Expressed Sequence Tags ; Fishes/genetics ; Gene Deletion ; Gene Duplication ; Genome ; Humans ; Invertebrates/genetics ; Phylogeny ; SNARE Proteins/classification/*genetics/physiology ; Vertebrates/genetics ; },
abstract = {Vesicle trafficking between intracellular compartments of eukaryotic cells is mediated by conserved protein machineries. In each trafficking step, fusion of the vesicle with the acceptor membrane is driven by a set of distinctive soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins that assemble into tight 4-helix bundle complexes between the fusing membranes. During evolution, about 20 primordial SNARE types were modified independently in different eukaryotic lineages by episodes of duplication and diversification. Here we show that 2 major changes in the SNARE repertoire occurred in the evolution of animals, each reflecting a main overhaul of the endomembrane system. In addition, we found several lineage-specific losses of distinct SNAREs, particularly in nematodes and platyhelminthes. The first major transformation took place during the transition to multicellularity. The primary event that occurred during this transformation was an increase in the numbers of endosomal SNAREs, but the SNARE-related factor lethal giant larvae also emerged. Apparently, enhanced endosomal sorting capabilities were an advantage for early multicellular animals. The second major transformation during the rise of vertebrates resulted in a robust expansion of the secretory set of SNAREs, which may have helped develop a more versatile secretory apparatus.},
}

Animals
Endosomes/metabolism
Eukaryotic Cells/physiology
*Evolution, Molecular
Expressed Sequence Tags
Fishes/genetics
Gene Deletion
Gene Duplication
Genome
Humans
Invertebrates/genetics
Phylogeny
SNARE Proteins/classification/*genetics/physiology
Vertebrates/genetics

@article {pmid18757919,
year = {2008},
author = {Lynch, M},
title = {The cellular, developmental and population-genetic determinants of mutation-rate evolution.},
journal = {Genetics},
volume = {180},
number = {2},
pages = {933-943},
pmid = {18757919},
issn = {0016-6731},
support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; GM36827/GM/NIGMS NIH HHS/United States ; },
mesh = {Alleles ; Animals ; *Evolution, Molecular ; Humans ; *Mutation ; Selection, Genetic ; },
abstract = {Although the matter has been subject to considerable theoretical study, there are numerous open questions regarding the mechanisms driving the mutation rate in various phylogenetic lineages. Most notably, empirical evidence indicates that mutation rates are elevated in multicellular species relative to unicellular eukaryotes and prokaryotes, even on a per-cell division basis, despite the need for the avoidance of somatic damage and the accumulation of germline mutations. Here it is suggested that multicellularity discourages selection against weak mutator alleles for reasons associated with both the cellular and the population-genetic environments, thereby magnifying the vulnerability to somatic mutations (cancer) and increasing the risk of extinction from the accumulation of germline mutations. Moreover, contrary to common belief, a cost of fidelity need not be invoked to explain the lower bound to observed mutation rates, which instead may simply be set by the inability of selection to advance very weakly advantageous antimutator alleles in finite populations.},
}

Alleles
Animals
*Evolution, Molecular
Humans
*Mutation
Selection, Genetic

@article {pmid18764950,
year = {2008},
author = {Bailly, X and Vanin, S and Chabasse, C and Mizuguchi, K and Vinogradov, SN},
title = {A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins.},
journal = {BMC evolutionary biology},
volume = {8},
number = {},
pages = {244},
pmid = {18764950},
issn = {1471-2148},
mesh = {Amino Acid Sequence ; Animals ; Annelida/*genetics ; Archaea/*genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Bayes Theorem ; Evolution, Molecular ; Exons ; Genes, Archaeal ; Genes, Bacterial ; Genome ; Hemerythrin/*genetics ; Introns ; Molecular Sequence Data ; *Phylogeny ; RNA/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; },
abstract = {BACKGROUND: Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated.

RESULTS: A search for putative Hrs in the genomes of 43 archaea, 444 bacteria and 135 eukaryotes, revealed their presence in 3 archaea, 118 bacteria, several fungi, one apicomplexan, a heterolobosan, a cnidarian and several annelids. About a fourth of the Hr sequences were identified as N- or C-terminal domains of chimeric, chemotactic gene regulators. The function of the remaining single domain bacterial Hrs remains to be determined. In addition to oxygen transport, the possible functions in annelids have been proposed to include cadmium-binding, antibacterial action and immunoprotection. A Bayesian phylogenetic tree revealed a split into two clades, one encompassing archaea, bacteria and fungi, and the other comprising the remaining eukaryotes. The annelid and sipunculan Hrs share the same intron-exon structure, different from that of the cnidarian Hr.

CONCLUSION: The phylogenomic profile of Hrs demonstrated a limited occurrence in bacteria and archaea and a marked absence in the vast majority of multicellular organisms. Among the metazoa, Hrs have survived in a cnidarian and in a few protostome groups; hence, it appears that in metazoans the Hr gene was lost in deuterostome ancestor(s) after the radiata/bilateria split. Signal peptide sequences in several Hirudinea Hrs suggest for the first time, the possibility of extracellular localization. Since the alpha-helical bundle is likely to have been among the earliest protein folds, Hrs represent an ancient family of iron-binding proteins, whose primary function in bacteria may have been that of an oxygen sensor, enabling aerophilic or aerophobic responses. Although Hrs evolved to function as O2 transporters in brachiopods, priapulids and sipunculans, their function in annelids remains to be elucidated. Overall Hrs exhibit a considerable lack of evolutionary success in metazoans.},
}

Amino Acid Sequence
Animals
Annelida/*genetics
Archaea/*genetics
Archaeal Proteins/genetics
Bacteria/*genetics
Bacterial Proteins/genetics
Bayes Theorem
Evolution, Molecular
Exons
Genes, Archaeal
Genes, Bacterial
Genome
Hemerythrin/*genetics
Introns
Molecular Sequence Data
*Phylogeny
RNA/genetics
Sequence Alignment
Sequence Homology, Amino Acid

@article {pmid18768474,
year = {2008},
author = {Page, MJ and Di Cera, E},
title = {Evolution of peptidase diversity.},
journal = {The Journal of biological chemistry},
volume = {283},
number = {44},
pages = {30010-30014},
pmid = {18768474},
issn = {0021-9258},
support = {HL49413/HL/NHLBI NIH HHS/United States ; HL58141/HL/NHLBI NIH HHS/United States ; HL73813/HL/NHLBI NIH HHS/United States ; },
mesh = {Databases, Protein ; Evolution, Molecular ; Genome ; Genome, Archaeal ; Genome, Bacterial ; Humans ; Hydrolases/chemistry ; Peptide Hydrolases/*chemistry ; Proteins/chemistry ; Sequence Analysis, Protein ; Species Specificity ; Trypsin/chemistry ; },
abstract = {A wide variety of peptidases associate with vital biological pathways, but the origin and evolution of their tremendous diversity are poorly defined. Application of the MEROPS classification to a comprehensive set of genomes yields a simple pattern of peptidase distribution and provides insight into the organization of proteolysis in all forms of life. Unexpectedly, a near ubiquitous core set of peptidases is shown to contain more types than those unique to higher multicellular organisms. From this core group, an array of eukaryote-specific peptidases evolved to yield well known intracellular and extracellular processes. The paucity of peptidase families unique to higher metazoa suggests gains in proteolytic network complexity required a limited number of biochemical inventions. These findings provide a framework for deeper investigation into the evolutionary forces that shaped each peptidase family and a roadmap to develop a timeline for their expansion as an interconnected system.},
}

Databases, Protein
Evolution, Molecular
Genome
Genome, Archaeal
Genome, Bacterial
Humans
Hydrolases/chemistry
Peptide Hydrolases/*chemistry
Proteins/chemistry
Sequence Analysis, Protein
Species Specificity
Trypsin/chemistry

@article {pmid18820252,
year = {2008},
author = {Domazet-Loso, T and Tautz, D},
title = {An ancient evolutionary origin of genes associated with human genetic diseases.},
journal = {Molecular biology and evolution},
volume = {25},
number = {12},
pages = {2699-2707},
pmid = {18820252},
issn = {1537-1719},
mesh = {Disease/*genetics ; *Evolution, Molecular ; Genome, Human ; Humans ; Multifactorial Inheritance ; },
abstract = {Several thousand genes in the human genome have been linked to a heritable genetic disease. The majority of these appear to be nonessential genes (i.e., are not embryonically lethal when inactivated), and one could therefore speculate that they are late additions in the evolutionary lineage toward humans. Contrary to this expectation, we find that they are in fact significantly overrepresented among the genes that have emerged during the early evolution of the metazoa. Using a phylostratigraphic approach, we have studied the evolutionary emergence of such genes at 19 phylogenetic levels. The majority of disease genes was already present in the eukaryotic ancestor, and the second largest number has arisen around the time of evolution of multicellularity. Conversely, genes specific to the mammalian lineage are highly underrepresented. Hence, genes involved in genetic diseases are not simply a random subset of all genes in the genome but are biased toward ancient genes.},
}

Disease/*genetics
*Evolution, Molecular
Genome, Human
Humans
Multifactorial Inheritance

@article {pmid18831774,
year = {2008},
author = {Dunker, AK and Oldfield, CJ and Meng, J and Romero, P and Yang, JY and Chen, JW and Vacic, V and Obradovic, Z and Uversky, VN},
title = {The unfoldomics decade: an update on intrinsically disordered proteins.},
journal = {BMC genomics},
volume = {9 Suppl 2},
number = {Suppl 2},
pages = {S1},
pmid = {18831774},
issn = {1471-2164},
support = {R01 LM007688/LM/NLM NIH HHS/United States ; R01 LM007688-01A1/LM/NLM NIH HHS/United States ; GM071714-01A2/GM/NIGMS NIH HHS/United States ; R01 GM071714/GM/NIGMS NIH HHS/United States ; R56 LM007688/LM/NLM NIH HHS/United States ; },
mesh = {Algorithms ; Alternative Splicing ; Amino Acid Sequence ; Binding Sites ; *Computational Biology ; Drug Design ; Humans ; Protein Conformation ; *Protein Folding ; Proteins/*chemistry/*metabolism ; Sequence Analysis, Protein ; Structure-Activity Relationship ; },
abstract = {BACKGROUND: Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90-95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of protein disorder. While the various prediction methodologies used for protein intrinsic disorder resemble those methodologies used for secondary structure prediction, the two types of structures are entirely different. For example, the two structural classes have very different dynamic properties, with the irregular secondary structure class being much less mobile than the disorder class. The prediction of secondary structure has been useful. On the other hand, the prediction of intrinsic disorder has been revolutionary, leading to major modifications of the more than 100 year-old views relating protein structure and function. Experimentalists have been providing evidence over many decades that some proteins lack fixed structure or are disordered (or unfolded) under physiological conditions. In addition, experimentalists are also showing that, for many proteins, their functions depend on the unstructured rather than structured state; such results are in marked contrast to the greater than hundred year old views such as the lock and key hypothesis. Despite extensive data on many important examples, including disease-associated proteins, the importance of disorder for protein function has been largely ignored. Indeed, to our knowledge, current biochemistry books don't present even one acknowledged example of a disorder-dependent function, even though some reports of disorder-dependent functions are more than 50 years old. The results from genome-wide predictions of intrinsic disorder and the results from other bioinformatics studies of intrinsic disorder are demanding attention for these proteins.

RESULTS: Disorder prediction has been important for showing that the relatively few experimentally characterized examples are members of a very large collection of related disordered proteins that are wide-spread over all three domains of life. Many significant biological functions are now known to depend directly on, or are importantly associated with, the unfolded or partially folded state. Here our goal is to review the key discoveries and to weave these discoveries together to support novel approaches for understanding sequence-function relationships.

CONCLUSION: Intrinsically disordered protein is common across the three domains of life, but especially common among the eukaryotic proteomes. Signaling sequences and sites of posttranslational modifications are frequently, or very likely most often, located within regions of intrinsic disorder. Disorder-to-order transitions are coupled with the adoption of different structures with different partners. Also, the flexibility of intrinsic disorder helps different disordered regions to bind to a common binding site on a common partner. Such capacity for binding diversity plays important roles in both protein-protein interaction networks and likely also in gene regulation networks. Such disorder-based signaling is further modulated in multicellular eukaryotes by alternative splicing, for which such splicing events map to regions of disorder much more often than to regions of structure. Associating alternative splicing with disorder rather than structure alleviates theoretical and experimentally observed problems associated with the folding of different length, isomeric amino acid sequences. The combination of disorder and alternative splicing is proposed to provide a mechanism for easily "trying out" different signaling pathways, thereby providing the mechanism for generating signaling diversity and enabling the evolution of cell differentiation and multicellularity. Finally, several recent small molecules of interest as potential drugs have been shown to act by blocking protein-protein interactions based on intrinsic disorder of one of the partners. Study of these examples has led to a new approach for drug discovery, and bioinformatics analysis of the human proteome suggests that various disease-associated proteins are very rich in such disorder-based drug discovery targets.},
}

Algorithms
Alternative Splicing
Amino Acid Sequence
Binding Sites
*Computational Biology
Drug Design
Humans
Protein Conformation
*Protein Folding
Proteins/*chemistry/*metabolism
Sequence Analysis, Protein
Structure-Activity Relationship

@article {pmid18832373,
year = {2008},
author = {Castro, MA and Dalmolin, RJ and Moreira, JC and Mombach, JC and de Almeida, RM},
title = {Evolutionary origins of human apoptosis and genome-stability gene networks.},
journal = {Nucleic acids research},
volume = {36},
number = {19},
pages = {6269-6283},
pmid = {18832373},
issn = {1362-4962},
mesh = {Animals ; Apoptosis/*genetics ; Computational Biology ; *Evolution, Molecular ; *Gene Regulatory Networks ; Genes, Lethal ; Genes, Neoplasm ; Genome, Human ; *Genomic Instability ; Humans ; Mice ; Saccharomyces cerevisiae/genetics ; },
abstract = {Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a 'molecular node' in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown. Here, using computational methods, we reconstruct the evolutionary scenario that linked apoptosis with genome stability pathways in a functional human gene/protein association network. We found that the entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2. Also, several critical nodes that entangle apoptosis and genome stability are cancer genes (e.g. ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6 and TP53), although their orthologs have arisen in different points of evolution. Our results demonstrate how genome stability and apoptosis were co-opted during evolution recruiting genes that merge both systems. We also provide several examples to exploit this evolutionary platform, where we have judiciously extended information on gene essentiality inferred from model organisms to human.},
}

Animals
Apoptosis/*genetics
Computational Biology
*Evolution, Molecular
*Gene Regulatory Networks
Genes, Lethal
Genes, Neoplasm
Genome, Human
*Genomic Instability
Humans
Mice
Saccharomyces cerevisiae/genetics

@article {pmid18926910,
year = {2008},
author = {Rokas, A},
title = {The molecular origins of multicellular transitions.},
journal = {Current opinion in genetics & development},
volume = {18},
number = {6},
pages = {472-478},
doi = {10.1016/j.gde.2008.09.004},
pmid = {18926910},
issn = {1879-0380},
mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology ; *Evolution, Molecular ; Genome/*genetics ; *Phylogeny ; Protein Structure, Tertiary ; Transcription Factors/*genetics ; },
abstract = {Multicellularity has evolved multiple times independently from a variety of ancestral unicellular lineages. Past research on multicellularity was focused more on explaining why it was repeatedly invented and less so on the molecular foundations associated with each transition. Several recent comparative functional analyses of microbial unicellular and multicellular genomes have begun to throw considerable light on the molecular commonalities exhibited by independent multicellular transitions. These have enabled the delineation of the likely functional components of the genetic toolkit required for multicellular existence and to surprising discoveries, such as the presence of several toolkit components in unicellular lineages. The study of these toolkit proteins in a unicellular context has begun yielding insights into their ancestral functions and how they were coopted for multicellular development.},
}

*Biological Evolution
Eukaryotic Cells/*cytology
*Evolution, Molecular
Genome/*genetics
*Phylogeny
Protein Structure, Tertiary
Transcription Factors/*genetics

@article {pmid18936483,
year = {2008},
author = {Pace, JK and Gilbert, C and Clark, MS and Feschotte, C},
title = {Repeated horizontal transfer of a DNA transposon in mammals and other tetrapods.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {105},
number = {44},
pages = {17023-17028},
pmid = {18936483},
issn = {1091-6490},
support = {R01 GM077582/GM/NIGMS NIH HHS/United States ; R01GM77582/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; Databases, Genetic ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Humans ; Mammals/genetics ; Mice ; Molecular Sequence Data ; Phylogeny ; Rats ; },
abstract = {Horizontal transfer (HT) is central to the evolution of prokaryotic species. Selfish and mobile genetic elements, such as phages, plasmids, and transposons, are the primary vehicles for HT among prokaryotes. In multicellular eukaryotes, the prevalence and evolutionary significance of HT remain unclear. Here, we identified a set of DNA transposon families dubbed SPACE INVADERS (or SPIN) whose consensus sequences are approximately 96% identical over their entire length (2.9 kb) in the genomes of murine rodents (rat/mouse), bushbaby (prosimian primate), little brown bat (laurasiatherian), tenrec (afrotherian), opossum (marsupial), and two non-mammalian tetrapods (anole lizard and African clawed frog). In contrast, SPIN elements were undetectable in other species represented in the sequence databases, including 19 other mammals with draft whole-genome assemblies. This patchy distribution, coupled with the extreme level of SPIN identity in widely divergent tetrapods and the overall lack of selective constraint acting on these elements, is incompatible with vertical inheritance, but strongly indicative of multiple horizontal introductions. We show that these germline infiltrations likely occurred around the same evolutionary time (15-46 mya) and spawned some of the largest bursts of DNA transposon activity ever recorded in any species lineage (nearly 100,000 SPIN copies per haploid genome in tenrec). The process also led to the emergence of a new gene in the murine lineage derived from a SPIN transposase. In summary, HT of DNA transposons has contributed significantly to shaping and diversifying the genomes of multiple mammalian and tetrapod species.},
}

Animals
Base Sequence
DNA Transposable Elements/*genetics
Databases, Genetic
Evolution, Molecular
*Gene Transfer, Horizontal
Genome
Humans
Mammals/genetics
Mice
Molecular Sequence Data
Phylogeny
Rats

@article {pmid18983257,
year = {2008},
author = {Rokas, A},
title = {The origins of multicellularity and the early history of the genetic toolkit for animal development.},
journal = {Annual review of genetics},
volume = {42},
number = {},
pages = {235-251},
doi = {10.1146/annurev.genet.42.110807.091513},
pmid = {18983257},
issn = {0066-4197},
mesh = {Animals ; Bacteria/cytology/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Cell Adhesion/*genetics ; Cell Communication/*genetics ; Cell Differentiation/genetics ; Eukaryota/cytology/genetics/physiology ; Eukaryotic Cells ; Phylogeny ; Transcription, Genetic ; },
abstract = {Multicellularity appeared early and repeatedly in life's history; its instantiations presumably required the confluence of environmental, ecological, and genetic factors. Comparisons of several independently evolved pairs of multicellular and unicellular relatives indicate that transitions to multicellularity are typically associated with increases in the numbers of genes involved in cell differentiation, cell-cell communication, and adhesion. Further examination of the DNA record suggests that these increases in gene complexity are the product of evolutionary innovation, tinkering, and expansion of genetic material. Arguably, the most decisive multicellular transition was the emergence of animals. Decades of developmental work have demarcated the genetic toolkit for animal multicellularity, a select set of a few hundred genes from a few dozen gene families involved in adhesion, communication, and differentiation. Examination of the DNA records of the earliest-branching animal phyla and their closest protist relatives has begun to shed light on the origins and assembly of this toolkit. Emerging data favor a model of gradual assembly, with components originating and diversifying at different time points prior to or shortly after the origin of animals.},
}

Animals
Bacteria/cytology/genetics
Bacterial Physiological Phenomena
*Biological Evolution
Cell Adhesion/*genetics
Cell Communication/*genetics
Cell Differentiation/genetics
Eukaryota/cytology/genetics/physiology
Eukaryotic Cells
Phylogeny
Transcription, Genetic

@article {pmid19026540,
year = {2008},
author = {Matz, MV and Frank, TM and Marshall, NJ and Widder, EA and Johnsen, S},
title = {Giant deep-sea protist produces bilaterian-like traces.},
journal = {Current biology : CB},
volume = {18},
number = {23},
pages = {1849-1854},
doi = {10.1016/j.cub.2008.10.028},
pmid = {19026540},
issn = {1879-0445},
mesh = {Amoeba/classification/genetics/*physiology/ultrastructure ; Animals ; Biological Evolution ; Cnidaria/physiology ; DNA, Protozoan/analysis ; Eukaryota/classification/genetics/*physiology/ultrastructure ; Fossils ; Geologic Sediments/parasitology ; Paleontology ; Phylogeny ; RNA, Ribosomal/genetics ; Seawater/parasitology ; Sequence Analysis, DNA ; },
abstract = {One of the strongest paleontological arguments in favor of the origin of bilaterally symmetrical animals (Bilateria) prior to their obvious and explosive appearance in the fossil record in the early Cambrian, 542 million years ago, is the occurrence of trace fossils shaped like elongated sinuous grooves or furrows in the Precambrian. Being restricted to the seafloor surface, these traces are relatively rare and of limited diversity, and they do not show any evidence of the use of hard appendages. They are commonly attributed to the activity of the early nonskeletonized bilaterians or, alternatively, large cnidarians such as sea anemones or sea pens. Here we describe macroscopic groove-like traces produced by a living giant protist and show that these traces bear a remarkable resemblance to the Precambrian trace fossils, including those as old as 1.8 billion years. This is the first evidence that organisms other than multicellular animals can produce such traces, and it prompts re-evaluation of the significance of Precambrian trace fossils as evidence of the early diversification of Bilateria. Our observations also render indirect support to the highly controversial interpretation of the enigmatic Ediacaran biota of the late Precambrian as giant protists.},
}

Amoeba/classification/genetics/*physiology/ultrastructure
Animals
Biological Evolution
Cnidaria/physiology
DNA, Protozoan/analysis
Eukaryota/classification/genetics/*physiology/ultrastructure
Fossils
Geologic Sediments/parasitology
Paleontology
Phylogeny
RNA, Ribosomal/genetics
Seawater/parasitology
Sequence Analysis, DNA

@article {pmid19079286,
year = {2009},
author = {Kourtis, N and Tavernarakis, N},
title = {Autophagy and cell death in model organisms.},
journal = {Cell death and differentiation},
volume = {16},
number = {1},
pages = {21-30},
doi = {10.1038/cdd.2008.120},
pmid = {19079286},
issn = {1476-5403},
mesh = {Animals ; Autophagy/*physiology ; Caenorhabditis elegans/physiology ; Cell Survival/physiology ; Dictyostelium/physiology ; Drosophila melanogaster ; Humans ; *Models, Biological ; Saccharomyces cerevisiae/physiology ; Signal Transduction/physiology ; Stress, Physiological/*physiology ; },
abstract = {Autophagy evolved in unicellular eukaryotes as a means for surviving nutrient stress. During the course of evolution, as multicellular organisms developed specialized cell types and complex intracellular signalling networks, autophagy has been summoned to serve additional cellular functions. Numerous recent studies indicate that apart from its pro-survival role under nutrient limitation, autophagy also participates in cell death. However, the precise role of this catabolic process in dying cells is not fully understood. Although in certain situations autophagy has a protective function, in other types of cell death it actually contributes to cellular destruction. Simple model organisms ranging from the unicellular Saccharomyces cerevisiae to the soil amoeba Dictyostelium discoideum and the metazoans Caenorhabditis elegans and Drosophila melanogaster provide clearly defined cell death paradigms that can be used to dissect the involvement of autophagy in cell death, at the molecular level. In this review, we survey current research in simple organisms, linking autophagy to cell death and discuss the complex interplay between autophagy, cell survival and cell death.},
}

Animals
Autophagy/*physiology
Caenorhabditis elegans/physiology
Cell Survival/physiology
Dictyostelium/physiology
Drosophila melanogaster
Humans
*Models, Biological
Saccharomyces cerevisiae/physiology
Signal Transduction/physiology
Stress, Physiological/*physiology

@article {pmid19093090,
year = {2008},
author = {Wu, H and Zou, D and Gao, K},
title = {Impacts of increased atmospheric CO2 concentration on photosynthesis and growth of micro- and macro-algae.},
journal = {Science in China. Series C, Life sciences},
volume = {51},
number = {12},
pages = {1144-1150},
doi = {10.1007/s11427-008-0142-5},
pmid = {19093090},
issn = {1006-9305},
mesh = {Atmosphere/*chemistry ; Carbon Dioxide/*metabolism ; Environment ; Eukaryota/*physiology ; Oceans and Seas ; Photosynthesis/*physiology ; Phytoplankton/physiology ; Seawater ; },
abstract = {Marine photosynthesis drives the oceanic biological CO(2) pump to absorb CO(2) from the atmosphere, which sinks more than one third of the industry-originated CO(2) into the ocean. The increasing atmospheric CO(2) and subsequent rise of pCO(2) in seawater, which alters the carbonate system and related chemical reactions and results in lower pH and higher HCO(3) (-) concentration, affect photosynthetic CO(2) fixation processes of phytoplanktonic and macroalgal species in direct and/or indirect ways. Although many unicellular and multicellular species can operate CO(2)-concentrating mechanisms (CCMs) to utilize the large HCO(3) (-) pool in seawater, enriched CO(2) up to several times the present atmospheric level has been shown to enhance photosynthesis and growth of both phytoplanktonic and macro-species that have less capacity of CCMs. Even for species that operate active CCMs and those whose photosynthesis is not limited by CO(2) in seawater, increased CO(2) levels can down-regulate their CCMs and therefore enhance their growth under light-limiting conditions (at higher CO(2) levels, less light energy is required to drive CCM). Altered physiological performances under high-CO(2) conditions may cause genetic alteration in view of adaptation over long time scale. Marine algae may adapt to a high CO(2) oceanic environment so that the evolved communities in future are likely to be genetically different from the contemporary communities. However, most of the previous studies have been carried out under indoor conditions without considering the acidifying effects on seawater by increased CO(2) and other interacting environmental factors, and little has been documented so far to explain how physiology of marine primary producers performs in a high-CO(2) and low-pH ocean.},
}

Atmosphere/*chemistry
Carbon Dioxide/*metabolism
Environment
Eukaryota/*physiology
Oceans and Seas
Photosynthesis/*physiology
Phytoplankton/physiology
Seawater

@article {pmid19100909,
year = {2008},
author = {Hall, MN},
title = {mTOR-what does it do?.},
journal = {Transplantation proceedings},
volume = {40},
number = {10 Suppl},
pages = {S5-8},
doi = {10.1016/j.transproceed.2008.10.009},
pmid = {19100909},
issn = {0041-1345},
mesh = {Animals ; Cell Division/physiology ; Cell Physiological Phenomena ; Growth Substances/physiology ; Homeostasis ; Humans ; Mammals ; Mechanistic Target of Rapamycin Complex 1 ; Multiprotein Complexes ; Phosphatidylinositol 3-Kinases/*metabolism ; Protein Kinases/*physiology ; Proteins ; Signal Transduction ; TOR Serine-Threonine Kinases ; Transcription Factors/physiology ; },
abstract = {Target of rapamycin (TOR) is a highly conserved serine/threonine kinase that controls cell growth and metabolism in response to nutrients, growth factors, cellular energy, and stress. TOR, which was originally discovered in yeast, is conserved in all eukaryotes including plants, worms, flies, and mammals. The discovery of TOR led to a fundamental change in how we think about cell growth. It is not a spontaneous process that just happens when building blocks (nutrients) are available, but rather a highly regulated, plastic process controlled by TOR-dependent signaling pathways. TOR is found in 2 structurally and functionally distinct multiprotein complexes, TORC1 and TORC2. The 2 TOR complexes, like TOR itself, are highly conserved. Mammalian TORC1 (mTORC1) is rapamycin sensitive and contains mTOR, raptor, and mLST8. TORC1 in yeast and mammals mediates temporal control of cell growth by regulating several cellular processes, including translation, transcription, ribosome biogenesis, nutrient transport, and autophagy. mTORC2 is rapamycin insensitive and contains mTOR, rictor, mSIN1, PRR5, and mLST8. TORC2 in yeast and mammals mediates spatial control of cell growth by regulating the actin cytoskeleton. Thus, the 2 TOR complexes constitute an ancestral signaling network conserved throughout eukaryotic evolution to control the fundamental process of cell growth. As a central controller of cell growth, TOR plays a key role in development and aging and has been implicated in disorders such as cancer, cardiovascular disease, obesity, and diabetes. The challenge now is to understand the role of mTOR signaling to coordinate and integrate overall body growth in multicellular organisms.},
}

Animals
Cell Division/physiology
Cell Physiological Phenomena
Growth Substances/physiology
Homeostasis
Humans
Mammals
Mechanistic Target of Rapamycin Complex 1
Multiprotein Complexes
Phosphatidylinositol 3-Kinases/*metabolism
Protein Kinases/*physiology
Proteins
Signal Transduction
TOR Serine-Threonine Kinases
Transcription Factors/physiology

@article {pmid19106296,
year = {2009},
author = {Payne, JL and Boyer, AG and Brown, JH and Finnegan, S and Kowalewski, M and Krause, RA and Lyons, SK and McClain, CR and McShea, DW and Novack-Gottshall, PM and Smith, FA and Stempien, JA and Wang, SC},
title = {Two-phase increase in the maximum size of life over 3.5 billion years reflects biological innovation and environmental opportunity.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {1},
pages = {24-27},
pmid = {19106296},
issn = {1091-6490},
mesh = {Animals ; Atmosphere ; *Biological Evolution ; *Body Size/genetics ; *Environment ; *Eukaryotic Cells ; Fossils ; History, Ancient ; Oxygen ; },
abstract = {The maximum size of organisms has increased enormously since the initial appearance of life >3.5 billion years ago (Gya), but the pattern and timing of this size increase is poorly known. Consequently, controls underlying the size spectrum of the global biota have been difficult to evaluate. Our period-level compilation of the largest known fossil organisms demonstrates that maximum size increased by 16 orders of magnitude since life first appeared in the fossil record. The great majority of the increase is accounted for by 2 discrete steps of approximately equal magnitude: the first in the middle of the Paleoproterozoic Era (approximately 1.9 Gya) and the second during the late Neoproterozoic and early Paleozoic eras (0.6-0.45 Gya). Each size step required a major innovation in organismal complexity--first the eukaryotic cell and later eukaryotic multicellularity. These size steps coincide with, or slightly postdate, increases in the concentration of atmospheric oxygen, suggesting latent evolutionary potential was realized soon after environmental limitations were removed.},
}

Animals
Atmosphere
*Biological Evolution
*Body Size/genetics
*Environment
*Eukaryotic Cells
Fossils
History, Ancient
Oxygen

@article {pmid19146945,
year = {2009},
author = {Guo, WJ and Ling, J and Li, P},
title = {Consensus features of microsatellite distribution: microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes.},
journal = {Genomics},
volume = {93},
number = {4},
pages = {323-331},
doi = {10.1016/j.ygeno.2008.12.009},
pmid = {19146945},
issn = {1089-8646},
mesh = {Arabidopsis/genetics ; Centromere/*genetics ; Chromosomes/genetics ; Eukaryotic Cells/metabolism ; *Genome ; Humans ; Microsatellite Repeats/*genetics ; Oryza/genetics ; Recombination, Genetic/*genetics ; },
abstract = {Microsatellite DNA is highly polymorphic and informative, which makes its distribution pattern and its associations very valuable for marker applications and genomic research in evolution. Using computational and statistical approaches, based on database technology, we have demonstrated that microsatellite content is consistently and significantly 2 to 5 fold lower than the average chromosomal level in the centromeric and pericentromeric regions of the chromosomes of two plant species, Arabidopsis thaliana and Oryza sativa. We conducted a path coefficient analysis to compare the direct effect of microsatellites (from mono-nucleotide through to penta-nucleotide repeats) on recombination rates. The results revealed that tri- and penta-nucleotide microsatellites significantly influence recombination rates. In the human genome, tri-, tetra- and mono-nucleotide microsatellites, in decreasing order, make significant direct contributions to recombination rates, according to DECODE, GENTHON, and MARSHFIELD averages. Path coefficient analysis in rice and human genomes of the impact of di-nucleotide microsatellites of different motifs on recombination rates indicate that motifs with either A or T have an effect, resulting in increased recombination rates for microsatellites with motifs consisting of 50% A or T, such as AG, TC, CA, TG. Conversely, microsatellites with motifs consisting of only A & T or G & C, such as AT, TA, GC or CG, have decreased recombination rates. The extremely low microsatellite content in centromeric and pericentromeric regions, as well as the quantitative association of microsatellite sequences with the recombination rate at the genome level, suggests that purifying selection in genome evolution creates a balance between genomic polymorphisms and the biological function of sequences in a genome.},
}

Arabidopsis/genetics
Centromere/*genetics
Chromosomes/genetics
Eukaryotic Cells/metabolism
*Genome
Humans
Microsatellite Repeats/*genetics
Oryza/genetics
Recombination, Genetic/*genetics

@article {pmid19150962,
year = {2008},
author = {Pearson, BJ and Sánchez Alvarado, A},
title = {Regeneration, stem cells, and the evolution of tumor suppression.},
journal = {Cold Spring Harbor symposia on quantitative biology},
volume = {73},
number = {},
pages = {565-572},
doi = {10.1101/sqb.2008.73.045},
pmid = {19150962},
issn = {1943-4456},
support = {//Howard Hughes Medical Institute/United States ; },
mesh = {Adult Stem Cells/cytology/physiology ; Animals ; Biological Evolution ; Cell Proliferation ; Drosophila ; Eukaryota ; Genes, Tumor Suppressor ; Humans ; Longevity ; Neoplasms/genetics/pathology/*prevention & control ; Planarians ; Regeneration/genetics/*physiology ; Stem Cells/cytology/*physiology ; Vertebrates ; },
abstract = {All multicellular organisms have requirements for tumor suppression to regulate cellular proliferation during either embryonic development or adult life. However, different organisms have vastly different requirements. Adult tumor suppression is probably not crucial to organisms possessing both short life spans and largely postmitotic soma. In contrast, animals with lifelong tissue turnover or those capable of regenerating body parts lost to injury must possess evolutionarily selected mechanisms to control rates of cell proliferation such that tissue homeostasis can be maintained or restored after injury. We hypothesize that these biological differences may help to explain why the lists of tumor suppressor genes in humans and Drosophila are largely nonoverlapping. Here, we address this disparity by examining the tumor suppressor gene content of two outgroups to the vertebrates and flies/nematodes: the freshwater planarian and the single-celled choanoflagellate. Both of these organisms have recently had their genomes sequenced, giving us a first glimpse of which known tumor suppressor genes have been maintained during evolution. In addition, we attempt to resolve which genes may have had ancestral tumor suppressor function and which may have acquired this function de novo.},
}

Adult Stem Cells/cytology/physiology
Animals
Biological Evolution
Cell Proliferation
Drosophila
Eukaryota
Genes, Tumor Suppressor
Humans
Longevity
Neoplasms/genetics/pathology/*prevention & control
Planarians
Regeneration/genetics/*physiology
Stem Cells/cytology/*physiology
Vertebrates

@article {pmid19154376,
year = {2009},
author = {Willensdorfer, M},
title = {On the evolution of differentiated multicellularity.},
journal = {Evolution; international journal of organic evolution},
volume = {63},
number = {2},
pages = {306-323},
doi = {10.1111/j.1558-5646.2008.00541.x},
pmid = {19154376},
issn = {1558-5646},
support = {R01GM078986/GM/NIGMS NIH HHS/United States ; },
mesh = {*Biological Evolution ; *Cell Differentiation ; Eukaryota/cytology ; Fungi/cytology ; *Models, Genetic ; },
abstract = {Most conspicuous organisms are multicellular and most multicellular organisms develop somatic cells to perform specific, nonreproductive tasks. The ubiquity of this division of labor suggests that it is highly advantageous. In this article I present a model to study the evolution of specialized cells. The model allows for unicellular and multicellular organisms that may contain somatic (terminally differentiated) cells. Cells contribute additively to a quantitative trait. The fitness of the organism depends on this quantitative trait (via a benefit function), the size of the organism, and the number of somatic cells. The model allows one to determine when somatic cells are advantageous and to calculate the optimum number (or fraction) of reproductive cells. I show that the fraction of reproductive cells is always surprisingly high. If somatic cells are very small, they can outnumber reproductive cells but their biomass is still less than the biomass of reproductive cells. I discuss the biology of primitive multicellular organisms with respect to the model predictions. I find a good agreement and outline how this work can be used to guide further quantitative studies of multicellularity.},
}

*Biological Evolution
*Cell Differentiation
Eukaryota/cytology
Fungi/cytology
*Models, Genetic

@article {pmid19168567,
year = {2009},
author = {Szöllosi, GJ and Derényi, I},
title = {Congruent evolution of genetic and environmental robustness in micro-RNA.},
journal = {Molecular biology and evolution},
volume = {26},
number = {4},
pages = {867-874},
doi = {10.1093/molbev/msp008},
pmid = {19168567},
issn = {1537-1719},
mesh = {Animals ; *Evolution, Molecular ; Humans ; MicroRNAs/*genetics ; Models, Genetic ; Selection, Genetic ; },
abstract = {Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic robustness, whether it evolves directly by natural selection or it is a correlated byproduct of other phenotypic traits, is, however, unresolved. Examining micro-RNA (miRNA) genes of several eukaryotic species, Borenstein and Ruppin (Borenstein E, Ruppin E. 2006. Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci USA. 103: 6593) showed that the structure of miRNA precursor stem loops exhibits significantly increased mutational robustness in comparison with a sample of random RNA sequences with the same stem-loop structure. The observed robustness was found to be uncorrelated with traditional measures of environmental robustness-implying that miRNA sequences show evidence of the direct evolution of genetic robustness. These findings are surprising as theoretical results indicate that the direct evolution of robustness requires high mutation rates and/or large effective population sizes only found among RNA viruses, not multicellular eukaryotes. We demonstrate that the sampling method used by Borenstein and Ruppin introduced significant bias that lead to an overestimation of robustness. Introducing a novel measure of environmental robustness based on the equilibrium thermodynamic ensemble of secondary structures of the miRNA precursor sequences, we demonstrate that the biophysics of RNA folding induces a high level of correlation between genetic (mutational) and environmental (thermodynamic) robustness, as expected from the theory of plastogenetic congruence introduced by Ancel and Fontana (Ancel LW, Fontana W. 2000. Plasticity, evolvability, and modularity in RNA. J Exp Zool. 288: 242-283). In light of theoretical considerations, we believe that this correlation strongly suggests that genetic robustness observed in miRNA sequences is the byproduct of selection for environmental robustness.},
}

Animals
*Evolution, Molecular
Humans
MicroRNAs/*genetics
Models, Genetic
Selection, Genetic

@article {pmid19198773,
year = {2009},
author = {Müller, WE and Wang, X and Schröder, HC},
title = {Paleoclimate and evolution: emergence of sponges during the neoproterozoic.},
journal = {Progress in molecular and subcellular biology},
volume = {47},
number = {},
pages = {55-77},
doi = {10.1007/978-3-540-88552-8_3},
pmid = {19198773},
issn = {0079-6484},
mesh = {Animals ; *Biological Evolution ; Body Patterning/physiology ; *Climate ; Ecosystem ; Fossils ; Marine Biology ; Porifera/cytology/*physiology ; Stem Cells ; },
abstract = {In the last 15 years, we had to cope with many technological and conceptual obstacles. The major hindrance was the view that sponges are primitive and exist separated from the other metazoan organisms. After answering these problems, the painful scientific process to position the most enigmatic metazoan phylum, the Porifera, into the correct phylogenetic place among the eukaryotes in general and the multicellular animals in particular came to an end. The well-studied taxon Porifera (sponges) was first grouped to the animal-plants or plant-animals, then to the Zoophyta or Mesozoa, and finally to the Parazoa. Only by the application of molecular biological techniques was it possible to place the Porifera monophyletically with the other metazoan phyla, justifying a unification of all multicellular animals to only one kingdom, the Metazoa. The first strong support came from the discovery that cell-cell and cell-matrix adhesion molecules, that were cloned from sponges (mainly the demosponges Suberites domuncula and Geodia cydonium) and that were subsequently expressed, share high DNA sequence and protein function similarity with the corresponding molecules of other metazoans. Together with the molecular biological studies and with the use of the cell culture technologies (primmorphs), which allowed an insight into the stem cell system of these simple organisms, it was possible to stethoscope back in the paleontological history of animals. These studies confirmed the view that the sponges evolved between two epochal ice times, 710-680 Ma (Sturtian glaciation) and 605-585 Ma (Varanger-Marinoan ice age), a period which allowed evolution to proceed but resulted also in a mass extinction of most animal taxa, with the exception of the Porifera. These animals could develop in the aqueous milieu which was rich in silica, due also to their ability to live in a symbiosis with unicellular organisms (prokaryotic and also eukaryotic). Those organisms provided the sponges with the nutrition to survive and to overcome the food deprivation in cold water and even in an environment under the ice. Based on the diverse genetic toolkit, the sponges could also resist the adverse temperature and sunlight climatic influences. It is fortunate that the sponges survived the last 800 million years with their basic body plan. This fact might qualify the sponges to become model organisms not only in biology and molecular biology but also to be used - as living fossils - as reference organisms to deduce important and new insights in the understanding of fossil records explored from the Neoproterozoic. Taken together, these data caused a paradigmatic change; the Porifera are complex and simple, but by far not primitive, and they contribute to the understanding of the deep evolution of animals in molecular biological and paleontological views.},
}

Animals
*Biological Evolution
Body Patterning/physiology
*Climate
Ecosystem
Fossils
Marine Biology
Porifera/cytology/*physiology
Stem Cells

@article {pmid19209377,
year = {2009},
author = {Nedelcu, AM},
title = {Comparative genomics of phylogenetically diverse unicellular eukaryotes provide new insights into the genetic basis for the evolution of the programmed cell death machinery.},
journal = {Journal of molecular evolution},
volume = {68},
number = {3},
pages = {256-268},
pmid = {19209377},
issn = {1432-1432},
mesh = {Amino Acid Sequence ; Animals ; Apoptosis Regulatory Proteins/*genetics ; Databases, Protein ; Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; Genomics ; Molecular Sequence Data ; *Phylogeny ; Plants/genetics ; },
abstract = {Programmed cell death (PCD) represents a significant component of normal growth and development in multicellular organisms. Recently, PCD-like processes have been reported in single-celled eukaryotes, implying that some components of the PCD machinery existed early in eukaryotic evolution. This study provides a comparative analysis of PCD-related sequences across more than 50 unicellular genera from four eukaryotic supergroups: Unikonts, Excavata, Chromalveolata, and Plantae. A complex set of PCD-related sequences that correspond to domains or proteins associated with all main functional classes--from ligands and receptors to executors of PCD--was found in many unicellular lineages. Several PCD domains and proteins previously thought to be restricted to animals or land plants are also present in unicellular species. Noteworthy, the yeast, Saccharomyces cerevisiae--used as an experimental model system for PCD research, has a rather reduced set of PCD-related sequences relative to other unicellular species. The phylogenetic distribution of the PCD-related sequences identified in unicellular lineages suggests that the genetic basis for the evolution of the complex PCD machinery present in extant multicellular lineages has been established early in the evolution of eukaryotes. The shaping of the PCD machinery in multicellular lineages involved the duplication, co-option, recruitment, and shuffling of domains already present in their unicellular ancestors.},
}

Amino Acid Sequence
Animals
Apoptosis Regulatory Proteins/*genetics
Databases, Protein
Eukaryotic Cells
*Evolution, Molecular
Fungi/genetics
Genomics
Molecular Sequence Data
*Phylogeny
Plants/genetics

@article {pmid19223580,
year = {2009},
author = {Herron, MD and Hackett, JD and Aylward, FO and Michod, RE},
title = {Triassic origin and early radiation of multicellular volvocine algae.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {9},
pages = {3254-3258},
pmid = {19223580},
issn = {1091-6490},
mesh = {*Phylogeny ; Time Factors ; Volvox/*genetics/*radiation effects ; },
abstract = {Evolutionary transitions in individuality (ETIs) underlie the watershed events in the history of life on Earth, including the origins of cells, eukaryotes, plants, animals, and fungi. Each of these events constitutes an increase in the level of complexity, as groups of individuals become individuals in their own right. Among the best-studied ETIs is the origin of multicellularity in the green alga Volvox, a model system for the evolution of multicellularity and cellular differentiation. Since its divergence from unicellular ancestors, Volvox has evolved into a highly integrated multicellular organism with cellular specialization, a complex developmental program, and a high degree of coordination among cells. Remarkably, all of these changes were previously thought to have occurred in the last 50-75 million years. Here we estimate divergence times using a multigene data set with multiple fossil calibrations and use these estimates to infer the times of developmental changes relevant to the evolution of multicellularity. Our results show that Volvox diverged from unicellular ancestors at least 200 million years ago. Two key innovations resulting from an early cycle of cooperation, conflict and conflict mediation led to a rapid integration and radiation of multicellular forms in this group. This is the only ETI for which a detailed timeline has been established, but multilevel selection theory predicts that similar changes must have occurred during other ETIs.},
}

*Phylogeny
Time Factors
Volvox/*genetics/*radiation effects

@article {pmid19243224,
year = {2009},
author = {Gordon, AJ and Halliday, JA and Blankschien, MD and Burns, PA and Yatagai, F and Herman, C},
title = {Transcriptional infidelity promotes heritable phenotypic change in a bistable gene network.},
journal = {PLoS biology},
volume = {7},
number = {2},
pages = {e44},
pmid = {19243224},
issn = {1545-7885},
mesh = {DNA-Directed RNA Polymerases/metabolism ; Epigenesis, Genetic ; Escherichia coli/*genetics/metabolism ; Feedback, Physiological ; *Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Genes, Switch ; Lac Operon/genetics ; Phenotype ; Protein Multimerization ; Stochastic Processes ; *Transcription, Genetic ; },
abstract = {Bistable epigenetic switches are fundamental for cell fate determination in unicellular and multicellular organisms. Regulatory proteins associated with bistable switches are often present in low numbers and subject to molecular noise. It is becoming clear that noise in gene expression can influence cell fate. Although the origins and consequences of noise have been studied, the stochastic and transient nature of RNA errors during transcription has not been considered in the origin or modeling of noise nor has the capacity for such transient errors in information transfer to generate heritable phenotypic change been discussed. We used a classic bistable memory module to monitor and capture transient RNA errors: the lac operon of Escherichia coli comprises an autocatalytic positive feedback loop producing a heritable all-or-none epigenetic switch that is sensitive to molecular noise. Using single-cell analysis, we show that the frequency of epigenetic switching from one expression state to the other is increased when the fidelity of RNA transcription is decreased due to error-prone RNA polymerases or to the absence of auxiliary RNA fidelity factors GreA and GreB (functional analogues of eukaryotic TFIIS). Therefore, transcription infidelity contributes to molecular noise and can effect heritable phenotypic change in genetically identical cells in the same environment. Whereas DNA errors allow genetic space to be explored, RNA errors may allow epigenetic or expression space to be sampled. Thus, RNA infidelity should also be considered in the heritable origin of altered or aberrant cell behaviour.},
}

DNA-Directed RNA Polymerases/metabolism
Epigenesis, Genetic
Escherichia coli/*genetics/metabolism
Feedback, Physiological
*Gene Expression Regulation, Bacterial
*Gene Regulatory Networks
Genes, Switch
Lac Operon/genetics
Phenotype
Protein Multimerization
Stochastic Processes
*Transcription, Genetic

@article {pmid19280701,
year = {2008},
author = {Chai, CL and Zhang, Z and Huang, FF and Wang, XY and Yu, QY and Liu, BB and Tian, T and Xia, QY and Lu, C and Xiang, ZH},
title = {A genomewide survey of homeobox genes and identification of novel structure of the Hox cluster in the silkworm, Bombyx mori.},
journal = {Insect biochemistry and molecular biology},
volume = {38},
number = {12},
pages = {1111-1120},
doi = {10.1016/j.ibmb.2008.06.008},
pmid = {19280701},
issn = {1879-0240},
mesh = {Amino Acid Sequence ; Animals ; Bombyx/*genetics ; Gene Expression Profiling ; Gene Expression Regulation/physiology ; *Genes, Homeobox ; Genes, Insect ; *Genome, Insect ; Insect Proteins/genetics/metabolism ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; },
abstract = {Homeobox genes encode transcriptional factors that play crucial roles in a variety of developmental pathways from unicellular to multicellular eukaryotes. We have identified 102 homeobox genes in the typical insect of Lepidoptera, Bombyx mori, based on the newly assembled genome sequence with 9X coverage. These identified homeobox genes were categorized into nine classes including at least 74 families. The available ESTs and microarray data at present confirmed that more than half of them were expressed during silkworm developmental processes. Orthologs of pb, zen and ftz were newly identified in the Bombyx Hox cluster on chromosome 6. Interestingly, a special group of 12 tandemly duplicated homeobox genes was found located between Bmpb and Bmzen in the Bombyx Hox cluster, suggesting that Hox cluster might have experienced a lineage-specific expansion in the silkworm. A detailed analysis on genome data reveals that a split exists between Bmlab and Bmpb. Our data provide valuable information for future research on the development and evolution of silkworm.},
}

Amino Acid Sequence
Animals
Bombyx/*genetics
Gene Expression Profiling
Gene Expression Regulation/physiology
*Genes, Homeobox
Genes, Insect
*Genome, Insect
Insect Proteins/genetics/metabolism
Molecular Sequence Data
*Multigene Family
Phylogeny

@article {pmid19281950,
year = {2009},
author = {Lopez, P and Bapteste, E},
title = {Molecular phylogeny: reconstructing the forest.},
journal = {Comptes rendus biologies},
volume = {332},
number = {2-3},
pages = {171-182},
doi = {10.1016/j.crvi.2008.07.003},
pmid = {19281950},
issn = {1768-3238},
mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Trees/*physiology ; },
abstract = {Phylogeny, be it morphological or molecular, has long tried to explain the extant biodiversity by the Tree of Species, which is a logical consequence of strict Darwinian evolutionary principles. Through constant improvement of both methods and data sets, some parts of this diversity have actually been demonstrated to be the result of a tree-like process. For some other parts, and especially for prokaryotes, different molecular markers have, however, produced different evolutionary trees, preventing the reconstruction of such a Tree. While technical artifacts could be blamed for these discrepancies, Lateral Gene Transfers are now largely held for responsible, and their existence requires an extension of the Darwinian framework, since genetic material is not always vertically inherited from parents to offspring. Through a variety of biological processes, sometimes large parts of DNA are exchanged between phylogenetically distant contemporary organisms, especially between those sharing the same environment. While mainly concerning prokaryotes, Lateral Gene Transfers have been also demonstrated to affect eukaryotes, and even multicellular ones, like plants or animals. Most of the time, these transfers allow important adaptations and the colonisation of new niches. The quantitative and qualitative importance of genetic transfers has thus severely challenged the very existence of a universal Tree of Species, since genetic connections, at least for microbes, seem more reticulated than tree-like. Even traditional biological concepts, like the concept of species, need to be re-evaluated in the light of recent discoveries. In short, instead of focusing on a elusive universal tree, biologists are now considering the whole forest corresponding to the multiple processes of inheritance, both vertical and horizontal. This constitutes the major challenge of evolutionary biology for the years to come.},
}

*Evolution, Molecular
Gene Transfer, Horizontal
Phylogeny
Trees/*physiology

@article {pmid19369262,
year = {2009},
author = {Acquisti, C and Kumar, S and Elser, JJ},
title = {Signatures of nitrogen limitation in the elemental composition of the proteins involved in the metabolic apparatus.},
journal = {Proceedings. Biological sciences},
volume = {276},
number = {1667},
pages = {2605-2610},
pmid = {19369262},
issn = {0962-8452},
mesh = {Animals ; Arabidopsis/genetics/metabolism ; Drosophila melanogaster/metabolism ; Gene Expression Regulation/*physiology ; Humans ; Metabolism ; Mice ; Nitrogen/*metabolism ; Proteins/*chemistry/*metabolism ; },
abstract = {Nitrogen (N) is a fundamental component of nucleotides and amino acids and is often a limiting nutrient in natural ecosystems. Thus, study of the N content of biomolecules may establish important connections between ecology and genomics. However, while significant differences in the elemental composition of whole organisms are well documented, how the flux of nutrients in the cell has shaped the evolution of different cellular processes remains poorly understood. By examining the elemental composition of major functional classes of proteins in four multicellular eukaryotic model organisms, we find that the catabolic machinery shows substantially lower N content than the anabolic machinery and the rest of the proteome. This pattern suggests that ecological selection for N conservation specifically targets cellular components that are highly expressed in response to nutrient limitation. We propose that the RNA component of the anabolic machineries is the mechanistic force driving the elemental imbalance we found, and that RNA functions as an intracellular nutrient reservoir that is degraded and recycled during starvation periods. A comparison of the elemental composition of the anabolic and catabolic machineries in species that have experienced different levels of N limitation in their evolutionary history (animals versus plants) suggests that selection for N conservation has preferentially targeted the catabolic machineries of plants, resulting in a lower N content of the proteins involved in their catabolic processes. These findings link the composition of major cellular components to the environmental factors that trigger the activation of those components, suggesting that resource availability has constrained the atomic composition and the molecular architecture of the biotic processes that enable cells to respond to reduced nutrient availability.},
}

Animals
Arabidopsis/genetics/metabolism
Drosophila melanogaster/metabolism
Gene Expression Regulation/*physiology
Humans
Metabolism
Mice
Nitrogen/*metabolism
Proteins/*chemistry/*metabolism

@article {pmid19384428,
year = {2007},
author = {Holt, JE and Ly-Huynh, JD and Efthymiadis, A and Hime, GR and Loveland, KL and Jans, DA},
title = {Regulation of Nuclear Import During Differentiation; The IMP alpha Gene Family and Spermatogenesis.},
journal = {Current genomics},
volume = {8},
number = {5},
pages = {323-334},
pmid = {19384428},
issn = {1389-2029},
abstract = {Access to nuclear genes in eukaryotes is provided by members of the importin (IMP) superfamily of proteins, which are of alpha- or beta-types, the best understood nuclear import pathway being mediated by a heterodimer of an IMP alpha and IMP beta1. IMP alpha recognises specific targeting signals on cargo proteins, while IMP beta1 mediates passage into, and release within, the nucleus by interacting with other components of the transport machinery, including the monomeric guanine nucleotide binding protein Ran. In this manner, hundreds of different proteins can be targeted specifically into the nucleus in a tightly regulated fashion. The IMP alpha gene family has expanded during evolution, with only a single IMP alpha (Srp1p) gene in budding yeast, and three (IMP alpha1, 2/pendulin and 3) and five (IMP alpha1, -2, -3, -4 and -6) IMP alpha genes in Drosophila melanogaster and mouse respectively, which fall into three phylogenetically distinct groups. The fact that IMP alpha3 and IMP alpha2 are only present in metazoans implies that they emerged during the evolution of multicellular animals to perform specialised roles in particular cells and tissues. This review describes what is known of the IMP alpha gene family in mouse and in D. melanogaster, including a comparitive examination of their mRNA expression profiles in a highly differentiated tissue, the testis. The clear implication of their highly regulated synthesis during the course of spermatogenesis is that the different IMP alphas have distinct expression patterns during cellular differentiation, implying tissue/cell type-specific roles.},
}

@article {pmid19416510,
year = {2009},
author = {Ros, VI and Hurst, GD},
title = {Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?.},
journal = {BMC biology},
volume = {7},
number = {},
pages = {20},
pmid = {19416510},
issn = {1741-7007},
mesh = {Animals ; Eukaryotic Cells/*cytology/*metabolism ; Gene Transfer, Horizontal/*genetics ; Prokaryotic Cells/*metabolism ; Symbiosis/genetics ; },
abstract = {The expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. However, it remains controversial whether these genes are of functional importance in their recipient host. Nikoh and Nakabachi, in a recent paper in BMC Biology, take a first step and show that two genes of bacterial origin are highly expressed in the pea aphid Acyrthosiphon pisum. Active gene expression of transferred genes is supported by three other recent studies. Future studies should reveal whether functional proteins are produced and whether and how these are targeted to the appropriate compartment. We argue that the transfer of genes between host and symbiont may occasionally be of great evolutionary importance, particularly in the evolution of the symbiotic interaction itself.},
}

Animals
Eukaryotic Cells/*cytology/*metabolism
Gene Transfer, Horizontal/*genetics
Prokaryotic Cells/*metabolism
Symbiosis/genetics

@article {pmid19416859,
year = {2009},
author = {Bengtson, S and Belivanova, V and Rasmussen, B and Whitehouse, M},
title = {The controversial "Cambrian" fossils of the Vindhyan are real but more than a billion years older.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {106},
number = {19},
pages = {7729-7734},
pmid = {19416859},
issn = {1091-6490},
mesh = {Archaeology/methods ; Biological Evolution ; Cyanobacteria/metabolism ; *Fossils ; Gases ; Geologic Sediments/microbiology ; Paleontology/methods ; Phylogeny ; Time ; },
abstract = {The age of the Vindhyan sedimentary basin in central India is controversial, because geochronology indicating early Proterozoic ages clashes with reports of Cambrian fossils. We present here an integrated paleontologic-geochronologic investigation to resolve this conundrum. New sampling of Lower Vindhyan phosphoritic stromatolitic dolomites from the northern flank of the Vindhyans confirms the presence of fossils most closely resembling those found elsewhere in Cambrian deposits: annulated tubes, embryo-like globules with polygonal surface pattern, and filamentous and coccoidal microbial fabrics similar to Girvanella and Renalcis. None of the fossils, however, can be ascribed to uniquely Cambrian or Ediacaran taxa. Indeed, the embryo-like globules are not interpreted as fossils at all but as former gas bubbles trapped in mucus-rich cyanobacterial mats. Direct dating of the same fossiliferous phosphorite yielded a Pb-Pb isochron of 1,650 +/- 89 (2sigma) million years ago, confirming the Paleoproterozoic age of the fossils. New U-Pb geochronology of zircons from tuffaceous mudrocks in the Lower Vindhyan Porcellanite Formation on the southern flank of the Vindhyans give comparable ages. The Vindhyan phosphorites provide a window of 3-dimensionally preserved Paleoproterozoic fossils resembling filamentous and coccoidal cyanobacteria and filamentous eukaryotic algae, as well as problematic forms. Like Neoproterozoic phosphorites a billion years later, the Vindhyan deposits offer important new insights into the nature and diversity of life, and in particular, the early evolution of multicellular eukaryotes.},
}

Archaeology/methods
Biological Evolution
Cyanobacteria/metabolism
*Fossils
Gases
Geologic Sediments/microbiology
Paleontology/methods
Phylogeny
Time

@article {pmid19468312,
year = {2007},
author = {Vitulo, N and Vezzi, A and Galla, G and Citterio, S and Marino, G and Ruperti, B and Zermiani, M and Albertini, E and Valle, G and Barcaccia, G},
title = {Characterization and evolution of the cell cycle-associated mob domain-containing proteins in eukaryotes.},
journal = {Evolutionary bioinformatics online},
volume = {3},
number = {},
pages = {121-158},
pmid = {19468312},
issn = {1176-9343},
abstract = {The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the 43 eukaryotic genomes so far sequenced. We show that genes for Mob-like proteins are present in at least 41 of these genomes, confirming the universal distribution of this protein family and suggesting its prominent biological function. The phylogenetic analysis reveals five distinct MOB domain classes, showing a progressive expansion of this family from unicellular to multicellular organisms, reaching the highest number in mammals. Plant Mob genes appear to have evolved from a single ancestor, most likely after the loss of one or more genes during the early stage of Viridiplantae evolutionary history. Three of the Mob classes are widespread among most of the analyzed organisms. The possible biological and molecular function of Mob proteins and their role in conserved signaling pathways related to cell proliferation, cell death and cell polarity are also presented and critically discussed.},
}

@article {pmid19513277,
year = {2009},
author = {Agnati, LF and Barlow, PW and Baldelli, E and Baluska, F},
title = {Are maternal mitochondria the selfish entities that are masters of the cells of eukaryotic multicellular organisms?.},
journal = {Communicative & integrative biology},
volume = {2},
number = {2},
pages = {194-200},
pmid = {19513277},
issn = {1942-0889},
abstract = {The Energide concept, as well as the endosymbiotic theory of eukaryotic cell organization and evolution, proposes that present-day cells of eukaryotic organisms are mosaics of specialized and cooperating units, or organelles. Some of these units were originally free-living prokaryotes, which were engulfed during evolutionary time. Mitochondria represent one of these types of previously independent organisms, the Energide, is another type. This new perspective on the organization of the cell has been further expanded to reveal the concept of a public milieu, the cytosol, in which Energides and mitochondria live, each with their own private internal milieu. The present paper discusses how the endosymbiotic theory implicates a new hypothesis about the hierarchical and communicational organization of the integrated prokaryotic components of the eukaryotic cell and provides a new angle from which to consider the theory of evolution and its bearing upon cellular complexity. Thus, it is proposed that the "selfish gene" hypothesis of Dawkins1 is not the only possible perspective for comprehending genomic and cellular evolution. Our proposal is that maternal mitochondria are the selfish "master" entities of the eukaryotic cell with respect not only to their propagation from cell-to-cell and from generation-to-generation but also to their regulation of all other cellular functions. However, it should be recognized that the concept of "master" and "servant" cell components is a metaphor; in present-day living organisms their organellar components are considered to be interdependent and inseparable.},
}