151
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Martin AP, Costello EK, Meyer AF, Nemergut DR, Schmidt SK. THE RATE AND PATTERN OF CLADOGENESIS IN MICROBES. Evolution 2004. [DOI: 10.1554/03-452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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152
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Abstract
In recent years, Bacteria and Archaea have been discovered living in practically every conceivable terrestrial environment, including some previously thought to be too extreme for survival. Exploration of our solar system has revealed a number of extraterrestrial bodies that harbor environments analogous to many of the terrestrial environments in which extremophiles flourish. The recent discovery of more than 105 extrasolar planets suggests that planetary systems are quite common. These three findings have led some to speculate that life is therefore common in the universe, as life as we know it can seemingly survive almost anywhere there is liquid water. It is suggested here that while environments capable of supporting life may be common, this does not in itself support the notion that life is common in the universe. Given that interplanetary transfer of life may be unlikely, the actual origin of life may require specific environmental and geological conditions that may be much less common than the mere existence of liquid water.
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Affiliation(s)
- H James Cleaves
- Geosciences Research Divison, Scripps Institution of Oceanography, La Jolla, California 92093-0212, USA.
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153
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Abstract
The initial analysis of complete genomes has suggested that horizontal gene transfer events are very frequent between microorganisms. This could potentially render the inference, and even the concept itself, of the organismal phylogeny impossible. However, a coherent phylogenetic pattern has recently emerged from an analysis of about a hundred genes, the so-called 'core', strongly suggesting that it is possible to infer the phylogeny of prokaryotes. Also, estimation of the frequency of horizontal gene transfers at the genome level in a phylogenetic context seems to indicate that it is rather low, although of significant biological impact. Nevertheless, it should be emphasized that the history of microorganisms cannot be properly represented by the phylogeny of the core, which represents only a tiny fraction of the genome. This history, even if horizontal gene transfers are rare, should be represented by a network surrounding the core phylogeny.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Département de Biochimie, Université de Montréal, Qc., H3C 3J7, Montréal, Canada.
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154
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Ben-Shem A, Frolow F, Nelson N. Crystal structure of plant photosystem I. Nature 2003; 426:630-5. [PMID: 14668855 DOI: 10.1038/nature02200] [Citation(s) in RCA: 546] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2003] [Accepted: 10/28/2003] [Indexed: 11/09/2022]
Abstract
Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4 A resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.
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Affiliation(s)
- Adam Ben-Shem
- Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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155
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Abstract
We screened a Thermotoga sp. strain RQ2 lambda library for genes present in that strain but absent from the closely related completely sequenced relative Thermotoga maritima strain MSB8, by using probes generated in an earlier genomic subtraction study. Five lambda insert fragments were sequenced, containing, respectively, an archaeal type ATPase operon, rhamnose biosynthetic genes, ORFs with similarity to an arabinosidase, a Thermotoga sp. strain RQ2-specific alcohol dehydrogenase and a novel archaeal Mut-S homologue. All but one of these fragments contained additional Thermotoga sp. strain RQ2-specific sequences not screened for, suggesting that many such strain-specific genes will be found clustered in the genome. Moreover, phylogenetic analyses, phylogenetic distribution and/or G + C content suggests that all the Thermotoga sp. strain RQ2 specific sequences in the sequenced lambda clones have been acquired by lateral gene transfer. We suggest that the use of strain-specific small insert clones obtained by subtractive hybridization to target larger inserts for sequencing is an efficient, economical way to identify environmentally (or clinically) relevant interstrain differences and novel gene clusters, and will be invaluable in comparative genomics.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Alcohol Dehydrogenase/genetics
- Bacterial Proteins/genetics
- Base Composition
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Archaeal/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA-Binding Proteins/genetics
- Gene Library
- Gene Order
- Gene Transfer, Horizontal/genetics
- Genes, Archaeal
- Genes, Bacterial
- Genomic Library
- Glycoside Hydrolases/genetics
- Molecular Sequence Data
- MutS DNA Mismatch-Binding Protein
- Phylogeny
- Rhamnose/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Thermotoga maritima/genetics
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Affiliation(s)
- Camilla L Nesbø
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
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156
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Aravind L, Anantharaman V, Iyer LM. Evolutionary connections between bacterial and eukaryotic signaling systems: a genomic perspective. Curr Opin Microbiol 2003; 6:490-7. [PMID: 14572542 DOI: 10.1016/j.mib.2003.09.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recent advances in microbial genomics suggest that several protein domains are common to bacterial and eukaryotic regulatory proteins. In particular, developmentally and morphologically complex prokaryotes appear to share several signaling modules with eukaryotes. New experimental studies and information from domain architectures point to several similar mechanistic themes in bacterial and eukaryotic signaling proteins. Laterally transferred protein domains, originally of bacterial provenance, appear to have contributed to the evolution of sensory pathways related to light, redox and nitric oxide signaling, and developmental pathways, such as Notch, cytokine and cytokinin signaling in eukaryotes.
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Affiliation(s)
- L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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157
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Zhaxybayeva O, Gogarten JP. An improved probability mapping approach to assess genome mosaicism. BMC Genomics 2003; 4:37. [PMID: 12974984 PMCID: PMC222983 DOI: 10.1186/1471-2164-4-37] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2003] [Accepted: 09/15/2003] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Maximum likelihood and posterior probability mapping are useful visualization techniques that are used to ascertain the mosaic nature of prokaryotic genomes. However, posterior probabilities, especially when calculated for four-taxon cases, tend to overestimate the support for tree topologies. Furthermore, because of poor taxon sampling four-taxon analyses suffer from sensitivity to the long branch attraction artifact. Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability. RESULTS Quartets of orthologous proteins were complemented with homologs from selected reference genomes. The mapping of bootstrap support values from these extended datasets gives results similar to the original maximum likelihood and posterior probability mapping. The more conservative nature of the plotted support values allows to focus further analyses on those protein families that strongly disagree with the majority or plurality of genes present in the analyzed genomes. CONCLUSION Posterior probability is a non-conservative measure for support, and posterior probability mapping only provides a quick estimation of phylogenetic information content of four genomes. This approach can be utilized as a pre-screen to select genes that might have been horizontally transferred. Better taxon sampling combined with subtree analyses prevents the inconsistencies associated with four-taxon analyses, but retains the power of visual representation. Nevertheless, a case-by-case inspection of individual multi-taxon phylogenies remains necessary to differentiate unrecognized paralogy and shared phylogenetic reconstruction artifacts from horizontal gene transfer events.
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Affiliation(s)
- Olga Zhaxybayeva
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269-3125, USA
| | - J Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269-3125, USA
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158
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Abstract
It has been suggested that horizontal gene transfer (HGT) is the "essence of phylogeny." In contrast, much data suggest that this is an exaggeration resulting in part from a reliance on inadequate methods to identify HGT events. In addition, the assumption that HGT is a ubiquitous influence throughout evolution is questionable. Instead, rampant global HGT is likely to have been relevant only to primitive genomes. In modern organisms we suggest that both the range and frequencies of HGT are constrained most often by selective barriers. As a consequence those HGT events that do occur most often have little influence on genome phylogeny. Although HGT does occur with important evolutionary consequences, classical Darwinian lineages seem to be the dominant mode of evolution for modern organisms.
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Affiliation(s)
- C G Kurland
- Department of Molecular Evolution, Evolutionary Biology Centre, University of Uppsala, S-75236 Uppsala, Sweden
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159
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Abstract
Gene acquisition is an ongoing process in many bacterial genomes, contributing to adaptation and ecological diversification. Lateral gene transfer is considered the primary explanation for discordance among gene phylogenies and as an obstacle to reconstructing the tree of life. We measured the extent of phylogenetic conflict and alien-gene acquisition within quartets of sequenced genomes. Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree.
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Affiliation(s)
- Vincent Daubin
- Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ, 85721, USA
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160
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Karr EA, Sattley WM, Jung DO, Madigan MT, Achenbach LA. Remarkable diversity of phototrophic purple bacteria in a permanently frozen Antarctic lake. Appl Environ Microbiol 2003; 69:4910-4. [PMID: 12902286 PMCID: PMC169089 DOI: 10.1128/aem.69.8.4910-4914.2003] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although anoxygenic photosynthesis is thought to play an important role in the primary productivity of permanently frozen lakes in the Antarctic dry valleys, the bacterial communities responsible for this metabolism remain uncharacterized. Here we report the composition and activity of phototrophic purple bacteria in Lake Fryxell, Antarctica, as determined by analysis of a photosynthesis-specific gene, pufM. The results revealed an extensive diversity and highly stratified distribution of purple nonsulfur bacteria in Lake Fryxell and showed which phylotypes produced pufM transcripts in situ. Enrichment cultures for purple bacteria yielded two morphotypes, each with a pufM signature identical to signatures detected by environmental screening. The isolates also contained gas vesicles, buoyancy structures previously unknown in purple nonsulfur bacteria, that may be necessary for these organisms to position themselves at specific depths within the nearly freezing water column.
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Affiliation(s)
- Elizabeth A Karr
- Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901-6508, USA
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161
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Raymond J, Zhaxybayeva O, Gogarten JP, Blankenship RE. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach. Philos Trans R Soc Lond B Biol Sci 2003; 358:223-30. [PMID: 12594930 PMCID: PMC1693105 DOI: 10.1098/rstb.2002.1181] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared.
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Affiliation(s)
- Jason Raymond
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
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162
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Green BR. The Evolution of Light-harvesting Antennas. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_4] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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163
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Affiliation(s)
- Satoshi Hanada
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)
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164
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Sato N, Terasawa K, Miyajima K, Kabeya Y. Organization, Developmental Dynamics, and Evolution of Plastid Nucleoids. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 232:217-62. [PMID: 14711120 DOI: 10.1016/s0074-7696(03)32006-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The plastid is a semiautonomous organelle essential in photosynthesis and other metabolic activities of plants and algae. Plastid DNA is organized into the nucleoid with various proteins and RNA, and the nucleoid is subject to dynamic changes during the development of plant cells. Characterization of the major DNA-binding proteins of nucleoids revealed essential differences in the two lineages of photosynthetic eukaryotes, namely nucleoids of green plants contain sulfite reductase as a major DNA-binding protein that represses the genomic activity, whereas the prokaryotic DNA-binding protein HU is abundant in plastid nucleoids of the rhodophyte lineage. In addition, current knowledge on DNA-binding proteins, as well as the replication and transcription systems of plastids, is reviewed from comparative and evolutionary points of view. A revised hypothesis on the discontinuous evolution of plastid genomic machinery is presented: despite the cyanobacterial origin of plastids, the genomic machinery of the plastid genome is fundamentally different from its counterpart in cyanobacteria.
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Affiliation(s)
- Naoki Sato
- Department of Molecular Biology, Faculty of Science, Saitama University, Saitama 338-8570, Japan
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165
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Green BR, Anderson JM, Parson WW. Photosynthetic Membranes and Their Light-Harvesting Antennas. LIGHT-HARVESTING ANTENNAS IN PHOTOSYNTHESIS 2003. [DOI: 10.1007/978-94-017-2087-8_1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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166
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003; 4:277-84. [PMID: 18629117 PMCID: PMC2447404 DOI: 10.1002/cfg.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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167
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In Brief. Nat Rev Genet 2003. [DOI: 10.1038/nrg992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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