Being Aquifex aeolicus: Untangling a Hyperthermophile’s Checkered Past

Genome Biology and Evolution - Tập 5 Số 12 - Trang 2478-2497 - 2013
Robert Eveleigh1,2, Conor J. Meehan1,2, John M. Archibald1, Robert G. Beiko2
1Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
2Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada

Tóm tắt

Từ khóa


Tài liệu tham khảo

Alain, 2004, Early steps in microbial colonization processes at deep-sea hydrothermal vents, Environ Microbiol., 6, 227, 10.1111/j.1462-2920.2003.00557.x

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389

Andam, 2010, Biased gene transfer mimics patterns created through shared ancestry, Proc Natl Acad Sci U S A., 107, 10679, 10.1073/pnas.1001418107

Asai, 1999, Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons, J Bacteriol., 181, 3803, 10.1128/JB.181.12.3803-3809.1999

Aravind, 1998, Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles, Trends Genet., 14, 442, 10.1016/S0168-9525(98)01553-4

Baker, 2009, Complete generic-level phylogenetic analyses of palms (Arecaceae) with comparisons of supertree and supermatrix approaches, Syst Biol., 58, 240, 10.1093/sysbio/syp021

Baldauf, 1996, The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny, Proc Natl Acad Sci., 93, 7749, 10.1073/pnas.93.15.7749

Bapteste, 2005, Do orthologous gene phylogenies really support tree-thinking?, BMC Evol Biol., 5, 33, 10.1186/1471-2148-5-33

Beiko, 2011, Telling the whole story in a 10,000-genome world, Biol Direct., 6, 34, 10.1186/1745-6150-6-34

Beiko, 2008, The impact of reticulate evolution on genome phylogeny, Syst Biol., 57, 844, 10.1080/10635150802559265

Beiko, 2005, Highways of gene sharing in prokaryotes, Proc Natl Acad Sci U S A., 102, 14332, 10.1073/pnas.0504068102

Beiko, 2006, Searching for convergence in phylogenetic Markov chain Monte Carlo, Syst Biol., 55, 553, 10.1080/10635150600812544

Berezovsky, 2005, Physics and evolution of thermophilic adaptation, Proc Natl Acad Sci U S A., 102, 12742, 10.1073/pnas.0503890102

Bininda-Emonds, 2001, Assessment of the accuracy of matrix representation with parsimony analysis supertree construction, Syst Biol., 50, 565, 10.1080/106351501750435112

Bocchetta, 1995, Arrangement and nucleotide sequence of the gene (fus) encoding elongation factor G (EF-G) from the hyperthermophilic bacterium Aquifex pyrophilus: phylogenetic depth of hyperthermophilic bacteria inferred from analysis of the EF-G/fus sequences, J Mol Evol., 41, 803, 10.1007/BF00173160

Bordenstein, 2005, Mobile DNA in obligate intracellular bacteria, Nat Rev Microbiol., 3, 688, 10.1038/nrmicro1233

Boucher, 2003, Lateral gene transfer and the origins of prokaryotic groups, Annu Rev Genet., 37, 283, 10.1146/annurev.genet.37.050503.084247

Boussau, 2008, Parallel adaptations to high temperatures in the Archaean eon, Nature, 456, 942, 10.1038/nature07393

Boussau, 2008, Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of bacteria, BMC Evol Biol., 8, 272, 10.1186/1471-2148-8-272

Bradley, 2009, Fast statistical alignment, PLoS Comput Biol., 5, e1000392, 10.1371/journal.pcbi.1000392

Brochier, 2000, The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome, Trends Genet., 16, 529, 10.1016/S0168-9525(00)02142-9

Brochier, 2005, An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences, BMC Evol Biol., 5, 16, 10.1186/1471-2148-5-36

Campbell, 2006, The versatile epsilon-proteobacteria: key players in sulphidic habitats, Nat Rev Microbiol., 4, 458, 10.1038/nrmicro1414

Cavalier-Smith, 2002, The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, Int J Syst Evol Microbiol., 52, 7, 10.1099/00207713-52-1-7

Chilcott, 2000, Coupling of flagellar gene expression to flagellar assembly in Salmonella enterica serovar typhimurium and Escherichia coli, Microbiol Mol Biol Rev., 64, 694, 10.1128/MMBR.64.4.694-708.2000

Ciccarelli, 2006, Toward automatic reconstruction of a highly resolved tree of life, Science, 311, 1283, 10.1126/science.1123061

Clason, 2010, The structure of eukaryotic and prokaryotic complex I, J Struct Biol., 169, 81, 10.1016/j.jsb.2009.08.017

Coenye, 2005, Organisation of the S10, spc and alpha ribosomal protein gene clusters in prokaryotic genomes, FEMS Microbiol Lett., 242, 117, 10.1016/j.femsle.2004.10.050

Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res., 37, 141, 10.1093/nar/gkn879

Dagan, 2010, Genome networks root the tree of life between prokaryotic domains, Genome Biol Evol., 2, 379, 10.1093/gbe/evq025

Deckert, 1998, The complete genome of the hyperthermophilic bacterium Aquifex aeolicus, Nature, 392, 353, 10.1038/32831

Doolittle, 2007, Evolution: reducible complexity—the case for bacterial flagella, Curr Biol., 17, 510, 10.1016/j.cub.2007.05.003

Doolittle, 2009, On the origin of prokaryotic species, Genome Res., 19, 744, 10.1101/gr.086645.108

Eddy, 2009, A new generation of homology search tools based on probabilistic inference, Genome Inform., 23, 205

Felsenstein, 1989, PHYLIP—phylogeny inference package (version 3.2), Cladistics, 5, 164

Gaasterland, 1998, Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes, Microb Comp Genomics., 3, 219, 10.1089/omi.1.1998.3.199

Galtier, 2007, A model of horizontal gene transfer and the bacterial phylogeny problem, Syst Biol., 56, 633, 10.1080/10635150701546231

García-Horsman, 1994, The superfamily of heme-copper respiratory oxidases, J Bacteriol., 176, 5587, 10.1128/jb.176.18.5587-5600.1994

Gaucher, 2008, Palaeotemperature trend for Precambrian life inferred from resurrected proteins, Nature, 451, 704, 10.1038/nature06510

Gene Ontology Consortium, 2000, Gene ontology: tool for the unification of biology, Nat Genet., 25, 25, 10.1038/75556

Gogarten, 2002, Prokaryotic evolution in light of gene transfer, Mol Biol Evol., 19, 2226, 10.1093/oxfordjournals.molbev.a004046

Gophna, 2006, Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus, Trends Microbiol., 14, 64, 10.1016/j.tim.2005.12.008

Griffiths, 2004, Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales, Int Microbiol., 7, 41

Gruber, 1998, Characterization of the group 1 and group 2 sigma factors of the green sulfur bacterium Chlorobium tepidum and the green non-sulfur bacterium Chloroflexus aurantiacus, Arch Microbiol., 170, 285, 10.1007/s002030050644

Hao, 2008, Uncovering rate variation of lateral gene transfer during bacterial genome evolution, BMC Genomics, 9, 235, 10.1186/1471-2164-9-235

Harshey, 2003, Bacterial motility on a surface: many ways to a common goal, Annu Rev Microbiol., 57, 249, 10.1146/annurev.micro.57.030502.091014

Hilario, 1993, Horizontal transfer of ATPase genes—the tree of life becomes a net of life, Biosystems, 31, 111, 10.1016/0303-2647(93)90038-E

Hirst, 2010, Towards the molecular mechanism of respiratory complex I, Biochem J., 425, 327, 10.1042/BJ20091382

Holloway, 2010, Assembling networks of microbial genomes using linear programming, BMC Evol Biol., 10, 360, 10.1186/1471-2148-10-360

Huber, 2006, Thermotogales, The Prokaryotes. An evolving electronic resource for the microbiological community, 3rd ed, 899

Huber, 1992, Aquifex pyrophilus gen nov., sp. nov., represents a novel group of marine hyperthermophilic hydrogen-oxidizing bacteria, Syst Appl Microbiol., 15, 340, 10.1016/S0723-2020(11)80206-7

Huber, 1998, Thermocrinis ruber gen. nov., sp. nov., a pink-filament-forming hyperthermophilic bacterium isolated from yellowstone national park, Appl Environ Microbiol., 64, 3576, 10.1128/AEM.64.10.3576-3583.1998

Iyer, 2004, Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer, Gene, 23, 73, 10.1016/j.gene.2004.03.017

Jain, 1999, Horizontal gene transfer among genomes: the complexity hypothesis, Proc Natl Acad Sci U S A., 96, 3801, 10.1073/pnas.96.7.3801

Kanehisa, 2000, KEGG: Kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27

Kanhere, 2009, Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes, BMC Evol Biol., 9, 9, 10.1186/1471-2148-9-9

Klenk, 1999, RNA polymerase of Aquifex pyrophilus: implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria, J Mol Evol., 48, 528, 10.1007/PL00006496

Koga, 2007, Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations, Microbiol Mol Biol Rev., 71, 97, 10.1128/MMBR.00033-06

Koski, 2001, The closest BLAST hit is often not the nearest neighbor, J Mol Evol., 52, 540, 10.1007/s002390010184

Lapointe, 2010, Clanistics: a multi-level perspective for harvesting unrooted gene trees, Trends Microbiol., 18, 341, 10.1016/j.tim.2010.03.009

Leif, 1995, Isolation and characterization of the proton-translocating NADH: ubiquinone oxidoreductase from Escherichia coli, Eur J Biochem., 230, 538, 10.1111/j.1432-1033.1995.tb20594.x

Leigh, 2008, Testing congruence in phylogenomic analysis, Syst Biol., 57, 104, 10.1080/10635150801910436

L’Haridon, 2006, Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the Bacteria, Int J Syst Evol Microbiol., 56, 2843, 10.1099/ijs.0.63994-0

Lindahl, 1986, Ribosomal genes in Escherichia coli, Annu Rev Genet., 20, 297, 10.1146/annurev.ge.20.120186.001501

Liu, 2007, Stepwise formation of the bacterial flagellar system, Proc Natl Acad Sci U S A., 104, 7116, 10.1073/pnas.0700266104

López-García, 2003, Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge, Environ Microbiol., 5, 961, 10.1046/j.1462-2920.2003.00495.x

Mamat, 2009, WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-d-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis, J Biol Chem., 284, 22248, 10.1074/jbc.M109.033308

Mathee, 2008, Dynamics of Pseudomonas aeruginosa genome evolution, Proc Natl Acad Sci U S A., 105, 3100, 10.1073/pnas.0711982105

Matte-Tailliez, 2002, Archaeal phylogeny based on ribosomal proteins, Mol Biol Evol., 19, 631, 10.1093/oxfordjournals.molbev.a004122

Nakagawa, 2005, Distribution, phylogenetic diversity and physiological characteristics of epsilon—proteobacteria in a deep-sea hydrothermal field, Environ Microbiol., 7, 1619, 10.1111/j.1462-2920.2005.00856.x

Nakagawa, 2007, Deep-sea vent epsilon-proteobacterial genomes provide insights into emergence of pathogens, Proc Natl Acad Sci U S A., 104, 12146, 10.1073/pnas.0700687104

Nelson, 1999, Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima, Nature, 399, 323, 10.1038/20601

Ng, 2006, Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications, J Mol Microbiol Biotechnol., 11, 167, 10.1159/000094053

Pellegrini, 1999, Assigning protein functions by comparative genome analysis: protein phylogenetic profiles, Proc Natl Acad Sci U S A., 96, 4285, 10.1073/pnas.96.8.4285

Philippe, 2004, Phylogenomics of eukaryotes: impact of missing data on large alignments, Mol Biol Evol., 21, 1740, 10.1093/molbev/msh182

Plötz, 2000, Characterization of a novel lipid A containing d-galacturonic acid that replaces phosphate residues. The structure of the lipid A of the lipopolysaccharide from the hyperthermophilic bacterium Aquifex pyrophilus, J Biol Chem., 275, 11222, 10.1074/jbc.275.15.11222

Puigbò, 2010, The tree and net components of prokaryote evolution, Genome Biol Evol., 2, 745, 10.1093/gbe/evq062

Raetz, 2007, Lipid A modification systems in Gram-negative bacteria, Annu Rev Biochem., 76, 295, 10.1146/annurev.biochem.76.010307.145803

Renesto, 2005, Some lessons from Rickettsia genomics, FEMS Microbiol Rev., 29, 99, 10.1016/j.femsre.2004.09.002

Reysenbach, 2009, Complete and draft genome sequences of six members of the Aquificales, J Bacteriol., 191, 1992, 10.1128/JB.01645-08

Rinke, 2013, Insights into the phylogeny and coding potential of microbial dark matter, Nature, 499, 431, 10.1038/nature12352

Scheide, 2002, The proton-pumping NADH: ubiquinone oxidoreductase (complex I) of Aquifex aeolicus, FEBS Lett., 512, 80, 10.1016/S0014-5793(02)02224-X

Schütz, 2000, Early evolution of cytochrome bc complexes, J Mol Biol., 300, 663, 10.1006/jmbi.2000.3915

Shimodaira, 2001, CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246, 10.1093/bioinformatics/17.12.1246

Simmons, 2011, Misleading results of likelihood-based phylogenetic analyses in the presence of missing data, Cladistics, 27, 1

Singleton, 1973, Proteins from thermophilic microorganisms, Bacteriol Rev., 37, 320, 10.1128/MMBR.37.3.320-342.1973

Slonim, 2006, Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks, Mol Syst Biol., 2, 2006.0005, 10.1038/msb4100047

Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446

Stohr, 2001, Hydrogenothermus marinus gen. nov., sp. nov., a novel thermophilic hydrogen-oxidizing bacterium, recognition of Calderobacterium hydrogenophilum as a member of the genus Hydrogenobacter and proposal of the reclassification of Hydrogenobacter acidophilus as Hydrogenobaculum acidophilum gen. nov., comb. nov., in the phylum “Hydrogenobacter/Aquifex”, Int J Syst Evol Microbiol., 51, 1853, 10.1099/00207713-51-5-1853

Sukumaran, 2010, DendroPy: a python library for phylogenetic computing, Bioinformatics, 26, 1569, 10.1093/bioinformatics/btq228

Tatusov, 1997, A genomic perspective on protein families, Science, 278, 631, 10.1126/science.278.5338.631

Typas, 2011, From the regulation of peptidoglycan synthesis to bacterial growth and morphology, Nat Rev Microbiol., 10, 123, 10.1038/nrmicro2677

Vollmer, 2008, Murein (peptidoglycan) structure, architecture and biosynthesis in Escherichia coli, Biochim Biophys Acta., 1778, 1714, 10.1016/j.bbamem.2007.06.007

Wang, 2010, Lipopolysaccharide: biosynthetic pathway and structure modification, Prog Lipid Res., 49, 97, 10.1016/j.plipres.2009.06.002

Whelan, 2001, A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol Biol Evol., 18, 459, 10.1093/oxfordjournals.molbev.a003851

Wolf, 2001, Genome trees constructed using five different approaches suggest new major bacterial clades, BMC Evol Biol., 1, 8, 10.1186/1471-2148-1-8

Wu, 2008, A simple, fast, and accurate method of phylogenomic inference, Genome Biol., 9, R151, 10.1186/gb-2008-9-10-r151

Wu, 2009, A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea, Nature, 462, 1056, 10.1038/nature08656

Yoshida, 2001, ATP synthase—a marvellous rotary engine of the cell, Nat Rev Mol Cell Biol., 2, 669, 10.1038/35089509

Zhaxybayeva, 2009, On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales, Proc Natl Acad Sci U S A., 106, 5865, 10.1073/pnas.0901260106