{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T01:43:46Z","timestamp":1782351826513,"version":"3.54.5"},"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2014,9,4]],"date-time":"2014-09-04T00:00:00Z","timestamp":1409788800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003821","type":"journal-article","created":{"date-parts":[[2014,9,5]],"date-time":"2014-09-05T01:53:01Z","timestamp":1409881981000},"page":"e1003821","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Evolution of the F0F1 ATP Synthase Complex in Light of the Patchy Distribution of Different Bioenergetic Pathways across Prokaryotes"],"prefix":"10.1371","volume":"10","author":[{"given":"Vassiliki Lila","family":"Koumandou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sophia","family":"Kossida","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,9,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1128\/MMBR.63.3.570-620.1999","article-title":"Bioenergetics of the Archaea","volume":"63","author":"G Schafer","year":"1999","journal-title":"Microbiol Mol Biol Rev"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1007\/s00018-002-8526-3","article-title":"Redox-driven proton translocation in methanogenic Archaea","volume":"59","author":"U Deppenmeier","year":"2002","journal-title":"Cell Mol Life Sci"},{"key":"ref3","doi-asserted-by":"crossref","unstructured":"Blankenship RE (2002) Molecular Mechanisms of Phtosynthesis. Oxford: Blackwell Science.","DOI":"10.1002\/9780470758472"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/S1389-1723(02)80232-8","article-title":"Structure and function of enzymes involved in the methanogenic pathway utilizing carbon dioxide and molecular hydrogen","volume":"93","author":"S Shima","year":"2002","journal-title":"J Biosci Bioeng"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1128\/AEM.68.1.316-325.2002","article-title":"Characterization of an autotrophic sulfide-oxidizing marine Arcobacter sp. that produces filamentous sulfur","volume":"68","author":"CO Wirsen","year":"2002","journal-title":"Appl Environ Microbiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.pbiomolbio.2004.11.003","article-title":"Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview","volume":"89","author":"PM Matias","year":"2005","journal-title":"Prog Biophys Mol Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/j.tim.2006.09.001","article-title":"Prokaryotic photosynthesis and phototrophy illuminated","volume":"14","author":"DA Bryant","year":"2006","journal-title":"Trends Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nrmicro1490","article-title":"Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction","volume":"4","author":"KA Weber","year":"2006","journal-title":"Nat Rev Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"e49793","DOI":"10.1371\/journal.pone.0049793","article-title":"Metagenomic and biochemical characterizations of sulfur oxidation metabolism in uncultured large sausage-shaped bacterium in hot spring microbial mats","volume":"7","author":"S Tamazawa","year":"2012","journal-title":"PLoS One"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1016\/B978-0-12-394423-8.00006-8","article-title":"Supramolecular organization in prokaryotic respiratory systems","volume":"61","author":"A Magalon","year":"2012","journal-title":"Adv Microb Physiol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.bbabio.2012.09.005","article-title":"On the universal core of bioenergetics","volume":"1827","author":"B Schoepp-Cothenet","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref12","article-title":"The Diversity of Procaryotic Metabolism","author":"K Todar","journal-title":"Online Textbook of Bacteriology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1126\/science.287.5453.605","article-title":"Perspectives: earth science and evolution. Genomics and the geosciences","volume":"287","author":"JF Banfield","year":"2000","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2148-4-44","article-title":"A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land","volume":"4","author":"FU Battistuzzi","year":"2004","journal-title":"BMC Evol Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1017\/S0263593300028650","article-title":"The evolution of ecological tolerance in prokaryotes","volume":"80","author":"AH Knoll","year":"1989","journal-title":"Trans R Soc Edinb Earth Sci"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/S0005-2728(01)00227-4","article-title":"Comparative genomics and bioenergetics","volume":"1506","author":"J Castresana","year":"2001","journal-title":"Biochim Biophys Acta"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1126\/science.1072483","article-title":"Merging genomes with geochemistry in hydrothermal ecosystems","volume":"296","author":"AL Reysenbach","year":"2002","journal-title":"Science"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1146\/annurev.genet.37.050503.084247","article-title":"Lateral gene transfer and the origins of prokaryotic groups","volume":"37","author":"Y Boucher","year":"2003","journal-title":"Annu Rev Genet"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1098\/rstb.2002.1184","article-title":"The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes","volume":"358","author":"F Baymann","year":"2003","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1023\/B:PRES.0000030457.06495.83","article-title":"Thinking about the evolution of photosynthesis","volume":"80","author":"JM Olson","year":"2004","journal-title":"Photosynthesis Research"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1093\/molbev\/msl079","article-title":"Conservation of distantly related membrane proteins: photosynthetic reaction centers share a common structural core","volume":"23","author":"S Sadekar","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.febslet.2004.08.065","article-title":"The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+\/ATP coupling ratio","volume":"576","author":"RL Cross","year":"2004","journal-title":"FEBS Lett"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.bbabio.2006.04.027","article-title":"Bioenergetics of archaea: ancient energy conserving mechanisms developed in the early history of life","volume":"1757","author":"K Lewalter","year":"2006","journal-title":"Biochim Biophys Acta"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1038\/nrmicro1767","article-title":"Inventing the dynamo machine: the evolution of the F-type and V-type ATPases","volume":"5","author":"AY Mulkidjanian","year":"2007","journal-title":"Nat Rev Microbiol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"4765","DOI":"10.1128\/JB.180.18.4765-4774.1998","article-title":"Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity","volume":"180","author":"P Hugenholtz","year":"1998","journal-title":"J Bacteriol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1006\/tpbi.2002.1589","article-title":"Critical issues in bacterial phylogeny","volume":"61","author":"RS Gupta","year":"2002","journal-title":"Theor Popul Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s11427-007-0084-3","article-title":"Prokaryote phylogeny meets taxonomy: an exhaustive comparison of composition vector trees with systematic bacteriology","volume":"50","author":"L Gao","year":"2007","journal-title":"Sci China C Life Sci"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1093\/molbev\/msm229","article-title":"Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny","volume":"25","author":"E Bapteste","year":"2008","journal-title":"Mol Biol Evol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e62510","DOI":"10.1371\/journal.pone.0062510","article-title":"Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices","volume":"8","author":"JM Lang","year":"2013","journal-title":"PLoS One"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1073\/pnas.0913033107","article-title":"Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution","volume":"107","author":"SR Jun","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nature08656","article-title":"A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea","volume":"462","author":"D Wu","year":"2009","journal-title":"Nature"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1093\/bioinformatics\/btq234","article-title":"Characterization of the N-ATPase, a distinct, laterally transferred Na+-translocating form of the bacterial F-type membrane ATPase","volume":"26","author":"DV Dibrova","year":"2010","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1080\/10635150500221028","article-title":"How much data are needed to resolve a difficult phylogeny?: case study in Lamiales","volume":"54","author":"AH Wortley","year":"2005","journal-title":"Syst Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"e38793","DOI":"10.1371\/journal.pone.0038793","article-title":"Specific evolution of F1-like ATPases in mycoplasmas","volume":"7","author":"L Beven","year":"2012","journal-title":"PLoS One"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.bbrc.2007.12.170","article-title":"UncI protein can mediate ring-assembly of c-subunits of FoF1-ATP synthase in vitro","volume":"367","author":"Y Ozaki","year":"2008","journal-title":"Biochem Biophys Res Commun"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"20776","DOI":"10.1073\/pnas.0708075105","article-title":"The product of uncI gene in F1Fo-ATP synthase operon plays a chaperone-like role to assist c-ring assembly","volume":"104","author":"T Suzuki","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"20537","DOI":"10.1073\/pnas.1209119109","article-title":"Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea","volume":"109","author":"S Nelson-Sathi","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"10039","DOI":"10.1073\/pnas.0800679105","article-title":"Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution","volume":"105","author":"T Dagan","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1101\/gr.1092603","article-title":"The balance of driving forces during genome evolution in prokaryotes","volume":"13","author":"V Kunin","year":"2003","journal-title":"Genome Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e1001284","DOI":"10.1371\/journal.pgen.1001284","article-title":"Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes","volume":"7","author":"TJ Treangen","year":"2011","journal-title":"PLoS Genet"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1016\/j.tree.2013.04.002","article-title":"Exploring the costs of horizontal gene transfer","volume":"28","author":"DA Baltrus","year":"2013","journal-title":"Trends Ecol Evol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1038\/nature10724","article-title":"Evolution of increased complexity in a molecular machine","volume":"481","author":"GC Finnigan","year":"2012","journal-title":"Nature"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"24465","DOI":"10.1074\/jbc.M113.465633","article-title":"Individual interactions of the b subunits within the stator of the Escherichia coli ATP synthase","volume":"288","author":"K Brandt","year":"2013","journal-title":"J Biol Chem"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"26441","DOI":"10.1074\/jbc.M113.503722","article-title":"Escherichia coli F1Fo-ATP synthase with a b\/delta fusion protein allows analysis of the function of the individual b subunits","volume":"288","author":"CS Gajadeera","year":"2013","journal-title":"J Biol Chem"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"5463","DOI":"10.1128\/JB.00191-07","article-title":"Functional incorporation of chimeric b subunits into F1Fo ATP synthase","volume":"189","author":"SB Claggett","year":"2007","journal-title":"J Bacteriol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1093\/bioinformatics\/btt064","article-title":"Phylogenomic clustering for selecting non-redundant genomes for comparative genomics","volume":"29","author":"G Moreno-Hagelsieb","year":"2013","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D115","DOI":"10.1093\/nar\/gkr1044","article-title":"IMG: the Integrated Microbial Genomes database and comparative analysis system","volume":"40","author":"VM Markowitz","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"JR Cole","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"i559","DOI":"10.1093\/bioinformatics\/btm226","article-title":"Multiple alignment by aligning alignments","volume":"23","author":"TJ Wheeler","year":"2007","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1471-2148-6-29","article-title":"Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified","volume":"6","author":"TM Keane","year":"2006","journal-title":"BMC Evol Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"RC Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"2104","DOI":"10.1093\/bioinformatics\/bti263","article-title":"ProtTest: selection of best-fit models of protein evolution","volume":"21","author":"F Abascal","year":"2005","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","article-title":"MrBayes 3: Bayesian phylogenetic inference under mixed models","volume":"19","author":"F Ronquist","year":"2003","journal-title":"Bioinformatics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","article-title":"RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models","volume":"22","author":"A Stamatakis","year":"2006","journal-title":"Bioinformatics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003821","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,24]],"date-time":"2020-08-24T02:25:07Z","timestamp":1598235907000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003821"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,9,4]]},"references-count":55,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2014,9,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003821","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,9,4]]}}}