{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T02:19:54Z","timestamp":1767925194657,"version":"3.49.0"},"reference-count":47,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2014,4,24]],"date-time":"2014-04-24T00:00:00Z","timestamp":1398297600000},"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.1003575","type":"journal-article","created":{"date-parts":[[2014,4,24]],"date-time":"2014-04-24T20:33:54Z","timestamp":1398371634000},"page":"e1003575","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":38,"title":["Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens"],"prefix":"10.1371","volume":"10","author":[{"given":"Adam M.","family":"Feist","sequence":"first","affiliation":[]},{"given":"Harish","family":"Nagarajan","sequence":"additional","affiliation":[]},{"given":"Amelia-Elena","family":"Rotaru","sequence":"additional","affiliation":[]},{"given":"Pier-Luc","family":"Tremblay","sequence":"additional","affiliation":[]},{"given":"Tian","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Kelly P.","family":"Nevin","sequence":"additional","affiliation":[]},{"given":"Derek R.","family":"Lovley","sequence":"additional","affiliation":[]},{"given":"Karsten","family":"Zengler","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,4,24]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1007\/BF00290916","article-title":"Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals","volume":"159","author":"DR Lovley","year":"1993","journal-title":"Archives of microbiology"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nrmicro2113","article-title":"Exoelectrogenic bacteria that power microbial fuel cells","volume":"7","author":"BE Logan","year":"2009","journal-title":"Nature reviews Microbiology"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1413","DOI":"10.1126\/science.1196526","article-title":"Direct exchange of electrons within aggregates of an evolved syntrophic coculture of anaerobic bacteria","volume":"330","author":"ZM Summers","year":"2010","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/330252a0","article-title":"Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism","volume":"330","author":"DR Lovley","year":"1987","journal-title":"Nature"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/B978-0-12-387661-4.00004-5","article-title":"Geobacter: the microbe electric&apos;s physiology, ecology, and practical applications","volume":"59","author":"DR Lovley","year":"2011","journal-title":"Adv Microb Physiol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/339297a0","article-title":"Oxidation of aromatic contaminants coupled to microbial iron reduction","volume":"339","author":"DR Lovley","year":"1989","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.copbio.2013.02.012","article-title":"Electrobiocommodities: powering microbial production of fuels and commodity chemicals from carbon dioxide with electricity","volume":"24","author":"DR Lovley","year":"2013","journal-title":"Curr Opin Biotechnol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/nrmicro1949","article-title":"Reconstruction of biochemical networks in microorganisms","volume":"7","author":"AM Feist","year":"2009","journal-title":"Nat Rev Microbiol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1038\/nprot.2009.203","article-title":"A protocol for generating a high-quality genome-scale metabolic reconstruction","volume":"5","author":"I Thiele","year":"2010","journal-title":"Nat Protoc"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/msb.2013.18","article-title":"Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli","volume":"9","author":"D McCloskey","year":"2013","journal-title":"Molecular Systems Biology"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/nrmicro2456","article-title":"In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling","volume":"9","author":"R Mahadevan","year":"2011","journal-title":"Nat Rev Microbiol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1128\/AEM.72.2.1558-1568.2006","article-title":"Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling","volume":"72","author":"R Mahadevan","year":"2006","journal-title":"Appl Environ Microbiol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1752-0509-3-15","article-title":"Genome-scale constraint-based modeling of Geobacter metallireducens","volume":"3","author":"J Sun","year":"2009","journal-title":"BMC Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1186\/1471-2180-9-109","article-title":"The genome sequence of Geobacter metallireducens: features of metabolism, physiology and regulation common and dissimilar to Geobacter sulfurreducens","volume":"9","author":"M Aklujkar","year":"2009","journal-title":"BMC Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2443","DOI":"10.1099\/mic.0.28849-0","article-title":"Succinate dehydrogenase functioning by a reverse redox loop mechanism and fumarate reductase in sulphate-reducing bacteria","volume":"152","author":"T Zaunmuller","year":"2006","journal-title":"Microbiology"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"17687","DOI":"10.1073\/pnas.0905073106","article-title":"Identification and characterization of the tungsten-containing class of benzoyl-coenzyme A reductases","volume":"106","author":"JW Kung","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"6493","DOI":"10.1128\/JB.00790-08","article-title":"Purification and characterization of active-site components of the putative p-cresol methylhydroxylase membrane complex from Geobacter metallireducens","volume":"190","author":"J Johannes","year":"2008","journal-title":"Journal of Bacteriology"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1016\/j.mib.2010.03.003","article-title":"The biomass objective function","volume":"13","author":"AM Feist","year":"2010","journal-title":"Curr Opin Microbiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"17480","DOI":"10.1073\/pnas.0603364103","article-title":"Systems approach to refining genome annotation","volume":"103","author":"JL Reed","year":"2006","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1038\/nbt.1672","article-title":"High-throughput generation, optimization and analysis of genome-scale metabolic models","volume":"28","author":"CS Henry","year":"2010","journal-title":"Nat Biotechnol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1093\/bioinformatics\/btq702","article-title":"Functional integration of a metabolic network model and expression data without arbitrary thresholding","volume":"27","author":"PA Jensen","year":"2011","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1038\/nrmicro2365","article-title":"Autotrophic carbon fixation in archaea","volume":"8","author":"IA Berg","year":"2010","journal-title":"Nature reviews Microbiology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.1099\/mic.0.2007\/006478-0","article-title":"Involvement of <italic>Geobacter sulfurreducens<\/italic> SfrAB in acetate metabolism rather than intracellular Fe(III) reduction","volume":"153","author":"MV Coppi","year":"2007","journal-title":"Microbiology"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1128\/MMBR.41.1.100-180.1977","article-title":"Energy conservation in chemotrophic anaerobic bacteria","volume":"41","author":"RK Thauer","year":"1977","journal-title":"Bacteriological reviews"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/S0005-2728(01)00234-1","article-title":"Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism","volume":"1553","author":"A Kroger","year":"2002","journal-title":"Biochimica et biophysica acta"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1128\/JB.188.2.450-455.2006","article-title":"Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens","volume":"188","author":"JE Butler","year":"2006","journal-title":"Journal of Bacteriology"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1128\/AEM.54.6.1472-1480.1988","article-title":"Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese","volume":"54","author":"DR Lovley","year":"1988","journal-title":"Applied and environmental microbiology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1128\/AEM.02954-12","article-title":"Outer cell surface components essential for Fe(III) oxide reduction by <italic>Geobacter metallireducens<\/italic>","volume":"79","author":"JA Smith","year":"2013","journal-title":"Appl Environ Microbiol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/nnano.2011.119","article-title":"Tunable metallic-like conductivity in nanostructured biofilms comprised of microbial nanowires","volume":"6","author":"NS Malvankar","year":"2011","journal-title":"Nature Nanotechnology"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1042\/bj1520547","article-title":"Proton translocation and the respiratory nitrate reductase of Escherichia coli","volume":"152","author":"PB Garland","year":"1975","journal-title":"The Biochemical journal"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/84379","article-title":"<italic>In silico<\/italic> predictions of <italic>Escherichia coli<\/italic> metabolic capabilities are consistent with experimental data","volume":"19","author":"JS Edwards","year":"2001","journal-title":"Nat Biotechnol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.copbio.2013.12.001","article-title":"Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms","volume":"27","author":"H Latif","year":"2014","journal-title":"Current Opinion in Biotechnology"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1186\/1471-2164-11-490","article-title":"The genome of Geobacter bemidjiensis, exemplar for the subsurface clade of Geobacter species that predominate in Fe(III)-reducing subsurface environments","volume":"11","author":"M Aklujkar","year":"2010","journal-title":"BMC Genomics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1186\/1471-2164-13-690","article-title":"The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features","volume":"13","author":"M Aklujkar","year":"2012","journal-title":"BMC Genomics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"D742","DOI":"10.1093\/nar\/gkr1014","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway\/genome databases","volume":"40","author":"R Caspi","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1038\/msb4100155","article-title":"A genome-scale metabolic reconstruction for <italic>Escherichia coli<\/italic> K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information","volume":"3","author":"AM Feist","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1007\/s10295-008-0486-7","article-title":"Polar lipid fatty acids, LPS-hydroxy fatty acids, and respiratory quinones of three Geobacter strains, and variation with electron acceptor","volume":"36","author":"DB Hedrick","year":"2009","journal-title":"J Ind Microbiol Biotechnol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nprot.2011.308","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0","volume":"6","author":"J Schellenberger","year":"2011","journal-title":"Nat Protoc"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1472","DOI":"10.1128\/AEM.54.6.1472-1480.1988","article-title":"Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese","volume":"54","author":"DR Lovley","year":"1988","journal-title":"Appl Environ Microbiol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1128\/JB.188.2.450-455.2006","article-title":"Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in <italic>Geobacter sulfurreducens<\/italic> and engineering of fumarate reduction in <italic>Geobacter metallireducens<\/italic>","volume":"188","author":"JE Butler","year":"2006","journal-title":"J Bacteriol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1007\/s002030000208","article-title":"Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture","volume":"174","author":"AS Galushko","year":"2000","journal-title":"Archives of microbiology"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1111\/j.1462-2920.2005.00731.x","article-title":"Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture","volume":"7","author":"A Esteve-Nunez","year":"2005","journal-title":"Environmental microbiology"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"5926","DOI":"10.1128\/AEM.05452-11","article-title":"Anaerobic oxidation of benzene by the hyperthermophilic archaeon Ferroglobus placidus","volume":"77","author":"DE Holmes","year":"2011","journal-title":"Applied and environmental microbiology"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/ismej.2011.88","article-title":"Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus","volume":"6","author":"DE Holmes","year":"2012","journal-title":"The ISME journal"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1186\/1752-0509-5-147","article-title":"TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks","volume":"5","author":"PA Jensen","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"M Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1186\/1475-2859-12-118","article-title":"Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii","volume":"12","author":"H Nagarajan","year":"2013","journal-title":"Microb Cell Fact"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003575","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,18]],"date-time":"2020-08-18T10:03:59Z","timestamp":1597745039000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003575"}},"subtitle":[],"editor":[{"given":"Costas D.","family":"Maranas","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,4,24]]},"references-count":47,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2014,4,24]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003575","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,24]]}}}