{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T14:59:49Z","timestamp":1769007589442,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008137","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,8,27]],"date-time":"2020-08-27T00:00:00Z","timestamp":1598486400000}}],"reference-count":50,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T00:00:00Z","timestamp":1597622400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-FC02-07ER64494"],"award-info":[{"award-number":["DE-FC02-07ER64494"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","award":["DE-SC0018409"],"award-info":[{"award-number":["DE-SC0018409"]}],"id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NIGMS 5 T32 GM08349"],"award-info":[{"award-number":["NIGMS 5 T32 GM08349"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1008137","type":"journal-article","created":{"date-parts":[[2020,8,17]],"date-time":"2020-08-17T18:17:00Z","timestamp":1597688220000},"page":"e1008137","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0972-1499","authenticated-orcid":true,"given":"Wai Kit","family":"Ong","sequence":"first","affiliation":[]},{"given":"Dylan K.","family":"Courtney","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3914-9278","authenticated-orcid":true,"given":"Shu","family":"Pan","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3531-0247","authenticated-orcid":true,"given":"Ramon Bonela","family":"Andrade","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8771-1782","authenticated-orcid":true,"given":"Patricia J.","family":"Kiley","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9232-9959","authenticated-orcid":true,"given":"Brian F.","family":"Pfleger","sequence":"additional","affiliation":[]},{"given":"Jennifer L.","family":"Reed","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,8,17]]},"reference":[{"issue":"5","key":"pcbi.1008137.ref001","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1128\/JB.187.5.1581-1590.2005","article-title":"Experimental identification and quantification of glucose metabolism in seven bacterial species","volume":"187","author":"T Fuhrer","year":"2005","journal-title":"J Bacteriol"},{"key":"pcbi.1008137.ref002","first-page":"73","volume-title":"Advances in Microbial Physiology","author":"U Kalnenieks","year":"2006"},{"issue":"1","key":"pcbi.1008137.ref003","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/MMBR.41.1.1-46.1977","article-title":"The biology of Zymomonas","volume":"41","author":"J Swings","year":"1977","journal-title":"Bacteriol Rev"},{"issue":"7","key":"pcbi.1008137.ref004","doi-asserted-by":"crossref","first-page":"2222","DOI":"10.1073\/pnas.1420663112","article-title":"N2 gas is an effective fertilizer for bioethanol production by Zymomonas mobilis","volume":"112","author":"TA Kremer","year":"2015","journal-title":"Proc Natl Acad Sci"},{"issue":"5195","key":"pcbi.1008137.ref005","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1126\/science.267.5195.240","article-title":"Metabolic engineering of a pentose metabolsim pathway in ethanologenic Zymomonas mobilis","volume":"267","author":"Min Zhang","year":"1995","journal-title":"Science (80-)"},{"issue":"12","key":"pcbi.1008137.ref006","doi-asserted-by":"crossref","first-page":"4465","DOI":"10.1128\/AEM.62.12.4465-4470.1996","article-title":"Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic pathway engineering","volume":"62","author":"K Deanda","year":"1996","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"pcbi.1008137.ref007","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/j.procbio.2004.01.041","article-title":"Optimization study for sorbitol production by Zymomonas mobilis in sugar cane molasses","volume":"40","author":"ML Cazetta","year":"2005","journal-title":"Process Biochem"},{"issue":"6","key":"pcbi.1008137.ref008","doi-asserted-by":"crossref","first-page":"1847","DOI":"10.1128\/AEM.57.6.1847-1849.1991","article-title":"Production of beta-carotene in Zymomonas mobilis and Agrobacterium tumefaciens by Introduction of the Biosynthetic Genes from Erwinia uredovora","volume":"57","author":"N Misawa","year":"1991","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"pcbi.1008137.ref009","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s13068-017-0714-3","article-title":"Enhancement of furan aldehydes conversion in Zymomonas mobilis by elevating dehydrogenase activity and cofactor regeneration","volume":"10","author":"X Wang","year":"2017","journal-title":"Biotechnol Biofuels"},{"key":"pcbi.1008137.ref010","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/j.ymben.2018.04.001","article-title":"Advances and prospects in metabolic engineering of Zymomonas mobilis","volume":"50","author":"X Wang","year":"2018","journal-title":"Metab Eng"},{"issue":"1","key":"pcbi.1008137.ref011","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nbt1045","article-title":"The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4","volume":"23","author":"JS Seo","year":"2005","journal-title":"Nat Biotechnol"},{"issue":"10","key":"pcbi.1008137.ref012","doi-asserted-by":"crossref","first-page":"893","DOI":"10.1038\/nbt1009-893","article-title":"Improved genome annotation for Zymomonas mobilis","volume":"27","author":"S Yang","year":"2009","journal-title":"Nat Biotechnol"},{"issue":"1","key":"pcbi.1008137.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13068-018-1116-x","article-title":"Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032","volume":"11","author":"S Yang","year":"2018","journal-title":"Biotechnol Biofuels"},{"issue":"1","key":"pcbi.1008137.ref014","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jbiotec.2013.02.014","article-title":"Biotechnological potential of respiring Zymomonas mobilis: A stoichiometric analysis of its central metabolism","volume":"165","author":"A Pentjuss","year":"2013","journal-title":"J Biotechnol"},{"key":"pcbi.1008137.ref015","doi-asserted-by":"crossref","DOI":"10.1186\/1475-2859-6-8","article-title":"Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis","volume":"6","author":"IC Tsantili","year":"2007","journal-title":"Microb Cell Fact"},{"issue":"PART 12","key":"pcbi.1008137.ref016","first-page":"2674","article-title":"Kinetic modelling of the Zymomonas mobilis Entner-Doudoroff pathway: Insights into control and functionality","volume":"159","author":"R Rutkis","year":"2013","journal-title":"Microbiol (United Kingdom)"},{"key":"pcbi.1008137.ref017","first-page":"1","article-title":"The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies","volume":"9","author":"KY Lee","year":"2010","journal-title":"Microb Cell Fact"},{"issue":"3","key":"pcbi.1008137.ref018","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1002\/bit.22965","article-title":"Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis","volume":"108","author":"H Widiastuti","year":"2011","journal-title":"Biotechnol Bioeng"},{"issue":"4","key":"pcbi.1008137.ref019","doi-asserted-by":"crossref","first-page":"30","DOI":"10.3390\/pr6040030","article-title":"Genome-Scale In Silico Analysis for Enhanced Production of Succinic Acid in Zymomonas mobilis","volume":"6","author":"H Widiastuti","year":"2018","journal-title":"Processes"},{"issue":"4","key":"pcbi.1008137.ref020","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1039\/C5MB00588D","article-title":"Reconstruction of a charge balanced genome-scale metabolic model to study the energy-uncoupled growth of Zymomonas mobilis ZM1","volume":"12","author":"E Motamedian","year":"2016","journal-title":"Mol Biosyst"},{"issue":"March","key":"pcbi.1008137.ref021","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.ymben.2019.05.006","article-title":"2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis","volume":"54","author":"TB Jacobson","year":"2019","journal-title":"Metab Eng"},{"key":"pcbi.1008137.ref022","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1007\/s002030050724","article-title":"Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures","volume":"171","author":"AA De Graaf","year":"1999","journal-title":"Arch Microbiol"},{"key":"pcbi.1008137.ref023","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2164-10-34","article-title":"Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations","volume":"10","author":"S Yang","year":"2009","journal-title":"BMC Genomics"},{"issue":"1\u20138","key":"pcbi.1008137.ref024","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1007\/s12010-009-8842-2","article-title":"Phenotype microarray profiling of Zymomonas mobilis ZM4","volume":"161","author":"B Bochner","year":"2010","journal-title":"Appl Biochem Biotechnol"},{"issue":"674","key":"pcbi.1008137.ref025","article-title":"Dissecting a complex chemical stress: Chemogenomic profiling of plant hydrolysates","volume":"9","author":"JM Skerker","year":"2013","journal-title":"Mol Syst Biol"},{"issue":"20","key":"pcbi.1008137.ref026","doi-asserted-by":"crossref","first-page":"3643","DOI":"10.1128\/JB.01836-14","article-title":"Towards an informative mutant phenotype for every bacterial gene","volume":"196","author":"A Deutschbauer","year":"2014","journal-title":"J Bacteriol"},{"issue":"10","key":"pcbi.1008137.ref027","doi-asserted-by":"crossref","first-page":"1836","DOI":"10.1101\/gr.093955.109","article-title":"Quantitative phenotyping via deep barcode sequencing","volume":"19","author":"AM Smith","year":"2009","journal-title":"Genome Res"},{"issue":"14","key":"pcbi.1008137.ref028","first-page":"1","article-title":"A universal tagmodule collection for parallel genetic analysis of microorganisms","volume":"38","author":"J Oh","year":"2010","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"pcbi.1008137.ref029","article-title":"Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection","volume":"6","author":"J Oh","year":"2010","journal-title":"PLoS Pathog"},{"issue":"3","key":"pcbi.1008137.ref030","doi-asserted-by":"crossref","first-page":"R30","DOI":"10.1186\/gb-2010-11-3-r30","article-title":"Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action","volume":"11","author":"ME Hillenmeyer","year":"2010","journal-title":"Genome Biol"},{"issue":"6","key":"pcbi.1008137.ref031","first-page":"1","article-title":"Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons","volume":"6","author":"KM Wetmore","year":"2015","journal-title":"MBio"},{"key":"pcbi.1008137.ref032","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1101\/gr.1926504","article-title":"Flux Coupling Analysis of Genome-Scale Metabolic Network","volume":"14","author":"AP Burgard","year":"2004","journal-title":"Genome Res"},{"issue":"24","key":"pcbi.1008137.ref033","doi-asserted-by":"crossref","first-page":"10250","DOI":"10.1074\/jbc.M116.763193","article-title":"Model-enabled gene search (MEGS) allows fast and direct discovery of enzymatic and transport gene functions in the marine bacterium Vibrio fischeri","volume":"292","author":"S Pan","year":"2017","journal-title":"J Biol Chem"},{"issue":"Database issue","key":"pcbi.1008137.ref034","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1093\/nar\/gkt1103","article-title":"The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway\/Genome Databases","volume":"38","author":"R Caspi","year":"2014","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pcbi.1008137.ref035","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mSystems.00284-18","article-title":"Systems-Level Analysis of Oxygen Exposure in Zymomonas mobilis: Implications for Isoprenoid Production","volume":"4","author":"JI Martien","year":"2019","journal-title":"mSystems"},{"key":"pcbi.1008137.ref036","first-page":"1","article-title":"Distinct functional roles for hopanoid composition in the chemical tolerance of Zymomonas mobilis","volume":"0","author":"L Brenac","year":"2019","journal-title":"Mol Microbiol"},{"issue":"535","key":"pcbi.1008137.ref037","first-page":"1","article-title":"A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011","volume":"7","author":"JD Orth","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"46","key":"pcbi.1008137.ref038","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":"Proc Natl Acad Sci"},{"issue":"SUPPL.1","key":"pcbi.1008137.ref039","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1093\/nar\/gkn741","article-title":"Database resources of the National Center for Biotechnology Information","volume":"38","author":"EW Sayers","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pcbi.1008137.ref040","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"M Kanehisa","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"pcbi.1008137.ref041","doi-asserted-by":"crossref","first-page":"D515","DOI":"10.1093\/nar\/gkv1049","article-title":"BiGG Models: A platform for integrating, standardizing and sharing genome-scale models","volume":"44","author":"ZA King","year":"2016","journal-title":"Nucleic Acids Res"},{"issue":"90001","key":"pcbi.1008137.ref042","doi-asserted-by":"crossref","first-page":"431D","DOI":"10.1093\/nar\/gkh081","article-title":"BRENDA, the enzyme database: updates and major new developments","volume":"32","author":"I Schomburg","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"SUPPL.1","key":"pcbi.1008137.ref043","first-page":"396","article-title":"MicrobesOnline: An integrated portal for comparative and functional genomics","volume":"38","author":"PS Dehal","year":"2009","journal-title":"Nucleic Acids Res"},{"issue":"SUPPL. 1","key":"pcbi.1008137.ref044","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1093\/nar\/gkl925","article-title":"TransportDB: A comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels","volume":"35","author":"Q Ren","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008137.ref045","first-page":"1","volume-title":"Memote: A community driven effort towards a standardized genome-scale metabolic model test suite","author":"C Lieven","year":"2018"},{"key":"pcbi.1008137.ref046","article-title":"Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants","volume":"2","author":"T Baba","year":"2006","journal-title":"The Keio collection. Mol Syst Biol"},{"issue":"12","key":"pcbi.1008137.ref047","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"KA Datsenko","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1008137.ref048","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev.ge.17.120183.001011","article-title":"The molecular genetics of bacteriophage P1","volume":"17","author":"N Sternberg","year":"1983","journal-title":"Annu Rev Genet"},{"issue":"5","key":"pcbi.1008137.ref049","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/nmeth.1318","article-title":"Enzymatic assembly of DNA molecules up to several hundred kilobases","volume":"6","author":"DG Gibson","year":"2009","journal-title":"Nat Methods"},{"issue":"4","key":"pcbi.1008137.ref050","doi-asserted-by":"crossref","first-page":"2646","DOI":"10.1093\/nar\/gkt1139","article-title":"Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites","volume":"42","author":"A Espah Borujeni","year":"2014","journal-title":"Nucleic Acids Res"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1008137","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,8,27]],"date-time":"2020-08-27T00:00:00Z","timestamp":1598486400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008137","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,27]],"date-time":"2020-08-27T17:58:25Z","timestamp":1598551105000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008137"}},"subtitle":[],"editor":[{"given":"Costas D.","family":"Maranas","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,17]]},"references-count":50,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2020,8,17]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008137","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1008137","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,8,17]]}}}