{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T09:42:12Z","timestamp":1789983732591,"version":"4.0.1"},"reference-count":60,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2013,6,19]],"date-time":"2013-06-19T00:00:00Z","timestamp":1371600000000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0066104","type":"journal-article","created":{"date-parts":[[2013,6,19]],"date-time":"2013-06-19T21:32:44Z","timestamp":1371677564000},"page":"e66104","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics"],"prefix":"10.1371","volume":"8","author":[{"given":"Becky M.","family":"Hess","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junfeng","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lye Meng","family":"Markillie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronald C.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H. Steven","family":"Wiley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Birgitte K.","family":"Ahring","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bryan","family":"Linggi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2013,6,19]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/nchembio.2007.5","article-title":"The function of terpene natural products in the natural world","volume":"3","author":"J Gershenzon","year":"2007","journal-title":"Nat Chem Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"13654","DOI":"10.1073\/pnas.1006138107","article-title":"Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control","volume":"107","author":"E Leonard","year":"2010","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"2399","DOI":"10.1128\/AEM.02341-10","article-title":"Enhancing Isoprene Production by Genetic Modification of the 1-Deoxy-d-Xylulose-5-Phosphate Pathway in <italic>Bacillus subtilis<\/italic>","volume":"77","author":"J Xue","year":"2011","journal-title":"Applied and Environmental Microbiology"},{"key":"ref4","doi-asserted-by":"crossref","unstructured":"Connolly JD (1991) Dictionary of terpenoids. In: Hall\/CRC C, editor. Dictionary of terpenoids. 2156.","DOI":"10.1007\/978-1-4899-4513-6"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"700","DOI":"10.1104\/pp.104.054445","article-title":"Evolution of the Isoprene Biosynthetic Pathway in Kudzu","volume":"137","author":"TD Sharkey","year":"2005","journal-title":"Plant Physiology"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1104\/pp.007138","article-title":"Elucidation of the Methylerythritol Phosphate Pathway for Isoprenoid Biosynthesis in Bacteria and Plastids. A Metabolic Milestone Achieved through Genomics","volume":"130","author":"M Rodr\u00edguez-Concepci\u00f3n","year":"2002","journal-title":"Plant Physiology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1007\/BF00294190","article-title":"Bacteria produce the volatile hydrocarbon isoprene","volume":"30","author":"J Kuzma","year":"1995","journal-title":"Curr Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S0006-291X(02)00435-7","article-title":"Isoprene synthase activity parallels fluctuations of isoprene release during growth of <italic>Bacillus subtilis<\/italic>","volume":"294","author":"TL Sivy","year":"2002","journal-title":"Biochemical and Biophysical Research Communications"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1007\/s00253-007-0953-5","article-title":"Functional analysis of genes involved in the biosynthesis of isoprene in <italic>Bacillus subtilis<\/italic>","volume":"75","author":"M Julsing","year":"2007","journal-title":"Applied Microbiology and Biotechnology"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/nbt833","article-title":"Engineering a mevalonate pathway in <italic>Escherichia coli<\/italic> for production of terpenoids","volume":"21","author":"VJJ Martin","year":"2003","journal-title":"Nat Biotech"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2376","DOI":"10.1271\/bbb.110572","article-title":"Evidence of Isoprenoid Precursor Toxicity in <italic>Bacillus subtilis<\/italic>","volume":"75","author":"TL Sivy","year":"2011","journal-title":"Bioscience, Biotechnology, and Biochemistry"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1016\/j.copbio.2008.10.014","article-title":"Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels","volume":"19","author":"SK Lee","year":"2008","journal-title":"Current Opinion in Biotechnology"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"7404","DOI":"10.1016\/j.ijhydene.2009.05.078","article-title":"Metabolic pathway engineering for enhanced biohydrogen production","volume":"34","author":"J Mathews","year":"2009","journal-title":"International Journal of Hydrogen Energy"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1016\/S0141-0229(00)00180-0","article-title":"Lactic acid bacteria as a cell factory: rerouting of carbon metabolism in Lactococcus lactis by metabolic engineering","volume":"26","author":"M Kleerebezemab","year":"2000","journal-title":"Enzyme and Microbial Technology"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1038\/75398","article-title":"Improving lycopene production in <italic>Escherichia coli<\/italic> by engineering metabolic control","volume":"18","author":"WR Farmer","year":"2000","journal-title":"Nat Biotech"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/S1369-5266(99)80026-0","article-title":"Metabolic engineering of plants for osmotic stress resistance","volume":"2","author":"ML Nuccio","year":"1999","journal-title":"Current Opinion in Plant Biology"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1007\/s00253-005-0081-z","article-title":"Global physiological understanding and metabolic engineering of microorganisms based on omics studies","volume":"68","author":"SJ Park","year":"2005","journal-title":"Applied Microbiology and Biotechnology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1675","DOI":"10.1126\/science.1904627","article-title":"Network rigidity and metabolic engineering in metabolite overproduction","volume":"252","author":"G Stephanopoulos","year":"1991","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"13172","DOI":"10.1073\/pnas.240454797","article-title":"Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes","volume":"97","author":"BM Lange","year":"2000","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/36786","article-title":"The complete genome sequence of the Gram-positive bacterium <italic>Bacillus subtilis<\/italic>","volume":"390","author":"F Kunst","year":"1997","journal-title":"Nature"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1021\/bp0255412","article-title":"Isoprene Formation in <italic>Bacillus subtilis<\/italic>: A Barometer of Central Carbon Assimilation in a Bioreactor?","volume":"18","author":"MC Shirk","year":"2002","journal-title":"Biotechnology Progress"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"D109","DOI":"10.1093\/nar\/gkr988","article-title":"KEGG for integration and interpretation of large-scale molecular data sets","volume":"40","author":"M Kanehisa","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref23","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 Research"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"8977","DOI":"10.1073\/pnas.0603148103","article-title":"Convergence of isoprene and polyketide biosynthetic machinery: Isoprenyl-S-carrier proteins in the pksX pathway of <italic>Bacillus subtilis<\/italic>","volume":"103","author":"CT Calderone","year":"2006","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1126\/science.1193990","article-title":"Manufacturing molecules through metabolic engineering","volume":"330","author":"JD Keasling","year":"2010","journal-title":"Science"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e33509","DOI":"10.1371\/journal.pone.0033509","article-title":"Enhancing Production of Bio-Isoprene Using Hybrid MVA Pathway and Isoprene Synthase in <italic>E. coli<\/italic>","volume":"7","author":"J Yang","year":"2012","journal-title":"PLoS ONE"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"6277","DOI":"10.1128\/AEM.00861-07","article-title":"Identification of Isopentenol Biosynthetic Genes from <italic>Bacillus subtilis<\/italic> by a Screening Method Based on Isoprenoid Precursor Toxicity","volume":"73","author":"ST Withers","year":"2007","journal-title":"Applied and Environmental Microbiology"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/s00284-006-0419-5","article-title":"Expression Vectors for the Rapid Purification of Recombinant Proteins in <italic>Bacillus subtilis<\/italic>","volume":"55","author":"H Nguyen","year":"2007","journal-title":"Current Microbiology"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"S Anders","year":"2010","journal-title":"Genome Biology"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1186\/1471-2105-8-426","article-title":"DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis","volume":"8","author":"B Sherman","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1261\/rna.620507","article-title":"RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria","volume":"13","author":"C Yanofsky","year":"2007","journal-title":"RNA"},{"key":"ref32","doi-asserted-by":"crossref","unstructured":"Gollnick P, Babitzke P, Antson A, Yanofsky C (2005) Complexity in regulation of tryptophan biosynthesis in <italic>Bacillus subtilis<\/italic>. Annual Review of Genetics. Palo Alto: Annual Reviews. 47\u201368.","DOI":"10.1146\/annurev.genet.39.073003.093745"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"5344","DOI":"10.1128\/JB.180.20.5344-5350.1998","article-title":"Nitrogen and Oxygen Regulation of <italic>Bacillus subtilis<\/italic> nasDEF Encoding NADH-Dependent Nitrite Reductase by TnrA and ResDE","volume":"180","author":"MM Nakano","year":"1998","journal-title":"Journal of Bacteriology"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1110\/ps.03330104","article-title":"Dimethyl sulfoxide at 2.5% (v\/v) alters the structural cooperativity and unfolding mechanism of dimeric bacterial NAD+ synthetase","volume":"13","author":"ZW Yang","year":"2004","journal-title":"Protein Science"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1882","DOI":"10.1111\/j.1365-3040.2008.01893.x","article-title":"Isoprene and nitric oxide reduce damages in leaves exposed to oxidative stress","volume":"31","author":"V Velikova","year":"2008","journal-title":"Plant, Cell & Environment"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1104\/pp.010497","article-title":"Isoprene Produced by Leaves Protects the Photosynthetic Apparatus against Ozone Damage, Quenches Ozone Products, and Reduces Lipid Peroxidation of Cellular Membranes","volume":"127","author":"F Loreto","year":"2001","journal-title":"Plant Physiology"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1146\/annurev.arplant.52.1.407","article-title":"Isoprene emission from plants","volume":"52","author":"TD Sharkey","year":"2001","journal-title":"Annual Review of Plant Physiology and Plant Molecular Biology"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"993","DOI":"10.1104\/pp.126.3.993","article-title":"Ozone quenching properties of isoprene and its antioxidant role in leaves","volume":"126","author":"F Loreto","year":"2001","journal-title":"Plant Physiology"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1021\/np990286p","article-title":"Isoprene Biosynthesis in <italic>Bacillus subtilis<\/italic> via the Methylerythritol Phosphate Pathway","volume":"63","author":"WP Wagner","year":"1999","journal-title":"Journal of Natural Products"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"8925","DOI":"10.1073\/pnas.171310598","article-title":"Progress in plant metabolic engineering","volume":"98","author":"P Broun","year":"2001","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1002\/1097-0290(20000220)72:4<408::AID-BIT1003>3.0.CO;2-H","article-title":"Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in <italic>Escherichia coli<\/italic> enhances lycopene production","volume":"72","author":"S-W Kim","year":"2001","journal-title":"Biotechnology and Bioengineering"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1042\/bj3240421","article-title":"Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in <italic>Escherichia coli<\/italic>","volume":"324","author":"S Kajiwara","year":"1997","journal-title":"Biochem J"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.ymben.2005.08.005","article-title":"Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in <italic>E. coli<\/italic>","volume":"8","author":"LZ Yuan","year":"2006","journal-title":"Metabolic Engineering"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"2676","DOI":"10.1074\/jbc.M610235200","article-title":"Crystal Structure of 1-Deoxy-d-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis","volume":"282","author":"S Xiang","year":"2007","journal-title":"Journal of Biological Chemistry"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/S0014-5793(99)00360-9","article-title":"Expression of prokaryotic 1-deoxy-d-xylulose-5-phosphatases in <italic>Escherichia coli<\/italic> increases carotenoid and ubiquinone biosynthesis","volume":"448","author":"M Harker","year":"1999","journal-title":"FEBS Letters"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1427","DOI":"10.1128\/JB.127.3.1427-1442.1976","article-title":"Autolytic enzyme-deficient mutants of <italic>Bacillus subtilis<\/italic> 168","volume":"127","author":"JE Fein","year":"1976","journal-title":"Journal of Bacteriology"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2061","DOI":"10.1099\/00221287-138-10-2061","article-title":"Cloning and characterization of genes induced by hydrogen peroxide in <italic>Bacillus subtilis<\/italic>","volume":"138","author":"OM Hartford","year":"1992","journal-title":"Journal of General Microbiology"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1099\/13500872-142-8-2031","article-title":"The phage-like element PBSX and part of the skin element, which are resident at different locations on the <italic>Bacillus subtilis<\/italic> chromosome, are highly homologous","volume":"142","author":"S Krogh","year":"1996","journal-title":"Microbiology"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"045004","DOI":"10.1088\/1478-3975\/9\/4\/045004","article-title":"Modeling the latent dimensions of multivariate signaling datasets","volume":"9","author":"JJ Karin","year":"2012","journal-title":"Physical Biology"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2500","DOI":"10.1128\/JB.184.9.2500-2520.2002","article-title":"<italic>Bacillus subtilis<\/italic> functional genomics: global characterization of the stringent response by proteome and transcriptome analysis","volume":"184","author":"C Eymann","year":"2002","journal-title":"Journal of Bacteriology"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"880","DOI":"10.1093\/nar\/gki232","article-title":"A novel method for accurate operon predictions in all sequenced prokaryotes","volume":"33","author":"MN Price","year":"2005","journal-title":"Nucleic Acids Research"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"D1278","DOI":"10.1093\/nar\/gkr923","article-title":"SubtiWiki\u2013a comprehensive community resource for the model organism <italic>Bacillus subtilis<\/italic>","volume":"40","author":"U M\u00e4der","year":"2012","journal-title":"Nucleic Acids Research"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1073\/pnas.0610503104","article-title":"The Identification of Bacillaene, the Product of the PksX Megacomplex in <italic>Bacillus subtilis<\/italic>","volume":"104","author":"RA Butcher","year":"2007","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1103","DOI":"10.1126\/science.1206848","article-title":"Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in <italic>Bacillus subtilis<\/italic>","volume":"335","author":"P Nicolas","year":"2012","journal-title":"Science"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nrmicro1772","article-title":"Control of key metabolic intersections in <italic>Bacillus subtilis<\/italic>","volume":"5","author":"AL Sonenshein","year":"2007","journal-title":"Nat Rev Micro"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"e47513","DOI":"10.1371\/journal.pone.0047513","article-title":"Metabolite Profiling Identified Methylerythritol Cyclodiphosphate Efflux as a Limiting Step in Microbial Isoprenoid Production","volume":"7","author":"K Zhou","year":"2012","journal-title":"PLoS ONE"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1126\/science.1206871","article-title":"Global Network Reorganization During Dynamic Adaptations of <italic>Bacillus subtilis<\/italic> Metabolism","volume":"335","author":"JM Buescher","year":"2012","journal-title":"Science"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/nbt.1499","article-title":"Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network","volume":"26","author":"G Chechik","year":"2008","journal-title":"Nat Biotech"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1752-0509-4-166","article-title":"Systems biology approach reveals that overflow metabolism of acetate in <italic>Escherichia coli<\/italic> is triggered by carbon catabolite repression of acetyl-CoA synthetase","volume":"4","author":"K Valgepea","year":"2010","journal-title":"BMC Systems Biology"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1111\/j.1365-3040.2009.01980.x","article-title":"Regulation of isoprene emission from poplar leaves throughout a day","volume":"32","author":"AE Wiberley","year":"2009","journal-title":"Plant, Cell & Environment"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0066104","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,28]],"date-time":"2020-07-28T20:06:53Z","timestamp":1595966813000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0066104"}},"subtitle":[],"editor":[{"given":"Michael","family":"Otto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2013,6,19]]},"references-count":60,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2013,6,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0066104","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,6,19]]}}}