{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:35:00Z","timestamp":1778632500220,"version":"3.51.4"},"reference-count":43,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2009,10,29]],"date-time":"2009-10-29T00:00:00Z","timestamp":1256774400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2009,12]]},"DOI":"10.1186\/1752-0509-3-104","type":"journal-article","created":{"date-parts":[[2009,10,30]],"date-time":"2009-10-30T11:37:59Z","timestamp":1256902679000},"source":"Crossref","is-referenced-by-count":23,"title":["13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose"],"prefix":"10.1186","volume":"3","author":[{"given":"Paula","family":"Jouhten","sequence":"first","affiliation":[]},{"given":"Esa","family":"Pitk\u00e4nen","sequence":"additional","affiliation":[]},{"given":"Tiina","family":"Pakula","sequence":"additional","affiliation":[]},{"given":"Markku","family":"Saloheimo","sequence":"additional","affiliation":[]},{"given":"Merja","family":"Penttil\u00e4","sequence":"additional","affiliation":[]},{"given":"Hannu","family":"Maaheimo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,10,29]]},"reference":[{"key":"372_CR1","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1007\/s10295-008-0327-8","volume":"35","author":"R Kumar","year":"2008","unstructured":"Kumar R, Singh S, Singh OV: Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 2008, 35: 377-391.","journal-title":"J Ind Microbiol Biotechnol"},{"key":"372_CR2","volume-title":"PhD thesis","author":"M Ilm\u00e9n","year":"1997","unstructured":"Ilm\u00e9n M: Molecular mechanisms of glucose repression in the filamentous fungus Trichoderma reesei. PhD thesis. 1997, VTT Publications VTT Espoo,"},{"key":"372_CR3","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1016\/j.femsre.2004.11.006","volume":"29","author":"N Aro","year":"2005","unstructured":"Aro N, Pakula T, Penttil\u00e4 M: Transcriptional regulation of plant cell wall degradation by filamentous fungi. FEMS Microbiol Rev. 2005, 29: 719-735.","journal-title":"FEMS Microbiol Rev"},{"key":"372_CR4","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s00253-007-1322-0","volume":"78","author":"AR Stricker","year":"2008","unstructured":"Stricker AR, Mach RL, de Graaf LH: Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei). Appl Microbiol Biotechnol. 2008, 78: 211-220.","journal-title":"Appl Microbiol Biotechnol"},{"key":"372_CR5","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/S0168-1656(97)00097-7","volume":"57","author":"M Margolles-Clark","year":"1997","unstructured":"Margolles-Clark M, Ilm\u00e9n M, Penttil\u00e4 M: Expression patterns of ten hemicellulase genes from filamentous fungus Trichoderma reesei on various carbon sources. J Biotechnol. 1997, 57: 167-179.","journal-title":"J Biotechnol"},{"key":"372_CR6","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1128\/AEM.63.4.1298-1306.1997","volume":"63","author":"M Ilm\u00e9n","year":"1997","unstructured":"Ilm\u00e9n M, Saloheimo A, Onnela M-L, Penttil\u00e4 ME: Regulation of Cellulase Gene Expression in the Filamentous Fungus Trichoderma reesei. Appl Env Microbiol. 1997, 63: 1298-1306.","journal-title":"Appl Env Microbiol"},{"key":"372_CR7","doi-asserted-by":"publisher","first-page":"2126","DOI":"10.1128\/AEM.72.3.2126-2133.2006","volume":"72","author":"IS Druzhinina","year":"2006","unstructured":"Druzhinina IS, Schmoll M, Seiboth B, Kubicek P: Global Carbon Utilization Profiles of Wild-Type, Mutant, and Transformant Strains of Hypcrea jecorina. Appl Env Microbiol. 2006, 72: 2126-2133.","journal-title":"Appl Env Microbiol"},{"key":"372_CR8","doi-asserted-by":"publisher","first-page":"6432","DOI":"10.1021\/bi025529i","volume":"41","author":"P Richard","year":"2002","unstructured":"Richard P, Putkonen M, V\u00e4\u00e4n\u00e4nen R, Londesborough J, Penttil\u00e4 M: The missing link in the fungal L-arabinose catabolic pathway: identification of the L-xylulose reductase gene. Biochemistry. 2002, 41: 6432-6437.","journal-title":"Biochemistry"},{"key":"372_CR9","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1007\/s002940000165","volume":"38","author":"M Nogawa","year":"2001","unstructured":"Nogawa M, Goto M, Okada H, Morikawa Y: L-sorbose induces cellulase gene transcription in the cellulolytic fungus Trichoderma reesei. Curr Genet. 2001, 38: 329-334.","journal-title":"Curr Genet"},{"key":"372_CR10","first-page":"1864","volume":"271","author":"M Pail","year":"2004","unstructured":"Pail M, Peterbauer T, Seiboth B, Hametner C, Druzhinina I, Kubicek CP: The metabolic role and evolution of L-arabinitol 4-dehydrogenase of Hypocrea. jecorina. 2004, 271: 1864-1872.","journal-title":"jecorina"},{"key":"372_CR11","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1111\/j.1432-1033.1975.tb03958.x","volume":"51","author":"C Bailey","year":"1975","unstructured":"Bailey C, Arst HN: Carbon catabolite repression in Aspergillus nidulans. Eur J Biochem. 1975, 51: 573-577.","journal-title":"Eur J Biochem"},{"key":"372_CR12","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0014-5793(95)01255-5","volume":"376","author":"J Strauss","year":"1995","unstructured":"Strauss J, Mach RL, Zeilinger S, Hartler G, St\u00f6ffler G, Wolschek M, Kubicek CP: Cre1, the carbon catabolite repressor protein from Trichoderma reesei. FEBS Lett. 1995, 376: 103-107.","journal-title":"FEBS Lett"},{"key":"372_CR13","first-page":"451","volume":"251","author":"M Ilm\u00e9n","year":"1996","unstructured":"Ilm\u00e9n M, Thrane C, Penttil\u00e4 M: The glucose repressor gene cre1 of Trichoderma: Isolation and expression of a full length and truncated mutant form. Mol Gen Genet. 1996, 251: 451-460.","journal-title":"Mol Gen Genet"},{"key":"372_CR14","doi-asserted-by":"publisher","first-page":"14688","DOI":"10.1074\/jbc.M200744200","volume":"277","author":"A Cziferszky","year":"2002","unstructured":"Cziferszky A, Mach RL, Kubicek CP: Phosphorylation Positively Regulates DNA Binding of the Carbon Catabolite Repressor Cre1 of Hypocrea jecorina (Trichoderma reesei). J Biol Chem. 2002, 277: 14688-14694.","journal-title":"J Biol Chem"},{"key":"372_CR15","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/S0014-5793(99)00691-2","volume":"453","author":"G Vautard","year":"1999","unstructured":"Vautard G, Cotton P, F\u00e8vre M: The glucose repressor CRE1 from Sclerotina sclerotiorum is functionally related to CREA from Aspergillus nidulans but not to the Mig proteins from Saccharomyces cerevisiae. FEBS Letters. 1999, 453: 54-58.","journal-title":"FEBS Letters"},{"key":"372_CR16","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1126\/science.1058079","volume":"292","author":"T Pfeiffer","year":"2001","unstructured":"Pfeiffer T, Schuster S, Bonhoeffer S: Cooperation and Competition in the Evolution of ATP-producing Pathways. Science. 2001, 292: 504-507.","journal-title":"Science"},{"key":"372_CR17","doi-asserted-by":"publisher","first-page":"13983","DOI":"10.1074\/jbc.M107651200","volume":"277","author":"FS Chambergo","year":"2002","unstructured":"Chambergo FS, Bonaccorsi ED, Ferreira AJS, Ramos ASP, Ribamar Ferreira J\u00fanior J, Abrahao-Neto J, Farah JPS, El-Dorry H: Elucidation of the Metabolic Fate of Glucose in the Filamentous Fungus Trichoderma reesei Using Expressed Sequence Tag (EST) Analysis and cDNA Microarrays. J Biol Chem. 2002, 277: 13983-13988.","journal-title":"J Biol Chem"},{"key":"372_CR18","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1128\/MMBR.62.2.334-361.1998","volume":"62","author":"JM Gancedo","year":"1998","unstructured":"Gancedo JM: Yeast carbon catabolite repression. Microbiol Mol Biol Rev. 1998, 62: 334-361.","journal-title":"Microbiol Mol Biol Rev"},{"key":"372_CR19","doi-asserted-by":"publisher","first-page":"2209","DOI":"10.1099\/mic.0.27787-0","volume":"151","author":"H David","year":"2005","unstructured":"David H, Krogh AM, Roca C, \u00c5kesson M, Nielsen J: CreA influences the metabolic fluxes of Aspergillus nidulans during growth on glucose and xylose. Microbiology. 2005, 151: 2209-2221.","journal-title":"Microbiology"},{"key":"372_CR20","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1038\/nbt1403","volume":"26","author":"D Martinez","year":"2008","unstructured":"Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EGJ, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parviainen A, Schoch CL, Yao J, Barbote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS: Genome sequencing and analysis of the biomass-degrading Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol. 2008, 26: 553-560.","journal-title":"Nat Biotechnol"},{"key":"372_CR21","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1186\/1752-0509-3-103","volume":"3","author":"E Pitk\u00e4nen","year":"2009","unstructured":"Pitk\u00e4nen E, Jouhten P, Rousu J: Inferring branching pathways in genome-scale metabolic networks with ReTrace. BMC Syst Biol. 2009, 3: 103-","journal-title":"BMC Syst Biol"},{"key":"372_CR22","doi-asserted-by":"publisher","first-page":"433","DOI":"10.1111\/j.1432-1033.1995.tb20829.x","volume":"232","author":"T Szyperski","year":"1995","unstructured":"Szyperski T: Biosynthetically directed fractional 13C-labelling of proteinogenic amino acids. An efficient tool to investigate intermediary metabolism. Eur J Biochem. 1995, 232: 433-448.","journal-title":"Eur J Biochem"},{"key":"372_CR23","doi-asserted-by":"publisher","first-page":"448","DOI":"10.1038\/nbt0597-448","volume":"15","author":"U Sauer","year":"1997","unstructured":"Sauer U, Hatzimanikatis V, Bailey JE, Hochuli M, Szyperski T, W\u00fcthrich K: Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat Biotechnol. 1997, 15: 448-452.","journal-title":"Nat Biotechnol"},{"key":"372_CR24","doi-asserted-by":"crossref","first-page":"6679","DOI":"10.1128\/JB.181.21.6679-6688.1999","volume":"181","author":"U Sauer","year":"1999","unstructured":"Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, W\u00fcthrich K, Bailey JE: Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol. 1999, 181: 6679-6688.","journal-title":"J Bacteriol"},{"key":"372_CR25","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1006\/mben.1999.0116","volume":"1","author":"T Szyperski","year":"1999","unstructured":"Szyperski T, Glaser RW, Hochuli M, Fiaux J, Sauer U, Bailey JE, W\u00fcthrich K: Bioreaction network topology and metabolic flux ratio analysis by biosynthetic fractional 13C labelling and two-dimensional NMR spectroscopy. Metab Eng. 1999, 1: 189-197.","journal-title":"Metab Eng"},{"key":"372_CR26","doi-asserted-by":"publisher","first-page":"2464","DOI":"10.1046\/j.1432-1327.2001.02126.x","volume":"268","author":"H Maaheimo","year":"2001","unstructured":"Maaheimo H, Fiaux J, \u00ccakar PZ, Bailey JE, Sauer U, Szyperski T: Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional 13C labelling of common amino acids. Eur J Biochem. 2001, 268: 2464-2479.","journal-title":"Eur J Biochem"},{"key":"372_CR27","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1128\/EC.2.1.170-180.2003","volume":"2","author":"J Fiaux","year":"2003","unstructured":"Fiaux J, \u00ccakar PZ, Sonderegger M, W\u00fcthrich K, Szyperski T, Sauer U: Metabolic-Flux Profiling of the Yeasts Saccharomyces cerevisiae and Pichia stipitis. Eukaryot Cell. 2003, 2: 170-180.","journal-title":"Eukaryot Cell"},{"key":"372_CR28","doi-asserted-by":"publisher","first-page":"2462","DOI":"10.1111\/j.1432-1033.2004.04176.x","volume":"271","author":"A Sola","year":"2004","unstructured":"Sola A, Maaheimo H, Ylonen K, Ferrer P, Szyperski T: Amino acid biosynthesis and metabolic flux profiling of Pichia pastoris. Eur J Biochem. 2004, 271: 2462-2470.","journal-title":"Eur J Biochem"},{"key":"372_CR29","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1385\/CBB:46:1:43","volume":"46","author":"H Xu","year":"2006","unstructured":"Xu H, Qian BAJ, West AH, Cook PF: The \u03b1-Aminoadipate Pathway for Lysine Biosynthesis in Fungi. Cell Biochem Biophys. 2006, 46: 43-46.","journal-title":"Cell Biochem Biophys"},{"key":"372_CR30","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/0076-6879(71)17021-8","volume":"17b","author":"HP Broquist","year":"1971","unstructured":"Broquist HP: Lysine biosynthesis (Yeast). Methods Enzymol. 1971, 17b: 112-119.","journal-title":"Methods Enzymol"},{"key":"372_CR31","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1016\/j.femsyr.2004.09.008","volume":"5","author":"LM Blank","year":"2005","unstructured":"Blank LM, Lehmbeck F, Sauer U: Metabolic-flux analysis of fourteen hemiascomycetous yeasts. FEMS Yeast Res. 2005, 5: 545-558.","journal-title":"FEMS Yeast Res"},{"key":"372_CR32","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/S0378-1097(97)00096-7","volume":"150","author":"N Monschau","year":"1997","unstructured":"Monschau N, Stahmann K-P, Sahm H, McNeil JB, Bognar AL: Identification of Saccharomyces cerevisiae GLY1 as a threonine aldolase: a key enzyme in glycine biosynthesis. FEMS Microbiology Letters. 1997, 150: 55-60.","journal-title":"FEMS Microbiology Letters"},{"key":"372_CR33","doi-asserted-by":"publisher","first-page":"953","DOI":"10.1038\/nprot.2007.131","volume":"2","author":"O Emanuelsson","year":"2007","unstructured":"Emanuelsson O, Brunak S, von Heijnen G, Nielsen H: Locating proteins in the cell using TargetP, SignalP and related tools. Nature Protocols. 2007, 2: 953-971.","journal-title":"Nature Protocols"},{"key":"372_CR34","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1006\/jmbi.2000.3903","volume":"300","author":"O Emanuelsson","year":"2000","unstructured":"Emanuelsson O, Nielsen H, Brunak B, von Heijnen G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequenc. J Mol Biol. 2000, 300: 1005-1016.","journal-title":"J Mol Biol"},{"key":"372_CR35","doi-asserted-by":"publisher","first-page":"686","DOI":"10.1038\/nature02026","volume":"425","author":"WK Huh","year":"2003","unstructured":"Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'shea EK: Global analysis of protein localization in budding yeast. Nature. 2003, 425: 686-691.","journal-title":"Nature"},{"key":"372_CR36","first-page":"595","volume":"28","author":"KE Christensen","year":"2006","unstructured":"Christensen KE, MacKenzie RE: Mitochondrial one-carbon metabolism is adapted to the specific needs of yeast, plants and mammals. Bio Essays. 2006, 28: 595-605.","journal-title":"Bio Essays"},{"key":"372_CR37","doi-asserted-by":"crossref","first-page":"9155","DOI":"10.1016\/S0021-9258(17)37089-8","volume":"269","author":"JB McNeil","year":"1994","unstructured":"McNeil JB, McIntosh EM, Taylor BV, Zhang F, Tang S, Bognar AL: Cloning and Molecular Characterization of Three Genes, Including Two Genes Encoding Serine Hydroxymethyltransferases, Whose Inactivation Is Required to Render Yeast Auxotrophic for Glycine. J Biol Chem. 1994, 269: 9155-9165.","journal-title":"J Biol Chem"},{"key":"372_CR38","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1093\/genetics\/142.2.371","volume":"142","author":"JB McNeil","year":"1996","unstructured":"McNeil JB, Bognar AL, Pearlman RE: In vivo analysis of folate coenzymes and their compartmentation in Saccharomyces cerevisiae. Genetics. 1996, 142: 371-381.","journal-title":"Genetics"},{"key":"372_CR39","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1128\/JB.73.2.269-278.1957","volume":"73","author":"M Mandels","year":"1957","unstructured":"Mandels M, Reese ET: Induction of cellulase in Trichoderma viride as influenced by carbon sources and metals. J Bacteriol. 1957, 73: 269-278.","journal-title":"J Bacteriol"},{"key":"372_CR40","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkm882","volume":"36","author":"M Kanehisa","year":"2008","unstructured":"Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y: KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36: D480-D484.","journal-title":"Nucleic Acids Res"},{"key":"372_CR41","doi-asserted-by":"publisher","first-page":"D193","DOI":"10.1093\/nar\/gkl929","volume":"35","author":"The UniProt Consortium","year":"2007","unstructured":", : The Universal Protein Resource (UniProt). Nucleic Acids Res. 2007, 35: D193-197.","journal-title":"Nucleic Acids Res"},{"key":"372_CR42","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402.","journal-title":"Nucleic Acids Res"},{"key":"372_CR43","first-page":"154","volume-title":"35th IEEE Symp Foundations of Comp Sci., Santa Fe","author":"D Eppstein","year":"1994","unstructured":"Eppstein D: Finding the k shortest paths. 35th IEEE Symp Foundations of Comp Sci., Santa Fe. 1994, 154-165."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-3-104\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-3-104.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T03:58:57Z","timestamp":1634097537000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-3-104"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,29]]},"references-count":43,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2009,12]]}},"alternative-id":["372"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-3-104","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,29]]},"article-number":"104"}}