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Volumn 7, Issue , 2013, Pages

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

Author keywords

Genome scale metabolic model; Integrated analysis; Saccharomyces cerevisiae; Transcriptionally controlled reactions

Indexed keywords

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84876789665     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-36     Document Type: Article
Times cited : (103)

References (41)
  • 1
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • 10.1101/gr.234503, 420374, 12566402
    • Forster J, Famili I, Fu P, Palsson B, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13(2):244-253. 10.1101/gr.234503, 420374, 12566402.
    • (2003) Genome Res , vol.13 , Issue.2 , pp. 244-253
    • Forster, J.1    Famili, I.2    Fu, P.3    Palsson, B.4    Nielsen, J.5
  • 2
    • 84864932596 scopus 로고    scopus 로고
    • Fifteen years of large scale metabolic modeling of yeast: developments and impacts
    • 10.1016/j.biotechadv.2011.07.021, 21846501
    • Österlund T, Nookaew I, Nielsen J. Fifteen years of large scale metabolic modeling of yeast: developments and impacts. Biotechnol Adv 2012, 30(5):979-988. 10.1016/j.biotechadv.2011.07.021, 21846501.
    • (2012) Biotechnol Adv , vol.30 , Issue.5 , pp. 979-988
    • Österlund, T.1    Nookaew, I.2    Nielsen, J.3
  • 5
    • 84861744439 scopus 로고    scopus 로고
    • Yeast 5-an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
    • 10.1186/1752-0509-6-55, 3413506, 22663945
    • Heavner BD, Smallbone K, Barker B, Mendes P, Walker LP. Yeast 5-an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 2012, 6(1):55. 10.1186/1752-0509-6-55, 3413506, 22663945.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 55
    • Heavner, B.D.1    Smallbone, K.2    Barker, B.3    Mendes, P.4    Walker, L.P.5
  • 6
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast
    • 10.1186/1752-0509-3-37, 2679711, 19321003
    • Mo ML, Palsson B, Herrgård MJ. Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst Biol 2009, 3(1):37. 10.1186/1752-0509-3-37, 2679711, 19321003.
    • (2009) BMC Syst Biol , vol.3 , Issue.1 , pp. 37
    • Mo, M.L.1    Palsson, B.2    Herrgård, M.J.3
  • 7
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • 10.1101/gr.3992505, 1240085, 16204195
    • Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005, 15(10):1421-1430. 10.1101/gr.3992505, 1240085, 16204195.
    • (2005) Genome Res , vol.15 , Issue.10 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 8
    • 52649105455 scopus 로고    scopus 로고
    • The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism
    • 10.1186/1752-0509-2-71, 2542360, 18687109
    • Nookaew I, Jewett M, Meechai A, Thammarongtham C, Laoteng K, Cheevadhanarak S, Nielsen J, Bhumiratana S. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Syst Biol 2008, 2:71. 10.1186/1752-0509-2-71, 2542360, 18687109.
    • (2008) BMC Syst Biol , vol.2 , pp. 71
    • Nookaew, I.1    Jewett, M.2    Meechai, A.3    Thammarongtham, C.4    Laoteng, K.5    Cheevadhanarak, S.6    Nielsen, J.7    Bhumiratana, S.8
  • 9
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • 10.1101/gr.2250904, 442145, 15197165
    • Duarte N, Herrgard M, Palsson B. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004, 14(7):1298-1309. 10.1101/gr.2250904, 442145, 15197165.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1298-1309
    • Duarte, N.1    Herrgard, M.2    Palsson, B.3
  • 10
    • 84857058761 scopus 로고    scopus 로고
    • A systems-level approach for metabolic engineering of yeast cell factories
    • 10.1111/j.1567-1364.2011.00779.x, 22188344
    • Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS yeast research 2012, 12(2):228-248. 10.1111/j.1567-1364.2011.00779.x, 22188344.
    • (2012) FEMS yeast research , vol.12 , Issue.2 , pp. 228-248
    • Kim, I.K.1    Roldão, A.2    Siewers, V.3    Nielsen, J.4
  • 11
    • 84861372886 scopus 로고    scopus 로고
    • Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth
    • 10.1186/1752-0509-6-49, 3390277, 22631437
    • Sohn SB, Kim TY, Lee JH, Lee SY. Genome-scale metabolic model of the fission yeast Schizosaccharomyces pombe and the reconciliation of in silico/in vivo mutant growth. BMC Syst Biol 2012, 6(1):49. 10.1186/1752-0509-6-49, 3390277, 22631437.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 49
    • Sohn, S.B.1    Kim, T.Y.2    Lee, J.H.3    Lee, S.Y.4
  • 12
    • 84860505042 scopus 로고    scopus 로고
    • A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica
    • 10.1186/1752-0509-6-35, 3443063, 22558935
    • Loira N, Dulermo T, Nicaud JM, Sherman D. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica. BMC Syst Biol 2012, 6(1):35. 10.1186/1752-0509-6-35, 3443063, 22558935.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 35
    • Loira, N.1    Dulermo, T.2    Nicaud, J.M.3    Sherman, D.4
  • 13
    • 84859199206 scopus 로고    scopus 로고
    • Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials
    • 10.1186/1752-0509-6-24, 3364918, 22472172
    • Caspeta L, Shoaie S, Agren R, Nookaew I, Nielsen J. Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in silico evaluation of their potentials. BMC Syst Biol 2012, 6(1):24. 10.1186/1752-0509-6-24, 3364918, 22472172.
    • (2012) BMC Syst Biol , vol.6 , Issue.1 , pp. 24
    • Caspeta, L.1    Shoaie, S.2    Agren, R.3    Nookaew, I.4    Nielsen, J.5
  • 14
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • 10.1073/pnas.0406811102, 549453, 15710883
    • Patil K, Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci 2005, 102(8):2685-2689. 10.1073/pnas.0406811102, 549453, 15710883.
    • (2005) Proc Natl Acad Sci , vol.102 , Issue.8 , pp. 2685-2689
    • Patil, K.1    Nielsen, J.2
  • 15
    • 78049304837 scopus 로고    scopus 로고
    • Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    • 10.1371/journal.pcbi.1000859, 2904763, 20657658
    • Bordel S, Agren R, Nielsen J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput Biol 2010, 6(7):e1000859. 10.1371/journal.pcbi.1000859, 2904763, 20657658.
    • (2010) PLoS Comput Biol , vol.6 , Issue.7
    • Bordel, S.1    Agren, R.2    Nielsen, J.3
  • 17
    • 0032904470 scopus 로고    scopus 로고
    • The dolichol pathway of N-linked glycosylation
    • 10.1016/S0304-4165(98)00127-5, 9878760
    • Burda P, Aebi M. The dolichol pathway of N-linked glycosylation. Biochim Biophys Acta 1999, 1426(2):239-257. 10.1016/S0304-4165(98)00127-5, 9878760.
    • (1999) Biochim Biophys Acta , vol.1426 , Issue.2 , pp. 239-257
    • Burda, P.1    Aebi, M.2
  • 18
    • 0035920193 scopus 로고    scopus 로고
    • The essential Smp3 protein is required for addition of the side-branching fourth mannose during assembly of yeast glycosylphosphatidylinositols
    • 10.1074/jbc.M101986200, 11356840
    • Grimme SJ, Westfall BA, Wiedman JM, Taron CH, Orlean P. The essential Smp3 protein is required for addition of the side-branching fourth mannose during assembly of yeast glycosylphosphatidylinositols. J Biol Chem 2001, 276(29):27731-27739. 10.1074/jbc.M101986200, 11356840.
    • (2001) J Biol Chem , vol.276 , Issue.29 , pp. 27731-27739
    • Grimme, S.J.1    Westfall, B.A.2    Wiedman, J.M.3    Taron, C.H.4    Orlean, P.5
  • 19
    • 84877119088 scopus 로고    scopus 로고
    • Genome-Scale Modeling of the Protein Secretory Machinery in Yeast
    • 10.1371/journal.pone.0063284, 3636087, 23637590
    • Feizi A, Österlund T, Petranovic D, Bordel S, Nielsen J. Genome-Scale Modeling of the Protein Secretory Machinery in Yeast. PLoS computational biology 2013, : . 10.1371/journal.pone.0063284, 3636087, 23637590.
    • (2013) PLoS computational biology
    • Feizi, A.1    Österlund, T.2    Petranovic, D.3    Bordel, S.4    Nielsen, J.5
  • 20
    • 84877615275 scopus 로고    scopus 로고
    • Mapping Condition Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae
    • Submitted for publication 2013
    • Jewett MC, Workman CT, Nookaew I, Pizarro FA, Agosin E, Hellgren LI, Nielsen J. Mapping Condition Dependent Regulation of Lipid Metabolism in Saccharomyces cerevisiae. Submitted for publication 2013.
    • Jewett, M.C.1    Workman, C.T.2    Nookaew, I.3    Pizarro, F.A.4    Agosin, E.5    Hellgren, L.I.6    Nielsen, J.7
  • 22
    • 0042816453 scopus 로고    scopus 로고
    • Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae
    • 10.1089/153623103322246584, 14506848
    • Förster J, Famili I, Palsson B, Nielsen J. Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae. OMICS A Journal of Integrative Biology 2003, 7(2):193-202. 10.1089/153623103322246584, 14506848.
    • (2003) OMICS A Journal of Integrative Biology , vol.7 , Issue.2 , pp. 193-202
    • Förster, J.1    Famili, I.2    Palsson, B.3    Nielsen, J.4
  • 23
    • 0033753004 scopus 로고    scopus 로고
    • Simultaneous overexpression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Saccharomyces cerevisiae
    • 10.1002/1097-0061(200010)16:14<1325::AID-YEA627>3.0.CO;2-E, 11015729
    • Smits HP, Hauf J, Müller S, Hobley TJ, Zimmermann FK, Hahn Hägerdal B, Nielsen J, Olsson L. Simultaneous overexpression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Saccharomyces cerevisiae. Yeast 2000, 16(14):1325-1334. 10.1002/1097-0061(200010)16:14<1325::AID-YEA627>3.0.CO;2-E, 11015729.
    • (2000) Yeast , vol.16 , Issue.14 , pp. 1325-1334
    • Smits, H.P.1    Hauf, J.2    Müller, S.3    Hobley, T.J.4    Zimmermann, F.K.5    Hahn Hägerdal, B.6    Nielsen, J.7    Olsson, L.8
  • 25
    • 0028363566 scopus 로고
    • INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter
    • Ambroziak J, Henry SA. INO2 and INO4 gene products, positive regulators of phospholipid biosynthesis in Saccharomyces cerevisiae, form a complex that binds to the INO1 promoter. J Biol Chem 1994, 269(21):15344-15349.
    • (1994) J Biol Chem , vol.269 , Issue.21 , pp. 15344-15349
    • Ambroziak, J.1    Henry, S.A.2
  • 26
    • 0034936617 scopus 로고    scopus 로고
    • The negative regulator Opi1 of phospholipid biosynthesis in yeast contacts the pleiotropic repressor Sin3 and the transcriptional activator Ino2
    • 10.1046/j.1365-2958.2001.02495.x, 11454208
    • Wagner C, Dietz M, Wittmann J, Albrecht A, Schüller HJ. The negative regulator Opi1 of phospholipid biosynthesis in yeast contacts the pleiotropic repressor Sin3 and the transcriptional activator Ino2. Mol Microbiol 2001, 41(1):155-166. 10.1046/j.1365-2958.2001.02495.x, 11454208.
    • (2001) Mol Microbiol , vol.41 , Issue.1 , pp. 155-166
    • Wagner, C.1    Dietz, M.2    Wittmann, J.3    Albrecht, A.4    Schüller, H.J.5
  • 27
    • 0032750741 scopus 로고    scopus 로고
    • Nitrogen catabolite repression in Saccharomyces cerevisiae
    • 10.1385/MB:12:1:35, 10554772
    • Hofman-Bang J. Nitrogen catabolite repression in Saccharomyces cerevisiae. Mol Biotechnol 1999, 12(1):35-73. 10.1385/MB:12:1:35, 10554772.
    • (1999) Mol Biotechnol , vol.12 , Issue.1 , pp. 35-73
    • Hofman-Bang, J.1
  • 28
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum
    • 10.1371/journal.pcbi.1002980, 3605104, 23555215
    • Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS computational biology 2013, 9(3):e1002980. 10.1371/journal.pcbi.1002980, 3605104, 23555215.
    • (2013) PLoS computational biology , vol.9 , Issue.3
    • Agren, R.1    Liu, L.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 31
    • 78650595350 scopus 로고    scopus 로고
    • Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data
    • 10.1186/1752-0509-4-178, 3023687, 21190580
    • Zomorrodi A, Maranas C. Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol 2010, 4(1):178. 10.1186/1752-0509-4-178, 3023687, 21190580.
    • (2010) BMC Syst Biol , vol.4 , Issue.1 , pp. 178
    • Zomorrodi, A.1    Maranas, C.2
  • 32
    • 0033893839 scopus 로고    scopus 로고
    • The mitochondrial alcohol dehydrogenase Adh3p is involved in a redox shuttle in Saccharomyces cerevisiae
    • 10.1128/JB.182.17.4730-4737.2000, 111347, 10940011
    • Bakker BM, Bro C, Kötter P, Luttik MAH, Van Dijken JP, Pronk JT. The mitochondrial alcohol dehydrogenase Adh3p is involved in a redox shuttle in Saccharomyces cerevisiae. J Bacteriol 2000, 182(17):4730-4737. 10.1128/JB.182.17.4730-4737.2000, 111347, 10940011.
    • (2000) J Bacteriol , vol.182 , Issue.17 , pp. 4730-4737
    • Bakker, B.M.1    Bro, C.2    Kötter, P.3    Luttik, M.A.H.4    Van Dijken, J.P.5    Pronk, J.T.6
  • 33
    • 0034057725 scopus 로고    scopus 로고
    • In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiaeMitochondria
    • 10.1128/JB.182.10.2823-2830.2000, 101991, 10781551
    • Overkamp KM, Bakker BM, Kötter P, Van Tuijl A, De Vries S, Van Dijken JP, Pronk JT. In Vivo Analysis of the Mechanisms for Oxidation of Cytosolic NADH by Saccharomyces cerevisiaeMitochondria. J Bacteriol 2000, 182(10):2823-2830. 10.1128/JB.182.10.2823-2830.2000, 101991, 10781551.
    • (2000) J Bacteriol , vol.182 , Issue.10 , pp. 2823-2830
    • Overkamp, K.M.1    Bakker, B.M.2    Kötter, P.3    Van Tuijl, A.4    De Vries, S.5    Van Dijken, J.P.6    Pronk, J.T.7
  • 34
    • 0035140099 scopus 로고    scopus 로고
    • Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression
    • 10.1128/JB.183.4.1441-1451.2001, 95019, 11157958, Moreira dos Santos M
    • Gombert AK, Christensen B, Nielsen J, . Moreira dos Santos M Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 2001, 183(4):1441-1451. 10.1128/JB.183.4.1441-1451.2001, 95019, 11157958, Moreira dos Santos M.
    • (2001) J Bacteriol , vol.183 , Issue.4 , pp. 1441-1451
    • Gombert, A.K.1    Christensen, B.2    Nielsen, J.3
  • 35
    • 33847785682 scopus 로고    scopus 로고
    • Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae
    • 10.1073/pnas.0607469104, 1892921, 17287356
    • Vemuri G, Eiteman M, McEwen J, Olsson L, Nielsen J. Increasing NADH oxidation reduces overflow metabolism in Saccharomyces cerevisiae. Proc Natl Acad Sci 2007, 104(7):2402-2407. 10.1073/pnas.0607469104, 1892921, 17287356.
    • (2007) Proc Natl Acad Sci , vol.104 , Issue.7 , pp. 2402-2407
    • Vemuri, G.1    Eiteman, M.2    McEwen, J.3    Olsson, L.4    Nielsen, J.5
  • 37
    • 0031015551 scopus 로고    scopus 로고
    • Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae
    • 10.1099/00221287-143-1-203, 9025295
    • Nissen TL, Schulze U, Nielsen J, Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 1997, 143(1):203-218. 10.1099/00221287-143-1-203, 9025295.
    • (1997) Microbiology , vol.143 , Issue.1 , pp. 203-218
    • Nissen, T.L.1    Schulze, U.2    Nielsen, J.3    Villadsen, J.4
  • 38
    • 0034873481 scopus 로고    scopus 로고
    • Involvement of nitrogen metabolism in the triggering of ethanol fermentation in aerobic chemostat cultures of Saccharomyces cerevisiae
    • 10.1006/mben.2001.0181, 11461147
    • Aon JC, Cortassa S. Involvement of nitrogen metabolism in the triggering of ethanol fermentation in aerobic chemostat cultures of Saccharomyces cerevisiae. Metab Eng 2001, 3(3):250-264. 10.1006/mben.2001.0181, 11461147.
    • (2001) Metab Eng , vol.3 , Issue.3 , pp. 250-264
    • Aon, J.C.1    Cortassa, S.2
  • 39
    • 33748766328 scopus 로고    scopus 로고
    • Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation
    • 10.1128/AEM.00548-06, 1563674, 16957246
    • Usaite R, Patil KR, Grotkjær T, Nielsen J, Regenberg B. Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation. Appl Environ Microbiol 2006, 72(9):6194-6203. 10.1128/AEM.00548-06, 1563674, 16957246.
    • (2006) Appl Environ Microbiol , vol.72 , Issue.9 , pp. 6194-6203
    • Usaite, R.1    Patil, K.R.2    Grotkjær, T.3    Nielsen, J.4    Regenberg, B.5
  • 40
    • 12844281816 scopus 로고    scopus 로고
    • Two-dimensional Transcriptome Analysis in Chemostat Cultures - Combinatorial Effects of Oxygen Availability and Macronutrient Limitation in Saccharomyces cerevisiae
    • Tai SL, Boer VM, Daran-Lapujade P, Walsh MC, de Winde JH, Daran JM, Pronk JT. Two-dimensional Transcriptome Analysis in Chemostat Cultures - Combinatorial Effects of Oxygen Availability and Macronutrient Limitation in Saccharomyces cerevisiae. J Biol Chem 2005, 280(1):437-447.
    • (2005) J Biol Chem , vol.280 , Issue.1 , pp. 437-447
    • Tai, S.L.1    Boer, V.M.2    Daran-Lapujade, P.3    Walsh, M.C.4    de Winde, J.H.5    Daran, J.M.6    Pronk, J.T.7
  • 41
    • 0028786431 scopus 로고
    • Energetics and product formation by Saccharomyces cerevisiae grown in anaerobic chemostats under nitrogen limitation
    • 10.1007/BF00166921, 8590653
    • Lidén G, Persson A, Niklasson C, Gustafsson L. Energetics and product formation by Saccharomyces cerevisiae grown in anaerobic chemostats under nitrogen limitation. Appl Microbiol Biotechnol 1995, 43(6):1034-1038. 10.1007/BF00166921, 8590653.
    • (1995) Appl Microbiol Biotechnol , vol.43 , Issue.6 , pp. 1034-1038
    • Lidén, G.1    Persson, A.2    Niklasson, C.3    Gustafsson, L.4


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