Skip to main content
SpringerLink
Log in

Metabolomics and Systems Biology in Saccharomyces cerevisiae

  • Chapter
Fungal Genomics

Part of the book series: The Mycota ((MYCOTA,volume 13))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 209.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Adams A (2003) Metabolomics: small-molecule omics. The Scientist 17:38–40

    Google Scholar 

  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002) Molecular biology of the cell, 4th edn. Garland Science, Taylor and Francis Group, New York

    Google Scholar 

  • Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB (2003) High-throughput classification of yeast mutants using metabolic footprinting. Nat Biotechnol 21:692–696

    Article  CAS  PubMed  Google Scholar 

  • Auesukaree C, Homma T, Tochio H, Shirakawa M, Kaneko Y, Harashima S (2004) Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae. J Biol Chem 279:17289–17294

    Article  CAS  PubMed  Google Scholar 

  • Baganz F, Hayes A, Farquhar R, Butler PR, Gardner DCJ, Oliver SG (1998) Quantitative analysis of yeast gene function using competition experiments in continuous culture. Yeast 14:1417–1427

    Article  CAS  PubMed  Google Scholar 

  • Bailey JE (1991) Toward a science of metabolic engineering. Science 252:1668–1675

    CAS  PubMed  Google Scholar 

  • Bailey JE, Ollis DF (1986) Biochemical engineering fundamentals, 2nd edn. McGraw Hill, New York

    Google Scholar 

  • Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell’s functional organization. Nat Rev Genet 5:101–113

    Article  PubMed  Google Scholar 

  • Boer VM, de Winde JH, Pronk JT, Piper MDW (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278:3265–3274

    Article  CAS  PubMed  Google Scholar 

  • Bro C, Regenberg B, Lagniel G, Labarre J, Montero-Lomeli M, Nielsen J (2003) Transcriptional, proteomic, and metabolic responses to lithiumin galactose-grown yeast cells. J Biol Chem 278:32141–323149

    Article  CAS  PubMed  Google Scholar 

  • Brown AJP (1997) Control of metabolic flux in yeasts and fungi. Trends Biotechnol 15:445–447

    Article  CAS  PubMed  Google Scholar 

  • Brown AJP, Tuite MF (1998) Yeast gene analysis. Academic Press, San Diego, Methods in Microbiology 26

    Google Scholar 

  • Brown GC, Hafner RP, Brand MD (1990) A ‘top-down’ approach to the determination of control coefficients in metabolic control theory. Eur J Biochem 188:321–325

    Article  CAS  PubMed  Google Scholar 

  • Burke D, Dawson D, Stearns T (2000) Methods in yeast genetics, 2000 edn. A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Castrillo JI, Oliver SG (2004) Yeast as a touchstone in post-genomic research. Strategies for integrative analysis in functional genomics. J Biochem Mol Biol 37:93–106

    CAS  PubMed  Google Scholar 

  • Castrillo JI, Ugalde UO (1994) A general model of yeast energy metabolism in aerobic chemostat culture. Yeast 10:185–197

    Article  CAS  PubMed  Google Scholar 

  • Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG (2003) An optimised protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62:929–937

    Article  CAS  PubMed  Google Scholar 

  • Cech TR (2004) RNA finds a simpler way. Nature 428:263–264

    CAS  PubMed  Google Scholar 

  • Choudhuri S (2004) The nature of gene regulation. Int Arch Biosci 2004:1001–1015

    Google Scholar 

  • Cornell M, Paton NW, Hedeler C, Kirby P, Delneri D, Hayes A, Oliver SG (2003) GIMS: an integrated data storage and analysis environment for genomic and functional data. Yeast 20:1291–1306

    Article  CAS  PubMed  Google Scholar 

  • Cortassa S, Aon MA (1994) Metabolic control analysis of glycolysis and branching to ethanol production in chemostat cultures of Saccharomyces cerevisiae under carbon, nitrogen, or phosphate limitations. Enzyme Microb Technol 16:761–770

    Article  CAS  Google Scholar 

  • Costanzo MC, Crawford ME, Hirschman JE, Kranz JE, Olsen P, Robertson LS, Skrzypek MS, Braun BR, Hopkins KL, Kondu P et al. (2001) YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res 29:75–79

    Article  CAS  PubMed  Google Scholar 

  • Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BØ (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92–96

    Article  CAS  PubMed  Google Scholar 

  • Csank C, Costanzo MC, Hirschman J, Hodges P, Kranz JE, Mangan M, O’Neill K, Robertson LS, Skrzypek MS, Brooks J et al. (2002) Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD). Methods Enzymol 350:347–373

    CAS  PubMed  Google Scholar 

  • Daran-Lapujade P, Jansen ML, Daran JM, van Gulik W, de Winde JH, Pronk JT (2004) Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 279:9125–9138

    Article  CAS  PubMed  Google Scholar 

  • Day DA, Tuite MF (1998) Post-transcriptional gene regulatory mechanisms in eukaryotes: an overview. J Endocrinol 157:361–371

    Article  CAS  PubMed  Google Scholar 

  • De la Fuente A, Snoep JL, Westerhoff HV, Mendes P (2002) Metabolic control in integrated biochemical systems. Eur J Biochem 269:4399–4408

    PubMed  Google Scholar 

  • Delneri D, Brancia FL, Oliver SG (2001) Towards a truly integrative biology through the functional genomics of yeast. Curr Opin Biotechnol 12:87–91

    Article  CAS  PubMed  Google Scholar 

  • Dong L, Xu CW (2004) Carbohydrates induce monoubiquitination of H2B in yeast. J Biol Chem 279:1577–1580

    CAS  PubMed  Google Scholar 

  • Duarte NC, Herrgard MJ, Palsson BØ (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298–1309

    Article  CAS  PubMed  Google Scholar 

  • Eisenstein M (2004) Getting down to the bare essentials. Nat Methods 20 July 2004. DOI 101038/nmteh030

    Google Scholar 

  • Fafournoux P, Bruhat A, Jousse C (2000) Amino acid regulation of gene expression. Biochem J 351:1–12

    Article  CAS  PubMed  Google Scholar 

  • Fell DA (1997) Understanding the control of metabolism. Portland Press, London

    Google Scholar 

  • Fell DA (1998) Increasing the flux in metabolic pathways: a metabolic control analysis perspective. Biotechnol Bioeng 58:121–124

    Article  CAS  PubMed  Google Scholar 

  • Fell DA (2001) Beyond genomics. Trends Genet 17:680–682

    Article  CAS  PubMed  Google Scholar 

  • Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L (2004) Metabolite profiling: fromdiagnostics to systems biology. Nat Rev Mol Cell Biol 5:763–769

    Article  CAS  PubMed  Google Scholar 

  • Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20:301–305

    Article  CAS  PubMed  Google Scholar 

  • Fiehn O (2001) Combining genomics, metabolome analysis and biochemical modelling to understand metabolic networks. Comp Funct Genomics 2:155–168

    CAS  Google Scholar 

  • Förster J, Famili I, Fu P, Palsson BØ, Nielsen J (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13:244–253

    PubMed  Google Scholar 

  • Gaisne M, Bécam AM, Verdière J, Herbert CJ (1999) A ‘natural’ mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet 36:195–200

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Martinez J, Aranda A, Perez-Ortin JE (2004) Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell 15:303–313

    CAS  PubMed  Google Scholar 

  • Gavin AC, Superti-Furga G (2003) Protein complexes and proteome organization from yeast to man. Curr Opin Chem Biol 7:21–27

    Article  CAS  PubMed  Google Scholar 

  • Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141–147

    Article  CAS  PubMed  Google Scholar 

  • Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O’Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737–741

    Article  CAS  PubMed  Google Scholar 

  • Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391

    Article  CAS  PubMed  Google Scholar 

  • Gill RT, Dodge T (2004) Special issue on inverse metabolic engineering. Metab Eng 6:175–176

    Article  CAS  Google Scholar 

  • Giuseppin ML, van Riel NA (2000) Metabolic modelling of Saccharomyces cerevisiae using the optimal control of homeostasis: a cybernetic model definition. Metab Eng 2:14–33

    Article  CAS  PubMed  Google Scholar 

  • Glanemann C, Loos A, Gorret N, Willis LB, O’Brien XM, Lessard PA, Sinskey AJ (2003) Disparity between changes in mRNA abundance and enzyme activity in Corynebacterium glutamicum and implications for DNA microarray analysis. Appl Microbiol Biotechnol 61:61–68

    CAS  PubMed  Google Scholar 

  • Goffeau A (2000) Four years of post-genomic life with 6000 yeast genes. FEBS Lett 480:37–41

    Article  CAS  PubMed  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M et al. (1996) Life with 6000 genes. Science 274:546–567

    Article  CAS  PubMed  Google Scholar 

  • Goffeau A, Aert R, Agostini-Carbone ML, Ahmed A, Aigle M, Alberghina L, Albermann K, Albers M, Aldea M, Alexandraki D et al (1997) The yeast genome directory. Nature 387 Suppl no 6632 (http://www.nature.com/genomics/papers/s_cerevisiae.html)

    Google Scholar 

  • Gonzalez B, François J, Renaud M (1997) A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast 13:1347–1355

    Article  CAS  PubMed  Google Scholar 

  • Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22:245–252

    Article  CAS  PubMed  Google Scholar 

  • Guthrie C, Fink GR (2002a) Guide to yeast genetics and molecular and cell biology. Part B. Academic Press, Elsevier Science, San Diego, Methods in Enzymology vol 350

    Google Scholar 

  • Guthrie C, Fink GR (2002b) Guide to yeast genetics and molecular and cell biology. Part C. Academic Press, Elsevier Science, San Diego, Methods in Enzymology vol 351

    Google Scholar 

  • Guthrie C, Fink GR (2004) Guide to yeast genetics and molecular biology. Part A. Academic Press, Elsevier Science, San Diego, Methods in Enzymology vol 194

    Google Scholar 

  • Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730

    CAS  PubMed  Google Scholar 

  • Hancock JT (1997) Cell signalling. Prentice Hall, Harlow

    Google Scholar 

  • Hansen J, Johannesen PF (2000) Cysteine is essential for transcriptional regulation of the sulfur assimilation genes in Saccharomyces cerevisiae. Mol Gen Genet 263:535–542

    CAS  PubMed  Google Scholar 

  • Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99–104

    Article  CAS  PubMed  Google Scholar 

  • Harrigan GG, Goodacre R (2003) Metabolic profiling: its role in biomarker discovery and gene function analysis. Kluwer, Boston

    Google Scholar 

  • Hayes A, Zhang N, Wu J, Butler PR, Hauser NC, Hoheisel JD, Lim F, Sharrocks AD, Oliver SG (2002) Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 26:281–290

    Article  CAS  PubMed  Google Scholar 

  • Hirayoshi K, Lis JT (1999) Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases. Methods Enzymol 304:351–362

    CAS  PubMed  Google Scholar 

  • Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180–183

    Article  CAS  PubMed  Google Scholar 

  • Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O’Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425:686–691

    Article  CAS  PubMed  Google Scholar 

  • Ideker T (2004a) Systems biology 101 — what you need to know. Nat Biotechnol 22:473–475

    Article  CAS  PubMed  Google Scholar 

  • Ideker T (2004b) A systems approach to discovering signalling and regulatory pathways — or, how to digest large interaction networks into relevant pieces. Adv Exp Med Biol 547:21–30

    PubMed  Google Scholar 

  • Ideker T, Galitski T, Hood L (2001a) A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet 2:343–372

    Article  CAS  PubMed  Google Scholar 

  • Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L (2001b) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292:929–934

    Article  CAS  PubMed  Google Scholar 

  • Ihmels J, Levy R, Barkai N (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22:86–92

    Article  CAS  PubMed  Google Scholar 

  • Ilyin SE, Belkowski SM, Plata-Salaman CR (2004) Biomarker discovery and validation: technologies and integrative approaches. Trends Biotechnol 22:411–416

    Article  CAS  PubMed  Google Scholar 

  • Iyer V, Struhl K (1996) Absolute mRN Alevels and transcriptional initiation rates in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 93:5208–5212

    CAS  PubMed  Google Scholar 

  • Kacser H (1995) Recent developments beyond metabolic control analysis. Biochem Soc Trans 23:387–391

    CAS  PubMed  Google Scholar 

  • Kacser H, Burns JA (1973) The control of flux. Symp Soc Exp Biol 27:65–104

    CAS  PubMed  Google Scholar 

  • Kafatos FC, Eisner T (2004) Unification in the century of biology. Science 303:1257

    Article  CAS  PubMed  Google Scholar 

  • Kapetanovic IM, Rosenfeld S, Izmirlian G (2004) Overview of commonly used bioinformatics methods and their applications. Ann N Y Acad Sci 1020:10–21

    CAS  PubMed  Google Scholar 

  • Kell DB, King RD (2000) On the optimization of classes for the assignment of unidentified reading frames in functional genomics programmes: the need for machine learning. Trends Biotechnol 18:93–98

    CAS  PubMed  Google Scholar 

  • Kell DB, Oliver SG (2004) Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 26:99–105

    Article  PubMed  Google Scholar 

  • Kitano H (2002) Systems biology: a brief overview. Science 295:1662–1664

    Article  CAS  PubMed  Google Scholar 

  • Klamt S, Stelling J (2003) Two approaches for metabolic pathway analysis? Trends Biotechnol 21:64–69

    Article  CAS  PubMed  Google Scholar 

  • Krauss S, Quant PA (1996) Regulation and control in complex, dynamic metabolic systems: experimental application of the top-down approaches of metabolic control analysis to fatty acid oxidation and ketogenesis. J Theor Biol 182:381–388

    Article  CAS  PubMed  Google Scholar 

  • Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci USA 94:13057–13062

    CAS  PubMed  Google Scholar 

  • Lee PS, Shaw LB, Choe LH, Mehra A, Hatzimanikatis V, Lee KH (2003) Insights into the relation between mRNA and protein expression patterns: II. Experimental observations in Escherichia coli. Biotechnol Bioeng 84:834–841

    CAS  PubMed  Google Scholar 

  • Lehninger AL (1975) Biochemistry, 2nd edn. Worth Publishers, New York

    Google Scholar 

  • Lei F, Rotboll M, Jorgensen SB (2001) A biochemically structured model for Saccharomyces cerevisiae. J Biotechnol 88:205–221

    CAS  PubMed  Google Scholar 

  • Loewen CJ, Gaspar ML, Jesch SA, Delon C, Ktistakis NT, Henry SA, Levine TP (2004) Phospholipid metabolism regulated by a transcription factor sensing phosphatidic acid. Science 304:1644–1647

    Article  CAS  PubMed  Google Scholar 

  • Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431:308–312

    Article  CAS  PubMed  Google Scholar 

  • McInerney JO (2002) Bioinformatics in a post-genomics world — the need for an inclusive approach. Pharmacogenomics J 2:207–208

    Article  CAS  PubMed  Google Scholar 

  • Mehra A, Lee KH, Hatzimanikatis V (2003) Insights into the relation between mRNA and protein expression patterns. I. Theoretical considerations. Biotechnol Bioeng 84:822–833

    Article  CAS  PubMed  Google Scholar 

  • Mendes P (2002) Emerging bioinformatics for the metabolome. Brief Bioinformatics 3:134–145

    CAS  PubMed  Google Scholar 

  • Merritt J, Edwards JS (2004) Assaying gene function by growth competition experiment. Metab Eng 6:212–219

    Article  CAS  PubMed  Google Scholar 

  • Mnaimneh S, Davierwala AP, Haynes J, Moffat J, Peng WT, Zhang W, Yang X, Pootoolal J, Chua G, Lopez A et al. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell 118:31–44

    Article  CAS  PubMed  Google Scholar 

  • Monod J, Changeux J-P, Jacob F (1963) Allosteric proteins and cellular control systems. J Mol Biol 6:306–329

    CAS  PubMed  Google Scholar 

  • Mortimer RK, Johnston JR (1986) Genealogy of principal strains of the yeast genetic stock center. Genetics 113:35–43

    CAS  PubMed  Google Scholar 

  • Muller D, Exler S, Aguilera-Vazquez L, Guerrero-Martin E, Reuss M (2003) Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20:351–367

    CAS  PubMed  Google Scholar 

  • Muratani M, Tansey WP (2003) How the ubiquitin-proteasome system controls transcription. Nat Rev Mol Cell Biol 4:192–201

    Article  CAS  PubMed  Google Scholar 

  • Nurse P (2003) Systemsbiology: understanding cells. Nature 424:883

    Article  CAS  PubMed  Google Scholar 

  • Oliver SG (1997) Yeast as a navigational aid in genome analysis. Microbiology 143:1483–1487

    CAS  PubMed  Google Scholar 

  • Oliver SG (2002) Functional genomics: lessons from yeast. Philos Trans R Soc B 357:17–23

    CAS  Google Scholar 

  • Oliver SG, Winson MK, Kell DB, Baganz F (1998) Systematic functional analysis of the yeast genome. Trends Biotechnol 16:373–378

    CAS  PubMed  Google Scholar 

  • Oliver DJ, Nikolau B, Wurtele ES (2002) Functional genomics: high-throughput mRNA, protein, and metabolite analyses. Metab Eng 4:98–106

    Article  CAS  PubMed  Google Scholar 

  • Olson OS, Nielsen J (2000) Metabolic engineering of Saccharomyces cerevisiae. Microbiol Mol Biol Rev 64:34–50

    Google Scholar 

  • Ozbudak EM, Thattai M, Lim HN, Shraiman BI, van Oudenaarden A (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427:737–740

    Article  CAS  PubMed  Google Scholar 

  • Papin JA, Palsson BØ (2004) Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk. J Theor Biol 227:283–297

    Article  PubMed  Google Scholar 

  • Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BØ (2004) Comparison of network-based pathway analysis methods. Trends Biotechnol 22:400–405

    Article  CAS  PubMed  Google Scholar 

  • Pasteur L (1857) Mémoire sur la fermentation appelée lactique. In: Mémoires Société Sciences Agriculture Arts Lille, séance 3 août 1857, 2ème Série, vol V, pp 13–26

    Google Scholar 

  • Peletier MA, Westerhoff HV, Kholodenko BN (2003) Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J Theor Biol 225:477–487

    Article  PubMed  Google Scholar 

  • Phelps TJ, Palumbo AV, Beliaev AS (2002) Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints. Curr Opin Biotechnol 13:20–24

    Article  CAS  PubMed  Google Scholar 

  • Plaxton WC (2004) Principles of metabolic control. In: Storey KB (ed) Functional metabolism of cells: control, regulation, and adaptation. Wiley, New York, pp 1–23

    Google Scholar 

  • Pratt JM, Petty J, Riba-Garcia I, Robertson DHL, Gaskell SJ, Oliver SG, Beynon RJ (2002) Dynamics of protein turnover, a missing dimension in proteomics. Mol Cell Proteomics 1:579–591

    CAS  PubMed  Google Scholar 

  • Quant PA (1993) Experimental applicationof top-down control analysis to metabolic systems. Trends Biochem Sci 18:26–30

    Article  CAS  PubMed  Google Scholar 

  • Raamsdonk LM, Teusink B, Broadhurst D, Zhang N, Hayes A, Walsh MC, Berden JA, Brindle KM, Kell DB, Rowland JJ et al. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19:45–50

    CAS  PubMed  Google Scholar 

  • Reed JL, Vo TD, Schilling CH, Palsson BØ (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4:R54

    Article  PubMed  Google Scholar 

  • Rose AH, Harrison JS (1987–1995) The yeasts, vols 1–6. Academic Press, London

    Google Scholar 

  • Rose AH, Harrison JS (1993) The yeasts, vol 5. Academic Press, London

    Google Scholar 

  • Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, Cheung KH, Sheehan A, Symoniatis D, Umansky L et al. (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413–418

    CAS  PubMed  Google Scholar 

  • Sage L (2004) Genome-scale model predicts gene regulation. The Scientist 18:42

    Google Scholar 

  • Scherens B, Goffeau A (2004) The uses of genome-wide yeast mutant collections. Genome Biol 5:229 (http://genomebiologycom/2004/5/7/229)

    Article  PubMed  Google Scholar 

  • Schwartz M (2001) The life and works of Louis Pasteur. J Appl Microbiol 91:597–601

    Article  CAS  PubMed  Google Scholar 

  • Sellick CA, Reece RJ (2003) Modulation of transcription factor function by an amino acid: activation of Put3p by proline. EMBO J 22:5147–5153

    Article  CAS  PubMed  Google Scholar 

  • Sherman F (1998) An introduction to the genetics and molecular biology of the yeast Saccharomyces cerevisiae (http://dbburmcrochester.edu/labs/sherman_f/yeast/)

    Google Scholar 

  • Sherman F (2002) Getting started with yeast. Methods Enzymol 350:3–41 (updated in http://dbburmcrochester.edu/labs/sherman_f/startedyeast.pdf)

    CAS  PubMed  Google Scholar 

  • Sinclair CG, Cantero D (1990) Fermentation modelling. In: McNeil B, Harvey LM (eds) Fermentation. A practical approach. IRL Press, Oxford University Press, Oxford, pp 65–112

    Google Scholar 

  • Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273–3297

    CAS  PubMed  Google Scholar 

  • Sprague GF Jr, Cullen PJ, Goehring AS (2004) Yeast signal transduction: regulation and interface with cell biology. In: Opresko LK, Gephart JM, Mann MB (eds) Advances in experimental medicine and biology. Kluwer/Plenum, New York, Advances in Systems Biology vol 547, pp 91–105

    Google Scholar 

  • Stelling J (2004) Mathematical models in microbial systems biology. Curr Opin Microbiol 7:513–518

    Article  PubMed  Google Scholar 

  • Stephanopoulos G (1999) Metabolic fluxes and metabolic engineering. Metab Eng 1:1–11

    Article  CAS  PubMed  Google Scholar 

  • Stephanopoulos G, Gill RT (2001) After a decade of progress, an expanded role for metabolic engineering. Adv Biochem Eng Biotechnol 73:1–8

    CAS  PubMed  Google Scholar 

  • Stephanopoulos G, Vallino JJ (1991) Network rigidity and metabolic engineering in metabolite overproduction. Science 252:1675–1681

    CAS  PubMed  Google Scholar 

  • ter Kuile BH, Westerhoff HV (2001) Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett 500:169–171

    PubMed  Google Scholar 

  • ter Linde JJ, Liang H, Davis RW, Steensma HY, van Dijken JP, Pronk JT (1999) Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. J Bacteriol 181:7409–7413

    PubMed  Google Scholar 

  • Teusink B, Baganz F, Westerhoff HV, Oliver SG (1998) Metabolic control analysis as a tool in the elucidation of the function of novel genes. In: Brown AJ, Tuite MF (eds) Methods in Microbiology, vol 26. Academic Press, London, pp 297–336

    Google Scholar 

  • The International Human Genome Mapping Consortium (2001a) Initial sequencing and analysis of the human genome. Nature 409:860–921

    Google Scholar 

  • The International Human Genome Mapping Consortium (2001b) A physical map of the human genome. Nature 409:934–941

    Google Scholar 

  • Tilstone C (2003) Vital statistics. Nature 424:610–613

    Article  CAS  PubMed  Google Scholar 

  • Ton VK, Rao R (2004) Functional expression of heterologous proteins in yeast: insights into Ca2+ signaling and Ca2+-transporting ATPases. Am J Physiol Cell Physiol 287:580–589

    Article  Google Scholar 

  • Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Willmitzer L, Fernie AR(2003) Parallel analysis of transcript and metabolic profiles: anew approach in systems biology. EMBO Rep 4:989–993

    Article  CAS  PubMed  Google Scholar 

  • US Patent Office (2003) US Patent 2003228567. Compositions and methods for modelling Saccharomyces cerevisiae metabolism. US Patent Office, Alexandria, VA

    Google Scholar 

  • Varma A, Palsson BØ (1994) Metabolic flux balancing: Basic concepts, scientific and practical use. Bio/Technology 12:994–998

    Article  CAS  Google Scholar 

  • Verger A, Perdomo J, Crossley M (2003) Modification with SUMO. A role in transcriptional regulation. EMBO Rep 4:137–142

    Article  CAS  PubMed  Google Scholar 

  • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417:399–403

    Google Scholar 

  • Wang S, Sim TB, Kim YS, Chang YT (2004) Tools for target identification and validation. Curr Opin Chem Biol 8:371–377

    Article  CAS  PubMed  Google Scholar 

  • Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54:669–689

    Article  CAS  PubMed  Google Scholar 

  • Wei GH, Liu DP, Liang CC (2004) Charting gene regulatory networks: strategies, challenges and perspectives. Biochem J 381:1–12

    CAS  PubMed  Google Scholar 

  • Wiechert W (2001) 13C metabolic flux analysis. Metab Eng 3:195–206

    CAS  PubMed  Google Scholar 

  • Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H et al. (1999) Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901–906

    Article  CAS  PubMed  Google Scholar 

  • Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 15:1359–1367

    Article  CAS  PubMed  Google Scholar 

  • Wohlschlegel JA, Yates JR (2003) Proteomics: where’s Waldo in yeast? Nature 425:671–672

    Article  CAS  PubMed  Google Scholar 

  • World Intellectual Property Organisation (2001a) WO Patent 0107567. Engineering of metabolic control. World Intellectual Property Organisation, Geneva

    Google Scholar 

  • World Intellectual Property Organisation (2001b) WO Patent 0178652. Methods for drug discovery, disease treatment and diagnosis using metabolomics. World Intellectual Property Organisation, Geneva

    Google Scholar 

  • Yao T (2002) Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era. Prog Biophys Mol Biol 80:23–42

    PubMed  Google Scholar 

  • Yeang CH, Ideker T, Jaakkola T (2004) Physical network models. J Comput Biol 11:243–262

    Article  CAS  PubMed  Google Scholar 

  • Yoon SH, Lee SY (2002) Comparison of transcript levels by DNA microarray and metabolic flux based on flux analysis for the production of poly-g-glutamic acid in recombinant Escherichia coli. Genome Informatics 13:587–588

    CAS  Google Scholar 

  • Yoon SH, Han MJ, Lee SY, Jeong KJ, Yoo JS (2003) Combined transcriptome and proteome analysis of Escherichia coli during the high cell density culture. Biotechnol Bioeng 81:753–767

    Article  CAS  PubMed  Google Scholar 

  • Zaragoza O, Lindley C, Gancedo JM (1999) Cyclic AMP can decrease expression of genes subject to catabolite repression in Saccharomyces cerevisiae. J Bacteriol 181:2640–2642

    CAS  PubMed  Google Scholar 

  • Zhu H, Snyder M (2003) Protein chip technology. Curr Opin Chem Biol 7:55–63

    Article  CAS  PubMed  Google Scholar 

  • Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T et al. (2001) Global analysis of protein activities using proteome chips. Science 293:2101–2105

    Article  CAS  PubMed  Google Scholar 

  • Zhu H, Bilgin M, Snyder M (2003) Proteomics. Annu Rev Biochem 72:783–812

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK

    J.I. Castrillo & S.G. Oliver

Authors
  1. J.I. Castrillo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. S.G. Oliver
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK

    Alistair J.P. Brown

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Castrillo, J., Oliver, S. (2006). Metabolomics and Systems Biology in Saccharomyces cerevisiae. In: Brown, A.J. (eds) Fungal Genomics. The Mycota, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-30809-1_1

Download citation

Publish with us

Policies and ethics

Search

Navigation