Skip to main content

Towards Integrative Functional Genomics Using Yeast as a Reference Model

Metabolomic analysis in the post-genomic era

  • Chapter
Metabolome Analyses: Strategies for Systems Biology

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

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. Metabolomics: Small-molecule ’omics. The Scientist, 17: 38–40 (2003).

    Google Scholar 

  • Aharoni A. Ric de Vos CH, Verhoeven HA, Maliepaard CA, Kruppa G, Bino R and Goodenowe DB. Nontargeted metabolome analysis by use of Fourier Transform Ion Cyclotron Mass Spectrometry. OMICS, 6: 217–234 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Alberts B, Johnson A, Lewis J, Raff M, Roberts K and Walter P. Molecular Biology of The Cell, 4th ed., Garland Science, Taylor and Francis Group, New York (2002).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Atkinson B and Mavituna F. Biochemical Engineering and Biotechnology Handbook, 2nd, ed., M. Stockton Press, New York (1991).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Bailey JE and Ollis DF. Biochemical Engineering Fundamentals, 2nd ed., McGraw Hill, New York (1986).

    Google Scholar 

  • Brindle KM, Fulton SM, Gillham H and Williams SP. Studies of metabolic control using NMR and molecular genetics. J. Mol. Recognit., 10: 182–187 (1997).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Brown AJP and Tuite MF. Yeast Gene Analysis. Methods in Microbiol., 26. Academic Press. San Diego (1998).

    Google Scholar 

  • Burke D, Dawson D and Stearns T. Methods in Yeast Genetics, 2000 Edition: A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press. New York (2000).

    Google Scholar 

  • Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ and Lee PW. Metabolic control analysis in drug discovery and disease. Nat. Biotechnol., 20: 243–249 (2002).

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Chen CN, Porubleva L, Shearer G, Svrakic M, Holden LG, Dover JL, Johnston M, Chitnis PR and Kohl DH. Associating protein activities with their genes: rapid identification of a gene encoding a methylglyoxal reductase in the yeast Saccharomyces cereviisiae. Yeast, 20: 545–554 (2003).

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Cortassa S and Aon MA. 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 (1994).

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • De Koning W and van Dam K. A method for the determination of changes in glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH. Anal. Biochem., 204: 118–123 (1992).

    Article  PubMed  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Demain AL. Induction of microbial secondary metabolism. Int. Microbiol., 1: 259–264 (1998).

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Farre EM, Tiessen A, Roessner U, Geigenberger P, Trethewey RN and Willmitzer L. Analysis of the compartmentation of glycolytic intermediates, nucleotides, sugars, organic acids, amino acids, and sugar alcohols in potato tubers using a nonaqueous fractionation method. Plant Physiol., 127: 685–700 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Fell DA. Understanding the Control of Metabolism, Portland Press Ltd., London (1997).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Fiehn O and Spranger J. Use of metabolomics to discover metabolic patterns associated with human diseases; in: Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, G. G. Harrigan, and R. Goodacre, eds., Kluwer Academic Publishers, Boston, pp. 199–216 (2003).

    Google Scholar 

  • Fiehn O and Weckwerth W. Deciphering metabolic networks. Eur. J. Biochem., 270: 579–588 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN and Willmitzer L. Metabolite profiling for plant functional genomics. Nat. Biotechnol., 18: 1157–1161 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Gancedo JM. Yeast carbon catabolite repression. Microbiol. Mol. Biol. Rev., 62: 334–361 (1998).

    PubMed  CAS  Google Scholar 

  • Gancedo JM and Gancedo C. Concentrations of intermediary metabolites in yeast. Biochimie, 55: 205–211 (1973).

    PubMed  CAS  Google Scholar 

  • Giaever G. et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature, 418, 387–391 (2002).

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Goffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H and Oliver SG. Life with 6000 genes. Science, 274: 546–567 (1996).

    Article  PubMed  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Gough NR, Adler EM and Ray LB. Focus Issue: Targeting signalling pathways for drug discovery. Sci STKE 225: eg5, March (2004).

    Google Scholar 

  • Griffin JL. Metabolic profiles to define the genome: can we hear the phenotypes? Phil. Trans. Biol. Sciences. R. Soc. Lond. B., 359: 857–571 (2004).

    Article  CAS  Google Scholar 

  • Griffin JL and Shockcor JP. Metabolic profiles of cancer cells. Nat. Rev. Cancer, 4: 551–561 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Griffin JL, Williams HJ, Sang E, Clarke K, Rae C and Nicholson JK. Metabolic profiling of genetic disorders: a multitissue 1H nuclear magnetic resonance spectroscopic and pattern recognition study into dystrophic tissue. Anal. Biochem., 293: 16–21 (2001).

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Hajjaj H, Blanc PJ, Goma J and François J. Sampling techniques and comparative extraction procedures for quantitative determination of intra-and extracellular metabolites in filamentous fungi. FEMS Microbiol. Lett., 164; 195–200 (1998).

    CAS  Google Scholar 

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

    Google Scholar 

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

    Article  CAS  Google Scholar 

  • Harrigan GG and Goodacre R. Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, Kluwer Academic Publishers, Boston (2003).

    Google Scholar 

  • He W, Miao FJ, Lin DC, Schwandner RT, Wang Z, Gao J, Chen JL, Tian H and Ling L. Citric acid cycle intermediates as ligands for orphan G-protein-coupled receptors. Nature, 429: 188–193 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Heaton JPW, Brien SE, Adams MA and Graham CH. Method for diagnosing a vascular condition. World Intellectual Property Organisation, WO Patent, 9957306 (1999).

    Google Scholar 

  • Hebert SC. Physiology: orphan detectors of metabolism. Nature, 429: 143–145 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Horinouchi S and Beppu T. Autoregulators. Biotechnol., 28, 103–119 (1995).

    CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Kaddurah-Daouk R and Kristal BS. Methods for drug discovery, disease treatment and diagnosis using metabolomics. World Intellectual Property Organisation, WO Patent, 0178652 (2001).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Kell DB and King RD. 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 (2000).

    Article  PubMed  CAS  Google Scholar 

  • Kell DB and Mendes P. Snapshots of systems: metabolic control analysis and biotechnology in the post-genomic era. In: Technological and Medical Implications of Metabolic Control Analysis, A. Cornish-Bowden, and M. L. Cardenas, eds., Kluwer Academic Publishers, Dordrecht, pp. 3–25 (2000).

    Google Scholar 

  • Kell DB, Darby RM and Draper J. Genomic computing: explanatory analysis of plant expression profiling data using machine learning. Plant Physiol., 126: 943–951 (2001).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Krauss S and Quant PA. 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 (1996).

    Article  PubMed  CAS  Google Scholar 

  • Kumar A, Harrison PM, Cheung K-H, Lan N, Echols N, Bertone P, Miller P, Gerstein MB and Snyder M. An integrated approach for finding overlooked genes in yeast. Nat. Biotechnol., 20: 58–63 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Lange HC, Eman M, van Zuijlen G, Visser D, van Dam JC, Frank J, Teixeira de Mattos MJ, and Heijnen JJ. Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiae. Biotechnol. Bioeng., 75: 406–415 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Lee W-NP and Boros LG. Stable isotope based dynamic metabolic profiling of living organisms for characterization of metabolic diseases, drug testing and drug development. US Patent Office, US Patent, 2003180800 (2003).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  • Martens JA, Laprade L, and Winston F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature, 429: 571–574 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Martinez-Force E and Benitez T. Separation of o-phtalaldehyde derivatives of amino acids of the internal pool of yeast by reverse-phase liquid chromatography. Biotechnol. Tech., 5: 209–214 (1991).

    Article  CAS  Google Scholar 

  • Mashego MR, van Gulik WM, Vinke JL and Heijnen JJ. Critical evaluation of sampling techniques for residual glucose determination in carbon-limited chemostat culture of Saccharomyces cerevisiae. Biotechnol. Bioeng., 83: 395–399 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Mashego MR, Wu L, Van Dam JC, Ras C, Vinke JL, Van Winden WA, Van Gulik WM and Heijnen JJ. MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol. Bioeng., 85: 620–628 (2004).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Moriya H and Johnston M. Glucose sensing and signalling in Saccharomyces cerevisiae through the Rgt2 glucose sensor and casein kinase I. Proc. Natl. Acad. Sci. USA., 101: 1572–1577 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Mosley AL, Lakshmanan J, Aryal BK and Ozcan S. Glucose-mediated phosphorylation converts the transcription factor Rgtl from a repressor to an activator. J. Biol. Chem., 278: 10322–10327 (2003).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Noble ME, Endicott JA and Johnson LN. Protein kinase inhibitors: insights into drug design from structure. Science, 303: 1800–1805 (2004).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Petroski RJ and McCormick SP. Secondary-metabolite biosynthesis and metabolism, Kluwer Academic/Plenum Publishers, New York (1992).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Plaxton WC. Principles of metabolic control, in: Functional Metabolism of Cells: Control, Regulation, and Adaptation, K B. Storey, ed., John Wiley and Sons, Inc., New York, pp. 1–23 (2004).

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Rohde JR and Cardenas ME. The tor pathway regulates gene expression by linking nutrient sensing to histone acetylation. Mol. Cell Biol., 23: 629–635 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Roncal T and Ugalde U. Conidiation induction in Penicillium. Res. Microbiol., 54: 539–546 (2003).

    Article  CAS  Google Scholar 

  • Rose AH and Harrison JS. The Yeasts. Vol. 1–6. Academic Press, London (1987–1995).

    Google Scholar 

  • Saez MJ and Lagunas R. Determination of intermediary metabolites in yeast. Critical examination of the effect of sampling conditions and recommendations for obtaining true levels. Mol. Cell. Biochem., 13: 73–78 (1976).

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J and Russell D. Molecular Cloning: a laboratory manual, 3rd edition. Cold Spring Harbor Laboratory Press. Cold Spring Harbor. New York (2000).

    Google Scholar 

  • Sandelin A, Hoglund A, Lenhard B and Wasserman WW. Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes. Funct. Integr. Genomics, 3: 125–134 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Schilter B and Constable A. Regulatory control of genetically modified (GM) foods: likely developments. Toxicol. Lett., 127: 341–349 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Schmitt S and Paro R. A reason for reading nonsense. Nature, 429: 510–511 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Segre D, Zucker J, Katz J, Lin X, D’Haeseleer P, Rindone WP, Kharchenko P, Nguyen DH, Wright MA and Church GM. From annotated genomes to metabolic flux models and kinetic parameter fitting. OMICS, 7: 301–316 (2003).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Sprague GF Jr, Cullen PJ and Goehring AS. Yeast signal transduction: Regulation and interface with cell biology, in: Advances in Experimental Medicine and Biology, Vol. 547, Advances in Systems Biology, L. K. Opresko, J. M. Gephart, and M. B. Mann, eds. Kluwer Academic/Plenum Publishers, New York, pp. 91–105 (2004).

    Google Scholar 

  • Stockton GW, Aranibar N and Ott K-H. Metabolome profiling methods using chromatographic and spectroscopic data in pattern recognition analysis. World Intellectual Property Organisation, WO Patent, 02057989 (2002).

    Google Scholar 

  • Sudarsan N, Barrick JE and Breaker RR. Metabolite-binding RNA domains are present in the genes of eukaryotes. RNA, 9: 644–647 (2003).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    Google Scholar 

  • Theobald U, Mailinger W, Reuss M and Rizzi M. In vivo analysis of glucose-induced fast changes in yeast adenine nucleotide pool applying a rapid sampling technique. Anal. Biochem., 214: 31–37 (1993).

    Article  PubMed  CAS  Google Scholar 

  • Trethewey RN. Gene discovery via metabolic profiling. Curr. Opin. Biotechnol., 12: 135–138 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Trethewey RN, Krotzky AJ and Willmitzer L. Metabolic profiling: a Rosetta Stone for genomics? Curr. Opin. Plant Biol., 2: 83–85 (1999).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Vaidyanathan S, Rowland JJ, Kell DB and Goodacre R. Discrimination of aerobic endospore-forming bacteria via electrospray ionization mass spectrometry of whole cell suspensions. Anal. Chem., 73: 4134–4144 (2001).

    Article  PubMed  CAS  Google Scholar 

  • Villas-Boas SG, Delicado DG, Akesson M and Nielsen J. Simultaneous analysis of amino and nonamino organic acids as methyl chloroformate derivatives using gas chromatography-mass spectrometry. Anal. Biochem., 322: 134–138 (2003).

    Article  PubMed  CAS  Google Scholar 

  • Watkins SM and German JB. Toward the implementation of metabolomic assessments of human health and nutrition. Curr. Opin. Biotechnol., 13: 512–516 (2002).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Weckwerth W and Fiehn O. Can we discover novel pathways using metabolomic analysis? Curr. Opin. Biotechnol., 13: 156–160 (2002).

    Article  PubMed  CAS  Google Scholar 

  • Weckwerth W and Fiehn O. Combined metabolomic, proteomic and transcriptomic analysis from one, single sample and suitable statistical evaluation data. World Intellectual Property Organisation, WO Patent, 03058238 (2003).

    Google Scholar 

  • Winkler WC, Nahvi A, Roth A, Collins JA and Breaker RR. Control of gene expression by a natural metabolite-responsive ribozyme. Nature, 428: 281–286 (2004).

    Article  PubMed  CAS  Google Scholar 

  • Wu LF, Hughes TR, Davierwala AP, Robinson MD, Stoughton R and Altschuler SJ. Largescale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters. Nat. Genet., 31: 255–265 (2002).

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer Science+Business Media, Inc.

About this chapter

Cite this chapter

Castrillo, J.I., Oliver, S.G. (2005). Towards Integrative Functional Genomics Using Yeast as a Reference Model. In: Vaidyanathan, S., Harrigan, G.G., Goodacre, R. (eds) Metabolome Analyses: Strategies for Systems Biology. Springer, Boston, MA. https://doi.org/10.1007/0-387-25240-1_2

Download citation

Publish with us

Policies and ethics