Sample preparation related to the intracellular metabolome of yeast: Methods for quenching, extraction, and metabolite quantitation

Methods in Enzymology

Volumn 500, Issue , 2011, Pages 277-297

  Dunn, Warwick B ^a   Winder, Catherine L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Extraction; Mass spectrometry; Metabolism; Metabolomics; Quenching; Saccharomyces cerevisiae; Yeast

Indexed keywords

2 OXOGLUTARIC ACID; CARBOXYLIC ACID; CITRIC ACID; FUMARIC ACID; MALIC ACID; MALONIC ACID; METHANOL; ORGANIC SOLVENT; SUCCINIC ACID;

ARTICLE; BACTERIUM CULTURE; BATCH CELL CULTURE; CELL METABOLISM; CELL WALL; CHEMICAL ANALYSIS; CITRIC ACID CYCLE; EXTRACTION; GAS CHROMATOGRAPHY; INTRACELLULAR METABOLISM; MASS SPECTROMETRY; METABOLITE; METABOLOME; PH MEASUREMENT; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SOLUBILITY; YEAST;

SACCHAROMYCES CEREVISIAE;

EID: 80053085575     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385118-5.00015-3     Document Type: Chapter

References (34)

1. J. Allen, H.M. Davey, D. Broadhurst, J.K. Heald, J.J. Rowland, S.G. Oliver, and D.B. Kell High-throughput classification of yeast mutants for functional genomics using metabolic footprinting Nat. Biotechnol. 21 2003 692 696 (Pubitemid 36638098)
2. D. Barik, W.T. Baumann, M.R. Paul, B. Novak, and J.J. Tyson A model of yeast cell-cycle regulation based on multisite phosphorylation Mol. Syst. Biol. 6 2010 405
3. P. Begley, S. Francis-McIntyre, W.B. Dunn, D.I. Broadhurst, A. Halsall, A. Tseng, J. Knowles, R. Goodacre, D.B. Kell, and H. Consortium Development and performance of a gas chromatography-time-of-flight mass spectrometry analysis for large-scale nontargeted metabolomic studies of human serum Anal. Chem. 81 2009 7038 7046
4. M. Brown, W.B. Dunn, D.I. Ellis, R. Goodacre, J. Handl, J.D. Knowles, S. O'Hagan, I. Spasic, and D.B. Kell A metabolome pipeline: From concept to data to knowledge Metabolomics 1 2005 39 51 (Pubitemid 40973872)
5. A.B. Canelas, C. Ras, A. ten Pierick, J.C. van Dam, J.J. Heijnen, and W.M. Van Gulik Leakage-free rapid quenching technique for yeast metabolomics Metabolomics 4 2008 226 239
6. J.I. Castrillo, A. Hayes, S. Mohammed, S.J. Gaskell, and S.G. Oliver An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry Phytochemistry 62 2003 929 937 (Pubitemid 36262396)
7. J.I. Castrillo, L.A. Zeef, D.C. Hoyle, N. Zhang, A. Hayes, D.C.J. Gardner, M.J. Cornell, J. Petty, L. Hakes, L. Wardleworth, B. Rash, and M. Brown Growth control of the eukaryote cell: A systems biology study in yeast J. Biol. 6 4 2007
8. W. De Koning, and K. Van Dam A method for the determination of changes of glycolytic metabolites in yeast on a subsecond time scale using extraction at neutral pH Anal. Biochem. 204 1992 118 123
9. P. Dejonggubbels, P. Vanrolleghem, S. Heijnen, J.P. Vandijken, and J.T. Pronk Regulation of carbon metabolism in chemostat cultures of Saccharomyces-cerevisiae grown on mixtures of glucose and ethanol Yeast 11 1995 407 418
10. P.D. Dobson, K. Smallbone, D. Jameson, E. Simeonidis, K. Lanthaler, P. Pir, C.A. Lu, N. Swainston, W.B. Dunn, P. Fisher, D. Hull, and M. Brown Further developments towards a genome-scale metabolic model of yeast BMC Syst. Biol. 4 145 2010
11. W.B. Dunn, D.I. Broadhurst, H.J. Atherton, R. Goodacre, and J.L. Griffin Systems level studies of mammalian metabolomes: The roles of mass spectrometry and nuclear magnetic resonance spectroscopy Chem. Soc. Rev. 40 2011 387 426
12. J.C. Ewald, S. Heux, and N. Zamboni High-throughput quantitative metabolomics: Workflow for cultivation, quenching, and analysis of yeast in a multiwell format Anal. Chem. 81 2009 3623 3629
13. A. Goldberg, C. Gregg, T. Boukh-Viner, S. Bourque, P. Kyryakov, T. Guo, Z. Aziz, D. Cyr, A. Naimi, F. Negoita, A. Oluoha, and M.H. Salah Molecular systems biology of aging: Using calorie-restricted yeast as a model system for defining a modular network controlling chronological aging Mol. Cell. Proteomics 5 2006 550
14. B. Gonzalez, J. Francois, and M. Renaud A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol Yeast 13 1997 1347 1355
15. M.J. Herrgard, N. Swainston, P. Dobson, W.B. Dunn, K.Y. Arga, M. Arvas, N. Bluthgen, S. Borger, R. Costenoble, M. Heinemann, M. Hucka, and N. Le Novere A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Nat. Biotechnol. 26 2008 1155 1160
16. D.B. Kell, and S.G. Oliver 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 2003 99 105 (Pubitemid 38095354)
17. M.R. Mashego, W.M. van Gulik, J.L. Vinke, D. Visser, and J.J. Heijnen In vivo kinetics with rapid perturbation experiments in Saccharomyces cerevisiae using a second-generation BioScope Metab. Eng. 8 2006 370 383 (Pubitemid 43903305)
18. M.R. Mashego, K. Rumbold, M. De Mey, E. Vandamme, W. Soetaert, and J.J. Heijnen Microbial metabolomics: Past, present and future methodologies Biotechnol. Lett. 29 2007 1 16 (Pubitemid 44950152)
19. M.L. Mo, N. Jamshidi, and B.O. Palsson A genome-scale, constraint-based approach to systems biology of human metabolism Mol. Biosyst. 3 2007 598 603 (Pubitemid 47258225)
20. R. Mustacchi, S. Hohmann, and J. Nielsen Yeast systems biology to unravel the network of life Yeast 23 2006 227 238
21. J.K. Nicholson, and I.D. Wilson Understanding 'global' systems biology: Metabonomics and the continuum of metabolism Nat. Rev. Drug Discov. 2 2003 668 676 (Pubitemid 37361770)
22. I. Nookaew, M.C. Jewett, A. Meechai, C. Thammarongtham, K. Laoteng, S. Cheevadhanarak, J. Nielsen, and S. Bhumiratana The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: A scaffold to query lipid metabolism BMC Syst. Biol. 2 71 2008
23. K. Robards, P.R. Haddad, and P.E. Jackson Principles and Practice of Modern Chromatographic Methods 1997 Academic Press London
24. M.J. Saez, and R. Lagunas Determination of intermediary metabolites in yeast - Critical-examination of effect of sampling conditions and recommendations for obtaining true levels Mol. Cell. Biochem. 13 1976 73 78 (Pubitemid 8003119)
25. J.L. Sporty, M.M. Kabir, K.W. Turteltaub, T. Ognibene, S.J. Lin, and G. Bench Single sample extraction protocol for the quantification of NAD and NADH redox states in Saccharomyces cerevisiae J. Sep. Sci. 31 2008 3202 3211
26. J. Spura, L.C. Reimer, P. Wieloch, K. Schreiber, S. Buchinger, and D. Schomburg A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast Anal. Biochem. 394 2009 192 201
27. B. Teusink, J. Passarge, C.A. Reijenga, E. Esgalhado, C.C. van der Weijden, M. Schepper, M.C. Walsh, B.M. Bakker, K. van Dam, H.V. Westerhoff, and J.L. Snoep Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry Eur. J. Biochem. 267 2000 5313 5329
28. S.G. Villas-Boas, and P. Bruheim Cold glycerol-saline: The promising quenching solution for accurate intracellular metabolite analysis of microbial cells Anal. Biochem. 370 2007 87 97 (Pubitemid 47404490)
29. S.G. VillasBoas, J. Nielsen, J. Smedsgaard, M.A.E. Hansen, and U. RoessnerTunali Metabolome Analysis: An Introduction 2007 John Wiley and Sons New Jersey
30. S.G. Villas-Boas, J. Hojer-Pedersen, M. Akesson, J. Smedsgaard, and J. Nielsen Global metabolite analysis of yeast: Evaluation of sample preparation methods Yeast 22 2005 1155 1169 (Pubitemid 41684146)
31. T. Wiken, and O. Richard Further research on the importance of oxygen in the fermentation of glucose with wine yeast Schweiz. Z. Pathol. Bakteriol. 18 1955 970 980
32. C.L. Winder, W.B. Dunn, S. Schuler, D. Broadhurst, R. Jarvis, G.M. Stephens, and R. Goodacre Global metabolic profiling of Escherichia coli cultures: An evaluation of methods for quenching and extraction of intracellular metabolites Anal. Chem. 80 2008 2939 2948 (Pubitemid 351556459)
33. C. Wittmann, J.O. Kromer, P. Kiefer, T. Binz, and E. Heinzle Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria Anal. Biochem. 327 2004 135 139 (Pubitemid 38367993)
34. E. Zelena, W.B. Dunn, D. Broadhurst, S. Francis-McIntyre, K.M. Carroll, P. Begley, S. O'Hagan, J.D. Knowles, A. Halsall, I.D. Wilson, D.B. Kell, and Consortium Husermet Development of a robust and repeatable UPLC-MS method for the long-term metabolomic study of human serum Anal. Chem. 81 2009 1357 1364