Global metabolite analysis of yeast: Evaluation of sample preparation methods

Yeast

Volumn 22, Issue 14, 2005, Pages 1155-1169

  Villas Bôas, Silas G ^a,b   Højer Pedersen, Jesper ^a   Åkesson, Mats ^a,c   Smedsgaard, Jørn ^a   Nielsen, Jens ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b AGRESEARCH GRASSLANDS   (New Zealand)

^c NOVO NORDISK A S   (Denmark)

Author keywords

Extraction; Freeze drying; Metabolome; Metabolomics; Quenching; Sample preparation

Indexed keywords

METHANOL; SOLVENT;

ARTICLE; CELL LOSS; CELL METABOLISM; CELL SEPARATION; COLD; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; EVAPORATION; FREEZE DRYING; FUNGAL METABOLISM; HIGH THROUGHPUT SCREENING; INTRACELLULAR SPACE; METHODOLOGY; MICROBIAL DIVERSITY; NONHUMAN; PHYSICAL CHEMISTRY; PRESSURE; PRIORITY JOURNAL; RELIABILITY; YEAST CELL;

FREEZE DRYING; METHANOL; MYCOLOGY; SACCHAROMYCES CEREVISIAE; SOLVENTS;

EUKARYOTA; PROKARYOTA;

EID: 28044440100     PISSN: 0749503X     EISSN: None     Source Type: Journal    
DOI: 10.1002/yea.1308     Document Type: Article

References (42)

1. Adams MA, Chen Z, Landman P, Colmer TD. 1999. Simultaneous determination by capillary gas chromatography of organic acids, sugars, and sugar alcohols in plant tissue extracts as their trimethylsilyl derivatives. Anal Biochem 266: 77-84.
2. Alfenore S, Délia ML, Strehaiano P. 2003. Use of ATP measurements by bioluminescence to quantify yeast's sensitivity against a killer toxin. Anal Chim Acta 495: 217-224.
3. Bouchereau A, Guénot P, Larher F. 2000. Analysis of amines in plant materials. J Chromatogr B 747: 49-67.
4. Buchholz A, Hurlebaus J, Wandrey C, Takors R. 2002. Metabolomics: quantification of intracellular metabolite dynamics. Biomol Eng 19: 5-15.
5. Buziol S, Bashir I, Baumeister A, et al. 2002. New bioreactor-coupled rapid stopped-flow sampling technique for measurements of metabolite dynamics on a subsecond time scale. Biotechnol Bioeng 80: 632-636.
6. Castrillo JI, Hayes A, Mohammed S, Gaskell SJ, Oliver SG. 2003. An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 62: 929-937.
7. Chen Z, Landman P, Colmer TD, Adams MA. 1998. Simultaneous analysis of amino and organic acids in extracts of plant leaves as tert-butyldimethylsilyl derivatives by capillary gas chromatography. Anal Biochem 259: 203-211.
8. Conneely A, Nugent A, O'Keeffe M. 2002. Use of solid phase extraction for the isolation and clean up of a derivatized furazolidone metabolite from animal tissues. Analyst 127: 705-709.
9. Cordeiro C, Freire AP. 1996. Methylglyoxal assay in cells as 2-methylquinoxaline using 1,2-diaminobenzene as derivatizing reagent. Anal Biochem 234: 221-224.
10. Cremin P, Donnelly DMX, Wolfender JL, Hostettmann K. 1995. Liquid chromatography-thermospray mass spectrometric analysis of sesquiterpenes of Armillaria (Eumycota: Basidiomycotina) species. J Chromatogr A 710: 273-285.
11. de Koning W, van Dam K. 1992. 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: 118-123.
12. Entian KD, Zimmermann FK, Scheel I. 1977. A partial defect in carbon catabolite repression mutants of Saccharomyces cerevisiae with reduced hexose phosphorylation. Mol Gen Genet 156: 99-105.
13. Folch J, Lees M, Stanley GH. 1957. A simple method for the isolation and purification of total lipids from animal tissue. Biol Chem 226: 497-509.
14. Gonzalez B, François J, Renaud M. 1997. A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast 13: 1347-1356.
15. 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.
16. Hajjaj H, Blanc PJ, Goma G, François J. 1998. Sampling techniques and comparative extraction procedures for quantitative determination of intra- and extracellular metabolites in filamentous fungi. FEMS Microbiol Lett 164: 195-200.
17. Hans MA, Heinzle E, Wittmann C. 2001. Quantification of intracellular amino acids in batch cultures of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 56: 776-779.
18. Jensen NB, Jokumsen KV, Villadsen J. 1999. Determination of the phosphorylated sugars of the Embden-Meyerhoff-Parnas pathway in Lactococcus lactis using a fast sampling technique and solid phase extraction. Biotechnol Bioeng 63: 357-362.
19. Kell DB. 2004. Metabolomics and systems biology: making sense of the soup. Curr Opin Microbiol 7: 296-307.
20. Kopka J, Ohlrogge JB, Jaworski JG. 1995. Analysis of in vivo levels of acyl-thioesters with gas chromatography/mass spectrometry of the butylamide derivative. Anal Biochem 224: 51-60.
21. Lange HC, Eman M, van Zuijlen G, et al. 2001. Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiae. Biotechnol Bioeng 75: 406-415.
22. 1H-NMR spectrometry. NMR Biomed 15: 37-44.
23. Letisse F, Lindley ND. 2000. An intracellular metabolite quantification technique applicable to polysaccharide-producing bacteria. Biotechnol Lett 22: 1673-1677.
24. Maharjan RP, Ferenci T. 2003. Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal Biochem 313: 145-154.
25. Martins AM, Cordeiro CA, Ponces Freire AM. 2001. In situ analysis of methylglyoxal metabolism in Saccharomyces cerevisiae. FEBS Lett 499: 41-44.
26. Mashego MR, Wu L, van Dam JC, et al. 2004. Miracle: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotech Bioeng 85: 620-628.
27. Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L. 2000. Simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23: 131-142.
28. Ruijter GJ, Visser J. 1996. Determination of intermediary metabolites in Aspergillus niger. J Microbiol Methods 25: 295-302.
29. Schaefer U, Boos W, Takors R, Weuster-Botz D. 1999. Automated sampling device for monitoring intracellular metabolite dynamics. Anal Biochem 270: 88-96.
30. Shryock JC, Rubio R, Berne RM. 1986. Extraction of adenine nucleotides from cultured endothelial cells. Anal Biochem 159: 73-81.
31. Smits HP, Cohen A, Buttler T, Nielsen J, Olsson L. 1998. Cleanup and analysis of sugar phosphates in biological extracts by using solid-phase extraction and anion-exchange chromatography with pulsed amperometric detection. Anal Biochem 261: 36-42.
32. Soga T, Ueno Y, Naraoka H, et al. 2002. Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem 74: 2233-2239.
33. Tweeddale H, Notley-Mcrobb L, Ferenci T. 1998. Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ('metabolome') analysis. J Bacteriol 180: 5109-5116.
34. van Dam JC, Eman MR, Frank J, et al. 2002. Analysis of glycolytic intermediates in Saccharomyces cerevisiae using anion exchange chromatography and electrospray ionization with tandem mass spectrometric detection. Anal Chim Acta 460: 209-218.
35. van der Greef J, van der Heijden R, Verheij ER. 2004. The role of mass spectrometry in systems biology: data processing and identification strategies in metabolomics. In Advances in Mass Spectrometry, vol 16, Ashcroft AE, Brenton G, Monaghan JJ (eds). Elsevier: Amsterdam; 145-165.
36. Vaseghi S, Baumeister A, Rizzi M, Reuss M. 1999. In vivo dynamics of pentose phosphate pathway in Saccharomyces cerevisiae. Metabolic Eng 1: 128-140.
37. Verduyn C, Postma E, Scheffers WA, van Dijken JP. 1992. Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
38. Villas-Bôas SG, Moxley JF, Åkesson M, Stephanopoulos G, Nielsen J. 2005. High-throughput metabolite state analysis: the missing link in integrated functional genomics. Biochem J 388: 669-677.
39. Visser D, van Zuylen GA, van Dam JC, et al. 2002. Rapid sampling for analysis of in vivo kinetics using the BioScope: a system for continuous-pulse experiments. Biotechnol Bioeng 79: 674-681.
40. Weuster-Botz D. 1997. Sampling tube device for monitoring intracellular metabolite dynamics. Anal Biochem 246: 225-233.
41. Wittmann C, Krömer JO, Kiefer P, Binz T, Heinzle E. 2004. Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria. Anal Biochem 327: 135-139.
42. Zaldivar J, Borges A, Johansson B, et al. 2002. Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose-fermenting Saccharomyces cerevisiae. Appl Microbiol Biotechnol 59: 436-442.