Advertisement

Metabolomics for Ethanologenic Yeast

Chapter
Part of the Microbiology Monographs book series (MICROMONO, volume 22)

Abstract

Metabolomics-based studies have been applied widely to improve our understanding of molecular mechanisms of yeast stress response as well as to seek foundational basis for further optimization of fermentation processes. In this chapter, the basic principles of metabolomic approaches including sample preparation, metabolomic analysis, metabolite identification and quantification, data mining, and biological interpretation are summarized, emphasizing on the gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled to mass spectrometry (LC-MS) based strategies. The major applications of metabolomics on ethanologenic yeast during ethanol production are highlighted, such as stress response to high cell density, inhibitory compounds in the lignocellulosic hydrolysates, different (batch and continuous) fermentation modes, and vacuum fermentation conditions.

Keywords

Partial Little Square Batch Fermentation Inoculum Density Metabolomic Analysis Furan Aldehyde 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

The authors are grateful for the financial support from the National Basic Research Program of China (“973” Program: 2007CB714301, 2011CBA00802), and the National Natural Science Foundation of China (Key Program: 20736006, Major International Joint Research Project: 21020102040).

References

  1. Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB (2003) High-throughput classification of yeast mutants for functional genomics via metabolic footprinting. Nat Biotechnol 21:692–696PubMedCrossRefGoogle Scholar
  2. Askenazi M, Driggers EM, Holtzman DA, Norman TC, Iverson S, Zimmer DP, Boers ME, Blomquist PR, Martinez EJ, Monreal AW, Feibelman TP, Mayorga ME, Maxon ME, Sykes K, Tobin JV, Cordero E, Salama SR, Trueheart J, Royer JC, Madden KT (2003) Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat Biotechnol 21:150–156PubMedCrossRefGoogle Scholar
  3. Attfield PV (1997) Stress tolerance: the key to effective strains of industrial baker’s yeast. Nat Biotechnol 15:1351–1357PubMedCrossRefGoogle Scholar
  4. Bai FW, Anderson WA, Moo-Young M (2008) Ethanol fermentation technologies from sugar and starch feedstocks. Biotechnol Adv 26:89–105PubMedCrossRefGoogle Scholar
  5. Brewster JL, de Valoir T, Dwyer ND, Winter E, Gustin MC (1993) An osmosensing signal transduction pathway in yeast. Science 259:1760–1763PubMedCrossRefGoogle Scholar
  6. Brindle JT, Antti H, Holmes E, Tranter G, Nicholson JK, Bethell HW, Clarke S, Schofield PM, McKilligin E, Mosedale DE, Grainger DJ (2002) Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat Med 8:1439–1444PubMedCrossRefGoogle Scholar
  7. Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD (2006) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34:511–516CrossRefGoogle Scholar
  8. Cheng JS, Ding MZ, Tian HC, Yuan YJ (2009a) Inoculation density-dependent responses and pathway shifts in Saccharomyces cerevisiae. Proteomics 9:4704–4713PubMedCrossRefGoogle Scholar
  9. Cheng JS, Zhou X, Ding MZ, Yuan YJ (2009b) Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Appl Microbiol Biotechnol 83:909–923PubMedCrossRefGoogle Scholar
  10. Corte L, Rellini P, Roscini L, Fatichenti F, Cardinali G (2010) Development of a novel, FTIR (Fourier transform infrared spectroscopy) based, yeast bioassay for toxicity testing and stress response study. Anal Chim Acta 659:258–265PubMedCrossRefGoogle Scholar
  11. Cowart LA, Shotwell M, Worley ML, Richards AJ, Montefusco DJ, Hannun YA, Lu X (2010) Revealing a signaling role of phytosphingosine-1-phosphate in yeast. Mol Syst Biol 6:349PubMedCrossRefGoogle Scholar
  12. Cysewski GR, Wilke CR (1977) Rapid ethanol fermentations using vacuum and cell cycle. Biotechnol Bioeng 19:1125–1143CrossRefGoogle Scholar
  13. Davis RA, Charlton AJ, Godward J, Jones SA, Harrison M, Wilson JC (2007) Adaptive binning: an improved binning method for metabolomics data using the undecimated wavelet transform. Chemom Intell Lab Syst 85:144–154CrossRefGoogle Scholar
  14. de Koning W, van Dam K (1992) A method for the determinations of changes of glycolytic metabolites in yeast on a sub second time scale using extraction at neutral pH. Anal Biochem 204:118–123PubMedCrossRefGoogle Scholar
  15. Devantier R, Scheithauer B, Villas-Bôas SG, Pedersen S, Olsson L (2005) Metabolite profiling for analysis of yeast stress response during very high gravity ethanol fermentations. Biotechnol Bioeng 90:703–714PubMedCrossRefGoogle Scholar
  16. Ding MZ, Tian HC, Cheng JS, Yuan YJ (2009a) Inoculum size-dependent interactive regulation of metabolism and stress response of Saccharomyces cerevisiae revealed by comparative metabolomics. J Biotechnol 144:279–286PubMedCrossRefGoogle Scholar
  17. Ding MZ, Cheng JS, Xiao WH, Qiao B, Yuan YJ (2009b) Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF/MS. Metabolomics 5:229–238CrossRefGoogle Scholar
  18. Ding MZ, Zhou X, Yuan YJ (2010a) Metabolome profiling reveals adaptive evolution of Saccharomyces cerevisiae during repeated vacuum fermentations. Metabolomics 6:42–55CrossRefGoogle Scholar
  19. Ding MZ, Li BZ, Cheng JS, Yuan YJ (2010b) Metabolome analysis of differential responses of diploid and haploid yeast to ethanol stress. OMICS 14:553–561PubMedCrossRefGoogle Scholar
  20. Ding MZ, Wang X, Yang Y, Yuan YJ (2011) Comparative metabolic profiling of parental and inhibitors-tolerant yeasts during lignocellulosic ethanol fermentation. Metabolomics. doi: 10.1007/s11306-011-0303-6
  21. Fiehn O (2002) Metabolomics-the link between genotypes and phenotypes. Plant Mol Biol 48:155–171PubMedCrossRefGoogle Scholar
  22. Fonseca ES, Guido RC, Scalassara PR, Maciel CD, Pereira JC (2007) Wavelet time-frequency analysis and least squares support vector machines for the identification of voice disorders. Comput Biol Med 37:571–578PubMedCrossRefGoogle Scholar
  23. Garcia DE, Baidoo EE, Benke PI, Pingitore F, Tang YJ, Villa S, Keasling JD (2008) Separation and mass spectrometry in microbial metabolomics. Curr Opin Microbiol 11:233–239PubMedCrossRefGoogle Scholar
  24. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241–4257PubMedCrossRefGoogle Scholar
  25. Gaspar ML, Aregullin MA, Jesch SA, Nunez LR, Villa-Garcia M, Henry SA (2007) The emergence of yeast lipidomics. Biochim Biophys Acta 1771:241–254PubMedCrossRefGoogle Scholar
  26. Gonzalez B, Francois J, Renaud M (1997) A rapid and reliable method for metabolite extraction in yeast using boiling buffered ethanol. Yeast 13:1347–1356PubMedCrossRefGoogle Scholar
  27. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22:245–252PubMedCrossRefGoogle Scholar
  28. Hajjaj H, Blanc PJ, Goma G, Francois J (1998) Sampling techniques and comparative extraction procedures for quantitative determination of intra- and extracellular metabolites in filamentous fungi. FEMS Microbiol Lett 164:195–200CrossRefGoogle Scholar
  29. Halket JM, Waterman D, Przyborowska AM, Patel RK, Fraser PD, Bramley PM (2005) Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J Exp Bot 56:219–243PubMedCrossRefGoogle Scholar
  30. Han PP, Yuan YJ (2009) Lipidomic analysis reveals activation of phospholipid signaling in mechanotransduction of Taxus cuspidata cells in response to shear stress. FASEB J 23:623–630PubMedCrossRefGoogle Scholar
  31. Hans MA, Heinzle E, Wittmann C (2001) Quantification of intracellular amino acids in batch cultures of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 56:776–779PubMedCrossRefGoogle Scholar
  32. Hill J, Nelson E, Tilman D, Polasky S, Tiffany D (2006) Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci USA 103:11206–11210PubMedCrossRefGoogle Scholar
  33. Hohmann S (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66:300–372PubMedCrossRefGoogle Scholar
  34. Ingram LO, Buttke TM (1984) Effects of alcohols on microorganisms. Adv Microb Physiol 25:253–300PubMedCrossRefGoogle Scholar
  35. Ivanova PT, Cerda BA, Horn DM, Cohen JS, McLafferty FW, Brown HA (2001) Electrospray ionization mass spectrometry analysis of changes in phospholipids in RBL-2 H3 mastocytoma cells during degranulation. Proc Natl Acad Sci USA 98:7152–7157PubMedCrossRefGoogle Scholar
  36. Jansen JJ, Hoefsloot HCJ, Boelens HFM, van der Greef J, Smilde AK (2004) Analysis of longitudinal metabolomics data. Bioinformatics 20:2438–2446PubMedCrossRefGoogle Scholar
  37. Kawai S, Phan TA, Kono E, Harada K, Okai C, Fukusaki E, Murata K (2009) Transcriptional and metabolic response in yeast Saccharomyces cerevisiae cells during polyethylene glycol-dependent transformation. J Basic Microbiol 49:73–81PubMedCrossRefGoogle Scholar
  38. Klinke HB, Thomsen AB, Ahring BK (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Appl Microbiol Biotechnol 66:10–26PubMedCrossRefGoogle Scholar
  39. Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmuller E, Dormann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D (2005) GMD@CSB.DB: the Golm metabolome database. Bioinformatics 21:1635–1638PubMedCrossRefGoogle Scholar
  40. Lafaye A, Junot C, Pereira Y, Lagniel G, Tabet JC, Ezan E, Labarre J (2005) Combined proteome and metabolite-profiling analyses reveal surprising insights into yeast sulfur metabolism. J Biol Chem 280:24723–24730PubMedCrossRefGoogle Scholar
  41. Lei J, Zhao X, Ge X, Bai F (2007) Ethanol tolerance and the variation of plasma membrane composition of yeast floc populations with different size distribution. J Biotechnol 131:270–275PubMedCrossRefGoogle Scholar
  42. Li BZ, Yuan YJ (2010c) Transcriptome shifts in response to furfural and acetic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 86:1915–1924PubMedCrossRefGoogle Scholar
  43. Li BZ, Cheng JS, Qiao B, Yuan YJ (2010a) Genome-wide transcriptional analysis of Saccharomyces cerevisiae during industrial bioethanol fermentation. J Ind Microbiol Biotechnol 37:43–55PubMedCrossRefGoogle Scholar
  44. Li BZ, Cheng JS, Ding MZ, Yuan YJ (2010b) Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress. J Biotechnol 148:194–203PubMedCrossRefGoogle Scholar
  45. Lin FM, Tang Y, Yuan YJ (2009) Temporal quantitative proteomics of Saccharomyces cerevisiae in response to a nonlethal concentration of furfural. Proteomics 9:5471–5483PubMedCrossRefGoogle Scholar
  46. Lindon JC, Holmes E, Nicholson JK (2001) Pattern recognition methods and applications in biomedical magnetic resonance. Prog Nucl Magn Reson Spectrosc 39:1–40CrossRefGoogle Scholar
  47. Liu ZL, Blaschek HP (2010) Biomass conversion inhibitors and in situ detoxification. In: Vertes A, Qureshi N, Yukawa H, Blaschek H (eds) Biomass to biofuels: strategies for global industries. Wiley, West Sussex, pp 233–258CrossRefGoogle Scholar
  48. Maharjan RP, Ferenci T (2003) Global metabolite analysis: the influence of extraction methodology on metabolome profiles of Escherichia coli. Anal Biochem 313:145–154PubMedCrossRefGoogle Scholar
  49. Maiorella B, Blanch HW, Wilke CR (1983) By-product inhibition effects of ethanolic fermentation by Saccharomyces cerevisiae. Biotechnol Bioeng 25:103–121PubMedCrossRefGoogle Scholar
  50. Mannazzu I, Angelozzi D, Budroni M, Farris GA, Gofffini P, Lodi T, Marzona M, Bardi L, Belviso S (2008) Behaviour of Saccharomyces cerevisiae wine strains during adaptation to unfavourable conditions of fermentation on synthetic medium: Cell lipid composition, membrane integrity, viability and fermentative activity. Int J Food Microbiol 121:84–91PubMedCrossRefGoogle Scholar
  51. Martinez A, Rodriguez ME, Wells ML, York SW, Preston JF, Ingram LO (2001) Detoxification of dilute acid hydrolysates of lignocellulose with lime. Biotechnol Prog 17:287–293PubMedCrossRefGoogle Scholar
  52. Mosier N, Wyman C, Dale B, Elander R, Lee YY, Holtzapple M, Ladisch M (2005) Features of promising technologies for pretreatment of lignocellulosic biomass. Bioresour Technol 96:673–686PubMedCrossRefGoogle Scholar
  53. Nielsen KF, Smedsgaard J, Larsen TO, Lund F, Thrane U, Frisvad JC (2003) Chemical identification of fungi: metabolite profiling and metabolomics. In: Arora DK (ed) Fungal biotechnology in agricultural, food, and environmental applications. Marcel Dekker, New York, pp 19–35Google Scholar
  54. Niessen WMA (1998) Advances in instrumentation in liquid chromatography mass spectrometry and related liquid-introduction techniques. J Chromatogr A 794:407–435PubMedCrossRefGoogle Scholar
  55. Paley SM, Karp PD (2006) The pathway tools cellular overview diagram and omics viewer. Nucleic Acids Res 34:3771–3778PubMedCrossRefGoogle Scholar
  56. Palmqvist E, Hahn-Hagerdal B (2000) Fermentation of lignocellulosic hydrolysates. II: inhibitors and mechanisms of inhibition. Bioresour Technol 74:25–33CrossRefGoogle Scholar
  57. Park JH, Lee SY, Kim TY, Kim HU (2008) Application of systems biology for bioprocess development. Trends Biotechnol 26:404–412PubMedCrossRefGoogle Scholar
  58. Pittner S, Kamarthi SV (1999) Feature extraction from wavelet coefficients for pattern recognition tasks. IEEE Trans Pattern Anal 21:83–88CrossRefGoogle Scholar
  59. Plumb RS, Johnson KA, Rainville P, Smith BW, Wilson ID, Castro-Perez JM, Nicholson JK (2006) UPLIC/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom 20:1989–1994PubMedCrossRefGoogle Scholar
  60. Roessner U, Wagner C, Kopka J, Trethewey RN, Willmitzer L (2000) Technical advance: simultaneous analysis of metabolites in potato tuber by gas chromatography-mass spectrometry. Plant J 23:131–142PubMedCrossRefGoogle Scholar
  61. Russell NJ, Evans RI, ter Steeg PF, Hellemons J, Verheul A, Abee T (1995) Membranes as a target for stress adaptation. Int J Food Microbiol 28:255–261PubMedCrossRefGoogle Scholar
  62. Scholz M, Gatzek S, Sterling A, Fiehn O, Selbig J (2004) Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20:2447–2454PubMedCrossRefGoogle Scholar
  63. Sen R, Swaminathan T (2004) Response surface modeling and optimization to elucidate and analyze the effects of inoculum age and size on surfactin production. Biochem Eng J 21:141–148CrossRefGoogle Scholar
  64. Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27:747–751PubMedCrossRefGoogle Scholar
  65. Stephanopoulos G, Alper H, Moxley J (2004) Exploiting biological complexity for strain improvement through systems biology. Nat Biotechnol 22:1261–1267PubMedCrossRefGoogle Scholar
  66. Takagi H (2008) Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications. Appl Microbiol Biotechnol 81:211–223PubMedCrossRefGoogle Scholar
  67. Takayama K, Fujikawa M, Nagai T (1999) Artificial neural network as a novel method to optimize pharmaceutical formulations. Pharm Res 16:1–6PubMedCrossRefGoogle Scholar
  68. Tanaka Y, Higashi T, Rakwal R, Wakida S, Iwahashi H (2007) Quantitative analysis of sulfur-related metabolites during cadmium stress response in yeast by capillary electrophoresis-mass spectrometry. J Pharm Biomed Anal 44:608–613PubMedCrossRefGoogle Scholar
  69. Turk M, Mejanelle L, Sentjurc M, Grimalt JO, Gunde-Cimerman N, Plemenitas A (2004) Salt-induced changes in lipid composition and membrane fluidity of halophilic yeast-like melanized fungi. Extremophiles 8:53–61PubMedCrossRefGoogle Scholar
  70. 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 180:5109–5116PubMedGoogle Scholar
  71. Urbanczyk-Wochniak E, Luedemann A, Kopka J, Selbig J, Roessner-Tunali U, Willmitzer L, Fernie AR (2003) Parallel analysis of transcript and metabolic profiles: a new approach in systems biology. EMBO Rep 4:989–993PubMedCrossRefGoogle Scholar
  72. Van Dijken JP, Scheffers WA (1986) Redox balances in the metabolism of sugars by yeasts. FEMS Microbiol Rev 32:199–224Google Scholar
  73. Van Hoek P, de Hulster E, Van Dijken JP, Pronk JT (2000) Fermentative capacity in high-cell-density fed-batch cultures of baker’s yeast. Biotechnol Bioeng 68:517–523PubMedCrossRefGoogle Scholar
  74. Van Mispelaar VG, Tas AC, Smilde AK, Schoenmakers PJ, van Asten AC (2003) Quantitative analysis of target components by comprehensive two-dimensional gas chromatography. J Chromatogr A 1019:15–29PubMedCrossRefGoogle Scholar
  75. Villas-Bôas SG, Hojer-Pedersen J, Akesson M, Smedsgaard J, Nielsen J (2005) Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 22:1155–1169PubMedCrossRefGoogle Scholar
  76. Ward JL, Harris C, Lewis J, Beale MH (2003) Assessment of H-1 NMR spectroscopy and multivariate analysis as a technique for metabolite fingerprinting of Arabidopsis thaliana. Phytochemistry 62:949–957PubMedCrossRefGoogle Scholar
  77. Weeks ME, Sinclair J, Butt A, Chung YL, Worthington JL, Wilkinson CR, Griffiths J, Jones N, Waterfield MD, Timms JF (2006) A parallel proteomic and metabolomic analysis of the hydrogen peroxide- and Sty1p-dependent stress response in Schizosaccharomyces pombe. Proteomics 6:2772–2796PubMedCrossRefGoogle Scholar
  78. 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 327:135–139PubMedCrossRefGoogle Scholar
  79. Wolf C, Quinn PJ (2008) Lipidomics: practical aspects and applications. Prog Lipid Res 47:15–36PubMedCrossRefGoogle Scholar
  80. Xia JM, Yuan YJ (2009) Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid. J Agr Food Chem 57:99–108CrossRefGoogle Scholar
  81. Xia JM, Wu XJ, Yuan YJ (2007) Integration of wavelet transform with PCA and ANN for metabolomics data-mining. Metabolomics 3:531–537CrossRefGoogle Scholar
  82. Xia JM, Jones AD, Lau MW, Yuan YJ, Dale BE, Balan V (2010) Comparative lipidomic profiling of xylose-metabolizing S. cerevisiae and its parental strain in different media reveals correlations between membrane lipids and fermentation capacity. Biotechnol Bioeng 108:12–21CrossRefGoogle Scholar
  83. Yang S, Qiao B, Lu SH, Yuan YJ (2007) Comparative lipidomics analysis of cellular development and apoptosis in two Taxus cell lines. Biochim Biophys Acta 1771:600–612PubMedCrossRefGoogle Scholar
  84. Zhang W, Li F, Nie L (2010) Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies. Microbiology 156:287–301PubMedCrossRefGoogle Scholar
  85. Zhou X, Zhou J, Tian HC, Yuan YJ (2010) Dynamic lipidomic insights into the adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. OMICS 14:563–574PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.Key Laboratory of Systems BioengineeringMinistry of EducationTianjinChina
  2. 2.Department of Pharmaceutical Engineering School of Chemical Engineering and TechnologyTianjin UniversityTianjinChina

Personalised recommendations