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Metabolome profiling reveals adaptive evolution of Saccharomyces cerevisiae during repeated vacuum fermentations

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Abstract

The adaptive evolution of Saccharomyces cerevisiae to repeated vacuum fermentations was investigated by metabolomic analysis using gas chromatography coupled to time-of-flight mass spectrometry. The first round (VFI, 30 cycles) and second round (VFII, 10 cycles) of repeated fermentations could be clearly distinguished by principal components analysis on intracellular metabolites, indicating that significant difference of metabolic states occurred between them. Further investigation revealed that higher levels of glycerol, trehalose, myo-inositol and glutamate might be involved in response to vacuum stress during initial cycles, while the decreases in their levels indicated that yeast cells adapted to vacuum condition as the fermentation progressed. Furthermore, lower levels of glycerol, myo-inositol, trehalose and glutamate during VFII indicated that the adapted yeast represented better vacuum tolerance. Additionally, glycolysis and TCA cycle intermediates were enhanced whereas glycerol biosynthesis was depressed by vacuum. The decreases of most amino acids might be related to increases in intermediates of glycolysis and TCA cycle as VFI progressed. These findings provided new insights into underlying mechanisms in adaptive evolution of yeast under vacuum condition.

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References

  • Alexandre, H., Ansanay-Galeote, V., Dequin, S., & Blondin, B. (2001). Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Letters, 498, 98–103.

    Article  CAS  PubMed  Google Scholar 

  • Attfield, P. V. (1997). Stress tolerance: the key to effective strains of industrial baker’s yeast. Nature Biotechnology, 15, 1351–1357.

    Article  CAS  PubMed  Google Scholar 

  • Balazs, R., Machiyama, Y., Hammond, B. J., Julian, T., & Richter, D. (1970). The operation of the 4-aminobutyrate bypath of the tricarboxylic acid cycle in the brain tissue in vitro. Biochemical Journal, 116, 445–467.

    CAS  PubMed  Google Scholar 

  • Blomberg, A., & Adler, L. (1989). Roles of glycerol and glycerol-3-phosphate dehydrogenase (NAD+) in acquired osmotolerance of Saccharomyces cerevisiae. Journal of Bacteriology, 171, 1087–1092.

    CAS  PubMed  Google Scholar 

  • Brandriss, M. C. (1983). Proline utilization in Saccharomyces cerevisiae: analysis of the cloned PUT2 gene. Molecular and Cellular Biology, 3, 1846–1856.

    CAS  PubMed  Google Scholar 

  • Brandriss, M. C., & Falvey, D. A. (1992). Proline biosynthesis in Saccharomyces cerevisiae: analysis of the PRO3 gene, which encodes Δ1-pyrroline-5-carboxylate reductase. Journal of Bacteriology, 174, 3782–3788.

    CAS  PubMed  Google Scholar 

  • Brewster, J. L., de Valoir, T., Dwyer, N. D., Winter, E., & Gustin, M. C. (1993). An osmosensing signal transduction pathway in yeast. Science, 259, 1760–1763.

    Article  CAS  PubMed  Google Scholar 

  • Caridi, A. (2002). Protective agents used to reverse the metabolic changes induced in wine yeasts by concomitant osmotic and thermal stress. Letters in Applied Microbiology, 35, 98–101.

    Article  CAS  PubMed  Google Scholar 

  • Cheng, J. S., Qiao, B., & Yuan, Y. J. (2008). Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation. Applied Microbiology and Biotechnology, 81, 327–338.

    Article  CAS  PubMed  Google Scholar 

  • Cheng, J. S., Zhou, X., Ding, M. Z., & Yuan, Y. J. (2009). Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Applied Microbiology and Biotechnology, 83, 909–923.

    Article  CAS  PubMed  Google Scholar 

  • Cysewski, G. R., & Wilke, C. R. (1977). Rapid ethanol fermentations using vacuum and cell cycle. Biotechnology and Bioengineering, 19, 1125–1143.

    Article  CAS  Google Scholar 

  • Devantier, R., Scheithauer, B., Villas-Bôas, S. G., Pedersen, S., & Olsson, L. (2005). Metabolite profiling for analysis of yeast stress response during very high gravity ethanol fermentations. Biotechnology and Bioengineering, 90, 703–714.

    Article  CAS  PubMed  Google Scholar 

  • Ding, M. Z., Cheng, J. S., Xiao, W. H., Qiao, B., & Yuan, Y. J. (2009). Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF-MS. Metabolomics, 5, 229–238.

    Article  CAS  Google Scholar 

  • Dinh, T. N., Nagahisa, K., Hirasawa, T., Furusawa, C., & Shimizu, H. (2008). Adaptation of Saccharomyces cerevisiae cells to high ethanol concentration and changes in fatty acid composition of membrane and cell size. PLoS One, 3, e2623.

    Article  PubMed  Google Scholar 

  • Estruch, F. (2000). Stress-controlled transcription factors, stress-induced genes and stress tolerance in budding yeast. FEMS Microbiology Reviews, 24, 469–486.

    Article  CAS  PubMed  Google Scholar 

  • Fiehn, O. (2002). Metabolomics–the link between genotypes and phenotypes. Plant Molecular Biology, 48, 155–171.

    Article  CAS  PubMed  Google Scholar 

  • Fiehn, O., Kopka, J., Dormann, P., Altmann, T., Trethewey, R. N., & Willmitzer, L. (2000). Metabolite profiling for plant functional genomics. Nature Biotechnology, 18, 1157–1161.

    Article  CAS  PubMed  Google Scholar 

  • Fornairon-Bonnefond, C., Demaretz, V., Rosenfeld, E., & Salmon, J. M. (2002). Oxygen addition and sterol synthesis in Saccharomyces cerevisiae during enological fermentation. Journal of Bioscience and Bioengineering, 93, 176–182.

    Article  CAS  PubMed  Google Scholar 

  • Francois, J., & Parrou, J. L. (2001). Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiology Reviews, 25, 125–145.

    Article  CAS  PubMed  Google Scholar 

  • Franzen, C. J. (2003). Metabolic flux analysis of RQ-controlled microaerobic ethanol production by Saccharomyces cerevisiae. Yeast, 20, 117–132.

    Article  CAS  PubMed  Google Scholar 

  • Furukawa, K., Kitano, H., Mizoguchi, H., & Hara, S. (2004). Effect of cellular inositol content on ethanol tolerance of Saccharomyces cerevisiae in sake brewing. Journal of Bioscience and Bioengineering, 98, 107–113.

    CAS  PubMed  Google Scholar 

  • Garcia, D. E., Baidoo, E. E., Benke, P. I., et al. (2008). Separation and mass spectrometry in microbial metabolomics. Current Opinion in Microbiology, 11, 233–239.

    Article  CAS  PubMed  Google Scholar 

  • Grant, C. M., MacIver, F. H., & Daves, I. W. (1996). Glutathione is an essential metabolite required for resistance to oxidative stress in the yeast Saccharomyces cerevisiae. Current Genetics, 29, 511–515.

    Article  CAS  PubMed  Google Scholar 

  • Graves, T., Narendranath, N. V., Dawson, K., & Power, R. (2007). Interaction effects of lactic acid and acetic acid at different temperatures on ethanol production by Saccharomyces cerevisiae in corn mash. Applied Microbiology and Biotechnology, 73, 1190–1196.

    Article  CAS  PubMed  Google Scholar 

  • Gustin, M. C., Albertyn, J., Alexander, M., & Davenport, K. (1998). MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews, 62, 1264–1300.

    CAS  PubMed  Google Scholar 

  • Han, P. P., & Yuan, Y. J. (2009a). Metabolic profiling as a tool for understanding defense response of Taxus cuspidata cells to shear stress. Biotechnology Progress. doi 10.1021/bp.209 [Epub ahead of print].

  • Han, P. P., & Yuan, Y. J. (2009b). Lipidomic analysis reveals activation of phospholipid signaling in mechanotransduction of Taxus cuspidata cells in response to shear stress. The FASEB Journal, 23, 623–630.

    Article  CAS  PubMed  Google Scholar 

  • Hernández, F., Portolés, T., Pitarch, E., & López, F. J. (2009). Searching for anthropogenic contaminants in human breast adipose tissues using gas chromatography-time-of-flight mass spectrometry. Journal of Mass Spectrometry, 44, 1–11.

    Article  PubMed  Google Scholar 

  • Hohmann, S. (2002). Osmotic stress signaling and osmoadaptation in yeasts. Microbiology and Molecular Biology Reviews, 66, 300–372.

    Article  CAS  PubMed  Google Scholar 

  • Ingram, L. O., & Buttke, T. M. (1984). Effects of alcohols on microorganisms. Advances in Microbial Physiology, 25, 253–300.

    Article  CAS  PubMed  Google Scholar 

  • Jouhten, P., Rintala, E., Huuskonen, A., et al. (2008). Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113–1A. BMC Systems Biology, 2, 60.

    Article  PubMed  Google Scholar 

  • Kaino, T., & Takagi, H. (2008). Gene expression profiles and intracellular contents of stress protectants in S. cerevisiae under ethanol and sorbitol stresses. Applied Microbiology and Biotechnology, 79, 273–283.

    Article  CAS  PubMed  Google Scholar 

  • Lloyd, D., Morrell, S., Carlsen, H. N., Degn, H., James, P. E., & Rowlands, C. C. (1993). Effects of growth with ethanol on fermentation and membrane fluidity of Saccharomyces cerevisiae. Yeast, 9, 825–833.

    Article  CAS  PubMed  Google Scholar 

  • MacKenzie, D. A., Defernez, M., Dunn, W. B., et al. (2008). Relatedness of medically important strains of Saccharomyces cerevisiae as revealed by phylogenetics and metabolomics. Yeast, 25, 501–512.

    Article  CAS  PubMed  Google Scholar 

  • Maiorella, B., Blanch, H. W., & Wilke, C. R. (1983). By-product inhibition effects of ethanolic fermentation by Saccharomyces cerevisiae. Biotechnology and Bioengineering, 25, 103–121.

    Article  CAS  PubMed  Google Scholar 

  • Maiorella, B., & Wilke, C. R. (1980). Energy requirements for the vacuferm process. Biotechnology and Bioengineering, 22, 1749–1751.

    Article  CAS  Google Scholar 

  • Mannazzu, I., Angelozzia, D., Belviso, S., et al. (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. International Journal of Food Microbiology, 121, 84–91.

    Article  CAS  PubMed  Google Scholar 

  • Mansure, J. J., Panek, A. D., Crowe, J. M., & Crowe, J. H. (1994). Trehalose inhibits ethanol effects on intact yeast cells and liposomes. Biochimica et Biophysica Acta, 1191, 309–316.

    Article  CAS  PubMed  Google Scholar 

  • Miura, D., Tanaka, H., & Wariishi, H. (2004). Metabolomic differential display analysis of the white-rot basidiomycete Phanerochaete chrysosporium grown under air and 100% oxygen. FEMS Microbiology Letters, 234, 111–116.

    Article  CAS  PubMed  Google Scholar 

  • Nasution, U., van Gulik, W. M., Ras, C., Proell, A., & Heijnen, J. J. (2008). A metabolome study of the steady-state relation between central metabolism, amino acid biosynthesis and penicillin production in Penicillium chrysogenum. Metabolic Engineering, 10, 10–23.

    Article  CAS  PubMed  Google Scholar 

  • Natera, V., Sobrevals, L., Fabra, A., & Castro, S. (2006). Glutamate is involved in acid stress response in Bradyrhizobium sp. SEMIA 6144 (Arachis hypogaea L.) microsymbiont. Current Microbiology, 53, 479–482.

    Article  CAS  PubMed  Google Scholar 

  • Nikawa, J., & Yamashita, S. (1997). Phosphatidylinositol synthase from yeast. Biochimica et Biophysica Acta, 1348, 173–178.

    CAS  PubMed  Google Scholar 

  • Noctor, G., Bergot, G., Mauve, C., et al. (2007). A comparative study of amino acid measurement in leaf extracts by gas chromatography-time of flight-mass spectrometry and high performance liquid chromatography with fluorescence detection. Metabolomics, 3, 161–174.

    Article  CAS  Google Scholar 

  • Orlowski, M., Richman, P. G., & Meister, A. (1969). Isolation and properties of gamma-l-glutamylcyclotransferase from human brain. Biochemistry, 8, 1048–1055.

    Article  CAS  PubMed  Google Scholar 

  • Panagiotou, G., Villas-Bôas, S. G., Christakopoulos, P., Nielsen, J., & Olsson, L. (2005). Intracellular metabolite profiling of Fusarium oxysporum converting glucose to ethanol. Journal of Biotechnology, 115, 425–434.

    Article  CAS  PubMed  Google Scholar 

  • Peter, P. W. (1993). Molecular events associated with acquisition of heat tolerance by the yeast Saccharomyces cerevisiae. FEMS Microbiology Reviews, 11, 339–355.

    Article  Google Scholar 

  • Querol, A., Fernández-Espinar, M. T., del Olmo, M., & Barrio, E. (2003). Adaptive evolution of wine yeast. International Journal of Food Microbiology, 86, 3–10.

    Article  CAS  PubMed  Google Scholar 

  • Ramalingham, A., & Finn, R. K. (1977). The vacuferm process: a new approach to fermentation alcohol. Biotechnology and Bioengineering, 19, 583–589.

    Article  CAS  Google Scholar 

  • Rodrigues-Pousada, C. A., Nevitt, T., Menezes, R., Azevedo, D., Pereira, J., & Amaral, C. (2004). Yeast activator proteins and stress response: an overview. FEBS Letters, 567, 80–85.

    Article  CAS  PubMed  Google Scholar 

  • Singer, M. A., & Lindquist, S. (1998). Thermotolerance in Saccharomyces cerevisiae: The Yin and Yang of trehalose. Trends in Biotechnology, 16, 460–468.

    Article  CAS  PubMed  Google Scholar 

  • Strom, A. R., & Kaasen, I. (1993). Trehalose metabolism in Escherichia coli: Stress protection and stress regulation of gene expression. Molecular Microbiology, 8, 205–210.

    Article  CAS  PubMed  Google Scholar 

  • Taherzadeh, M. J., Niklasson, C., & Liden, G. (1997). Acetic acid—friend or foe in anaerobic batch conversion of glucose to ethanol by Saccharomyces cerevisiae? Chemical Engineering Science, 52, 2653–2659.

    Article  CAS  Google Scholar 

  • Takagi, H. (2008). Proline as a stress protectant in yeast: physiological functions, metabolic regulations, and biotechnological applications. Applied Microbiology and Biotechnology, 81, 211–223.

    Article  CAS  PubMed  Google Scholar 

  • Takagi, H., Iwamoto, F., & Nakamori, S. (1997). Isolation of freeze-tolerant laboratory strains of Saccharomyces cerevisiae from proline analogue-resistant mutants. Applied Microbiology and Biotechnology, 47, 405–411.

    Article  CAS  PubMed  Google Scholar 

  • Takagi, H., Takaoka, M., Kawaguchi, A., & Kubo, Y. (2005). Effect of L-proline on sake brewing and ethanol stress in Saccharomyces cerevisiae. Applied and Environmental Microbiology, 71, 8656–8662.

    Article  CAS  PubMed  Google Scholar 

  • Tamás, M. J., Luyten, K., Sutherland, F. C., et al. (1999). Fps1p controls the accumulation and release of the compatible solute glycerol in yeast osmoregulation. Molecular Microbiology, 31, 1087–1104.

    Article  PubMed  Google Scholar 

  • Thevelein, J. M., & Hohmann, S. (1995). Trehalose synthase: guard to the gate of glycolysis in yeast? Trends in Biochemical Sciences, 20, 3–10.

    Article  CAS  PubMed  Google Scholar 

  • Thomas, D. S., Hossack, J. A., & Rose, A. H. (1978). Plasma-membrane lipid composition and ethanol tolerance in Saccharomyces cerevisiae. Archives of Microbiology, 117, 239–245.

    Article  CAS  PubMed  Google Scholar 

  • Thomas, D. S., & Rose, A. H. (1979). Inhibitory effect of ethanol on growth and solute accumulation by Saccharomyces cerevisiae as affected by plasma-membrane lipid composition. Archives of Microbiology, 122, 49–55.

    Article  CAS  PubMed  Google Scholar 

  • Van den Brink, J., Daran-Lapujade, P., Pronk, J. T., & de Winde, J. H. (2008). New insights into the Saccharomyces cerevisiae fermentation switch: Dynamic transcriptional response to anaerobicity and glucose-excess. BMC Genomics, 9, 100.

    Article  PubMed  Google Scholar 

  • Van Dijken, J. P., & Scheffers, W. A. (1986). Redox balances in the metabolism of sugars by yeasts. FEMS Microbiology Reviews, 32, 199–224.

    Google Scholar 

  • Villas-Bôas, S. G., Højer-Pedersen, J., Akesson, M., Smedsgaard, J., & Nielsen, J. (2005). Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast, 22, 1155–1169.

    Article  PubMed  Google Scholar 

  • Wiklund, S., Johansson, E., Sjöström, L., et al. (2008). Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models. Analytical Chemistry, 80, 115–122.

    Article  CAS  PubMed  Google Scholar 

  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., et al. (2008). Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites. Analytical Chemistry, 80, 2939–2948.

    Article  CAS  PubMed  Google Scholar 

  • Xia, J. M., Wu, X. J., & Yuan, Y. J. (2007). Integration of wavelet transform with PCA and ANN for metabolomics data-mining. Metabolomics, 3, 531–537.

    Article  CAS  Google Scholar 

  • Xia, J. M., & Yuan, Y. J. (2009). Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid. Journal of Agricultural and Food Chemistry, 57, 99–108.

    Article  CAS  PubMed  Google Scholar 

  • Yap, S. F., & Lim, S. T. (1983). Response of Rhizobium sp. UMKL 20 to sodium chloride stress. Archives of Microbiology, 135, 224–228.

    Article  CAS  Google Scholar 

  • York, J. D. (2006). Regulation of nuclear processes by inositol polyphosphates. Biochimica et Biophysica Acta, 1761, 552–559.

    CAS  PubMed  Google Scholar 

  • You, K. M., Rosenfield, C. L., & Knipple, D. C. (2003). Ethanol tolerance in the yeast Saccharomyces cerevisiae is dependent on cellular oleic acid content. Applied and Environmental Microbiology, 69, 1499–1503.

    Article  CAS  PubMed  Google Scholar 

  • Zuzuarregui, A., Monteoliva, L., Gil, C., & del Olmo, M. (2006). Transcriptomic and proteomic approach for understanding the molecular basis of adaptation of Saccharomyces cerevisiae to wine fermentation. Applied and Environmental Microbiology, 72, 836–847.

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors are grateful for the financial support from the National Natural Science Foundation of China (Key Program Grant No.20736006), the National Basic Research Program of China (“973” Program: 2007CB714301), international collaboration project of MOST(2006DFA62400) and Key Projects in the National Science and Technology Pillar Program (No.2007BAD42B02).

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  1. Key Laboratory of Systems Bioengineering, Ministry of Education, Department of Pharmaceutical Engineering, School of Chemical Engineering and Technology, Tianjin University, P. O. Box 6888, Tianjin, 300072, People’s Republic of China

    Ming-Zhu Ding, Xiao Zhou & Ying-Jin Yuan

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Ding, MZ., Zhou, X. & Yuan, YJ. Metabolome profiling reveals adaptive evolution of Saccharomyces cerevisiae during repeated vacuum fermentations. Metabolomics 6, 42–55 (2010). https://doi.org/10.1007/s11306-009-0173-3

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