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Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation

  • Genomics and Proteomics
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Abstract

The responses and adaptation mechanisms of the industrial Saccharomyces cerevisiae to vacuum fermentation were explored using proteomic approach. After qualitative and quantitative analyses, a total of 106 spots corresponding to 68 different proteins were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The differentially expressed proteins were involved in amino acid and carbohydrate metabolisms, various signal pathways (Ras/MAPK, Ras–cyclic adenosine monophosphate, and HOG pathway), and heat shock and oxidative responses. Among them, alternations in levels of 17 proteins associated with carbohydrate metabolisms, in particular, the upregulations of proteins involved in glycolysis, trehalose biosynthesis, and the pentose phosphate pathway, suggested vacuum-induced redistribution of the metabolic fluxes. The upregulation of 17 heat stress and oxidative response proteins indicated that multifactors contributed to oxidative stresses by affecting cell redox homeostasis. Taken together with upregulation in 14-3-3 proteins levels, 22 proteins were detected in multispots, respectively, indicating that vacuum might have promoted posttranslational modifications of some proteins in S. cerevisiae. Further investigation revealed that the elevations of the differentially expressed proteins were mainly derived from vacuum stress rather than the absence of oxygen. These findings provide new molecular mechanisms for understanding of adaptation and tolerance of yeast to vacuum fermentation.

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References

  • Atala DIP, Maugeri F (2005) Experimental development, instrumentation and control of a novel vacuum extractive fermentation process for ethanol production. J Biotechnol 118:S106–S106

    Google Scholar 

  • Blomberg A, Adler L (1992) Physiology of osmotolerance in fungi. Adv Microb Physiol 33:145–212

    CAS  PubMed  Google Scholar 

  • Boucherie H, Dujardin G, Kermorgant M, Monribot C, Slonimski P, Perrot M (1995) Two-dimensional protein map of Saccharomyces cerevisiae: construction of a gene-protein index. Yeast 11:601–613

    CAS  PubMed  Google Scholar 

  • Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254

    CAS  Google Scholar 

  • Brown SW, Oliver SG, Harrison DEF, Righelato RC (1981) Ethanol inhibition of yeast growth and fermentation: differences in the magnitude and complexity of the effect. Appl Microbiol Biotechnol 11:151–155

    CAS  Google Scholar 

  • Bruckmann A, Hensbergen PJ, Balog CI, Deelder AM, de Steensma HY, van Heusden GP (2007) Post-transcriptional control of the Saccharomyces cerevisiae proteome by 14-3-3 proteins. J Proteome Res 6:1689–1699

    CAS  PubMed  Google Scholar 

  • Bukau B, Horwich AL (1998) The Hsp70 and Hsp60 chaperone machines. Cell 92:351–366

    CAS  PubMed  Google Scholar 

  • Caesar R, Blomberg A (2004) The stress-induced Tfs1p requires NatB-mediated acetylation to inhibit carboxypeptidase Y and to regulate the protein kinase A pathway. J Biol Chem 279:38532–38543

    CAS  PubMed  Google Scholar 

  • Cheng JS, Yuan YJ (2006) Proteomic analysis reveals the spatial heterogeneity of immobilized Taxus cuspidata cells in support matrices. Proteomics 6:2199–2207

    CAS  PubMed  Google Scholar 

  • Cheng JS, Qiao B, Yuan YJ (2008) Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation. Appl Microbiol Biotechnol 81:327–338

    CAS  PubMed  Google Scholar 

  • Cysewski GR, Wilke CR (1977) Rapid ethanol fermentations using vacuum and cell recycle. Biotechnol Bioeng 19:1125–1143

    CAS  Google Scholar 

  • de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Fröhlich F, Walther TC, Mann M (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455:1251–1254

    PubMed  Google Scholar 

  • de Groot MJ, Daran-Lapujade P, van Breukelen B, Knijnenburg TA, de Hulster EA, Reinders MJ, Pronk JT, Heck AJ, Slijper M (2007) Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology 153:3864–3878

    PubMed  Google Scholar 

  • Ding MZ, Cheng JS, Xiao WH, Yuan YJ (2009) Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF-MS. Metabolomics 5:229–238

    CAS  Google Scholar 

  • Garay-Arroyo A, Covarrubias AA, Clark I, Nino I, Gossett G, Martinez A (2004) Response to different environmental stress conditions of industrial and laboratory Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 63:734–741

    CAS  PubMed  Google Scholar 

  • Giaever G, Chu AM, Ni L, Connelly C, Riles L, Veronneau S, Dow S, Lucau-Danila A, Anderson K, Andre B et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391

    CAS  PubMed  Google Scholar 

  • Godon C, Lagniel G, Lee J, Buhler JM, Kieffer S, Perrot M, Boucherie H, Toledano MB, Labarre J (1998) The H2O2 stimulon in Saccharomyces cerevisiae. J Biol Chem 273:22480–22489

    CAS  PubMed  Google Scholar 

  • Graves T, Narendranath NV, 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. Appl Microbiol Biotechnol 73:1190–1196

    CAS  PubMed  Google Scholar 

  • Gruhler A, Olsen JV, Mohammed S, Mortensen P, Faergeman NJ, Mann M, Jensen ON (2005) Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol Cell Proteomics 4:310–327

    CAS  PubMed  Google Scholar 

  • Hansen R, Pearson SY, Brosnan JM, Meaden PG, Jamieson DJ (2006) Proteomic analysis of a distilling strain of Saccharomyces cerevisiae during industrial grain fermentation. Appl Microbiol Biotechnol 72:116–125

    CAS  PubMed  Google Scholar 

  • Heux S, Cadiere A, Dequin S (2008) Glucose utilization of strains lacking PGI1 and expressing a transhydrogenase suggests differences in the pentose phosphate capacity among Saccharomyces cerevisiae strains. FEMS Yeast Res 8:217–224

    CAS  PubMed  Google Scholar 

  • Hohmann S (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev 66:300–372

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hu Y, Wang G, Chen GY, Fu X, Yao SQ (2003) Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 24:1458–1470

    CAS  PubMed  Google Scholar 

  • Izawa S, Maeda K, Miki T, Mano J, Inoue Y, Kimura A (1998) Importance of glucose-6-phosphate dehydrogenase in the adaptive response to hydrogen peroxide in Saccharomyces cerevisiae. Biochem J 330:811–817

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jouhten P, Rintala E, Huuskonen A, Tamminen A, Toivari M, Wiebe M, Ruohonen L, Penttilä M, Maaheimo H (2008) Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. BMC Sys Bio 2:60

    Google Scholar 

  • Kakiuchi K, Yamauchi Y, Taoka M, Iwago M, Fujita T, Ito T, Song SY, Sakai A, Isobe T, Ichimura T (2007) Proteomic analysis of in vivo 14-3-3 interactions in the yeast Saccharomyces cerevisiae. Biochemistry 46:7781–7792

    CAS  PubMed  Google Scholar 

  • Kolkman A, Olsthoorn MM, Heeremans CE, Heck AJ, Slijper M (2005) Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol Cell Proteomics 4:1–11

    CAS  PubMed  Google Scholar 

  • Kolkman A, Daran-Lapujade P, Fullaondo A, Olsthoorn MM, Pronk JT, Slijper M, Heck AJ (2006) Proteome analysis of yeast response to various nutrient limitations. Mol Syst Biol 2:1–16

    Google Scholar 

  • Lahti R, Kolakowski LF Jr, Heinonen J, Vihinen M, Pohjanoksa K, Cooperman BS (1990) Conservation of functional residues between yeast and E. coli inorganic pyrophosphatases. Biochim Biophys Acta 1038:338–345

    CAS  PubMed  Google Scholar 

  • Lloyd D, Morrell S, Carlsen HN, Degn H, James PE, Rowlands CC (1993) Effects of growth with ethanol on fermentation and membrane fluidity of Saccharomyces cerevisiae. Yeast 9:825–833

    CAS  PubMed  Google Scholar 

  • Maiorella BL, Blanch HW, Wilke CR (1983) By-product inhibition effects on ethanolic fermentation by Saccharomyces cerevisiae. Biotechnol Bioeng 25:103–121

    CAS  PubMed  Google Scholar 

  • Maiorella BL, Blanch HW, Wilke CR (1984) Economic evaluation of alternative ethanol fermentation processes. Biotechnol Bioeng 26:1003–1025

    CAS  PubMed  Google Scholar 

  • Nie Y, Liu H, Du G, Chen J (2008) Acetate yield increased by gas circulation and fed-batch fermentation in a novel syntrophic acetogenesis and homoacetogenesis coupling system. Bioresour Technol 99:2989–2995

    CAS  PubMed  Google Scholar 

  • Pahlman AK, Granath K, Ansell R, Hohmann S, Adler L (2001) The yeast glycerol 3-phosphatases Gpp 1p and Gpp2p are required for glycerol biosynthesis and differentially involved in the cellular responses to osmotic, anaerobic, and oxidative stress. J Biol Chem 276:3555–3563

    CAS  PubMed  Google Scholar 

  • Pham TK, Wright PC (2008a) Proteomic analysis of calcium alginate-immobilized Saccharomyces cerevisiae under high-gravity fermentation conditions. J Proteome Res 7:515–525

    CAS  PubMed  Google Scholar 

  • Pham TK, Wright PC (2008b) The proteomic response of Saccharomyces cerevisiae in very high glucose conditions with amino acid supplementation. J Proteome Res 7:4766–4774

    CAS  PubMed  Google Scholar 

  • Pham TK, Chong PK, Gan CS, Wright PC (2006) Proteomic analysis of Saccharomyces cerevisiae under high gravity fermentation conditions. J Proteome Res 5:3411–3419

    CAS  PubMed  Google Scholar 

  • Pinto Mariano A, Bastos Borba Costa C, de Franceschi de Angelis D, Maugeri Filho F, Pires Atala DI, Wolf Maciel MR, Maciel Filho R (2008) Optimization strategies based on sequential quadratic programming applied for a fermentation process for butanol production. Appl Biochem Biotechnol. doi:https://doi.org/10.1007/s12010-008-8450-6

    PubMed  Google Scholar 

  • Pronk JT, Yde Steensma H, Van Dijken JP (1996) Pyruvate metabolism in Saccharomyces cerevisiae. Yeast 12:1607–1633

    CAS  PubMed  Google Scholar 

  • Querol A, Fernández-Espinar MT, del Olmo M, Barrio E (2003) Adaptive evolution of wine yeast. Int J Food Microbiol 86:3–10

    CAS  PubMed  Google Scholar 

  • Ragu S, Faye G, Iraqui I, Masurel-Heneman A, Kolodner RD, Huang ME (2007) Oxygen metabolism and reactive oxygen species cause chromosomal rearrangements and cell death. Proc Natl Acad Sci USA 104:9747–9752

    CAS  PubMed  Google Scholar 

  • Ramalingham A, Finn RK (1977) The vacuferm process: a new approach to fermentation alcohol. Biotechnol Bioeng 19:583–589

    CAS  Google Scholar 

  • Rand JD, Grant CM (2006) The thioredoxin system protects ribosomes against stress-induced aggregation. Mol Biol Cell 17:387–401

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rep M, Proft M, Remize F, Tamás M, Serrano R, Thevelein JM, Hohmann S (2001) The Saccharomyces cerevisiae Sko1p transcription factor mediates HOG pathway-dependent osmotic regulation of a set of genes encoding enzymes implicated in protection from oxidative damage. Mol Microbiol 40:1067–1083

    CAS  PubMed  Google Scholar 

  • Roberts RL, Mösch HU, Fink GR (1997) 14-3-3 proteins are essential for RAS/MAPK cascade signaling during pseudohyphal development in S. cerevisiae. Cell 89:1055–1065

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Santivarangkna C, Kulozik U, Foerst P (2006) Effect of carbohydrates on the survival of Lactobacillus helveticus during vacuum drying. Lett Appl Microbiol 42:271–276

    CAS  PubMed  Google Scholar 

  • Santos PM, Simões T, Sá-Correia I (2009) Insights into yeast adaptive response to the agricultural fungicide mancozeb: a toxicoproteomics approach. Proteomics 9:657–670

    CAS  PubMed  Google Scholar 

  • Skoneczna A, Micialkiewicz A, Skoneczny M (2007) Saccharomyces cerevisiae Hsp31p, a stress response protein conferring protection against reactive oxygen species. Free Radic Biol Med 42:1409–1420

    CAS  PubMed  Google Scholar 

  • Stirling PC, Srayko M, Takhar KS, Pozniakovsky A, Hyman AA, Leroux MR (2007) Functional interaction between phosducin-like protein 2 and cytosolic chaperonin is essential for cytoskeletal protein function and cell cycle progression. Mol Biol Cell 18:2336–2345

    CAS  PubMed  PubMed Central  Google Scholar 

  • Taherzadeh MJ, Niklasson C, Liden G (1997) Acetic acid-friend or foe in anaerobic batch conversion of glucose to ethanol by Saccharomyces cerevisiae? Chem Eng Sci 52:2653–2659

    CAS  Google Scholar 

  • Trabalzini L, Paffetti A, Scaloni A, Talamo F, Ferro E, Coratza G, Bovalini L, Lusini P, Martelli P, Santucci A (2003) Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae. Biochem J 370(Pt 1):35–46

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ursic D, Sedbrook JC, Himmel KL, Culbertson MR (1994) The essential yeast Tcp1 protein affects actin and microtubules. Mol Biol Cell 5:1065–1080

    CAS  PubMed  PubMed Central  Google Scholar 

  • Visser W, van der Baan AA, Batenburg-van der Vegte W, Scheffers WA, Krämer R, van Dijken JP (1994) Involvement of mitochondria in the assimilatory metabolism of anaerobic Saccharomyces cerevisiae cultures. Microbiology 140:3039–3046

    CAS  PubMed  Google Scholar 

  • Wang W, Sun J, Hartlep M, Deckwer WD, Zeng AP (2003) Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae. Biotechnol Bioeng 83:525–536

    CAS  PubMed  Google Scholar 

  • Wegele H, Haslbeck M, Reinstein J, Buchner J (2003) Sti1 is a novel activator of the Ssa proteins. J Biol Chem 278:25970–25976

    CAS  PubMed  Google Scholar 

  • Winderickx J, de Winde JH, Crauwels M, Hino A, Hohmann S, Van Dijck P, Thevelein JM (1996) Regulation of genes encoding subunits of the trehalose synthase complex in Saccharomyces cerevisiae: novel variations of STRE-mediated transcription control? Mol Gen Genet 252:470–482

    CAS  PubMed  Google Scholar 

  • Wiseman A (2005) Avoidance of oxidative-stress perturbation in yeast bioprocesses by proteomic and genomic biostrategies? Lett Appl Microbiol 40:37–43

    CAS  PubMed  Google Scholar 

  • Wu CY, Bird AJ, Winge DR, Eide DJ (2007) Regulation of the yeast TSA1 peroxiredoxin by ZAP1 is an adaptive response to the oxidative stress of zinc deficiency. J Biol Chem 282:2184–2195

    CAS  PubMed  Google Scholar 

  • Xia JM, Yuan YJ (2009) Comparative lipidomics of four strains of Saccharomyces cerevisiae reveals different responses to furfural, phenol, and acetic acid. J Agric Food Chem 57:99–108

    CAS  PubMed  Google Scholar 

  • Yin Z, Stead D, Selway L, Walker J, Riba-Garcia I, McLnerney T, Gaskell S, Oliver SG, Cash P, Brown AJ (2004) Proteomic response to amino acid starvation in Candida albicans and Saccharomyces cerevisiae. Proteomics 4:2425–2436

    CAS  PubMed  Google Scholar 

  • Yoda K, Kawada T, Kaibara C, Fujie A, Abe M, Hitoshi H, Shimizu J, Tomishige N, Noda Y, Yamasaki M (2000) Defect in cell wall integrity of the yeast Saccharomyces cerevisiae caused by a mutation of the GDP-mannose pyrophosphorylase gene VIG9. Biosci Biotechnol Biochem 64:1937–1941

    CAS  PubMed  Google Scholar 

  • Zelenaya-Troitskaya O, Perlman PS, Butow RA (1995) An enzyme in yeast mitochondria that catalyzes a step in branched-chain amino acid biosynthesis also functions in mitochondrial DNA stability. EMBO J 14:3268–3276

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang R, Ou HY, Zhang CT (2004) DEG: a database of essential genes. Nucleic Acids Res 32(Database issue):D271–D272

    CAS  PubMed  PubMed Central  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), Key Projects in the National Science and Technology Pillar Program (No. 2007BAD42B02), and the National Natural Science Foundation of China (No. 20706044).

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

    Jing-Sheng Cheng, Xiao Zhou, Ming-Zhu Ding & Ying-Jin Yuan

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  1. Jing-Sheng Cheng
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Cheng, JS., Zhou, X., Ding, MZ. et al. Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Appl Microbiol Biotechnol 83, 909–923 (2009). https://doi.org/10.1007/s00253-009-2037-1

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