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Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation

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Abstract

A robust Saccharomyces cerevisiae strain has been widely applied in continuous and batch/fed-batch industrial fermentation. However, little is known about the molecular basis of fermentative behavior of this strain in the two realistic fermentation processes. In this paper, we presented comparative proteomic profiling of the industrial yeast in the industrial fermentation processes. The expression levels of most identified protein were closely interrelated with the different stages of fermentation processes. Our results indicate that, among the 47 identified protein spots, 17 of them belonging to 12 enzymes were involved in pentose phosphate, glycolysis, and gluconeogenesis pathways and glycerol biosynthetic process, indicating that a number of pathways will need to be inactivated to improve ethanol production. The differential expressions of eight oxidative response and heat-shock proteins were also identified, suggesting that it is necessary to keep the correct cellular redox or osmotic state in the two industrial fermentation processes. Moreover, there are significant differences in changes of protein levels between the two industrial fermentation processes, especially these proteins associated with the glycolysis and gluconeogenesis pathways. These findings provide a molecular understanding of physiological adaptation of industrial strain for optimizing the performance of industrial bioethanol fermentation.

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References

  1. Aguilera A (1986) Deletion of the phosphoglucose isomerase structural gene makes growth and sporulation glucose dependent in Saccharomyces cerevisiae. Mol Gen Genet 204:310–316

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

  3. Alfenore S, Molina-Jouve C, Guillouet SE, Uribelarrea JL, Goma G, Benbadis L (2002) Improving ethanol production and viability of Saccharomyces cerevisiae by a vitamin feeding strategy during fed-batch process. Appl Microbiol Biotechnol 60:67–72

  4. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565–1568

  5. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA (2003) Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature 423:181–185

  6. Ansell R, Granath K, Hohmann S, Thevelein JM, Adler L (1997) The two isoenzymes for yeast NAD+-dependent glycerol 3-phosphate dehydrogenase encoded by GPD1 and GPD2 have distinct roles in osmoadaptation and redox regulation. EMBO J 16:2179–2187

  7. Bai FW, Anderson WA, Moo-Young M (2008) Ethanol fermentation technologies from sugar and starch feedstocks. Biotechnol Adv 26:89–105

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

  9. 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

  10. 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

  11. Caesar R, Palmfeldt J, Gustafsson JS, Pettersson E, Hashemi SH, Blomberg A (2007) Comparative proteomics of industrial lager yeast reveals differential expression of the cerevisiae and non-cerevisiae parts of their genomes. Proteomics 7:4135–4147

  12. Cakar ZP, Seker UO, Tamerler C, Sonderegger M, Sauer U (2005) Evolutionary engineering of multiple-stress resistant Saccharomyces cerevisiae. FEMS Yeast Res 5:569–578

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

  14. Cheraiti N, Sauvage FX, Salmon JM (2008) Acetaldehyde addition throughout the growth phase alleviates the phenotypic effect of zinc deficiency in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 77:1093–1109

  15. 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

  16. Dickinson JR, Smith ME, Swanson TR, Williams AS, Wingfield JM (1988) The cdc30 mutation in Saccharomyces cerevisiae affects phosphoglucose isomerase, the cell cycle and sporulation. J Gen Microbiol 134:2475–2480

  17. Du C, Zhang Y, Li Y, Cao Z (2007) Novel redox potential-based screening strategy for rapid isolation of Klebsiella pneumoniae mutants with enhanced 1,3-propanediol-producing capability. Appl Environ Microbiol 73:4515–4521

  18. Fabrizio P, Longo VD (2003) The chronological life span of Saccharomyces cerevisiae. Aging Cell 2:73–81

  19. Gallo CM, Smith DL Jr, Smith JS (2004) Nicotinamide clearance by Pnc1 directly regulates Sir2-mediated silencing and longevity. Mol Cell Biol 24:1301–1312

  20. Gibson BR, Lawrence SJ, Leclaire JP, Powell CD, Smart KA (2007) Yeast responses to stresses associated with industrial brewery handling. FEMS Microbiol Rev 31:535–569

  21. 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

  22. Gurden SP, Westerhuis JA, Smilde AK (2002) Monitoring of batch processes using spectroscopy. AIChE J 48:2283–2297

  23. 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

  24. Hohmann S (1997) Pyruvate decarboxylases. In: Zimmermann F, Entian KD (eds) Yeast sugar metabolism. Biochemistry, genetics, biotechnology, and applications. Technomic, Lancaster, pp 187–212

  25. Hohmann S (2005) The yeast systems biology network: mating communities. Curr Opin Biotechnol 16:356–360

  26. 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

  27. Jules M, François J, Parrou JL (2005) Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose. FEBS J 272:1490–1500

  28. Kim YH, Han KY, Lee K, Lee J (2005) Proteome response of Escherichia coli fed-batch culture to temperature downshift. Appl Microbiol Biotechnol 68:786–793

  29. Klein-Marcuschamer D, Stephanopoulos G (2008) Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci USA 105:2319–2324

  30. 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

  31. 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

  32. Longo VD, Gralla EB, Valentine JS (1996) Superoxide dismutase activity is essential for stationary phase survival in Saccharomyces cerevisiae. Mitochondrial production of toxic oxygen species in vivo. J Biol Chem 271:12275–12280

  33. Ludwig JR 2nd, Foy JJ, Elliott SG, McLaughlin CS (1982) Synthesis of specific identified, phosphorylated, heat shock, and heat stroke proteins through the cell cycle of Saccharomyces cerevisiae. Mol Cell Biol 2:117–126

  34. Maestre O, García-Martínez T, Peinado RA, Mauricio JC (2008) Effects of ADH2 overexpression in Saccharomyces bayanus during alcoholic fermentation. Appl Environ Microbiol 74:702–707

  35. Magherini F, Tani C, Gamberi T, Caselli A, Bianchi L, Bini L, Modesti A (2007) Protein expression profiles in Saccharomyces cerevisiae during apoptosis induced by H2O2. Proteomics 7:1434–1445

  36. McAlister L, Holland MJ (1985) Differential expression of the three yeast glyceraldehyde-3-phosphate dehydrogenase genes. J Biol Chem 260:15019–15027

  37. Pahlman AK, Granath K, Ansell R, Hohmann S, Adler L (2001) The yeast glycerol 3-phosphatases Gpp1p 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

  38. Pérez-Torrado R, Bruno-Bárcena JM, Matallana E (2005) Monitoring stress-related genes during the process of biomass propagation of Saccharomyces cerevisiae strains used for wine making. Appl Environ Microbiol 71:6831–6837

  39. Perrot M, Guieysse-Peugeot AL, Massoni A, Espagne C, Claverol S, Monteiro Silva R, Jenö P, Santos M, Bonneu M, Boucherie H (2007) Yeast proteome map (update 2006). Proteomics 7:1117–1120

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

  41. 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

  42. Querin L, Sanvito R, Magni F, Busti S, Dorsselaer AV, Alberghina L, Vanoni M (2008) Proteomic analysis of a nutritional shift-up in Saccharomyces cerevisiae identifies Gvp36 as a BAR-containing protein involved in vesicular traffic and nutritional adaptation. J Biol Chem 283:4730–4743

  43. 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

  44. Rossignol T, Postaire O, Storaï J, Blondin B (2006) Analysis of the genomic response of a wine yeast to rehydration and inoculation. Appl Microbiol Biotechnol 71:699–712

  45. Talebnia F, Taherzadeh MJ (2006) In situ detoxification and continuous cultivation of dilute-acid hydrolyzate to ethanol by encapsulated S. cerevisiae. J Biotechnol 125:377–384

  46. Thomsson E, Gustafsson L, Larsson C (2005) Starvation response of Saccharomyces cerevisiae grown in anaerobic nitrogen- or carbon-limited chemostat cultures. Appl Environ Microbiol 71:3007–3013

  47. 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 370:35–46

  48. 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 68:517–523

  49. Varela JC, van Beekvelt C, Planta RJ, Mager WH (1992) Osmostress-induced changes in yeast gene expression. Mol Microbiol 6:2183–2190

  50. Walfridsson M, Hallborn J, Penttilä M, Keränen S, Hahn-Hägerdal B (1995) Xylose-metabolizing Saccharomyces cerevisiae strains overexpressing the TKL1 and TAL1 genes encoding the pentose phosphate pathway enzymes transketolase and transaldolase. Appl Environ Microbiol 61:4184–4190

  51. 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

  52. Wang J, Xue Y, Feng X, Li X, Wang H, Li W, Zhao C, Cheng X, Ma Y, Zhou P, Yin J, Bhatnagar A, Wang R, Liu S (2004) An analysis of the proteomic profile for Thermoanaerobacter tengcongensis under optimal culture conditions. Proteomics 4:136–150

  53. Wang Y, Wu SL, Hancock WS, Trala R, Kessler M, Taylor AH, Patel PS, Aon JC (2005) Proteomic profiling of Escherichia coli proteins under high cell density fed-batch cultivation with overexpression of phosphogluconolactonase. Biotechnol Prog 21:1401–1411

  54. Wildgruber R, Reil G, Drews O, Parlar H, Görg A (2002) Web-based two-dimensional database of Saccharomyces cerevisiae proteins using immobilized pH gradients from pH 6 to pH 12 and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Proteomics 2:727–732

  55. 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

  56. 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

  57. 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. Appl Environ Microbiol 72:836–847

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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 & Technology Pillar Program (No.2007BAD42B02), and the National Natural Science Foundation of China (No. 20706044).

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Correspondence to Ying-Jin Yuan.

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Cheng, J., Qiao, B. & Yuan, Y. Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation. Appl Microbiol Biotechnol 81, 327–338 (2008). https://doi.org/10.1007/s00253-008-1733-6

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Keywords

  • Continuous fermentation
  • Batch/fed-batch fermentation
  • Proteomic analysis
  • Bioethanol
  • Saccharomyces cerevisiae