Abstract
Saccharomyces cerevisiae is widely applied in large-scale industrial bioethanol fermentation; however, little is known about the molecular responses of industrial yeast during large-scale fermentation processes. We investigated the global transcriptional responses of an industrial strain of S. cerevisiae during industrial continuous and fed-batch fermentation by oligonucleotide-based microarrays. About 28 and 62% of all genes detected showed differential gene expression during continuous and fed-batch fermentation, respectively. The overrepresented functional categories of differentially expressed genes in continuous fermentation overlapped with those in fed-batch fermentation. Downregulation of glycosylation as well as upregulation of the unfolded protein stress response was observed in both fermentation processes, suggesting dramatic changes of environment in endoplasmic reticulum during industrial fermentation. Genes related to ergosterol synthesis and genes involved in glycogen and trehalose metabolism were downregulated in both fermentation processes. Additionally, changes in the transcription of genes involved in carbohydrate metabolism coincided with the responses to glucose limitation during the early main fermentation stage in both processes. We also found that during the late main fermentation stage, yeast cells exhibited similar but stronger transcriptional changes during the fed-batch process than during the continuous process. Furthermore, repression of glycosylation has been suggested to be a secondary stress in the model proposed to explain the transcriptional responses of yeast during industrial fermentation. Together, these findings provide insights into yeast performance during industrial fermentation processes for bioethanol production.
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References
Adams BG, Parks LW (1969) Differential effect of respiratory inhibitors on ergosterol synthesis by Saccharomyces cerevisiae during adaptation to oxygen. J Bacteriol 100:370–376
Aguilera F, Peinado RA, Millán C, Ortega JM, Mauricio JC (2006) Relationship between ethanol tolerance, H+-ATPase activity and the lipid composition of the plasma membrane in different wine yeast strains. Int J Food Microbiol 110:34–42. doi:10.1016/j.ijfoodmicro.2006.02.002
Bai FW, Anderson WA, Moo-Young M (2008) Ethanol fermentation technologies from sugar and starch feedstocks. Biotechnol Adv 26:89–105. doi:10.1016/j.biotechadv.2007.09.002
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. doi:10.1007/s00253-008-1733-6
Cheng JS, Zhou X, Ding MZ, Yuan YJ (2009) Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Appl Microbiol Biotechnol 83:909–923. doi:10.1007/s00253-009-2037-1
Cullen PJ, Xu-Friedman R, Delrow J, Sprague GF (2006) Genome-wide analysis of the response to protein glycosylation deficiency in yeast. FEMS Yeast Res 6:1264–1273. doi:10.1111/j.1567-1364.2006.00120.x
Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, Bakker BM (2007) The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci USA 104:15753–15758. doi:10.1073/pnas.0707476104
Ding MZ, Cheng JS, Xiao WH, Qiao B, Yuan YJ (2008) Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF–MS. Metabolomics 5:229–238. doi:10.1007/s11306-008-0145-z
Francois J, Parrou JL (2001) Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 25:125–145. doi:10.1111/j.1574-6976.2001.tb00574.x
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 11:233–239. doi:10.1016/j.mib.2008.04.002
Gibson BR, Boulton CA, Box WG, Graham NS, Lawrence SJ, Linforth RS, Smart KA (2008) Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation. Yeast 25:549–562. doi:10.1002/yea.1609
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. doi:10.1111/j.1574-6976.2007.00076.x
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 23:623–630. doi:10.1096/fj.08-119362
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. doi:10.1007/s00253-006-0508-1
Herdeiro RS, Pereira MD, Panek AD, Eleutherio EC (2006) Trehalose protects Saccharomyces cerevisiae from lipid peroxidation during oxidative stress. Biochim Biophys Acta 1760:340–346. doi:10.1016/j.bbagen.2006.01.010
James TC, Campbell S, Donnelly D, Bond U (2003) Transcription profile of brewery yeast under fermentation conditions. J Appl Microbiol 94:432–448. doi:10.1046/j.1365-2672.2003.01849.x
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 2:2006.0026. doi:10.1038/msb4100069
Lin FM, Qiao B, Yuan YJ (2009) Comparative proteomic analysis of tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to furfural, a lignocellulosic inhibitory compound. Appl Environ Microbiol 75:3765–3776. doi:10.1128/AEM.02594-08
Marks VD, Ho Sui SJ, Erasmus D, van der Merwe GK, Brumm J, Wasserman WW, Bryan J, van Vuuren HJ (2008) Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res 8:35–52. doi:10.1111/j.1567-1364.2007.00338.x
Maury J, Asadollahi MA, Møller K, Schalk M, Clark A, Formenti LR, Nielsen J (2008) Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae. FEBS Lett 582:4032–4038. doi:10.1016/j.febslet.2008.10.045
Melamed D, Pnueli L, Arava Y (2008) Yeast translational response to high salinity: global analysis reveals regulation at multiple levels. RNA 14:1337–1351. doi:10.1261/rna.864908
Mendes-Ferreira A, del Olmo M, García-Martínez J, Jiménez-Martí E, Mendes-Faia A, Pérez-Ortín JE, Leão C (2007) Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation. Appl Environ Microbiol 73:3049–3060. doi:10.1128/AEM.02754-06
Merksamer PI, Trusina A, Papa FR (2008) Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions. Cell 135:933–947. doi:10.1016/j.cell.2008.10.011
Miller GL (1959) Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal Chem 31:426–428
Mitra N, Sinha S, Ramya TN, Surolia A (2006) N-linked oligosaccharides as outfitters for glycoprotein folding, form and function. Trends Biochem Sci 31:156–163. doi:10.1016/j.tibs.2006.01.003
Mononen I, Karjalainen E (1984) Structural comparison of protein sequences around potential N-glycosylation sites. Biochim Biophys Acta 788:364–367
Mukhopadhyay K, Kohli A, Prasad R (2002) Drug susceptibilities of yeast cells are affected by membrane lipid composition. Antimicrob Agents Chemother 46:3695–3705. doi:10.1128/AAC.46.12.3695-3705.2002
Payne T, Hanfrey C, Bishop AL, Michael AJ, Avery SV, Archer DB (2008) Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae. FEBS Lett 582:503–509. doi:10.1016/j.febslet.2008.01.009
Pizarro FJ, Jewett MC, Nielsen J, Agosin E (2008) Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae. Appl Environ Microbiol 74:6358–6368. doi:10.1128/AEM.00602-08
Rodríguez A, De La Cera T, Herrero P, Moreno F (2001) The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae. Biochem J 355:625–631
Rossignol T, Dulau L, Julien A, Blondin B (2003) Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 20:1369–1385. doi:10.1002/yea.1046
Roth S, Schüller HJ (2001) Cat8 and Sip4 mediate regulated transcriptional activation of the yeast malate dehydrogenase gene MDH2 by three carbon source-responsive promoter elements. Yeast 18:151–162. doi:10.1002/1097-0061(20010130)18:2<151:AID-YEA662>3.0.CO;2-Q
Samokhvalov V, Ignatov V, Kondrashova M (2004) Reserve carbohydrates maintain the viability of Saccharomyces cerevisiae cells during chronological aging. Mech Ageing Dev 125:229–235. doi:10.1016/j.mad.2003.12.006
Schmitt ME, Brown TA, Trumpower BL (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18:3091–3092
Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R (2005) EXPANDER—an integrative program suite for microarray data analysis. BMC Bioinformatics 6:232. doi:10.1186/1471-2105-6-232
Shobayashi M, Mitsueda S, Ago M, Fujii T, Iwashita K, Iefuji H (2005) Effects of culture conditions on ergosterol biosynthesis by Saccharomyces cerevisiae. Biosci Biotechnol Biochem 69:2381–2388. doi:10.1271/bbb.69.2381
Tachibana C, Yoo JY, Tagne JB, Kacherovsky N, Lee TI, Young ET (2005) Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8. Mol Cell Biol 25:2138–2146. doi:10.1128/MCB.25.6.2138-2146.2005
Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101:249–258. doi:10.1016/S0092-8674(00)80835-1
Varela C, Cárdenas J, Melo F, Agosin E (2005) Quantitative analysis of wine yeast gene expression profiles under winemaking conditions. Yeast 22:369–383. doi:10.1002/yea.1217
Wu H, Zheng X, Araki Y, Sahara H, Takagi H, Shimoi H (2006) Global gene expression analysis of yeast cells during sake brewing. Appl Environ Microbiol 72:7353–7358. doi:10.1128/AEM.01097-06
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. doi:10.1021/jf802720t
Yin Z, Smith RJ, Brown AJ (1996) Multiple signalling pathways trigger the exquisite sensitivity of yeast gluconeogenic mRNAs to glucose. Mol Microbiol 20:751–764
Acknowledgments
The authors are grateful for 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 international collaboration project of MOST (2006DFA62400).
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Li, BZ., Cheng, JS., Qiao, B. et al. Genome-wide transcriptional analysis of Saccharomyces cerevisiae during industrial bioethanol fermentation. J Ind Microbiol Biotechnol 37, 43–55 (2010). https://doi.org/10.1007/s10295-009-0646-4
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DOI: https://doi.org/10.1007/s10295-009-0646-4