Genome-wide transcriptional analysis of Saccharomyces cerevisiae during industrial bioethanol fermentation

Journal of Industrial Microbiology and Biotechnology

Volumn 37, Issue 1, 2010, Pages 43-55

  Li, Bing Zhi ^a   Cheng, Jing Sheng ^a   Qiao, Bin ^a   Yuan, Ying Jin ^a  

^a TIANJIN UNIVERSITY   (China)

Author keywords

Bioethanol; Continuous fermentation; Fed batch fermentation; Saccharomyces cerevisiae; Transcriptome

Indexed keywords

ALCOHOL; ERGOSTEROL; GLYCOGEN; TRANSCRIPTOME; TREHALOSE;

ARTICLE; CARBOHYDRATE METABOLISM; CONTINUOUS FERMENTATION; CONTINUOUS PROCESS; CONTROLLED STUDY; DNA MICROARRAY; DOWN REGULATION; ENDOPLASMIC RETICULUM; FED BATCH FERMENTATION; FERMENTATION; FERMENTATION MONITORING; FUNGAL GENETICS; FUNGAL STRAIN; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GLYCOGEN METABOLISM; GLYCOSYLATION; INDUSTRIALIZATION; LARGE SCALE PRODUCTION; LIPOGENESIS; NONHUMAN; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE; STRESS; TRANSCRIPTION REGULATION; UPREGULATION; YEAST CELL;

BIOFUELS; BIOREACTORS; CARBOHYDRATE METABOLISM; ETHANOL; FERMENTATION; GENE EXPRESSION PROFILING; GENOME, FUNGAL; GENOME-WIDE ASSOCIATION STUDY; GLYCOGEN; GLYCOSYLATION; INDUSTRIAL MICROBIOLOGY; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE; TREHALOSE;

SACCHAROMYCES CEREVISIAE;

EID: 76949100778     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-009-0646-4     Document Type: Article

References (42)

1. BG Adams LW Parks 1969 Differential effect of respiratory inhibitors on ergosterol synthesis by Saccharomyces cerevisiae during adaptation to oxygen J Bacteriol 100 370 376 1:CAS:528:DyaF1MXltFSisbg%3D 5344101
2. +-ATPase activity and the lipid composition of the plasma membrane in different wine yeast strains Int J Food Microbiol 110 34 42 10.1016/j.ijfoodmicro.2006.02.002 10.1016/j. ijfoodmicro.2006.02.002 1:CAS:528:DC%2BD28XntVymtbg%3D 16690148 (Pubitemid 44041089)
3. FW Bai WA Anderson M Moo-Young 2008 Ethanol fermentation technologies from sugar and starch feedstocks Biotechnol Adv 26 89 105 10.1016/j.biotechadv. 2007.09.002 10.1016/j.biotechadv.2007.09.002 1:CAS:528:DC%2BD2sXhtlGnsrfJ 17964107 (Pubitemid 350141683)
4. JS Cheng B Qiao YJ Yuan 2008 Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation Appl Microbiol Biotechnol 81 327 338 10.1007/s00253-008-1733-6 10.1007/s00253-008-1733-6 1:CAS:528:DC%2BD1cXhtlaqsbnL 18923828
5. JS Cheng X Zhou MZ Ding YJ Yuan 2009 Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation Appl Microbiol Biotechnol 83 909 923 10.1007/s00253-009-2037-1 10.1007/s00253-009- 2037-1 1:CAS:528:DC%2BD1MXnsVOlsrs%3D 19488749
6. PJ Cullen R Xu-Friedman J Delrow GF Sprague 2006 Genome-wide analysis of the response to protein glycosylation deficiency in yeast FEMS Yeast Res 6 1264 1273 10.1111/j.1567-1364.2006.00120.x 10.1111/j.1567-1364.2006.00120.x 1:CAS:528:DC%2BD28XhtlWqsbnL 17156023 (Pubitemid 44800323)
7. P Daran-Lapujade S Rossell WM van Gulik MA Luttik MJ de Groot M Slijper AJ Heck JM Daran JH de Winde HV Westerhoff JT Pronk BM Bakker 2007 The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels Proc Natl Acad Sci USA 104 15753 15758 10.1073/pnas.0707476104 10.1073/pnas.0707476104 1:CAS:528:DC%2BD2sXhtFGns7%2FE 17898166 (Pubitemid 350035372)
8. MZ Ding JS Cheng WH Xiao B Qiao YJ Yuan 2008 Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF-MS Metabolomics 5 229 238 10.1007/s11306-008-0145-z 10.1007/s11306-008- 0145-z
9. J Francois JL Parrou 2001 Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae FEMS Microbiol Rev 25 125 145 10.1111/j.1574-6976.2001. tb00574.x 10.1016/S0168-6445(00)00059-0 1:CAS:528:DC%2BD3MXitl2lsA%3D%3D 11152943
10. DE Garcia EE Baidoo PI Benke F Pingitore YJ Tang S Villa JD Keasling 2008 Separation and mass spectrometry in microbial metabolomics Curr Opin Microbiol 11 233 239 10.1016/j.mib.2008.04.002 10.1016/j.mib.2008.04.002 1:CAS:528:DC%2BD1cXotlOjtb0%3D 18538626
11. BR Gibson CA Boulton WG Box NS Graham SJ Lawrence RS Linforth KA Smart 2008 Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation Yeast 25 549 562 10.1002/yea.1609 10.1002/yea.1609 1:CAS:528:DC%2BD1cXhtVeht73P 18668645
12. BR Gibson SJ Lawrence JP Leclaire CD Powell KA Smart 2007 Yeast responses to stresses associated with industrial brewery handling FEMS Microbiol Rev 31 535 569 10.1111/j.1574-6976.2007.00076.x 10.1111/j.1574-6976.2007.00076.x 1:CAS:528:DC%2BD2sXhtVSmsLnI 17645521 (Pubitemid 47246179)
13. PP Han YJ Yuan 2009 Lipidomic analysis reveals activation of phospholipid signaling in mechanotransduction of Taxus cuspidata cells in response to shear stress FASEB J 23 623 630 10.1096/fj.08-119362 10.1096/fj.08-119362 1:CAS:528:DC%2BD1MXhs1Klsr0%3D 18922880
14. R Hansen SY Pearson JM Brosnan PG Meaden DJ Jamieson 2006 Proteomic analysis of a distilling strain of Saccharomyces cerevisiae during industrial grain fermentation Appl Microbiol Biotechnol 72 116 125 10.1007/s00253-006-0508- 1 10.1007/s00253-006-0508-1 1:CAS:528:DC%2BD28XotVyguro%3D 16820951 (Pubitemid 44222430)
15. RS Herdeiro MD Pereira AD Panek EC Eleutherio 2006 Trehalose protects Saccharomyces cerevisiae from lipid peroxidation during oxidative stress Biochim Biophys Acta 1760 340 346 10.1016/j.bbagen.2006.01.010 1:CAS:528: DC%2BD28Xis1egsLk%3D 16510250
16. TC James S Campbell D Donnelly U Bond 2003 Transcription profile of brewery yeast under fermentation conditions J Appl Microbiol 94 432 448 10.1046/j.1365-2672.2003.01849.x 10.1046/j.1365-2672.2003.01849.x 1:CAS:528:DC%2BD3sXis1yisLw%3D 12588552 (Pubitemid 36321783)
17. A Kolkman P Daran-Lapujade A Fullaondo MM Olsthoorn JT Pronk M Slijper AJ Heck 2006 Proteome analysis of yeast response to various nutrient limitations Mol Syst Biol 2 2006.0026 10.1038/msb4100069 10.1038/msb4100069 16738570 (Pubitemid 43948169)
18. FM Lin B Qiao YJ Yuan 2009 Comparative proteomic analysis of tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to furfural, a lignocellulosic inhibitory compound Appl Environ Microbiol 75 3765 3776 10.1128/AEM.02594-08 10.1128/AEM.02594-08 1:CAS:528:DC%2BD1MXntlSgtrc%3D 19363068
19. VD Marks SJ Ho Sui D Erasmus GK van der Merwe J Brumm WW Wasserman J Bryan HJ van Vuuren 2008 Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response FEMS Yeast Res 8 35 52 10.1111/j.1567-1364.2007.00338.x 10.1111/j.1567-1364.2007.00338.x 1:CAS:528:DC%2BD1cXitVCqtLs%3D 18215224
20. J Maury MA Asadollahi K Møller M Schalk A Clark LR Formenti J Nielsen 2008 Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae FEBS Lett 582 4032 4038 10.1016/j.febslet.2008.10.045 10.1016/j.febslet.2008.10.045 1:CAS:528:DC%2BD1cXhsVGhtLvO 18996117
21. D Melamed L Pnueli Y Arava 2008 Yeast translational response to high salinity: global analysis reveals regulation at multiple levels RNA 14 1337 1351 10.1261/rna.864908 10.1261/rna.864908 1:CAS:528:DC%2BD1cXot1amtL8%3D 18495938 (Pubitemid 351872191)
22. A Mendes-Ferreira M del Olmo J García-Martínez E Jiménez-Martí A Mendes-Faia JE Pérez-Ortín C Leão 2007 Transcriptional response of Saccharomyces cerevisiae to different nitrogen concentrations during alcoholic fermentation Appl Environ Microbiol 73 3049 3060 10.1128/AEM.02754-06 10.1128/AEM.02754-06 1:CAS:528:DC%2BD2sXlsFeqtb0%3D 17337556 (Pubitemid 46718590)
23. PI Merksamer A Trusina FR Papa 2008 Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions Cell 135 933 947 10.1016/j.cell.2008.10.011 10.1016/j.cell.2008.10.011 1:CAS:528:DC%2BD1cXhsV2jtrzN 19026441
24. GL Miller 1959 Use of dinitrosalicylic acid reagent for determination of reducing sugar Anal Chem 31 426 428 10.1021/ac60147a030 1:CAS:528: DyaG1MXmtFKiuw%3D%3D
25. N Mitra S Sinha TN Ramya A Surolia 2006 N-linked oligosaccharides as outfitters for glycoprotein folding, form and function Trends Biochem Sci 31 156 163 10.1016/j.tibs.2006.01.003 10.1016/j.tibs.2006.01.003 1:CAS:528: DC%2BD28Xit1yms7c%3D 16473013 (Pubitemid 43357996)
26. I Mononen E Karjalainen 1984 Structural comparison of protein sequences around potential N-glycosylation sites Biochim Biophys Acta 788 364 367 1:CAS:528:DyaL2cXlt1Ghu70%3D
27. K Mukhopadhyay A Kohli R Prasad 2002 Drug susceptibilities of yeast cells are affected by membrane lipid composition Antimicrob Agents Chemother 46 3695 3705 10.1128/AAC.46.12.3695-3705.2002 10.1128/AAC.46.12.3695-3705.2002 1:CAS:528:DC%2BD38XptVyntr4%3D 12435664 (Pubitemid 35403239)
28. T Payne C Hanfrey AL Bishop AJ Michael SV Avery DB Archer 2008 Transcript-specific translational regulation in the unfolded protein response of Saccharomyces cerevisiae FEBS Lett 582 503 509 10.1016/j.febslet.2008.01.009 10.1016/j.febslet.2008.01.009 1:CAS:528:DC%2BD1cXhslejtrc%3D 18206654
29. FJ Pizarro MC Jewett J Nielsen E Agosin 2008 Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae Appl Environ Microbiol 74 6358 6368 10.1128/AEM.00602-08 10.1128/AEM.00602-08 1:CAS:528:DC%2BD1cXht1ygu7bJ 18723660
30. A Rodríguez T De La Cera P Herrero F Moreno 2001 The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae Biochem J 355 625 631 11311123
31. T Rossignol L Dulau A Julien B Blondin 2003 Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation Yeast 20 1369 1385 10.1002/yea.1046 10.1002/yea.1046 1:CAS:528:DC%2BD2cXhtVGktA%3D%3D 14663829 (Pubitemid 38016631)
32. S Roth HJ Schüller 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 10.1002/1097- 0061(20010130)18:2<151:AID-YEA662>3.0.CO;2-Q 10.1002/1097-0061(20010130) 18:2<151::AID-YEA662>3.0.CO;2-Q 1:CAS:528:DC%2BD3MXht1Slsb8%3D 11169757
33. V Samokhvalov V Ignatov M Kondrashova 2004 Reserve carbohydrates maintain the viability of Saccharomyces cerevisiae cells during chronological aging Mech Ageing Dev 125 229 235 10.1016/j.mad.2003.12.006 10.1016/j.mad.2003.12.006 1:CAS:528:DC%2BD2cXhvFajtr0%3D 15013667 (Pubitemid 38317278)
34. ME Schmitt TA Brown BL Trumpower 1990 A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae Nucleic Acids Res 18 3091 3092 10.1093/nar/18.10.3091 1:CAS:528:DyaK3cXktlOgsrk%3D 2190191
35. R Shamir A Maron-Katz A Tanay C Linhart I Steinfeld R Sharan Y Shiloh R Elkon 2005 EXPANDER-an integrative program suite for microarray data analysis BMC Bioinformatics 6 232 10.1186/1471-2105-6-232 10.1186/1471-2105-6-232 16176576 (Pubitemid 41548723)
36. M Shobayashi S Mitsueda M Ago T Fujii K Iwashita H Iefuji 2005 Effects of culture conditions on ergosterol biosynthesis by Saccharomyces cerevisiae Biosci Biotechnol Biochem 69 2381 2388 10.1271/bbb.69.2381 10.1271/bbb.69.2381 1:CAS:528:DC%2BD28XjtVaqtg%3D%3D 16377897 (Pubitemid 43004381)
37. C Tachibana JY Yoo JB Tagne N Kacherovsky TI Lee ET Young 2005 Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8 Mol Cell Biol 25 2138 2146 10.1128/MCB.25.6.2138-2146.2005 10.1128/MCB.25.6.2138-2146.2005 1:CAS:528:DC%2BD2MXisVOitLs%3D 15743812 (Pubitemid 40354614)
38. KJ Travers CK Patil L Wodicka DJ Lockhart JS Weissman P Walter 2000 Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation Cell 101 249 258 10.1016/S0092-8674(00)80835-1 10.1016/S0092-8674(00)80835-1 1:CAS:528: DC%2BD3cXjtFSrtL4%3D 10847680
39. C Varela J Cárdenas F Melo E Agosin 2005 Quantitative analysis of wine yeast gene expression profiles under winemaking conditions Yeast 22 369 383 10.1002/yea.1217 10.1002/yea.1217 1:CAS:528:DC%2BD2MXjslGqsro%3D 15806604 (Pubitemid 40561553)
40. H Wu X Zheng Y Araki H Sahara H Takagi H Shimoi 2006 Global gene expression analysis of yeast cells during sake brewing Appl Environ Microbiol 72 7353 7358 10.1128/AEM.01097-06 10.1128/AEM.01097-06 1:CAS:528: DC%2BD28Xht1GksrrO 16997994 (Pubitemid 44748454)
41. JM Xia YJ Yuan 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 10.1021/jf802720t 10.1021/jf802720t 1:CAS:528:DC%2BD1cXhsVCrurbK 19049411
42. Z Yin RJ Smith AJ Brown 1996 Multiple signalling pathways trigger the exquisite sensitivity of yeast gluconeogenic mRNAs to glucose Mol Microbiol 20 751 764 10.1111/j.1365-2958.1996.tb02514.x 1:CAS:528:DyaK28XjsFGjtr8%3D 8793872 (Pubitemid 26173803)