Comparative transcriptomic and proteomic profiling of industrial wine yeast strains

Applied and Environmental Microbiology

Volumn 76, Issue 12, 2010, Pages 3911-3923

  Rossouw, Debra ^a   Van Den Dool, Adri H ^a   Jacobson, Dan ^a   Bauer, Florian F ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOLIC FERMENTATION; CELLULAR NETWORK; COMPARATIVE APPROACH; DATA SETS; GENE ONTOLOGY; IN-LINE; INDUSTRIAL ENVIRONMENTS; METABOLIC ENZYMES; MOLECULAR ORIGINS; ON THE GO; PHENOTYPIC DIVERSITY; PHENOTYPIC TRAITS; PROTEOMES; PROTEOMIC ANALYSIS; PROTEOMIC PROFILING; SACCHAROMYCES CEREVISIAE; TIME POINTS; TRANSCRIPTIONAL CONTROL; TRANSCRIPTOMES; WINE YEAST;

CATALYSTS; CELLULAR NEURAL NETWORKS; ENZYMES; FERMENTATION; GENES; INDUSTRY; ONTOLOGY; WINE;

YEAST;

FUNGAL PROTEIN; PROTEOME;

ALCOHOL; BREWING INDUSTRY; COMMERCIAL SPECIES; COMPARATIVE STUDY; DATA SET; ENZYME ACTIVITY; FERMENTATION; GENE EXPRESSION; GENOTYPE; HYPOTHESIS TESTING; METABOLISM; MOLECULAR ANALYSIS; PHENOTYPE; PROTEOMICS; SPECIES DIVERSITY; YEAST;

ARTICLE; BIOSYNTHESIS; CHEMISTRY; COMPARATIVE STUDY; DNA MICROARRAY; FERMENTATION; GENE EXPRESSION PROFILING; GENETICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MICROBIOLOGY; WINE; YEAST;

CHROMATOGRAPHY, HIGH PRESSURE LIQUID; FERMENTATION; FUNGAL PROTEINS; GENE EXPRESSION PROFILING; INDUSTRIAL MICROBIOLOGY; MASS SPECTROMETRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; WINE; YEASTS;

LONCHOCARPUS GLAUCIFOLIUS; SACCHAROMYCES CEREVISIAE;

EID: 77953645863     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00586-10     Document Type: Article

References (51)

1. Abbott, D. A., T. A. Knijnenburg, L. M. de Poorter, M. J. Reinders, J. T. Pronk, and A. J. van Maris. 2007. Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEMS Yeast Res. 7:819-833.
2. Aggarwal, K., L. H. Choe, and K. H. Lee. 2005. Quantitative analysis of protein expression using amine-specific isobaric tags in Escherichia coli cells expressing rhsA elements. Proteomics 5:2297-2308. (Pubitemid 40835397)
3. Alexandre, H., V. Ansanay-Galeote, S. Dequin, and B. Blondin. 2001. Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett. 498:98-103.
4. Andreadis, A., Y. P. Hsu, M. Hermodson, G. Kohlhaw, and P. Schimmel. 1984. Yeast LEU2. Repression of mRNA by leucine and primary structure of the gene product. J. Biol. Chem. 259:8059-8062.
5. Ashby, M., and J. Rine. October 2006. Methods for drug screening. U.S. patent 5,569,588.
6. Bakalinsky, A. T., and R. Snow. 1990. The chromosomal constitution of wine strains of Saccharomyces cerevisiae. Yeast 6:367-382.
7. Bely, L., J. Sablayrolles, and P. Barre. 1990. Description of alcoholic fermentation kinetics: its variability and significance. Am. J. Enol. Viticult. 40:319-324.
8. Borkovich, K. A., F. W. Farrelly, D. B. Finkelstein, J. Taulien, and S. Lindquist. 1989. hsp82 is an essential protein that is required in higher concentrations for growth of cells at higher temperatures. Mol. Cell. Biol. 9:3919-3930.
9. Borneman, A. R., A. Forgan, I. S. Pretorius, and P. J. Chambers. 2008. Comparative genome analysis of a Saccharomyces cerevisiae wine strain. FEMS Yeast Res. 8:1185-1195.
10. Brejning, J., N. Arneborg, and L. Jespersen. 2005. Identification of genes and proteins induced during the lag and early exponential phase of lager brewing yeasts. J. Appl. Microbiol. 98:261-271.
11. Chen, X., L. W. Sun, Y. P. Yu, Y. Xue, and P. Yang. 2007. Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev. Proteomics 4:25-37. (Pubitemid 46239470)
12. Cline, M. S., M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, K. Hanspers, R. Isserlin, R. Kelley, S. Killcoyne, S. Lotia, S. Maere, J. Morris, K. Ono, V. Pavlovic, A. R. Pico, A. Vailaya, P. L. Wang, A. Adler, B. R. Conklin, L. Hood, M. Kuiper, C. Sander, I. Schmulevich, B. Schwikowski, G. J. Warner, T. Ideker, and G. D. Bader. 2007. Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc. 2:2366-2382.
13. Daran-Lapujade, P., M. L. Jansen, J. M. Daran, W. van Gulik, J. H. de Winde, and J. T. Pronk. 2004. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J. Biol. Chem. 279:9125-9138.
14. de Godoy, L. M. F., J. V. Olsen, J. Cox, M. L. Nielsen, N. C. Hubner, F. Fröhlich, T. C. Walther, and M. Mann. 2008. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455:1251-1254.
15. De Groot, M. J. L., P. Daran-Lapujade, B. van Breukelen, T. A. Knijnenburg, E. A. F. de Hulster, M. J. T. Reinders, J. T. Pronk, A. J. R. Heck, and M. Slij per. 2007. Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology 153:3864-3878.
16. Erasmus, D. J., G. K. van der Merwe, and H. J. J. van Vuuren. 2003. Genome-wide expression analyses: metabolic adaptation of Saccharomyces cerevisiae to high sugar stress. FEMS Yeast Res. 3:375-399.
17. Fey, S. J., and P. M. Larsen. 2001. 2D or not 2D. Two-dimensional gel electrophoresis. Curr. Opin. Chem. Biol. 5:26-33.
18. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldman, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274:546, 563-567.
19. Griffin, T. J., S. P. Gygi, T. Ideker, B. Rist, J. Eng, L. Hood, and R. Aebersold. 2002. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1:323-333.
20. Holmberg, S., and J. G. Petersen. 1988. Regulation of isoleucine-valine biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 13:207-217.
21. Kanehisa, M., and S. Goto. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27-30. (Pubitemid 30047706)
22. Kanehisa, M., S. Goto, M. Hattori, K. F. Aoki-Kinoshita, M. Itoh, S. Kawashima, T. Katayama, M. Araki, and M. Hirakawa. 2006. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34:D354-D357.
23. Kanehisa, M., M. Araki, S. Goto, M. Hattori, M. Hirakawa, M. Itoh, T. Katayama, S. Kawashima, S. Okuda, T. Tokimatsu, and Y. Yamanishi. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 36:D480-D484. (Pubitemid 351149770)
24. Kispal, G., H. Steiner, D. A. Court, B. Rolinski, and R. Lill. 1996. Mitochondrial and cytosolic branched chain amino acid transaminases from yeast, homologs of the myc oncogene-regulated Eca39 protein. J. Biol. Chem. 271:24458-24464.
25. Kobi, D., S. Zugmeyer, S. Potier, and L. Jaquet-Gutfreund. 2004. Twodimensional map of an "ale"-brewing yeast strain: proteome dynamics during fermentation. FEMS Yeast Res. 5:213-230.
26. Kolkman, A., P. Daran-Lapujade, A. Fullaondo, M. M. A. Olsthoorn, J. T. Pronk, M. Slijper, and A. J. R. Heck. 2006. Proteome analysis of yeast response to various nutrient limitations. Mol. Sys. Biol. 2:0026.
27. Maillet, I., G. Lagniel, M. Perrot, H. Boucherie, and J. Labarre. 1996. Rapid identification of yeast proteins on two-dimensional gels. J. Biol. Chem. 271: 10263-10270.
28. Mann, M., R. C. Hendricksen, and A. Pandey. 2001. Analysis of proteins and proteomes by mass spectrometry. Annu. Rev. Biochem. 70:437-473.
29. Marks, V. D., S. J. Ho Sui, D. Erasmus, G. K. van den Merwe, J. Brumm, W. W. Wasserman, J. Bryan, and H. J. van Vuuren. 2008. Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res. 8:35-52.
30. Nägele, E., M. Vollmer, and P. Hörth. 2004. Improved 2D nano-LC/MS for proteomics applications: a comparative analysis using yeast proteome. J. Biomol. Tech. 15:134-143.
31. Novo, M., F. Bigey, E. Beyne, V. Galeote, F. Gavory, S. Mallet, B. Cambon, J.-L. Legras, P. Wincker, S. Casaregola, and S. Dequin. 2009. Eukaryoteto-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc. Natl. Acad. Sci. U. S. A. 106:16333-16338.
32. O'Farrell, P. H. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250:4007-4021.
33. Parks, L. W., S. J. Smith, and J. H. Crowley. 1995. Biochemical and physiological effects of sterol alterations in yeast - a review. Lipids 30:227-230.
34. Peng, J., J. E. Elias, C. C. Thoreen, L. J. Licklider, and S. P. Gygi. 2002. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2:43-50. (Pubitemid 36207189)
35. Rabilloud, T. 2002. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs the mountains. Proteomics 2:3-10. (Pubitemid 34273093)
36. Rossignol, T., D. Kobi, L. Jacquet-Gutfreund, and B. Blondin. 2009. The proteome of a wine yeast strain during fermentation, correlation with the transcriptome. J. Appl. Microbiol. 107:47-55.
37. Rossouw, D., T. Naes, and F. F. Bauer. 2008. Linking gene regulation and the exo-metabolome: a comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast. BMC Genomics 9:530-548.
38. Rossouw, D., R. Olivares-Hernandes, J. Nielsen, and F. F. Bauer. 2009. Comparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation. Appl. Environ. Microbiol. 75:6600-6612.
39. Salvado, Z., R. Chiva, S. Rodriguez-Vargas, F. Rández-Gil, A. Mas, and J. M. Guillamón. 2008. Proteomic evolution of a wine yeast during the first hours of fermentation. FEMS Yeast Res. 8:1137-1146.
40. Sanyal, A., A. Harington, C. J. Herbert, O. Groudinsky, P. P. Slonimsky, B. Tung, and G. S. Getz. 1995. Heat shock protein HSP60 can alleviate the phenotype of mitochondrial RNA-deflcient temperature-sensitive mna2 pet mutants. Mol. Gen. Genet. 246:56-64.
41. Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 11:2498-2504. (Pubitemid 37428274)
42. Smolka, M., H. Zhou, and R. Aebersold. 2002. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol. Cell. Proteomics 1:19-29.
43. Swiegers, J. H., D. L. Capone, K. H. Pardon, G. M. Elsey, M. A. Sefton, I. L. Francis, and I. S. Pretorius. 2007. Engineering volatile thiol release in Saccharomyces cerevisiae for improved wine aroma. Yeast 24:561-574.
44. Tong, A. H., B. Drees, G. Nardelli, G. D. Bader, B. Brannetti, L. Castagnoli, M. Evangelista, S. Ferracuti, B. Nelson, S. Paoluzi, M. Quondam, A. Zucconi, C. W. Hogue, S. Fields, C. Boone, and G. Cesareni. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295:321-324.
45. Trabalzini, L., A. Paffeti, A. Scaloni, F. Tálamo, E. Ferro, G. Coratza, L. Bovalini, P. Lusini, P. Martelli, and A. Santucci. 2003. Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae. Biochem. J. 370:35-46.
46. Vido, K., D. Spector, G. Lagniel, S. Lopez, M. B. Toledano, and J. Labarre. 2001. A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J. Biol. Chem. 276:8469-8474.
47. Walhout, A. J., J. Reboul, O. Shtanko, N. Bertin, P. Vaglio, H. Ge, H. Lee, L. Doucette-Stamm, K. C. Gunsalus, A. J. Schetter, D. G. Morton, K. J. Kernphues, V. Reinke, S. K. Kim, F. Piano, and M. Vidal. 2002. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr. Biol. 12:1952-1958.
48. Washburn, M. P., R. Ulaszek, C. Deciu, D. M. Schielts, and J. R. Yates. 2002. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 74:1650-1657.
49. Wong, C. M., Y. Zhou, R. W. Ng, H. F. Kung, and D. Y. Jin. 2002. Cooperation of yeast peroxiredoxins Tsalp and Tsa2p in the cellular defense against oxidative and nitrosative stress. J. Biol. Chem. 277:5385-5394.
50. Wu, Z., R. Irizarry, R. Gentleman, F. M. Murillo, and F. Spencer. 2004. A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 99:909-917.
51. Yoshikawa, K., T. Tanaka, C. Furusawa, K. Nagahisa, T. Hirasawa, and H. Shimizu. 2009. Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae. FEMS Yeast Res. 9:32-44.