Transcriptional regulation and the diversification of metabolism in wine yeast strains

Genetics

Volumn 190, Issue 1, 2012, Pages 251-261

  Rossouw, Debra ^a   Jacobson, Dan ^a   Bauer, Florian F ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; FERMENTATION; FUNGAL STRAIN; GENE CONTROL; GENE EXPRESSION; GENETIC VARIABILITY; GENOTYPE; METABOLISM; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; WINE; WINE INDUSTRY; YEAST;

FERMENTATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; INDUSTRIAL MICROBIOLOGY; REPRESSOR PROTEINS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; WINE;

LONCHOCARPUS GLAUCIFOLIUS; SACCHAROMYCES CEREVISIAE;

EID: 84855466087     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.111.132720     Document Type: Article

References (55)

1. Abbott, D. A., T. A. Knijnenburg, L. M. De Poorter, M. J. Reinders, J. T. Pronk et al., 2007 Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae. FEM. Yeast Res. 7: 819-833.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, 1990 Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, and J. G. Seidman, 1994 Current Protocols In Molecular Biology. John Wiley, New York.
4. Bakalinsky, A. T., and R. Snow, 1990 The chromosomal constitution of wine strains of Saccharomyces cerevisiae. Yeast 6: 367-382.
5. Bely, L., J. Sablayrolles, and P. Barre, 1990 Description of alcoholic fermentation kinetics: its variability and significance. Am. J. Enol. Vitic. 40: 319-324.
6. Bidenne, C., B. Blondin, S. Dequin, and F. Vezinhet, 1992 Analysis of the chromosomal DNA polymorphism of wine strains of Saccharomyces cerevisiae. Curr. Genet. 22: 1-7.
7. Borneman, A. R., J. A. Leigh-Bell, H. Yu, P. Bertone, M. Gerstein et al., 2006 Target hub proteins serve as master regulators of development in yeast. Genes Dev. 20: 435-448.
8. Borneman, A. R., Z. D. Zhang, J. Rozowsky, M. R. Seringhaus, M. Gerstein et al., 2007a Transcription factor bindind site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct. Integr. Genomics 4: 335-345.
9. Borneman, A. R., T. A. Gianoulis, Z. D. Zhang, H. Yu, J. Rozowsky et al., 2007b Divergence of transcription factor binding sites across related yeast species. Science 317: 815-819.
10. Breiman, L., 2001 Random forests. Mach. Learn. 45: 5-22.
11. Chua, G., Q. D. Morris, R. Sopko, M. D. Robinson, O. Ryan et al., 2006 Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl. Acad. Sci. USA 103: 12045-12050.
12. Dermitzakis, E. T., and A. G. Clark, 2002 Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19: 1114-1121.
13. Dickinson, J. R., L. Eshantha, J. Salgado, and M. J. E. Hewlins, 2002 The catabolism of amino acids to long chain and com-plex alcohols in Saccharomyces cerevisiae. J. Biol. Chem. 278: 8028-8034.
14. Ernst, J., and Z. Bar-Joseph, 2006 STEM: a tool for the analysis of short time series gene expression data. BMC Bioinformatics 7: 191.
15. Frezier, V., and D. Dubourdieu, 1992 Ecology of yeast strain Saccharomyces cerevisiae during spontaneous fermentation in a Bordeaux winery. Am. J. Enol. Vitic. 43: 375-380.
16. Gimeno, C. J., and G. R. Fink, 1994 Induction of pseudohyphal growth by overexpression of PHD1, a Saccharomyces cerevisiae gene related to transcriptional regulators of fungal development. Mol. Cell. Biol. 14: 2100-2112.
17. Haugen, A. C., R. Kelley, J. B. Collins, C. J. Tucker, C. Deng et al., 2004 Integrating phenotypic and expression profiles to map arsenic-response networks. Genome Biol. 5: R95.
18. Holmberg, S., and J. G. Petersen, 1988 Regulation of isoleucinevaline biosynthesis in Saccharomyces cerevisiae. Curr. Genet. 13: 207-217.
19. Horak, C. E., N. M. Luscombe, J. Qian, P. Bertone, S. Piccirrillo et al., 2002 Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16: 3017-3033.
20. Hou, L., X. Cao, M. Wang, and M. Lu, 2009 Effect of overexpression of transcription factors on the fermentation properties of Saccharomyces cerevisiae industrial strains. Lett. Appl. Microbiol. 49: 14-19.
21. Irizarry, R. A., B. M. Bolstad, F. Collin, L. M. Cope, B. Hobbs et al., 2003 Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31: e15.
22. Johnston, J. R., C. Baccari, and R. K. Mortimer, 2000 Genotypic characterization of strains of commercial wine yeasts by tetrad analysis. Res. Microbiol. 151: 583-590.
23. Kasahara, K., K. Ohtsuki, and S. Ki, K. Aoyama, H. Takahashi et al., 2007 Assembly of regulatory factors on rRNA and ribosomal protein genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 27: 6686-6705.
24. Lee, T. I., N. J. Rinaldi, F. Robert, D. T. Odom, Z. Bar-Joseph et al., 2002 Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
25. Li, X., S. Macartur, R. Bourgon, D. Nix, D. A. Pollard et al., 2008 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6: e190.
26. Liaw, A., and M. Wiener, 2002 Classification and Regression by randomForest. R News 2: 18-22.
27. Libkind, D., C. T. Hittinger, E. Valério, C. Gonçalves, J. Dover et al., 2011 Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc. Natl. Acad. Sci. USA 108: 14539-14544.
28. Lilly, M., F. F. Bauer, G. Styger, M. G. Lambrechts, and I. S. Pretorius, 2006 The effect of increased branched-chain amino acid transaminase activity in yeast on the production of higher alcohols and on the flavour profiles of wine and distillates. FEM. Yeast Res. 6: 726-743.
29. Mardia, K. V., J. T. Kent, and J. H. Bibby, 1979 Multivariate Analysis. Academic Press, London.
30. Mortimer, R., and J. Johnston, 1986 Geneology of principal strains of the Yeast Genetics Stock Center. Genetics 113: 35-43.
31. Mortimer, R., R. Lerner, and J. Barr, 1957 Ultraviolet-induced biochemical mutants of Saccharomyces cerevisiae. U.S. Afon.Energy. Comm. Doc. UCRL 3746: 1-10.
32. Ni, L., C. Bruce, C. Hart, J. Leigh-Bell, D. Gelperin et al., 2009 Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev. 23: 1351-1363.
33. Okazaki, S., T. Tachibana, A. Naganuma, N. Mano, and S. Kuge, 2007 Multistep disulfide bond formation in Yap1 is required for sensing and transduction of H2O2 stress signal. Mol. Cell 27: 675-688.
34. Pan, X., and J. Heitman, 2000 Sok2 regulates yeast pseudohyphal differentiation via a transcription factor cascade that regulates cell-cell adhesion. Mol. Cell. Biol. 20: 8364-8372.
35. Puig, S., and J. E. Perez-Ortin, 2000 Stress response and expression patterns in wine fermentations of yeast genes induced at the diauxic shift. Yeast 16: 139-148.
36. Rachidi, N., P. Barre, and B. Blondin, 1999 Multiple Ty-mediated chromosomal translocation lead to karyotype changes in a wine strain of Saccharomyces cerevisiae. Mol. Gen. Genet. 261: 841-850.
37. Ramakers, C., J. M. Ruijter, R. H. Deprez, and A. F. Moorman, 2003 Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 339: 62-66.
38. 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.
39. 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.
40. Rossouw, D., A. H. Van Den Dool, D. Jacobson, and F. F. Bauer, 2010 Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. Appl. Environ. Microbiol. 10.1128/AEM.00586-10.
41. Saint-Prix, F., L. Bönquist, and S. Dequin, 2004 Functional analysis of the ALD gene family of Saccharomyces cerevisiae during anaerobic growth on glucose: the NADP+ -dependent Aldp6p and Aldp5p isoforms play a major role in acetate formation. Microbiology 150: 2209-2220.
42. Salmon, J. M., 1997 Enological fermentation kinetics of an isogenic ploidy series derived form an industrial Saccharomyces cerevisiae strain. J. Ferment. Bioeng. 83: 253-260.
43. Sambrook, J., E. F. Fritsch, and T. Maniatis, 1989 Molecular Cloning: A Laboratory Manual, Ed. 2. Cold Spring Harbor Laboratory Press, New York.
44. Sauer, F., and H. Jäckle, 1991 Concentration-dependent transcriptional activation or repression by Krüppel from a single binding site. Nature 10: 563-566.
45. Schütz, M., and J. Gafner, 1994 Dynamics of the yeast strain population during spontaneous alcoholic fermentation determined by CHEF gel electrophoresis. Lett. Appl. Microbiol. 19: 253-257.
46. Smoot, M., K. Ono, J. Ruscheinski, P.-L. Wang, and T. Ideker, 2011 Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431-432.
47. Tan, K., H. Feizi, C. Luo, S. H. Fan, T. Ravasi et al., 2008 A systems approach to delineate functions of paralogous transcription factors: role of the Yap family in the DNA damage response. Proc. Natl. Acad. Sci. USA 105: 2934-2939.
48. Teixeira, M. C., P. Monteiro, P. Jain, S. Tenreiro, A. R. Fernandes et al., 2006 The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 34: D446-D451.
49. Thorsen, M., G. Lagniel, E. Kristiansson, C. Junot, O. Nerman et al., 2007 Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite. Physiol. Genomics 30: 35-43.
50. Tusher, C. G., R. Tibshirani, and G. Chu, 2001 Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98: 5116-5121.
51. Vestrepen, K. J., S. D. Van Laere, B. M. Vanderhaegen, G. Derdelinckx, J. P. Dufour et al., 2003 Expression levels of the yeast alcohol acetyltransferase genes ATF1, Lg-ATF1, and ATF2 control the formation of a broad range of volatile esters. Appl. Environ. Microbiol. 69: 5228-5237.
52. Wenzel, T. J., A. Migliazza, H. Y. Steensma, and J. A. Van Den Berg, 1992 Efficient selection of phleomycin-resistant Saccharomyces cerevisiae transformants. Yeast 8: 667-668.
53. Workman, C. T., H. C. Mak, S. Mccuine, J. B. Tagne, M. Agarwal et al., 2006 A systems approach to mapping DNA damage response pathways. Science 312: 1054-1059.
54. Yarragudi, A., L. W. Parfrey, and R. H. Morse, 2007 Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae. Nucleic Acids Res. 35: 193-202.
55. Zheng, W., H. Zhao, E. Mancera, L. M. Steinmetz, and M. Snyder, 2010 Genetic analysis of variation in transcription factor binding in yeast. Nature 464: 1187-1191.