Transcription profile of brewery yeast under fermentation conditions

Journal of Applied Microbiology

Volumn 94, Issue 3, 2003, Pages 432-448

  James, T C ^a   Campbell, S ^a   Donnelly, D ^b   Bond, U ^a  

^a TRINITY COLLEGE DUBLIN   (Ireland)

^b DIAGEO PLC   (Ireland)

Author keywords

Anaerobiosis; Brewing; Fermentation; Lager yeast transcriptome; Metabolic changes; Stress response

Indexed keywords

BIOCHEMISTRY; BIOSYNTHESIS; FATTY ACIDS; METABOLISM; NUCLEIC ACIDS; PROTEINS; TRANSCRIPTION; YEAST;

ANAEROBIOSIS; BREWING; CONDITION; FERMENTATION CONDITIONS; LAGER YEAST TRANSCRIPTOME; METABOLIC CHANGES; PROTEIN SYNTHESIS; STRESSES RESPONSE; TRANSCRIPTION PROFILES; TRANSCRIPTOMES;

FERMENTATION;

FERMENTATION; YEAST;

ANAEROBIC GROWTH; ARTICLE; BIOTECHNOLOGY; BREWING; CARBOHYDRATE METABOLISM; DNA PROBE; FERMENTATION TECHNIQUE; GENE EXPRESSION REGULATION; METABOLIC ACTIVATION; SAMPLING; STRESS; TRANSCRIPTION REGULATION; YEAST;

EUKARYOTA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES PASTORIANUS;

EID: 0037221382     PISSN: 13645072     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2672.2003.01849.x     Document Type: Article

References (80)

1. Abramova, N., Sertil, O., Mehta, S. and Lowry, C.V. (2001a) Reciprocal regulation of anaerobic and aerobic cell wall mannoprotein gene expression in Saccharomyces cerevisiae. Journal of Bacteriology 183, 2881-2887.
2. Abramova, N.E., Cohen, B.D., Sertil, O., Kapoor, R., Davies, K.J. and Lowry, C.V. (2001b) Regulatory mechanisms controlling expression of the DAN/TIR mannoprotein genes during anaerobic remodeling of the cell wall in Saccharomyces cerevisiae. Genetics 157, 1169-1177.
3. Alexandre, H., Ansanay-Galeote, V., Dequin, S. and Blondin, B. (2001) Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Letters 498, 98-103.
4. Amillet, J.M., Buisson, N. and Labbe-Bois, R. (1996) Characterization of an upstream activation sequence and two Rox1p-responsive sites controlling the induction of the yeast HEM13 gene by oxygen and heme deficiency. Journal of Biological Chemistry 271, 24425-24432.
5. Attfield, P.V. and Kletsas, S. (2000) Hyperosmotic stress response by strains of bakers' yeasts in high sugar concentration medium. Letters in Applied Microbiology 31, 323-327.
6. Backhus, L.E., DeRisi, J., , P.O. and Bisson, L.F. (2001) Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Research 1, 111-125.
7. Bakker, B.M., Overkamp, K.M., van Maris, A.J., Kotter, P., Luttik, M.A., van Dijken, J.P. and Pronk, J.T. (2001) Stoichiometry and compartmentation of NADH metabolism in Saccharomyces cerevisiae. FEMS Microbiology Reviews 25, 15-37.
8. Banno, I. and Kaneko, Y. (1989) A genetic analysis of taxonomic relation between Saccharomyces cerevisiae and Saccharomyces bayanus. Yeast 5, 373-377.
9. Bracken, A.P. and Bond, U. (1999) Reassembly and protection of small nuclear ribonucleoprotein particles by heat shock proteins in yeast cells. RNA 5, 1586-1596.
10. Brewster, N.K., Val, D.L., Walker, M.E. and Wallace, J.C. (1994) Regulation of pyruvate carboxylase isozyme (PYC1, PYC2) gene expression in Saccharomyces cerevisiae during fermentative and nonfermentative growth. Archives in Biochemistry and Biophysics 311, 62-71.
11. Brosnan, M.P., Donnelly, D., James, T.C. and Bond, U. (2000) The stress response is repressed during fermentation in brewery strains of yeast. Journal of Applied Microbiology 88, 746-755.
12. Cahill, G., Walsh, P.K. and Donnelly, D. (2000) Determination of yeast glycogen content by individual cell spectroscopy using image analysis. Biotechnology and Bioengineering 69, 312-322.
13. Carrasco, P., Querol, A. and del Olmo, M. (2001) Analysis of the stress resistance of commercial wine yeast strains. Archives in Microbiology 175, 450-457.
14. Casaregola, S., Nguyen, H.V., Lapathitis, G., Kotyk, A. and Gaillardin, C. (2001) Analysis of the constitution of the beer yeast genome by PCR, sequencing and subtelomeric sequence hybridization. International Journal of Systematics and Evolutionary Microbiology 51, 1607-1618.
15. Causton, H.C., Ren, B., Koh, S.S., Harbison, C.T., Kanin, E., Jennings, E.G., Lee, T.I., True, H.L., Lander, E.S. and Young, R.A. (2001) Remodeling of yeast genome expression in response to environmental changes. Molecular Biology of the Cell 12, 323-337.
16. Cavalieri, D., Townsend, J.P. and Hartl, D.L. (2000) Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proceedings of the National Academy of Sciences of the United States of America 97, 12369-12374.
17. Charron, M.J., Dubin, R.A. and Michels, C.A. (1986) Structural and functional analysis of the MAL1 locus of Saccharomyces cerevisiae. 6, 3891-3899.
18. Chelstowska, A. and Butow, R.A. (1995) RTG genes in yeast that function in communication between mitochondria and the nucleus are also required for expression of genes encoding peroxisomal proteins. Journal of Biological Chemistry 270, 18141-18146.
19. Cohen, R., Yokoi, T., Holland, J.P., Pepper, A.E. and Holland, M.J. (1987) Transcription of the constitutively expressed yeast enolase gene ENO1 is mediated by positive and negative cis-acting regulatory sequences. Molecular Cell Biology 7, 2753-2761.
20. Dawes, I., Day, R., Duan, D., Roddick, F., Stanley, G., Chambers, P., Chandler, Higgins, V., Lentini, A. and Rogers, P. (2002) Brewing yeast, gene expression and beer quality. In American Society of Brewing Chemists Abstracts, 2002 meeting 14p. http:/www.asbcnetorg/meetings/2002/abstracts/p-14.htm.
21. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680-686.
22. el Moualij, B., Duyckaerts, C., Lamorte-Brasseur, J. and Sluse, F.E. (1997) Phylogenetic classifcation of the mitochondrial carrier family of Saccharomyces cerevisiae. Yeast 13, 573-581.
23. Entian, K.D. and Barnett, J.A. (1992) Regulation of sugar utilization by Saccharomyces cerevisiae. Trends in Biochemical Sciences 17, 506-510.
24. Epstein, C.B., Waddle, J.A., Hale, W. IV, Dave, V., Thornton, J., Macatee, T.L., Garner, H.R. and Butow, R.A. (2001) Genome-wide responses to mitochondrial dysfunction. Molecular Biology of the Cell 12, 297-308.
25. Fazzio, T.G., Kooperberg, C., Goldmark, J.P., Neal, C., Basom, R., Delrow, J. and Tsukiyama, T. (2001) Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodehng complexes in transcriptional repression. Molecular Cell Biology 21, 6450-6460.
26. Ferguson, L.R. and von Borstel, R.C. (1992) Induction of the cytoplasmic 'petite' mutation by chemical and physical agents in Saccharomyces cerevisiae. Mutation Research 268, 103-148.
27. Galitski, T., Saldanha, A.J., Styles, C.A., Lander, E.S. and Fink, G.R. (1999) Ploidy regulation of gene expression. Science 285, 251-254.
28. Gasch, A.P., Huang, M., Metzner, S., Botstein, D., Elledge, S.J. and Brown, P.O. (2001) Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Molecular Biology of the Cell 12, 2987-3003.
29. Grunwald-Raij, H. and Margalith, P. (1990) Ethanol fermentation by nystatin-resistant strains of Saccharomyces cerevisiae. Journal of Applied Bacteriology 68, 247-252.
30. Guijo, S., Mauricio, J.C., Salmon, J.M. and Ortega, J.M. (1997) Determination of the relative ploidy in different Saccharomyces cerevisiae strains used for fermentation and 'flor' film ageing of dry sherry-type wines. Yeast 13, 101-117.
31. Hammond, J.R. (1995) Genetically-modified brewing yeasts for the 21st century. Progress to date. Yeast 11, 1613-1627.
32. Haselbeck, R.J. and McAlister-Henn, L. (1993) Function and expression of yeast mitochondrial NAD- and NADP-specific isocitrate dehydrogenases. Journal of Biological Chemistry 268, 12116-12122.
33. Herrero, P., Galindez, J., Ruiz, N., Martinez-Campa, C. and Moreno, F. (1995) Transcriptional regulation of the Saccharomyces cerevisiae HXK1, HXK2 and GLK1 genes. Yeast 11, 137-144.
34. Higgins, J.V., Oliver, A.D., Day, R.E., Dawes, I.W. and Rogers, P.J. (2001) Application of genome-wide transcriptional analysis to identify genetic markers useful in industrial fermentations. In European Brewery Convention Congress, Budapest, Hungary, 2001. Nurnberg, Germany: EBC Publications, Fachverlag Hans Carl.
35. Hohmann, S. (1991) Characterization of PDC6, a third structural gene for pyruvate decarboxylase in Saccharomyces cerevisiae. Journal of Bacteriology 173, 7963-7969.
36. Hohmann, S. (2002) Osmotic stress signaling and osmoadaptation in yeasts. Microbiology and Molecular Biology Reviews 66, 300-372.
37. Jensen-Pergakes, K., Guo, Z., Giattina, M., Sturley, S.L. and Bard, M. (2001) Transcriptional regulation of the two sterol esterification genes in the yeast Saccharomyces cerevisiae. Journal of Bacteriology 183, 4950-4957.
38. Joubert, R., Brignon, P., Lehmann, C., Monribot, C., Gendre, F. and Boucherie, H. (2000) Two-dimensional gel analysis of the proteome of lager brewing yeasts. Yeast 16, 511-522.
39. Joubert, R., Strub, J.M., Zugmeyer, S., Kobi, D., Carte, N., VanDorsselaer, A., Boucherie, H. and Jaquet-Guffreund, L. (2001) Identification by mass spectrometry of two-dimensional gel electrophoresis-separated proteins extracted from lager brewing yeast. Electrophoresis 22, 2969-2982.
40. Kapteyn, J.C., ter Riet, B., Vink, E., Blad, S., De Nobel, H., Van Den Ende, H. and Klis, F.M. (2001) Low external pH induces HOG1-dependent changes in the organization of the Saccharomyces cerevisiae cell wall. Molecular Microbiology 39, 469-479.
41. Karpichev, I.V. and Small, G.M. (1998) Global regulatory functions of Oaf1p and Pip2p (Oaf2p), transcription factors that regulate genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Molecular Cellular Biology 18, 6560-6570.
42. Karst, F. and Lacroute, F. (1977) Ertosterol biosynthesis in Saccharomyces cerevisiae: mutants deficient in the early steps of the pathway. Molecular and General Genetics 154, 269-277.
43. Kastaniotis, A.J. and Zitomer, R.S. (2000) Roxl mediated repression. Oxygen dependent repression in yeast. Advances in Experimental Medicine and Biology 475, 185-195.
44. Kennedy, A. (2000) Yeast handling in brewery. In Brewing Yeast Fermentation Performance ed. Smart, K. pp. 129-134. Oxford, UK: Blackwell Science Ltd.
45. Kleyn, J. and Hough, J. (1971) The microbiology of brewing. Annual Reviews in Microbiology 25, 583-608.
46. Kunau, W.H. (1998) Peroxisome biogenesis: from yeast to man. Current Opinions in Microbiology 1, 232-237.
47. Kunau, W.H., Beyer, A., Franken, T., Gotte, K., Marzioch, M., Saidowsky, J., Skaletz-Rorowski, A. and Wiebel, F.F. (1993) Two complementary approaches to study peroxisome biogenesis in Saccharomyces cerevisiae: forward and reversed genetics. Biochimie 78, 209-224.
48. Kunau, W.H. and Hartig, A. (1992) Peroxisome biogenesis in Saccharomyces cerevisiae. Antonie Van Leeuwenhoek 62, 63-78.
49. Lawson, J.E., Behal, R.H. and Reed, L.J. (1991) Disruption and mutagenesis of the Saccharomyces cerevisiae PDX1 gene encoding the protein X component of the pyruvate dehydrogenase complex. Biochemistry 30, 2834-2839.
50. Lawson, J.E., Gawaz, M., Klingenberg, M. and Douglas, M.G. (1990) Structure-function studies of adenine nucleotide transport in mitochondria. 1. Construction and genetic analysis of yeast mutants encoding the ADP/ATP carrier protein of mitochondria. Journal of Biological Chemistry 265, 14195-14201.
51. Liu, X.D., Liu, P.C., Santoro, N. and Thiele, D.J. (1997) Conservation of a stress response: human heat shock transcription factors functionally substitute for yeast HSF. EMBO Journal 16, 6466-6477.
52. Maris, A.F., Assumpcao, A.L., Bonatto, D., Brendel, M. and Henriques, J.A. (2001) Diauxic shift-induced stress resistance against hydroperoxides in Saccharomyces cerevisiae is not an adaptive stress response and does not depend on functional mitochondria. Current Genetics 39, 137-149.
53. Millan, C., Mauricio, J.C. and Ortega, J.M. (1990) Alcohol and aldehyde dehydrogenase from Saccharomyces cerevisiae: specific activity and influence on the production of acetic acid, ethanol and higher alcohols in the first 48 h of fermentation of grape must. Microbios 64, 93-101.
54. Moore, P.A., Sagliocco, F.A., Wood, R.M. and Brown, A.J. (1991) Yeast glycolytic mRNAs are differentially regulated. Molecular Cellular Biology 11, 5330-5337.
55. Moskvina, E., Schuller, C., Maurer, C.T., Mager, W.H. and Ruis, H. (1998) A search in the genome of Saccharomyces cerevisiae for genes regulated via stress response elements. Yeast 14, 1041-1050.
56. Neuser, F., Zorn, H., Richter, U. and Berger, R.G. (2000) Purification, characterisation and cDNA sequencing of pyruvate decarboxylase from Zygosaccharomyces bisporus. Journal of Biological Chemistry 381, 349-353.
57. Parrou, J.L., Enjalbert, B., Plourde, L., Bauche, A., Gonzalez, B. and Francois, J. (1999) Dynamic responses of rcserve carbohydrate metabolism under carbon and nitrogen limitations in Saccharomyces cerevisiae. Yeast 15, 191-203.
58. Parrou, J.L., Teste, M.A. and Francois, J. (1997) Effects of various types of stress on the metabolism of reserve carbohydrates in Saccharomyces cerevisiae: genetic evidence for a stress-induced recycling of glycogen and trehalose. Microbiology (Reading, England) 143, 1891-1900.
59. Plapp, B.V., Ganzhorn, A.J., Gould, R.M., Green, D.W. and Hershey, A.D. (1987) Structure and function in yeast alcohol dehydrogenases. Advances in Biophysics 232, 227-236.
60. Pronk, J.T., Yde Steensma, H. and Van Dijken, J.P. (1996) Pyruvate metabolism in Saccharomyces cerevisiae. Yeast 12, 1607-1633.
61. Pugh, T., Dunn, B., Venteicher, A., Metzner, S., Bower, P., Bondre, C., Seabrooks, J., Ryder, D., Botstein, D. and Brown, P. (2002) Global analysis of yeast gene expression during a brewery fermentation. In Annual meeting of the American Society of Brewing Chemists, 2002, Abstracts, o2. http://www.asbcnetorg/meetings/2002/abstracts/o-2.htm.
62. Puig, S. and Perez-Ortin, J.E. (2000) Stress response and expression patterns in wine fermentations of yeast genes induced at the diauxic shift. Yeast 16, 139-148.
63. Purdue, P.E. and Lazarow, P.B. (2001) Peroxisome biogenesis. Annual Reviews in Cell and Developmental Biology 17, 701-752.
64. Rachidi, N., Martinez, M.J., Barre, P. and Blondin, B. (2000) Saccharomyces cerevisiae PAU genes are induced by anaerobiosis. Molecular Microbiology 35, 1421-1430.
65. Randez-Gil, F., Sanz, P. and Prieto, J.A. (1999) Engineering baker's yeast:room for improvement. Trends in Biotechnology 17, 237-244.
66. Reed, L.J., Browning, K.S., Niu, X.D., Behal, R.H. and Uhlinger, D.J. (1989) Biochemical and molecular genetic aspects of pyruvate dehydrogenase complex from Saccharomyces cerevisiae. Annals of the New York Academy of Sciences 573, 155-167.
67. Ruis, H. and Schuller, C. (1995) Stress signaling in yeast. Bioessays 17, 959-965.
68. Sekito, T., Thornton, J. and Butow, R.A. (2000) Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Molecular Biology of the Cell 11, 2103-2115.
69. Sherman, F. (1991) Getting started with yeast. Methods in Enzymology, 194, 3-21.
70. Smith, S.J., Crowley, J.H. and Parks, L.W. (1996) Transcriptional regulation by ergosterol in the yeast Saccharomyces cerevisiae. Molecular Cell Biology 16, 5427-5432.
71. Stambuk, B.U., da Silva, M.A., Panek, A.D. and de Araujo, P.S. (1999) Active α-glucoside transport in Saccharomyces cerevisiae. FEMS Microbiology Letters 170, 105-110.
72. Stoops, J.K., Cheng, R.H., Yazdi, M.A., Maeng, C.Y., Schroeter, J.P., Klueppelberg, U., Kolodziej, S.J., Baker, T.S. and Reed, L.J. (1997) On the unique structural organization of the Saccharomyces cerevisiae pyruvate dehydrogenase complex. Journal of Biological Chemistry 272, 5757-5756.
73. Swan, T.M. and Watson, K. (1999) Stress tolerance in a yeast lipid mutant: membrane lipids influence tolerance to heat and ethanol independently of heat shock proteins and trehalose. Canadian Journal of Microbiology 45, 472-479.
74. ter Linde, J.J., Liang, H., Davis, R.W., Steensma, H.Y., van Dijken, J.P. and Pronk, J.T. (1999) Genome-wide transcriptional analysis of aerobic and anaerobic chemostat cultures of Saccharomyces cerevisiae. Journal of Bacteriology 181, 7409-7413.
75. Trotter, P.J. (2001) The genetics of fatty acid metabolism in Saccharomyces cerevisiae. Annual Reviews in Nutrition, 21, 97-119.
76. Turkel, S. and Bisson, L.F. (1999) Transcription of the HXT4 gene is regulated by Gcr1p and Gcr2p in the yeast S. cerevisiae. Yeast (Chichester, England) 15, 1045-1057.
77. Uemura, H. and Jigami, Y. (1992) Role of GCR2 in transcriptional activation of yeast glycolytic genes. Molecular and Cellular Biology 12, 3834-3842.
78. Uemura, H., Koshio, M., Inoue, Y., Lopez, M.C. and Baker, H.V. (1997) The role of Gcr1p in the transcriptional activation of glycolytic genes in yeast Saccharomyces cerevisiae. Genetics 147, 521-532.
79. Velmurugan, S., Lobo, Z. and Maitra, P.K. (1997) Suppression of pdc2 regulating pyruvate decarboxylase synthesis in yeast. Genetics 145, 587-594.
80. Winderickx, J., de Winde, J.H., Crauwels, M., Hino, A., Hohmann, S., Van Dijck, P. and Thevelein, J.M. (1996) Regulation of genes encoding subunits of the trehalose synthase complex in Saccharomyces cerevisiae: novel variations of STRE-mediated transcription control? Molecular and General Genetics 252, 470-482.