Saccharomyces cerevisiae and DNA microarray analyses: What did we learn from it for a better understanding and exploitation of yeast biotechnology?

Applied Microbiology and Biotechnology

Volumn 87, Issue 2, 2010, Pages 391-400

  Hirasawa, Takashi ^a   Furusawa, Chikara ^a   Shimizu, Hiroshi ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

Biotechnology; DNA microarray; Metabolic engineering; Saccharomyces cerevisiae; Transcriptome

Indexed keywords

DNA MICRO-ARRAY; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOME; TRANSCRIPTOMES;

BINDING ENERGY; BINDING SITES; BIOASSAY; BIOCHEMISTRY; BIOCHIPS; BIOTECHNOLOGY; DNA; INDUSTRIAL CHEMICALS; METABOLISM; PRODUCTION ENGINEERING; TRANSCRIPTION; TRANSCRIPTION FACTORS; WINE; YEAST;

GENES;

BACTERIAL DNA; TRANSCRIPTOME;

BIOTECHNOLOGY; BREWING INDUSTRY; ENVIRONMENTAL STRESS; FERMENTATION; FOOD INDUSTRY; GENETIC ANALYSIS; GENETIC ENGINEERING; GENOME; INDUSTRIAL PRODUCTION; PHENOTYPE; POLYMORPHISM; TOLERANCE; YEAST;

BIOTECHNOLOGY; DNA MICROARRAY; FERMENTATION TECHNIQUE; GENE IDENTIFICATION; GENE TARGETING; GENETIC TRANSCRIPTION; NONHUMAN; PHENOTYPE; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SHORT SURVEY; SINGLE NUCLEOTIDE POLYMORPHISM; EVALUATION STUDY; FERMENTATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PROCEDURES;

BIOTECHNOLOGY; FERMENTATION; GENE EXPRESSION REGULATION, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 77953081255     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-010-2582-7     Document Type: Short Survey

References (73)

1. Abbott DA, Suir E, van Maris AJ, Pronk JT (2008) Physiological and transcriptional responses to high concentrations of lactic acid in anaerobic chemostat cultures of Saccharomyces cerevisiae. Appl Environ Microbiol 74:5759-5768
2. Alexandre H, Ansanay-Galeote V, Dequin S, Blondin B (2001) Global gene expression during short-term ethanol stress in Saccharomyces cerevisiae. FEBS Lett 498:98-103 (Pubitemid 32522899)
3. Argueso JL, Carazzolle MF, Mieczkowski PA, Duarte FM, Netto OV, Missawa SK, Galzerani F, Costa GG, Vidal RO, Noronha MF, Dominska M, Andrietta MG, Andrietta SR, Cunha AF, Gomes LH, Tavares FC, Alcarde AR, Dietrich FS, McCusker JH, Petes TD, Pereira GA (2009) Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 19:2258-2270
4. Arima C, Hakamada K, Okamoto M, Hanai T (2008) Modified fuzzy gap statistic for estimating preferable number of clusters in fuzzy k-means clustering. J Biosci Bioeng 105:273-281
5. Beltran G, Novo M, Leberre V, Sokol S, Labourdette D, Guillamon JM, Mas A, Francois J, Rozes N (2006) Integration of tran-scriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations. FEMS Yeast Res 6:1167-1183
6. Bengtsson O, Jeppsson M, Sonderegger M, Parachin NS, Sauer U, Hahn-Hagerdal B, Gorwa-Grauslund MF (2008) Identification of common traits in improved xylose-growing Saccharomyces cerevisiae for inverse metabolic engineering. Yeast 25:835-847
7. Blieck L, Toye G, Dumortier F, Verstrepen KJ, Delvaux FR, Thevelein JM, Van Dijck P (2007) Isolation and characterization of brewer's yeast variants with improved fermentation performance under high-gravity conditions. Appl Environ Microbiol 73:815-824
8. Bro C, Regenberg B, Forster J, Nielsen J (2006) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 8:102-111
9. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA (2001) Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12:323-337
10. Chen JP, Wu KW, Fukuda H (2008) Bioethanol production from uncooked raw starch by immobilized surface-engineered yeast cells. Appl Biochem Biotechnol 145:59-67
11. De Schutter K, Lin YC, Tiels P, Van Hecke A, Glinka S, Weber-Lehmann J, Rouze P, Van de Peer Y, Callewaert N (2009) Genome sequence of the recombinant protein production host Pichia pastoris. Nat Biotechnol 27:561-566
12. DeRisi JL, Iyer VR, Brown PO (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686
13. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuvéglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisramé A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wésolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004) Genome evolution in yeasts. Nature 430:35-44
14. Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95:14863-14868
15. Erasmus DJ, van der Merwe GK, van Vuuren HJ (2003) Genome-wide expression analyses: metabolic adaptation of Saccharomyces cerevisiae to high sugar stress. FEMS Yeast Res 3:375-399
16. Furusawa C, Ono N, Suzuki S, Agata T, Shimizu H, Yomo T (2009) Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. Bioinformatics 25:36-41
17. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11:4241-4257
18. Giaever G, Flaherty P, Kumm J, Proctor M, Nislow C, Jaramillo DF, Chu AM, Jordan MI, Arkin AP, Davis RW (2004) Chemogenomic profiling: identifying the functional interactions of small molecules in yeast. Proc Natl Acad Sci U S A 101:793-798
19. Gibson BR, Boulton CA, Box WG, Graham NS, Lawrence SJ, Linforth RS, Smart KA (2008a) Carbohydrate utilization and the lager yeast transcriptome during brewery fermentation. Yeast 25:549-562
20. Gibson BR, Lawrence SJ, Boulton CA, Box WG, Graham NS, Linforth RS, Smart KA (2008b) The oxidative stress response of a lager brewing yeast strain during industrial propagation and fermentation. FEMS Yeast Res 8:574-585
21. Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M (2001) Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. Genome Res 11:1463-1468
22. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, Kruglyak L (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311:1932-1936
23. Halbeisen RE, Gerber AP (2009) Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol 7:e105
24. Hirasawa T, Nakakura Y, Yoshikawa K, Ashitani K, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S (2006) Comparative analysis of transcriptional responses to saline stress in the laboratory and brewing strains of Saccharomyces cerevisiae with DNA microarray. Appl Microbiol Biotechnol 70:346-357
25. Hirasawa T, Yoshikawa K, Nakakura Y, Nagahisa K, Furusawa C, Katakura Y, Shimizu H, Shioya S (2007) Identification of target genes conferring ethanol stress tolerance to Saccharomyces cerevisiae based on DNA microarray data analysis. J Biotechnol 131:34-44
26. Hirasawa T, Ookubo A, Yoshikawa K, Nagahisa K, Furusawa C, Sawai H, Shimizu H (2009) Investigating the effectiveness of DNA microarray analysis for identifying the genes involved in L-lactate production by Saccharomyces cerevisiae. Appl Microbiol Biotechnol 84:1149-1159
27. Holter NS, Maritan A, Cieplak M, Fedoroff NV, Banavar JR (2001) Dynamic modeling of gene expression data. Proc Natl Acad Sci U S A 98:1693-1698
28. Hu XH, Wang MH, Tan T, Li JR, Yang H, Leach L, Zhang RM, Luo ZW (2007) Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae. Genetics 175:1479-1487
29. Ishida N, Saitoh S, Tokuhiro K, Nagamori E, Matsuyama T, Kitamoto K, Takahashi H (2005) Efficient production of L-Lactic acid by metabolically engineered Saccharomyces cerevisiae with a genome-integrated L-lactate dehydrogenase gene. Appl Environ Microbiol 71:1964-1970
30. Ishida N, Saitoh S, Ohnishi T, Tokuhiro K, Nagamori E, Kitamoto K, Takahashi H (2006a) Metabolic engineering of Saccharomyces cerevisiae for efficient production of pure L-(+)-lactic acid. Appl Biochem Biotechnol 131:795-807
31. Ishida N, Saitoh S, Onishi T, Tokuhiro K, Nagamori E, Kitamoto K, Takahashi H (2006b) The effect of pyruvate decarboxylase gene knockout in Saccharomyces cerevisiae on L-lactic acid production. Biosci Biotechnol Biochem 70:1148-1153
32. James TC, Campbell S, Donnelly D, Bond U (2003) Transcription profile of brewery yeast under fermentation conditions. J Appl Microbiol 94:432-448
33. Jeffries TW, Grigoriev IV, Grimwood J, Laplaza JM, Aerts A, Salamov A, Schmutz J, Lindquist E, Dehal P, Shapiro H, Jin YS, Passoth V, Richardson PM (2007) Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis. Nat Biotechnol 25:319-326
34. Jones T, Federspiel NA, Chibana H, Dungan J, Kalman S, Magee BB, Newport G, Thorstenson YR, Agabian N, Magee PT, Davis RW, Scherer S (2004) The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A 101:7329-7334
35. Katahira S, Mizuike A, Fukuda H, Kondo A (2006) Ethanol fermentation from lignocellulosic hydrolysate by a recombinant xylose- and cellooligosaccharide- assimilating yeast strain. Appl Microbiol Biotechnol 72:1136-1143
36. Katou T, Namise M, Kitagaki H, Akao T, Shimoi H (2009) QTL mapping of sake brewing characteristics of yeast. J Biosci Bioeng 107:383-393
37. Kim S, Imoto S, Miyano S (2004) Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems 75:57-65
38. Li C, Hung Wong W (2001) Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2:RESEARCH0032
39. 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
40. Marullo P, Aigle M, Bely M, Masneuf-Pomarede I, Durrens P, Dubourdieu D, Yvert G (2007) Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cerevisiae strains. FEMS Yeast Res 7:941-952
41. Matsushika A, Sawayama S (2008) Efficient bioethanol production from xylose by recombinant Saccharomyces cerevisiae requires high activity of xylose reductase and moderate xylulokinase activity. J Biosci Bioeng 106:306-309
42. Matsushika A, Watanabe S, Kodaki T, Makino K, Sawayama S (2008) Bioethanol production from xylose by recombinant Saccharomyces cerevisiae expressing xylose reductase, NADP+-dependent xylitol dehydrogenase, and xylulokinase. J Biosci Bioeng 105:296-299
43. Matsushika A, Inoue H, Watanabe S, Kodaki T, Makino K, Sawayama S (2009) Efficient bioethanol production by a recombinant flocculent Saccharomyces cerevisiae strain with a genome-integrated NADP+-dependent xylitol dehydrogenase gene. Appl Environ Microbiol 75:3818-3822
44. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfeiffer F, Zollner A (1997) Overview of the yeast genome. Nature 387:7-65
45. Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S, Nakamura N, Shimonaga T, Hattori M, Ashikari T (2009) Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res 16:115-129
46. Nakata T, Miyafuji H, Saka S (2006) Bioethanol from cellulose with supercritical water treatment followed by enzymatic hydrolysis. Appl Biochem Biotechnol 129-132:476-485
47. Ogawa Y, Nitta A, Uchiyama H, Imamura T, Shimoi H, Ito K (2000) Tolerance mechanism of the ethanol-tolerant mutant of sake yeast. J Biosci Bioeng 90:313-320
48. Ookubo A, Hirasawa T, Yoshikawa K, Nagahisa K, Furusawa C, Shimizu H (2008) Improvement of L-lactate production by CYB2 gene disruption in a recombinant Saccharomyces cerevisiae strain under low pH condition. Biosci Biotechnol Biochem 72:3063-3066
49. Pandey G, Yoshikawa K, Hirasawa T, Nagahisa K, Katakura Y, Furusawa C, Shimizu H, Shioya S (2007) Extracting the hidden features in saline osmotic tolerance in Saccharomyces cerevisiae from DNA microarray data using the self-organizing map: biosynthesis of amino acids. Appl Microbiol Biotechnol 75:415-426
50. Parsons AB, Lopez A, Givoni IE, Williams DE, Gray CA, Porter J, Chua G, Sopko R, Brost RL, Ho CH, Wang J, Ketela T, Brenner C, Brill JA, Fernandez GE, Lorenz TC, Payne GS, Ishihara S, Ohya Y, Andrews B, Hughes TR, Frey BJ, Graham TR, Andersen RJ, Boone C (2006) Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast. Cell 126:611-625
51. Pilpel Y, Sudarsanam P, Church GM (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet 29:153-159
52. 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
53. Rep M, Krantz M, Thevelein JM, Hohmann S (2000) The transcriptional response of Saccharomyces cerevisiae to osmotic shock. Hot1p and Msn2p/Msn4p are required for the induction of subsets of high osmolarity glycerol pathway-dependent genes. J Biol Chem 275:8290-8300
54. Rossignol T, Dulau L, Julien A, Blondin B (2003) Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 20:1369-1385
55. Sahara T, Goda T, Ohgiya S (2002) Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature. J Biol Chem 277:50015-50021
56. Saitoh S, Ishida N, Onishi T, Tokuhiro K, Nagamori E, Kitamoto K, Takahashi H (2005) Genetically engineered wine yeast produces a high concentration of L-lactic acid of extremely high optical purity. Appl Environ Microbiol 71:2789-2792
57. Schacherer J, Ruderfer DM, Gresham D, Dolinski K, Botstein D, Kruglyak L (2007) Genome-wide analysis of nucleotide-level variation in commonly used Saccharomyces cerevisiae strains. PLoS ONE 2:e322
58. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470
59. Serrano R, Ruiz A, Bernal D, Chambers JR, Arino J (2002) The transcriptional response to alkaline pH in Saccharomyces cerevisiae: evidence for calcium-mediated signalling. Mol Microbiol 46:1319-1333
60. Shobayashi M, Ukena E, Fujii T, Iefuji H (2007) Genome-wide expression profile of sake brewing yeast under shaking and static conditions. Biosci Biotechnol Biochem 71:323-335
61. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 96:2907-2912
62. Tavazoie S, Hughes JD, Campbell MJ, Cho RJ, Church GM (1999) Systematic determination of genetic network architecture. Nat Genet 22:281-285
63. Tegner J, Yeung MK, Hasty J, Collins JJ (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A 100:5944-5949
64. Toh H, Horimoto K (2002) Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling. Bioinformatics 18:287-297
65. Tokuhiro K, Ishida N, Nagamori E, Saitoh S, Onishi T, Kondo A, Takahashi H (2009) Double mutation of the PDC1 and ADH1 genes improves lactate production in the yeast Saccharomyces cerevisiae expressing the bovine lactate dehydrogenase gene. Appl Microbiol Biotechnol 82:883-890
66. Tomida S, Hanai T, Honda H, Kobayashi T (2002) Analysis of expression profile using fuzzy adaptive resonance theory. Bioinformatics 18:1073-1083
67. Wood V, Gwilliam R, Rajandream MA, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Düsterhöft A, Fritzc C, Holzer E, Moestl D, Hilbert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sánchez M, del Rey F, Benito J, Domínguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880
68. 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 (Pubitemid 44748454)
69. Yale J, Bohnert HJ (2001) Transcript expression in Saccharomyces cerevisiae at high salinity. J Biol Chem 276:15996-16007
70. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP (2002) Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 30:e15
71. Yoshida S, Hashimoto K, Shimada E, Ishiguro T, Minato T, Mizutani S, Yoshimoto H, Tashiro K, Kuhara S, Kobayashi O (2007) Identification of bottom-fermenting yeast genes expressed during lager beer fermentation. Yeast 24:599-606 (Pubitemid 47082726)
72. Yoshikawa K, Furusawa C, Hirasawa T, Shimizu H (2008) Genome-wide analysis of the effects of location and number of stress response elements on gene expression in Saccharomyces cerevisiae. J Biosci Bioeng 106:507-510
73. Yoshikawa K, Tanaka T, Furusawa C, Nagahisa K, Hirasawa T, Shimizu H (2009) Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stress in Saccharomyces cerevisiae. FEMS Yeast Res 9:32-44