Genome-Wide Study of the Adaptation of Saccharomyces cerevisiae to the Early Stages of Wine Fermentation

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Novo, Maite ^a,b   Mangado, Ana ^a   Quirós, Manuel ^a   Morales, Pilar ^a   Salvadó, Zoel ^a   Gonzalez, Ramon ^a  

^a UNIVERSITY OF LA RIOJA   (Spain)

^b UNIVERSITAT ROVIRA I VIRGILI   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCOSE;

ADAPTATION; ARTICLE; CONTINUOUS CULTURE; CONTROLLED STUDY; FERMENTATION; FUNGAL GENE; FUNGAL GENOME; FUNGAL STRAIN; FUNGUS GROWTH; GENE DELETION; HAPLOINSUFFICIENCY; HOMOZYGOTE; NONHUMAN; PEROXISOME; PROTEIN SYNTHESIS; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE; WINE;

ADAPTATION, BIOLOGICAL; FERMENTATION; GENE DELETION; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HAPLOINSUFFICIENCY; HOMOZYGOTE; MUTATION; PHENOTYPE; SACCHAROMYCES CEREVISIAE; WINE;

EID: 84883498349     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0074086     Document Type: Article

References (34)

1. Gonzalez R, Muñoz R, Carrascosa AV, (2011) Production of wine starter cultures. In: Carrascosa AV, Muñoz R, Gonzalez R, eds. Molecular Wine Microbiology. Academic Press. pp. pp. 279-298.
2. Trabalzini L, Paffetti A, Scaloni A, Talamo F, Ferro E, et al. (2003) Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae. Biochem J 370: 35-36. doi:10.1042/BJ20020140. PubMed: 12401115.
3. Rossignol T, Postaire O, Storaï J, Blondin B, (2006) Analysis of the genomic response of a wine yeast to rehydration and inoculation. Appl Microbiol Biotechnol 71: 699-712. doi:10.1007/s00253-006-0398-2. PubMed: 16607525.
4. Novo M, Beltran G, Rozes N, Guillamon JM, Sokol S, et al. (2007) Early transcriptional response of wine yeast after rehydration: osmotic shock and metabolic activation. FEMS Yeast Res 7: 304-316. doi:10.1111/j.1567-1364.2006.00175.x. PubMed: 17132143.
5. Salvadó Z, Chiva R, Rodríguez-Vargas S, Rández-Gil F, Mas Aet al. (2008) Proteomic evolution of a wine yeast during the first hours of fermentation. FEMS Yeast Res 8: 1137-1146.
6. Pérez-Torrado R, Carrasco P, Aranda A, Gimeno-Alcañiz J, Pérez-Ortín JE, et al. (2002) Study of the first hours of microvinification by the use of osmotic stress-response genes as probes. Syst Appl Microbiol 25: 153-161. doi:10.1078/0723-2020-00087. PubMed: 12086182.
7. Rossignol T, Dulau L, Julien A, Blondin B, (2003) Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 20: 1369-1385. doi:10.1002/yea.1046. PubMed: 14663829.
8. Varela C, Cárdenas J, Melo F, Agosin E, (2003) Quantitative analysis of wine yeast gene expression profiles under winemaking conditions. Yeast 22: 369-383. PubMed: 15806604.
9. Beltran G, Novo M, Leberre V, Sokol S, Labourdette D, et al. (2006) Integration of transcriptomic and metabolic analyses for understanding the global responses of low-temperature winemaking fermentations. FEMS Yeast Res 6: 1167-1183. doi:10.1111/j.1567-1364.2006.00106.x. PubMed: 17156014.
10. Marks VD, Ho Sui SJ, Erasmus D, van der Merwe GK, Brumm J, et al. (2008) Dynamics of the yeast transcriptome during wine fermentation reveals a novel fermentation stress response. FEMS Yeast Res 8: 35-52. doi:10.1111/j.1567-1364.2007.00338.x. PubMed: 18215224.
11. Rossouw D, Olivares-Hernandes R, Nielsen J, Bauer FF, (2009) Comparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation. Appl Environ Microbiol 75: 6600-6612. doi:10.1128/AEM.01251-09. PubMed: 19700545.
12. Birrell GW, Brown JA, Wu HI, Giaever G, Chu AM, et al. (2002) Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc Natl Acad Sci U S A 99: 8778-8783. doi:10.1073/pnas.132275199. PubMed: 12077312.
13. Tai SL, Snoek I, Luttik MA, Almering MJ, Walsh MC, et al. (2007) Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae. Microbiology 153: 877-886. doi:10.1099/mic.0.2006/002873-0. PubMed: 17322208.
14. Delneri D, Hoyle DC, Gkargkas K, Cross EJ, Rash B, et al. (2008) Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nat Genet 40: 113-117. doi:10.1038/ng.2007.49. PubMed: 18157128.
15. Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, et al. (1999) Functional characterization of the Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906. doi:10.1126/science.285.5429.901. PubMed: 10436161.
16. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391. doi:10.1038/nature00935. PubMed: 12140549.
17. Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, et al. (2009) Quantitative phenotyping via deep barcode sequencing. Genome Res 19: 1836-1842. doi:10.1101/gr.093955.109. PubMed: 19622793.
18. van Voorst F, Houghton-Larsen J, Jønson L, Kielland-Brandt MC, Brandt A, (2006). Genome-wide identification of genes required for growth of Saccharomyces cerevisiae underethanol stress. Yeast 23: 351-359.
19. Kumar GR, Goyashiki R, Ramakrishnan V, Karpel JE, Bisson LF, (2008) Genes required for ethanol tolerance and utilization in Saccharomyces cerevisiae. Am J Enol Vitic 59: 401-411.
20. Yazawa H, Iwahashi H, Uemura H, (2007) Disruption of URA7 and GAL6 improves the ethanol tolerance and fermentation capacity of Saccharomyces cerevisiae. Yeast 24: 551-560.
21. Fujita K, Matsuyama A, Kobayashi Y, Iwahashi H, (2006) The genome-wide screening of yeast deletion mutants to identify the genes required fortolerance to ethanol and other alcohols. FEMS Yeast Res 6: 744-750. doi:10.1111/j.1567-1364.2006.00040.x. PubMed: 16879425.
22. Auesukaree C, Damnernsawad A, Kruatrachue M, Pokethitiyook P, Boonchird C, et al. (2009) Genome-wide identification of genes involved in tolerance to various environmental stresses in Saccharomyces cerevisiae. J Appl Genet 50: 301-310.
23. Yoshikawa K, Tanaka T, Furusawa C, Nagahisa K, Hirasawa T, et al. (2009) Comprehensive phenotypic analysis for identification of genes affecting growth under ethanol stressin Saccharomyces cerevisiae. FEMS Yeast Res 9: 32-44.
24. Teixeira MC, Raposo LR, Mira NP, Lourenço AB, Sá-Correia I, (2009) Genome-wide identification of Saccharomyces cerevisiae genes required for maximal tolerance to ethanol. Appl Environ Microbiol 75: pp. 5761-5772.
25. Ando A, Tanaka F, Murata Y, Takagi H, Shima J, (2006) Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae. FEMS Yeast Res 6: 249-267. doi:10.1111/j.1567-1364.2006.00035.x. PubMed: 16487347.
26. Teixeira MC, Raposo LR, Palma M, Sá-Correia I, (2010) Identification of genes required for maximal tolerance to high-glucose concentrations, as those present in industrial alcoholic fermentation media, through a chemogenomics approach. Omics 14: 201-210. doi:10.1089/omi.2009.0149. PubMed: 20210661.
27. Piggott N, Cook MA, Tyers M, Measday V, (2011). Genome-wide fitness profiles reveal a requirement for autophagy during yeast fermentation. G3 (Bethesda) 1: 353-367.
28. Varela C, Pizarro F, Agosin E, (2004) Biomass content governs fermentation rate in nitrogen-deficient wine musts. Appl Environ Microbiol 70: 3392-3400. doi:10.1128/AEM.70.6.3392-3400.2004. PubMed: 15184136.
29. Pierce SE, Davis RW, Nislow C, Giaever G, (2007) Genome-wide analysis of barcoded Saccharomyces cerevisiae gene-deletion mutants in pooled cultures. Nat Protoc 2: 2958-2974. doi:10.1038/nprot.2007.427. PubMed: 18007632.
30. Bely M, Sablayrolles JM, Barre P, (1990) Automatic detection of assimilable nitrogen deficiencies during alcoholic fermentation in oenological conditions. J Ferment Bioeng 70: 246-252. doi:10.1016/0922-338X(90)90057-4.
31. Harsch MJ, Lee SA, Goddard MR, Gardner RC, (2010) Optimized fermentation of grape juice by laboratory strains of Saccharomyces cerevisiae. FEMS Yeast Res 10: 72-82. doi:10.1111/j.1567-1364.2009.00580.x. PubMed: 19840118.
32. Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210. doi:10.1093/nar/30.1.207. PubMed: 11752295.
33. Balakrishnan R, Park J, Karra K, Hitz BC, Binkly G, et al. (2012) YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database(2012) pp. bar062. doi:10.1093/database/bar062.
34. MIDAS. Microarray Data Analysis System. Available: http://www.tm4.org/midas.html. Accessed 2013 August 5.