title: Comparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation.
abstract: Commercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.
authors.affiliation: Institute for Wine Biotechnology, Department of Viticulture and Oenology, University of Stellenbosch, Matieland 7602, South Africa.
authors.forename: Debra
authors.initials: D
authors.lastname: Rossouw
authors.forename: Roberto
authors.initials: R
authors.lastname: Olivares-Hernandes
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
authors.forename: Florian F
authors.initials: FF
authors.lastname: Bauer
mesh_terms: D001709:Biotechnology; D002244:Carbon / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism; D005285:Fermentation; D005427:Flocculation; D005516:Food Microbiology; D020869:Gene Expression Profiling; D005800:Genes, Fungal; D008562:Membrane Glycoproteins / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics* / Q000378:metabolism / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D013045:Species Specificity; D013312:Stress, Physiological; D014920:Wine / Q000382:microbiology*
chemical_list: D008562:Membrane Glycoproteins; D029701:Saccharomyces cerevisiae Proteins; C025363:mannoproteins; D002244:Carbon
references.citation: Mol Biol Cell. 1998 Jan;9(1):161-71
references.pmid: 9436998
references.citation: J Comput Biol. 1999 Fall-Winter;6(3-4):281-97
references.pmid: 10582567
references.citation: Trends Biotechnol. 2002 Oct;20(10):426-32
references.pmid: 12220905
references.citation: FEMS Yeast Res. 2003 May;3(3):269-87
references.pmid: 12689635
references.citation: Biotechnol Bioeng. 1999 Sep 20;64(6):698-708
references.pmid: 10417219
references.citation: Mol Biol Cell. 2003 Oct;14(10):4272-84
references.pmid: 14517335
references.citation: J Appl Microbiol. 2005;98(2):299-307
references.pmid: 15659184
references.citation: Science. 2001 Feb 2;291(5505):878-81
references.pmid: 11157168
references.citation: FEMS Yeast Res. 2004 May;4(7):711-9
references.pmid: 15093774
references.citation: Science. 1996 Oct 25;274(5287):546, 563-7
references.pmid: 8849441
references.citation: Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5116-21
references.pmid: 11309499
references.citation: Yeast. 2003 Dec;20(16):1369-85
references.pmid: 14663829
references.citation: Yeast. 1997 Dec;13(15):1477-89
references.pmid: 9434352
references.citation: Mol Microbiol. 1996 Jun;20(5):981-91
references.pmid: 8809751
references.citation: J Biol Chem. 2003 Mar 7;278(10):8028-34
references.pmid: 12499363
references.citation: Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2685-9
references.pmid: 15710883
references.citation: FEMS Yeast Res. 2007 Jan;7(1):78-83
references.pmid: 17311586
references.citation: Nat Biotechnol. 1997 Dec;15(13):1351-7
references.pmid: 9415886
references.citation: J Biol Chem. 2003 Jan 31;278(5):3265-74
references.pmid: 12414795
references.citation: Appl Environ Microbiol. 2008 Oct;74(20):6358-68
references.pmid: 18723660
references.citation: Genome Res. 2003 Feb;13(2):244-53
references.pmid: 12566402
references.citation: Curr Genet. 2006 Jun;49(6):375-83
references.pmid: 16568252
references.citation: Nature. 1999 Dec 2;402(6761 Suppl):C47-52
references.pmid: 10591225
references.citation: Mol Biol Cell. 2000 Dec;11(12):4241-57
references.pmid: 11102521
references.citation: Nat Rev Microbiol. 2004 Jul;2(7):533-40
references.pmid: 15197389
references.citation: Microbiol Mol Biol Rev. 2005 Jun;69(2):197-216
references.pmid: 15944454
references.citation: Nucleic Acids Res. 2001 Feb 1;29(3):799-808
references.pmid: 11160904
references.citation: Annu Rev Genomics Hum Genet. 2001;2:343-72
references.pmid: 11701654
references.citation: J Biosci Bioeng. 2005 Apr;99(4):354-60
references.pmid: 16233801
references.citation: Appl Microbiol Biotechnol. 2003 May;61(3):197-205
references.pmid: 12698276
references.citation: FEMS Yeast Res. 2006 Dec;6(8):1167-83
references.pmid: 17156014
references.citation: Appl Environ Microbiol. 2008 Oct;74(19):6041-52
references.pmid: 18708514
references.citation: BMC Genomics. 2008 Nov 07;9:530
references.pmid: 18990252
references.citation: FEMS Yeast Res. 2007 Sep;7(6):819-33
references.pmid: 17484738
references.citation: J Biol Chem. 2001 Dec 28;276(52):49244-50
references.pmid: 11673473
references.citation: FEMS Yeast Res. 2008 Feb;8(1):35-52
references.pmid: 18215224