iTRAQ-based proteome profiling of Saccharomyces cerevisiae and cryotolerant species Saccharomyces uvarum and Saccharomyces kudriavzevii during low-temperature wine fermentation

Journal of Proteomics - Tập 146 - Trang 70-79 - 2016
Estéfani García-Ríos1, Amparo Querol1, José Manuel Guillamón1
1Departamento de Biotecnología de los alimentos, Instituto de Agroquímica y Tecnología de los Alimentos (CSIC), Avda. Agustín Escardino, 7, E-46980, Paterna, Valencia, Spain

Tài liệu tham khảo

Torija, 2003, Effects of fermentation temperature and Saccharomyces species on the cell fatty acid composition and presence of volatile compounds, Int. J. Food Microbiol., 85, 127, 10.1016/S0168-1605(02)00506-8 Beltran, 2008, Effect of fermentation temperature and culture media on the yeast lipid composition and wine volatile compounds, Int. J. Food Microbiol., 121, 169, 10.1016/j.ijfoodmicro.2007.11.030 Bisson, 1999, Stuck and sluggish fermentation, Am. J. Enol. Vitic., 50, 107, 10.5344/ajev.1999.50.1.107 Aguilera, 2007, Cold response in Saccharomyces cerevisiae: new functions for old mechanisms, FEMS Microbiol. Rev., 31, 327, 10.1111/j.1574-6976.2007.00066.x Sahara, 2002, Comprehensive expression analysis of time-dependent genetic responses in yeast cells to low temperature, J. Biol. Chem., 277, 50015, 10.1074/jbc.M209258200 Schade, 2004, Cold adaptation in budding yeast, Mol. Biol. Cell, 15, 5492, 10.1091/mbc.E04-03-0167 Tai, 2007, Acclimation of Saccharomyces cerevisiae to low temperature: a chemostat-based transcriptome analysis, Mol. Biol. Cell, 18, 5100, 10.1091/mbc.E07-02-0131 Masneuf-Pomarède, 2010, Reassessment of phenotypic traits for Saccharomyces bayanus var. uvarum wine yeast strains, Int. J. Food Microbiol., 139, 79, 10.1016/j.ijfoodmicro.2010.01.038 Gamero, 2013, Production of aroma compounds by cryotolerant Saccharomyces species and hybrids at low and moderate fermentation temperatures, J. Appl. Microbiol., 114, 1405, 10.1111/jam.12126 González, 2006, Natural hybrids from Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces kudriavzevii in wine fermentations, FEMS Yeast Res., 6, 1221, 10.1111/j.1567-1364.2006.00126.x González, 2007, Enological characterization of natural hybrids from Saccharomyces cerevisiae and S. kudriavzevii, Int. J. Food Microbiol., 11, 11, 10.1016/j.ijfoodmicro.2006.10.047 Sampaio, 2008, Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and sympatric with S. cerevisiae and S. paradoxus, Appl. Environ. Microbiol., 74, 2144, 10.1128/AEM.02396-07 Lopes, 2010, Natural hybrids of S. cerevisiae×S. kudriavzevii share alleles with European wild populations of Saccharomyces kudriavzevii, FEMS Yeast Res., 10, 412, 10.1111/j.1567-1364.2010.00614.x Tronchoni, 2009, Differences in the glucose and fructose consumption profiles in diverse Saccharomyces wine species and their hybrids during grape juice fermentation, Int. J. Food Microbiol., 134, 237, 10.1016/j.ijfoodmicro.2009.07.004 Tronchoni, 2012, Lipid composition of wine strains of Saccharomyces kudriavzevii and Saccharomyces cerevisiae grown at low temperature, Int. J. Food Microbiol., 155, 191, 10.1016/j.ijfoodmicro.2012.02.004 Salvadó, 2011, Temperature adaptation markedly determines the growth and evolution within the genus Saccharomyces, Appl. Environ. Microbiol., 77, 2292, 10.1128/AEM.01861-10 López-Malo, 2013, Metabolomic comparison of Saccharomyces cerevisiae and the cryotolerant species S. bayanus var. uvarum and S. kudriavzevii during wine fermentation at low temperature, PLoS One, 8, e60135, 10.1371/journal.pone.0060135 Tronchoni, 2014, Transcriptomics of cryophilic Saccharomyces kudriavzevii reveals the key role of gene translation efficiency in cold stress adaptations, BMC Genomics, 15, 432, 10.1186/1471-2164-15-432 Regenberg, 2006, Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae, Genome Biol., 7, R107, 10.1186/gb-2006-7-11-r107 Castrillo, 2007, Growth control of the eukaryote cell: a systems biology study in yeast, J. Biol., 6, 4, 10.1186/jbiol54 Ross, 2004, Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol. Cell. Proteomics, 3, 1154, 10.1074/mcp.M400129-MCP200 Casado-Vela, 2010, iTRAQ-based quantitative analysis of protein mixtures with large fold change and dynamic range, Proteomics, 10, 343, 10.1002/pmic.200900509 Chiva, 2012, Analysis of low temperature-induced genes (LTIG) in wine yeast during alcoholic fermentation, FEMS Yeast Res., 12, 831, 10.1111/j.1567-1364.2012.00834.x Salvadó, 2012, Functional analysis to identified genes in wine yeast adaptation to low temperature fermentation, J. Appl. Microbiol., 113, 76, 10.1111/j.1365-2672.2012.05308.x Bely, 2002, Description of alcoholic fermentation kinetics: its variability and significance, Am. J. Enol. Vitic., 41, 319, 10.5344/ajev.1990.41.4.319 Dukes, 1999, Rapid determination of primary amino acids in grape juice using an o-phthaldialdehyde/N-acetyl-l-cysteine spectrophotometric assay, Am. J. Enol. Vitic., 49, 125, 10.5344/ajev.1998.49.2.125 Shevchenko, 1996, Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels, Proc. Natl. Acad. Sci. U. S. A., 93, 14440, 10.1073/pnas.93.25.14440 Franceschini, 2013, STRING v10.0: protein–protein interaction networks, with increased coverage and integration, Nucleic Acids Res., 41, D808, 10.1093/nar/gks1094 Clement, 2011, Use a multistage bioreactor to mimic winemaking fermentations, Int. J. Food Microbiol., 150, 42, 10.1016/j.ijfoodmicro.2011.07.016 Vázquez-Lima, 2014, Use of chemostat cultures mimicking different phases of wine fermentations as a tool for quantitative physiological analysis, Microb. Cell Factories, 13, 85, 10.1186/1475-2859-13-85 García-Ríos, 2014, Global phenotypic and genomic comparison of two Saccharomyces cerevisiae wine strains reveals a novel role of the sulfur assimilation pathway in adaptation at low temperature fermentations, BMC Genomics, 15, 1059, 10.1186/1471-2164-15-1059 Kurata, 2010, Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP, Proc. Natl. Acad. Sci. U. S. A., 106, 2571 Zavanelli, 1994, Mutations in an essential U2 small nuclear RNA structure cause cold-sensitive U2 small nuclear ribonucleoprotein function by favoring competing alternative U2 RNA structures, Mol. Cell. Biol., 14, 1689, 10.1128/MCB.14.3.1689 Fortner, 1994, A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing, Genes Dev., 8, 221, 10.1101/gad.8.2.221 Li, 1996, A spontaneous duplication in U6 spliceosomal RNA uncouples the early and late functions of the ACAGA element in vivo, RNA, 2, 879 Staley, 1999, An RNA switch at the 5′ splice site requires ATP and the DEAD box protein Prp28p, Mol. Cell, 3, 55, 10.1016/S1097-2765(00)80174-4 Hilliker, 2007, U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing, Genes Dev., 21, 821, 10.1101/gad.1536107 Perriman, 2007, Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing, Genes Dev., 21, 811, 10.1101/gad.1524307 Pizarro, 2008, Growth temperature exerts differential physiological and transcriptional responses in laboratory and wine strains of Saccharomyces cerevisiae, Appl. Environ. Microbiol., 74, 6358, 10.1128/AEM.00602-08 A.G. Macdonald, The role of membrane fluidity in complex processes under high pressure. R.E. In Marquis, A.M. Zimmerman, H.W. Jannasch, Ed. Current perspectives in high pressure biology, Academic Press, London, England. Abe, 2000, Tryptophan permease gene TAT2 confers high-pressure growth in Saccharomyces cerevisiae, Mol. Cell. Biol., 20, 8093, 10.1128/MCB.20.21.8093-8102.2000 Beltran, 2008, Effect of fermentation temperature and culture media on the yeast lipid composition and wine volatile compounds, Int. J. Food Microbiol., 121, 169, 10.1016/j.ijfoodmicro.2007.11.030 Paget, 2014, Environmental systems biology of cold-tolerant phenotype in Saccharomyces species adapted to grow at different temperatures, Mol. Ecol., 23, 5241, 10.1111/mec.12930 Piškur, 2006, How did Saccharomyces evolve to become a good brewer?, Trends Genet., 22, 183, 10.1016/j.tig.2006.02.002 Arroyo-López, 2010, Modulation of the glycerol and ethanol syntheses in the yeast Saccharomyces kudriavzevii differs from that exhibited by Saccharomyces cerevisiae and their hybrid, Food Microbiol., 27, 628, 10.1016/j.fm.2010.02.001