Wine yeast genomics: adaptation of S.cerevisiae to fermentation stress

酿酒葡萄球菌已经发展出复杂的调控机制来应对发酵葡萄汁中初始糖浓度高、营养物质消耗和逐渐增加的乙醇浓度。工业酿酒酵母在葡萄发酵过程中对这些长期环境胁迫的分子和细胞适应性尚未得到很好的研究。为了研究酵母如何适应葡萄发酵过程中的恶劣条件，在酒精发酵过程中的五个时间点检测了全基因组转录。对于每个基因，整个发酵过程的时间趋势用两个参数值来描述表达谱的总体变化和形状。应用种子聚类算法对20个基因的表达模式进行分组，这些基因的时间趋势跨越了整个转录组中观察到的模式范围。在整个葡萄酒发酵过程中对酵母转录组的分析表明，40%的酵母基因组显著改变了表达水平，介导了对发酵应激的长期适应；223个基因在发酵过程的不同阶段被显著诱导，并被命名为发酵应激反应（FSR）基因。FSR是新颖的，62%的相关基因未涉及全球应激反应；28%的FSR基因没有功能注释。这62个未加注释的FSR基因的功能分析正在进行中。此外，我们发现20个非注释基因在葡萄酒发酵过程中显著下调，31个非注释基因显著上调。在这项拨款申请中，我们将构建所有51个未注释基因的零突变体，并使用系统生物学方法，转录组学，蛋白质组学和代谢组学，来建立这些未注释基因在葡萄酒发酵过程中被调节的功能。

Wine strains of S. cerevisiae have developed complex regulatory mechanisms to cope with high initial sugar concentrations, depleting nutrients, and gradually increasing ethanol concentrations in fermenting grape juice. The molecular and cellular adaptations of industrial wine yeasts to these long-term environmental stresses during grape must fermentation have not been well studied. To investigate how yeast adapts to the harsh conditions during the fermentation of grape must, genome-wide transcription was assayed at five time points during alcoholic fermentation. For each gene, the temporal trend throughout the fermentation process was summarized with two parameter values that describe the overall change and shape of the expression profile. A seeded clustering algorithm was applied in order to group the genes around the expression patterns exhibited by 20 genes whose temporal trends span the range of patterns observed across the entire transcriptome. Analyses of the yeast transcriptome throughout wine fermentations revealed that 40% of the yeast genome significantly changed expression levels to mediate long-term adaptation to fermentation stress; 223 genes were dramatically induced at various points during fermentation and were designated as Fermentation Stress Response (FSR) genes. The FSR is novel and 62% of the genes involved have not been implicated in global stress responses; 28% of the FSR genes have no functional annotation. Functional analyses of these 62 non-annotated FSR genes are in currently in progress. In addition, we found 20 non-annotated genes that were significantly down-regulated and 31 non-annotated genes that were significantly up-regulated during wine fermentations. In this grant application we will construct null mutants of all 51 non-annotated genes and use a systems biology approach, transcriptomics, proteomics and metabolomics, to establish functions of these non-annotated genes that are regulated during wine fermentations.