Exploration of the genetic makeup and expression of the glycolytic and fermentative pathways within the Saccharomyces genus

The ability of the yeast Saccharomyces cerevisiae to convert glucose, even in the presence of oxygen, via glycolysis and the fermentative pathway to ethanol has played an important role in its domestication. Despite the extensive knowledge on these pathways in S. cerevisiae, relatively little is known about these pathways in other industrially-relevant Saccharomyces yeast species. In this study we explore the diversity of the glycolytic and fermentative pathways within the Saccharomyces genus using S. cerevisiae, S. kudriavzevii and S. eubayanus as paradigms. Sequencing data revealed a highly conserved genetic makeup of the glycolytic and fermentative pathways in the three species in terms of number of paralogous genes. Although promoter regions were less conserved between the three species as compared to coding sequences, binding sites for Rap1, Gcr1 and Abf1, main transcriptional regulators of glycolytic and fermentative genes, were highly conserved. Transcriptome profiling of these three strains grown in aerobic batch cultivation in chemically defined medium with glucose as carbon source, revealed a remarkably similar expression of the glycolytic and fermentative genes across species, and the conserved classification of genes into major and minor paralogs. Furthermore, transplantation of the promoters of major paralogs of S. kudriavzevii and S. eubayanus into S. cerevisiae demonstrated not only the transferability of these promoters, but also the similarity of their strength and response to various environmental stimuli. The relatively low homology of S. kudriavzevii and S. eubayanus promoters to their S. cerevisiae relatives makes them very attractive alternatives for strain construction in S. cerevisiae, thereby expanding S. cerevisiae molecular toolbox.酿酒酵母（Saccharomyces cerevisiae）即便在有氧条件下，仍可通过糖酵解与发酵途径将葡萄糖转化为乙醇，这一特性在其驯化进程中发挥了重要作用。尽管学界对酿酒酵母的上述代谢途径已有较为充分的研究，但对其他工业相关的酿酒酵母属（Saccharomyces）物种的同类途径却所知甚少。本研究以酿酒酵母、库德里阿兹威酵母（S. kudriavzevii）与欧巴诺亚酵母（S. eubayanus）为模式物种，探究酿酒酵母属内糖酵解与发酵途径的多样性。测序数据显示，这三个物种的糖酵解与发酵途径在旁系同源基因的数量层面，拥有高度保守的遗传构成。尽管相较于编码序列，三个物种的启动子区域保守性稍弱，但作为糖酵解与发酵基因主要转录调控因子的Rap1、Gcr1及Abf1的结合位点却保持了高度保守。对这三株菌株在以葡萄糖为碳源的化学成分限定培养基中进行好氧分批培养后的转录组谱分析显示，不同物种间的糖酵解与发酵基因表达模式极为相似，且基因可被保守地划分为主要与次要旁系同源基因两类。此外，将库德里阿兹威酵母与欧巴诺亚酵母的主要旁系同源基因启动子移植到酿酒酵母中的实验表明，这些启动子不仅可被成功移植，其表达强度与对各类环境刺激的响应模式也高度相似。由于库德里阿兹威酵母与欧巴诺亚酵母的启动子与酿酒酵母同源启动子的同源性较低，它们成为酿酒酵母菌株构建中极具吸引力的替代元件，进而拓展了酿酒酵母的分子工具箱。