Targeted proteome analysis of single-gene deletion strains of Saccharomyces cerevisiae lacking enzymes in the central carbon metabolism

Central carbon metabolism is controlled by modulating the protein abundance profiles of enzymes that maintain the essential systems in living organisms. In this study, metabolic adaptation mechanisms in the model organism Saccharomyces cerevisiae were investigated by direct determination of enzyme abundance levels in 30 wild type and mutant strains. We performed a targeted proteome analysis using S. cerevisiae strains that lack genes encoding the enzymes responsible for central carbon metabolism. Our analysis revealed that at least 30% of the observed variations in enzyme abundance levels could be explained by global regulatory mechanisms. A enzyme-enzyme co-abundance analysis revealed that the abundances of enzyme proteins involved in the trehalose metabolism and glycolysis changed in a coordinated manner under the control of the transcription factors for global regulation. The remaining variations were derived from local mechanisms such as a mutant-specific increase in the abundances of remote enzymes. The proteome data also suggested that, although the functional compensation of the deficient enzyme was attained by using more resources for protein biosynthesis, available resources for the biosynthesis of the enzymes responsible for central metabolism were not abundant in S. cerevisiae cells. These results showed that global and local regulation of enzyme abundance levels shape central carbon metabolism in S. cerevisiae by using a limited resource for protein biosynthesis.中心碳代谢（central carbon metabolism）的调控依赖于对维持生命体必需系统的酶类蛋白质丰度谱的调控。本研究以模式生物酿酒酵母（Saccharomyces cerevisiae）为研究对象，通过直接测定30株野生型与突变株的酶丰度水平，探究其代谢适应机制。本研究针对敲除了中心碳代谢相关酶编码基因的酿酒酵母菌株，开展了靶向蛋白质组学分析。分析结果显示，观测到的酶丰度水平变异中，至少30%可通过全局调控机制予以解释。酶-酶共丰度分析显示，在全局调控转录因子的作用下，参与海藻糖代谢与糖酵解过程的酶类蛋白质丰度呈现协同变化模式。剩余的丰度变异则源自局部调控机制，例如远端酶类的丰度出现突变株特异性升高。蛋白质组数据同时表明，尽管通过投入更多蛋白质生物合成资源可实现缺陷酶的功能补偿，但酿酒酵母细胞内用于中心代谢相关酶生物合成的可用资源并不充足。上述结果证实，酿酒酵母的中心碳代谢过程，是通过有限的蛋白质生物合成资源，由酶丰度水平的全局与局部调控共同塑造而成。