State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE412 96 Gothenburg, Sweden.
Biomolecules. 2022 Nov 3;12(11):1632. doi: 10.3390/biom12111632.
Yeasts are increasingly employed in synthetic biology as chassis strains, including conventional and non-conventional species. It is still unclear how genomic evolution determines metabolic diversity among various yeast species and strains. In this study, we constructed draft GEMs for 332 yeast species using two alternative procedures from the toolbox RAVEN v 2.0. We found that draft GEMs could reflect the difference in yeast metabolic potentials, and therefore, could be utilized to probe the evolutionary trend of metabolism among 332 yeast species. We created a pan-draft metabolic model to account for the metabolic capacity of every sequenced yeast species by merging all draft GEMs. Further analysis showed that the pan-reactome of yeast has a "closed" property, which confirmed the great conservatism that exists in yeast metabolic evolution. Lastly, the quantitative correlations among trait similarity, evolutionary distances, genotype, and model similarity were thoroughly investigated. The results suggest that the evolutionary distance and genotype, to some extent, determine model similarity, but not trait similarity, indicating that multiple mechanisms shape yeast trait evolution. A large-scale reconstruction and integrative analysis of yeast draft GEMs would be a valuable resource to probe the evolutionary mechanism behind yeast trait variety and to further refine the existing yeast species-specific GEMs for the community.
酵母作为底盘菌株，越来越多地被应用于合成生物学，包括传统和非常规物种。基因组进化如何决定不同酵母物种和菌株的代谢多样性仍不清楚。在这项研究中，我们使用 RAVEN v 2.0 中的两种替代程序为 332 种酵母物种构建了 GEM 草案。我们发现 GEM 草案可以反映酵母代谢潜力的差异，因此可以用于探究 332 种酵母物种代谢的进化趋势。我们创建了一个泛 GEM 草案代谢模型，通过合并所有 GEM 草案来解释每个已测序酵母物种的代谢能力。进一步的分析表明，酵母的泛反应组具有“封闭”的特性，这证实了酵母代谢进化中存在的巨大保守性。最后，深入研究了性状相似性、进化距离、基因型和模型相似性之间的定量相关性。结果表明，进化距离和基因型在某种程度上决定了模型的相似性，但不能决定性状的相似性，这表明多种机制影响了酵母性状的进化。对酵母 GEM 草案进行大规模重建和综合分析，将有助于探究酵母性状多样性背后的进化机制，并进一步完善现有的酵母物种特异性 GEM 草案，供社区使用。
