A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism
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DOI：
10.1038/s41467-019-11581-3
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发表时间：
2019-08-08
影响因子：
16.6
通讯作者：
Nielsen, Jens
中科院分区：
文献类型：
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作者：
Lu, Hongzhong;Li, Feiran;Nielsen, Jens
基因组尺度代谢模型（GEM）代表了广泛的知识库，为模型模拟和组学数据的综合分析提供了平台。本研究介绍了酵母8和相关的生态系统的模型，代表了一个全面的计算资源进行模拟的代谢酵母菌的一个重要的模式生物和广泛使用的细胞工厂。Yeast8通过版本控制跟踪社区开发，为如何以简单和可复制的方式持续更新GEM设定了标准。我们使用Yeast8开发了衍生模型panYeast8和coreYeast8，从而能够为1，011种不同的酵母菌株重建GEM。通过与酶约束（ecYeast8）和蛋白质3D结构（proYeast8（DB））的整合，Yeast8进一步促进了在多尺度水平上探索酵母代谢，从而能够预测单核苷酸变异如何转化为表型性状。
Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae-an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8(DB)), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.