乳酸菌基因组代谢网络模型的研究进展

Research Progress of Lactic Acid Bacteria Genome-Scale Metabolic Models

基因组代谢网络模型(genome-scale metabolic models,GEMs/GSMM)是基因组规模的细胞生化反应网络,可以定量描述基因与表型的关系,广泛应用于系统生物学、代谢工程、环境科学等领域。微生物基因组代谢网络模型是基于微生物基因组构建的生理生化知识库,通过数学模型实现对目标微生物生理生化反应的模拟,已成为研究微生物代谢调控的重要工具。基因组代谢网络模型的构建步骤通常包括构建模型草图、人工精炼、模型转换、验证评估4个阶段。在介绍以模式微生物(大肠杆菌、枯草芽孢杆菌、酿酒酵母)为代表的微生物基因组代谢网络模型发展过程基础上,重点聚焦乳酸菌基因组代谢网络模型的研究现状,系统介绍了已构建的乳酸菌基因组代谢网络模型及其应用。对乳酸菌基因组代谢网络模型的发展方向进行了展望,提出未来乳酸菌基因组代谢网络模型的研究应在现有模型的基础上构建更高质量的代谢与大分子表达模型和泛基因组模型,为乳酸菌的研究提供更高效的工具。

Genome-scale metabolic models(GEMs/GSMM)are cellular biochemical reaction networks of the genomic scale,which can quantitatively describe the relationship between genes and phenotypes,and be widely used in systems biology,metabolic engineering,environmental science and other fields.Microbial GEMs are constructed based on physiological and biochemical knowledge bases of microbial genomes to simulate the physiological and biochemical reactions of targeted microorganism via mathematic model.Microbial GEMs have become important tools for studying the regulation of microbial metabolism.The work flows of GEMs reconstruction usually included four steps:draft reconstruction,refinement reconstruction,conversion of reconstruction,network evaluation.Based on the introduction of the development process of GEMs represented by model microorganisms(Escherichia coli,Bacillus subtilis,and Saccharomyces cerevisiae),the current research status of the lactic acid bacteria GEMs was focused.The reconstructed lactic acid bacteria GEMs and its application were systemically introduced.The development direction of the lactic acid bacteria GEMs was prospected.The future research on lactic acid bacteria GEMs was proposed to build higher-quality metabolic and macromolecular expression models and pan-genome models on the basis of existing models,so as to provide more efficient tools for the research of lactic acid bacteria.