A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
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DOI：
10.1038/msb4100155
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发表时间：
2007
影响因子：
9.9
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中科院分区：
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更新的基因组规模重建的代谢网络在大肠杆菌K-12 MG 1655。更新后的代谢重建包括：（1）与最新的基因组注释和EcoCyc的代谢内容进行比对，从而包括1260个ORF的活性;（2）表征和定量与E.大肠杆菌的热力学信息;（3）所包含化学反应的热力学信息。详细介绍了这种代谢网络重建到计算机模型的转换。在代谢重建过程中的一个新的步骤，称为热力学一致性分析，介绍了，其中反应进行了检查与热力学可逆性估计的一致性。展示基因组规模的代谢模型的能力，以预测高通量的实验生长和基因缺失表型筛选的应用。利用这种新的重建方法所增加的范围和计算能力有望拓宽大肠杆菌基础生物学和应用系统生物学研究的范围。大肠杆菌代谢
An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.