An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
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DOI：
10.1186/gb-2003-4-9-r54
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发表时间：
2003
期刊：
影响因子：
12.3
通讯作者：
Palsson BO
中科院分区：
文献类型：
--
作者：
Reed JL;Vo TD;Schilling CH;Palsson BO
建立了E.杆菌 包括904个基因和931个独特的生化反应，从而对E.大肠杆菌的代谢比以前的模型。 不同的数据集，包括基因组，转录组，蛋白质组和代谢组学数据，正在变得容易获得特定的生物体。目前需要将这些数据集集成到计算机建模框架中。大肠杆菌K-12 MG 1655的基于约束的模型已被开发并用于研究细菌的代谢和表型行为。最全面的E。coli模型（E. coliJE 660 aGSM）占660个基因，包括627个独特的生化反应。建立了大肠杆菌基因组规模的代谢模型。coli（iJR 904 GSM/GPR）中的904个基因和931个独特的生化反应。扩展模型中的反应是元素平衡和电荷平衡的。网络缺口分析导致55个开放阅读框架（ORF）的推定分配。基因到蛋白质到反应关联（GPR）现在直接包括在模型中。比较iJR 904和iJE 660 a模型的预测结果表明，它们基本相似，但在某些情况下存在差异。对基因组规模的质子平衡的分析表明，进出培养基的质子流量对于最大化细胞生长是多么重要。E.大肠杆菌iJR 904具有比iJE 660 a更高的能力。iJR 904是E.大肠杆菌的代谢能力高于iJE 660 a。也许最重要的是，iJR 904可以用于分析和整合不同的数据集。iJR 904将有助于阐明E. coliK-12，因为它可以同时解释基因组、转录组、蛋白质组和通量组数据。
A genome-scale metabolic model of E. coli has been reconstructed, including 904 genes and 931 unique biochemical reactions, which gives a more complete and chemically accurate description of E. coli metabolism than previous models. Diverse datasets, including genomic, transcriptomic, proteomic and metabolomic data, are becoming readily available for specific organisms. There is currently a need to integrate these datasets within an in silico modeling framework. Constraint-based models of Escherichia coli K-12 MG1655 have been developed and used to study the bacterium's metabolism and phenotypic behavior. The most comprehensive E. coli model to date (E. coli iJE660a GSM) accounts for 660 genes and includes 627 unique biochemical reactions. An expanded genome-scale metabolic model of E. coli (iJR904 GSM/GPR) has been reconstructed which includes 904 genes and 931 unique biochemical reactions. The reactions in the expanded model are both elementally and charge balanced. Network gap analysis led to putative assignments for 55 open reading frames (ORFs). Gene to protein to reaction associations (GPR) are now directly included in the model. Comparisons between predictions made by iJR904 and iJE660a models show that they are generally similar but differ under certain circumstances. Analysis of genome-scale proton balancing shows how the flux of protons into and out of the medium is important for maximizing cellular growth. E. coli iJR904 has improved capabilities over iJE660a. iJR904 is a more complete and chemically accurate description of E. coli metabolism than iJE660a. Perhaps most importantly, iJR904 can be used for analyzing and integrating the diverse datasets. iJR904 will help to outline the genotype-phenotype relationship for E. coli K-12, as it can account for genomic, transcriptomic, proteomic and fluxomic data simultaneously.
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影响因子：
5.8
作者：
Zdobnov, EM;Lopez, R;Etzold, T
通讯作者：
Etzold, T
影响因子：
14.9
作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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