An integrated network approach identifies the isobutanol response network of Escherichia coli.
An integrated network approach identifies the isobutanol response network of Escherichia coli.
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DOI：
10.1038/msb.2009.34
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发表时间：
2009
影响因子：
9.9
通讯作者：
Liao, James C.
中科院分区：
文献类型：
--
作者：
Brynildsen, Mark P.;Liao, James C.
由于最近的代谢工程努力，异丁醇已成为一种潜在的生物燃料。在这里，我们使用基因表达和转录网络连接数据、基因敲除和网络成分分析（NCA）来绘制大肠杆菌在有氧条件下的初始异丁醇反应网络。 NCA 揭示了呼吸的严重扰动。进一步的调查显示 ArcA 是这种反应的重要调解者。在本研究中，假设醌/醌故障会激活 ArcA、Fur 和 PhoB。为了支持这一假设，在发酵生长过程中，醌连接的 ArcA 和 Fur 靶标表达受异丁醇的干扰明显较小，而对苯二酚连接的 PhoB 靶标表达则保持激活状态，并且异丁醇在需要醌的甘油上比在葡萄糖上更能阻碍生长。此外，还比较了乙醇、正丁醇和异丁醇响应网络。正丁醇和异丁醇反应在性质上相似，而乙醇对 pspABCDE 和 ndh 具有显着的诱导差异，其基因产物管理质子动力。这里描述的网络可以帮助设计和理解酒精耐受性，而该方法提供了一个通用框架来表征系统级别的复杂现象。
Isobutanol has emerged as a potential biofuel due to recent metabolic engineering efforts. Here we used gene expression and transcription network connectivity data, genetic knockouts, and network component analysis (NCA) to map the initial isobutanol response network of Escherichia coli under aerobic conditions. NCA revealed profound perturbations to respiration. Further investigation showed ArcA as an important mediator of this response. Quinone/quinol malfunction was postulated to activate ArcA, Fur, and PhoB in this study. In support of this hypothesis, quinone-linked ArcA and Fur target expressions were significantly less perturbed by isobutanol under fermentative growth whereas quinol-linked PhoB target expressions remained activated, and isobutanol impeded growth on glycerol, which requires quinones, more than on glucose. In addition, ethanol, n-butanol, and isobutanol response networks were compared. n-Butanol and isobutanol responses were qualitatively similar, whereas ethanol had notable induction differences of pspABCDE and ndh, whose gene products manage proton motive force. The network described here could aid design and comprehension of alcohol tolerance, whereas the approach provides a general framework to characterize complex phenomena at the systems level.
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影响因子：
2.9
作者：
Braatsch, Stephan;Bernstein, Jeffrey R.;Beatty, J. Thomas
通讯作者：
Beatty, J. Thomas
影响因子：
2.8
作者：
Bekker, M.;Kramer, G.;de Mattos, M. J. Teixeira
通讯作者：
de Mattos, M. J. Teixeira
DOI：
10.1073/pnas.2136632100
发表时间：
2003-12-23
影响因子：
11.1
作者：
Liao, JC;Boscolo, R;Roychowdhury, VP
通讯作者：
Roychowdhury, VP
大肠杆菌K-12的构造框架，单基因敲除突变体：Keio Collection。
影响因子：
9.9
作者：
通讯作者：
--
影响因子：
5.8
作者：
Galbraith, Simon J.;Tran, Linh M.;Liao, James C.
通讯作者：
Liao, James C.