Metabolomic and transcriptomic stress response of Escherichia coli.
Metabolomic and transcriptomic stress response of Escherichia coli.
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DOI：
10.1038/msb.2010.18
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发表时间：
2010-05-11
影响因子：
9.9
通讯作者：
中科院分区：
文献类型：
--
作者：
环境的波动导致了大肠杆菌生理的快速调整，需要在潜在的细胞和分子网络的每一个层面上进行改变。到目前为止，大多数对大肠杆菌应激反应的全球分析仅限于一个水平，即基因表达。在这里，我们将代谢物组成与基因表达数据结合在一起，通过描述详细的时间分辨大肠杆菌对五种不同扰动(冷、热、氧化应激、乳糖脱氢和静止相)的响应，提供对系统水平压力调节的更全面的见解。与在转录本水平上观察到的一般反应相比，代谢物反应更具特异性，并在早期胁迫适应阶段以及将静止阶段的反应与其他扰动进行比较时反映出更高的特异性。尽管存在这些差异，但这两个水平上的反应仍然遵循相同的动力学和总体节能策略，反映在中枢碳代谢中间产物迅速减少的同时，与细胞生长相关的基因下调。对组合的代谢物和转录物数据应用共聚类和典型相关分析，发现代谢物和转录物之间有许多显著的条件依赖关系。结果证实和扩展了现有的基因表达和代谢物之间的共同调控模型，展示了面向集成系统的分析的能力。
Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here, we incorporate the metabolite composition together with gene expression data to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared with the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with downregulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition-dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.
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影响因子：
7.4
作者：
Bolten, Christoph J.;Kiefer, Patrick;Wittmann, Christoph
通讯作者：
Wittmann, Christoph
影响因子：
9.8
作者：
Hondorp ER;Matthews RG
通讯作者：
Matthews RG
影响因子：
5.6
作者：
Barker, MM;Gaal, T;Gourse, RL
通讯作者：
Gourse, RL
影响因子：
56.9
作者：
Kuroda, A;Nomura, K;Kornberg, A
通讯作者：
Kornberg, A
影响因子：
2.7
作者：
Hotelling, H
通讯作者：
Hotelling, H