谷氨酸棒杆菌转录调控以外的调控：包含小RNA和蛋白质相互作用介导的调控的扩展调控网络的组织原理和重建
Corynebacterium glutamicum regulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions
摘要：
谷氨酸棒杆菌是在土壤中发现的革兰氏阳性细菌，其中条件变化需要调节机制的可塑性。由于缺乏数据整合，在全球范围内对这种机制的研究受到了挑战。在这里，我们报告了三个调控网络模型的C。谷氨酸：强相互作用（3040个相互作用）仅由先前由定向实验支持的调控构建;所有证据（4665个相互作用）包含强网络、先前由非定向实验支持的调控和对基因转录有直接影响的蛋白质相互作用; sRNA（5222个相互作用）包含所有证据网络和sRNA介导的调控。与上一版本（2018）相比，强证据网络和全证据网络分别增加了75次和1225次交互。我们分析了这三个网络的系统级组件，以确定它们之间的差异，并将它们的结构与40多个物种的网络进行了比较。sRNA规则的引入改变了系统级组件的比例，增加了模块的数量，但减小了它们的大小。梭谷氨酸调控结构与其他细菌调控网络形成对比。最后，我们使用三个模式生物的强大网络来提供见解和未来的发展方向。谷氨酸调控网络表征。
英文摘要：
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; and sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNAs regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C. glutamicum regulatory network characterization.
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