Escorcia-Rodríguez Juan M, Tauch Andreas, Freyre-González Julio A
Regulatory Systems Biology Research Group, Laboratory of Systems and Synthetic Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca 62210, Morelos, Mexico.
Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstraße 27, 33615 Bielefeld, Germany.
Microorganisms. 2021 Jun 28;9(7):1395. doi: 10.3390/microorganisms9071395.
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 : (3040 interactions) constructed solely with regulations previously supported by directed experiments; (4665 interactions) containing the network, regulations previously supported by nondirected experiments, and protein-protein interactions with a direct effect on gene transcription; (5222 interactions) containing the network and sRNA-mediated regulations. Compared to the previous version (2018), the and 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 sRNA-mediated regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the networks of three model organisms to provide insights and future directions of the regulatory network characterization.
是一种存在于土壤中的革兰氏阳性细菌,在这种环境中,条件变化要求调控机制具有可塑性。由于缺乏数据整合,在全球范围内对这种机制的研究面临挑战。在此,我们报告了三种调控网络模型:(3040个相互作用)仅由先前有直接实验支持的调控构建而成;(4665个相互作用)包含网络、先前有非直接实验支持的调控以及对基因转录有直接影响的蛋白质-蛋白质相互作用;(5222个相互作用)包含网络和小RNA介导的调控。与先前版本(2018年)相比,和网络分别增加了75个和1225个相互作用。我们分析了这三种网络的系统级组件,以确定它们的差异,并将其结构与40多种物种的网络结构进行比较。包含小RNA介导的调控改变了系统级组件的比例,增加了模块数量,但减小了其规模。的调控结构与其他细菌调控网络不同。最后,我们使用三种模式生物的网络,为调控网络表征提供见解和未来方向。