Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.
Nat Commun. 2013;4:1755. doi: 10.1038/ncomms2743.
Bacteria contain multiple sigma factors, each targeting diverse, but often overlapping sets of promoters, thereby forming a complex network. The layout and deployment of such a sigma factor network directly impacts global transcriptional regulation and ultimately dictates the phenotype. Here we integrate multi-omic data sets to determine the topology, the operational, and functional states of the sigma factor network in Geobacter sulfurreducens, revealing a unique network topology of interacting sigma factors. Analysis of the operational state of the sigma factor network shows a highly modular structure with σ(N) being the major regulator of energy metabolism. Surprisingly, the functional state of the network during the two most divergent growth conditions is nearly static, with sigma factor binding profiles almost invariant to environmental stimuli. This first comprehensive elucidation of the interplay between different levels of the sigma factor network organization is fundamental to characterize transcriptional regulatory mechanisms in bacteria.
细菌含有多个 σ 因子，每个 σ 因子都针对不同的、但往往重叠的启动子组，从而形成一个复杂的网络。这种 σ 因子网络的布局和部署直接影响全局转录调控，并最终决定表型。在这里，我们整合多组学数据集来确定 Geobacter sulfurreducens 中 σ 因子网络的拓扑结构、操作和功能状态，揭示了相互作用的 σ 因子的独特网络拓扑结构。对 σ 因子网络操作状态的分析表明，其具有高度模块化的结构，σ（N）是能量代谢的主要调节剂。令人惊讶的是，在两个差异最大的生长条件下，网络的功能状态几乎是静态的，σ 因子结合谱几乎不受环境刺激的影响。这是首次全面阐明 σ 因子网络组织的不同层次之间的相互作用，对于细菌转录调控机制的特征具有重要意义。
