Department of Biochemistry, University of Regina, Regina, SK, Canada.
Nat Commun. 2022 Jul 14;13(1):4085. doi: 10.1038/s41467-022-31819-x.
Bacterial transcription factors (TFs) are widely studied in Escherichia coli. Yet it remains unclear how individual genes in the underlying pathways of TF machinery operate together during environmental challenge. Here, we address this by applying an unbiased, quantitative synthetic genetic interaction (GI) approach to measure pairwise GIs among all TF genes in E. coli under auxotrophic (rich medium) and prototrophic (minimal medium) static growth conditions. The resulting static and differential GI networks reveal condition-dependent GIs, widespread changes among TF genes in metabolism, and new roles for uncharacterized TFs (yjdC, yneJ, ydiP) as regulators of cell division, putrescine utilization pathway, and cold shock adaptation. Pan-bacterial conservation suggests TF genes with GIs are co-conserved in evolution. Together, our results illuminate the global organization of E. coli TFs, and remodeling of genetic backup systems for TFs under environmental change, which is essential for controlling the bacterial transcriptional regulatory circuits.
细菌转录因子（TFs）在大肠杆菌中被广泛研究。然而，在环境挑战下，TF 机制的基础途径中的各个基因如何协同作用仍不清楚。在这里，我们通过应用一种无偏的、定量的合成遗传相互作用（GI）方法来解决这个问题，该方法用于测量大肠杆菌中所有 TF 基因在营养缺陷型（丰富培养基）和原养型（最小培养基）静态生长条件下的成对 GI。由此产生的静态和差异 GI 网络揭示了条件依赖性 GI、代谢中 TF 基因的广泛变化，以及未表征的 TF（yjdC、yneJ、ydiP）作为细胞分裂、腐胺利用途径和冷休克适应调节剂的新作用。泛细菌保守性表明，具有 GI 的 TF 基因在进化中是共同保守的。总之，我们的结果阐明了大肠杆菌 TF 的全局组织，以及 TF 在环境变化下遗传备份系统的重塑，这对于控制细菌转录调控回路是必不可少的。
