NIZO, Ede, The Netherlands.
Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands.
BMC Microbiol. 2023 Jan 18;23(1):17. doi: 10.1186/s12866-022-02700-0.
Sigma factor B (SigB) is the central regulator of the general stress response in Bacillus subtilis and regulates a group of genes in response to various stressors, known as the SigB regulon members. Genes that are directly regulated by SigB contain a promotor binding motif (PBM) with a previously identified consensus sequence.
In this study, refined SigB PBMs were derived and different spacer compositions and lengths (N-N) were taken into account. These were used to identify putative SigB-regulated genes in the B. subtilis genome, revealing 255 genes: 99 had been described in the literature and 156 genes were newly identified, increasing the number of SigB putative regulon members (with and without a SigB PBM) to > 500 in B. subtilis. The 255 genes were assigned to five categories (I-V) based on their similarity to the original SigB consensus sequences. The functionalities of selected representatives per category were assessed using promoter-reporter fusions in wt and ΔsigB mutants upon exposure to heat, ethanol, and salt stress. The activity of the P (I) positive control was induced upon exposure to all three stressors. P (II) showed SigB-dependent activity only upon exposure to ethanol, whereas P (II) with a N spacer and P (III) with a N spacer showed mild induction regardless of heat/ethanol/salt stress. P (III) and P (IV) displayed ethanol-specific SigB-dependent activities despite a lower-level conserved - 10 binding motif. P (V) was SigB-induced under ethanol and salt stress while lacking a conserved - 10 binding region. The activities of P and P (III) did not show evident changes under the conditions tested despite having a SigB PBM that highly resembled the consensus. The identified extended SigB regulon candidates in B. subtilis are mainly involved in coping with stress but are also engaged in other cellular processes. Orthologs of SigB regulon candidates with SigB PBMs were identified in other Bacillales genomes, but not all showed a SigB PBM. Additionally, genes involved in the integration of stress signals to activate SigB were predicted in these genomes, indicating that SigB signaling and regulon genes are species-specific.
The entire SigB regulatory network is sophisticated and not yet fully understood even for the well-characterized organism B. subtilis 168. Knowledge and information gained in this study can be used in further SigB studies to uncover a complete picture of the role of SigB in B. subtilis and other species.
西格玛因子 B（SigB）是枯草芽孢杆菌中一般应激反应的中央调节剂，可调节一组基因以响应各种应激源，这些基因被称为 SigB 调控子成员。直接受 SigB 调控的基因包含一个先前鉴定的共有序列的启动子结合基序（PBM）。
在这项研究中，推导出了经过改进的 SigB PBM，并考虑了不同的间隔组成和长度（N-N）。这些 PBM 用于鉴定枯草芽孢杆菌基因组中潜在的 SigB 调控基因，共鉴定出 255 个基因：99 个已在文献中描述，156 个是新鉴定的，这使得枯草芽孢杆菌中的 SigB 假定调控子成员（有和没有 SigB PBM）的数量增加到>500 个。这 255 个基因根据与原始 SigB 共有序列的相似性被分为五个类别（I-V）。基于与原始 SigB 共有序列的相似性，选择每个类别的代表进行功能评估。在 wt 和 ΔsigB 突变体中，使用启动子-报告基因融合，在受到热、乙醇和盐胁迫时，对选定代表进行评估。P（I）阳性对照在受到三种应激源的刺激时都会被诱导。P（II）仅在暴露于乙醇时表现出 SigB 依赖性活性，而具有 N 间隔的 P（II）和具有 N 间隔的 P（III）无论受到热/乙醇/盐胁迫都有轻微诱导。P（III）和 P（IV）显示出乙醇特异性 SigB 依赖性活性，尽管它们的-10 结合基序的保守性较低。P（V）在乙醇和盐胁迫下被 SigB 诱导，而缺乏保守的-10 结合区。尽管具有高度相似的共有序列，但 P 和 P（III）在测试条件下的活性并未显示出明显变化。鉴定的枯草芽孢杆菌中扩展的 SigB 调控子候选物主要参与应对应激，但也参与其他细胞过程。在其他芽孢杆菌目中的基因组中鉴定到了具有 SigB PBM 的 SigB 调控子候选物的同源物，但并非所有的都具有 SigB PBM。此外，还预测了这些基因组中参与整合应激信号以激活 SigB 的基因，这表明 SigB 信号和调控子基因是具有物种特异性的。
即使是在特征明确的枯草芽孢杆菌 168 中，整个 SigB 调控网络也很复杂，尚未完全理解。在这项研究中获得的知识和信息可用于进一步的 SigB 研究，以揭示 SigB 在枯草芽孢杆菌和其他物种中的作用的全貌。
