Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA.
Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York, USA
mBio. 2019 May 21;10(3):e00273-19. doi: 10.1128/mBio.00273-19.
Mycobacterial σ belongs to the group II family of sigma factors, which are widely considered to transcribe genes required for stationary-phase survival and the response to stress. Here we explored the mechanism underlying the observed hypersensitivity of Δ deletion mutants of , , and to rifampin (RIF) and uncovered an additional constitutive role of σ during exponential growth of mycobacteria that complements the function of the primary sigma factor, σ Using chromatin immunoprecipitation sequencing (ChIP-Seq), we show that during exponential phase, σ binds to over 200 promoter regions, including those driving expression of essential housekeeping genes, like the rRNA gene. ChIP-Seq of ectopically expressed σ-FLAG demonstrated that at least 61 promoter sites are recognized by both σ and σ These results together suggest that RNA polymerase holoenzymes containing either σ or σ transcribe housekeeping genes in exponentially growing mycobacteria. The RIF sensitivity of the Δ mutant possibly reflects a decrease in the effective housekeeping holoenzyme pool, which results in susceptibility of the mutant to lower doses of RIF. Consistent with this model, overexpression of σ restores the RIF tolerance of the Δ mutant to that of the wild type, concomitantly ruling out a specialized role of σ in RIF tolerance. Although the properties of mycobacterial σ parallel those of σ in its ability to transcribe a subset of housekeeping genes, σ presents a clear departure from the paradigm, wherein the cellular levels of σ are tightly controlled during exponential growth, such that the transcription of housekeeping genes is initiated exclusively by a holoenzyme containing σ (E.σ). All mycobacteria encode a group II sigma factor, σ, closely related to the group I principal housekeeping sigma factor, σ Group II sigma factors are widely believed to play specialized roles in the general stress response and stationary-phase transition in the bacteria that encode them. Contrary to this widely accepted view, we show an additional housekeeping function of σ that complements the function of σ in logarithmically growing cells. These findings implicate a novel and dynamic partnership between σ and σ in maintaining the expression of housekeeping genes in mycobacteria and can perhaps be extended to other bacterial species that possess multiple group II sigma factors.
Mycobacterial σ 属于 II 组 σ 因子家族,该家族被广泛认为能转录与静止期生存和应激反应相关的基因。在这里,我们探索了观察到的 、 、 和 缺失突变体对抗结核药物利福平(RIF)敏感性增加的机制,并发现了 σ 在分枝杆菌指数生长期的一个额外的组成型功能,该功能补充了主要 σ 因子 σ 的功能。通过染色质免疫沉淀测序(ChIP-Seq),我们表明在指数生长期,σ 结合到超过 200 个启动子区域,包括那些驱动必需的管家基因,如 rRNA 基因表达的启动子。异位表达 σ-FLAG 的 ChIP-Seq 表明,至少有 61 个启动子位点被 σ 和 σ 识别。这些结果共同表明,含有 σ 或 σ 的 RNA 聚合酶全酶在指数生长期的分枝杆菌中转录管家基因。Δ 突变体对 RIF 的敏感性可能反映了有效管家全酶池的减少,这导致突变体对较低剂量的 RIF 敏感。与该模型一致,σ 的过表达恢复了 Δ 突变体对野生型的 RIF 耐受性,同时排除了 σ 在 RIF 耐受性中的特殊作用。尽管分枝杆菌 σ 的特性与其在转录一组管家基因方面的能力与大肠杆菌中的 σ 相似,但 σ 明显偏离了 σ 的范例,在指数生长期,σ 的细胞水平受到严格控制,因此管家基因的转录仅由含有 σ(E.σ)的全酶启动。所有分枝杆菌都编码一个 II 组 σ 因子,σ,与 I 组主要的管家 σ 因子 σ 密切相关。II 组 σ 因子被广泛认为在编码它们的细菌的一般应激反应和静止期过渡中发挥特殊作用。与这一被广泛接受的观点相反,我们展示了 σ 的另一个管家功能,该功能补充了 σ 在对数生长期细胞中的功能。这些发现暗示了 σ 和 σ 之间存在一种新的和动态的伙伴关系,以维持分枝杆菌中管家基因的表达,并可能扩展到其他具有多个 II 组 σ 因子的细菌物种。