Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, Russia.
RNA Biol. 2021 Nov;18(11):2028-2037. doi: 10.1080/15476286.2021.1889254. Epub 2021 Feb 25.
The bacterial σ factor plays the central role in promoter recognition by RNA polymerase (RNAP). The primary σ factor, involved in transcription of housekeeping genes, was also shown to participate in the initiation of RNA synthesis and promoter escape by RNAP. In the open promoter complex, the σ finger formed by σ region 3.2 directly interacts with the template DNA strand upstream of the transcription start site. Here, we analysed the role of the σ finger in transcription initiation by four alternative σ factors in , σ, σ, σ and σ. We found that deletions of the σ finger to various extent compromise the activity of RNAP holoenzymes containing alternative σ factors, especially at low NTP concentrations. All four σs are able to utilize NADH as a noncanonical priming substrate but it has only mild effects on the efficiency of transcription initiation. The mediators of the stringent response, transcription factor DksA and the alarmone ppGpp decrease RNAP activity and promoter complex stability for all four σ factors on tested promoters. For all σs except σ, deletions of the σ finger conversely increase the stability of promoter complexes and decrease their sensitivity to DksA and ppGpp. The result suggests that the σ finger plays a universal role in transcription initiation by alternative σ factors and sensitizes promoter complexes to the action of global transcription regulators DksA and ppGpp by modulating promoter complex stability.
细菌 σ 因子在 RNA 聚合酶 (RNAP) 识别启动子中起着核心作用。参与管家基因转录的主要 σ 因子也被证明参与了 RNAP 的 RNA 合成起始和启动子逃避。在开放启动复合物中，由 σ 区域 3.2 形成的 σ 指直接与转录起始位点上游的模板 DNA 链相互作用。在这里，我们分析了替代 σ 因子中的四个 σ 因子在转录起始中的作用，它们分别是 σ、σ、σ 和 σ。我们发现，不同程度地删除 σ 指会损害包含替代 σ 因子的全酶 RNAP 的活性，尤其是在低 NTP 浓度下。所有四个 σ 因子都能够利用 NADH 作为非典型的起始底物，但它对转录起始效率只有轻微的影响。严格反应的介质，转录因子 DksA 和警报素 ppGpp，降低了所有四个σ因子在测试启动子上的 RNAP 活性和启动子复合物稳定性。对于除了 σ 之外的所有 σ 因子，σ 指的缺失反而会增加启动子复合物的稳定性，并降低它们对 DksA 和 ppGpp 的敏感性。结果表明，σ 指在替代 σ 因子的转录起始中起着普遍作用，并通过调节启动子复合物稳定性使启动子复合物对全局转录调节剂 DksA 和 ppGpp 的作用敏感。
