Abstract

Although transcription by RNA polymerase (RNAP) is highly processive, elongation can be transiently halted by RNAP pausing. Pausing provides time for diverse regulatory events to occur such as RNA folding and regulatory factor binding. The transcription elongation factors NusA and NusG dramatically affect the frequency and duration of RNAP pausing, and hence regulation of transcription. NusG is the only transcription factor conserved in all three domains of life; its homolog in archaea and eukaryotes is Spt5. This review focuses on NusG-dependent pausing, which is a common occurrence in Bacillus subtilis. B. NusG induces pausing about once per 3 kb at a consensus TTNTTT motif in the non-template DNA strand within the paused transcription bubble. A conserved region of NusG contacts the TTNTTT motif to stabilize the paused transcription elongation complex (TEC) in multiple catalytically inactive RNAP conformations. The density of NusG-dependent pause sites is 3-fold higher in untranslated regions, suggesting that pausing could regulate the expression of hundreds of genes in B. subtilis. We describe how pausing in 5' leader regions contributes to regulating the expression of B. subtilis genes by transcription attenuation and translation control mechanisms. As opposed to the broadly accepted view that NusG is an anti-pausing factor, phylogenetic analyses suggest that NusG-dependent pausing is a widespread mechanism in bacteria. This function of NusG is consistent with the well-established role of its eukaryotic homolog Spt5 in promoter-proximal pausing. Since NusG is present in all domains of life, NusG-dependent pausing could be a conserved mechanism in all organisms.

摘要

尽管 RNA 聚合酶 (RNAP) 的转录是高度进行性的，但 RNAP 暂停可以暂时停止延伸。暂停为各种调节事件的发生提供了时间，例如 RNA 折叠和调节因子结合。转录延伸因子 NusA 和 NusG 显着影响 RNAP 暂停的频率和持续时间，从而影响转录的调节。NusG 是唯一在所有三个生命领域都保守的转录因子；它在古细菌和真核生物中的同源物是 Spt5。这篇综述的重点是 NusG 依赖的停顿，这在枯草芽孢杆菌中很常见。B.NusG 在暂停的转录气泡内的非模板 DNA 链中，每 3 kb 诱导一个共有 TTNTTT 基序暂停一次。NusG 的一个保守区域与 TTNTTT 基序接触，以稳定多个无催化活性 RNAP 构象中的暂停转录延伸复合物 (TEC)。NusG 依赖性暂停位点的密度在非翻译区域高出 3 倍，这表明暂停可以调节枯草芽孢杆菌中数百个基因的表达。我们描述了 5' 前导区域的暂停如何有助于调节枯草芽孢杆菌的表达基因通过转录衰减和翻译控制机制。与广泛接受的 NusG 是一种抗暂停因子的观点相反，系统发育分析表明，NusG 依赖性暂停是细菌中普遍存在的机制。NusG 的这一功能与其真核同源物Spt5 在启动子近端暂停中的既定作用是一致的。由于 NusG 存在于生命的所有领域，因此依赖于 NusG 的暂停可能是所有生物体中的一种保守机制。