Kriner Michelle A, Groisman Eduardo A
Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.
Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.
Nucleic Acids Res. 2017 Jan 25;45(2):631-642. doi: 10.1093/nar/gkw889. Epub 2016 Oct 5.
Transcription termination events in bacteria often require the RNA helicase Rho. Typically, Rho promotes termination at the end of coding sequences, but it can also terminate transcription within leader regions to implement regulatory decisions. Rho-dependent termination requires initial recognition of a Rho utilization (rut) site on a nascent RNA by Rho's primary binding surface. However, it is presently unclear what factors determine the location of transcription termination, how RNA secondary structures influence this process and whether mechanistic differences distinguish constitutive from regulated Rho-dependent terminators. We previously demonstrated that the 5' leader mRNA of the Salmonella corA gene can adopt two mutually exclusive conformations that dictate accessibility of a rut site to Rho. We now report that the corA leader also controls two subsequent steps of Rho-dependent termination. First, the RNA conformation that presents an accessible rut site promotes pausing of RNA polymerase (RNAP) at a single Rho-dependent termination site over 100 nt downstream. Second, an additional RNA stem-loop promotes Rho activity and controls the location at which Rho-dependent termination occurs, despite having no effect on initial Rho binding to the corA leader. Thus, the multi-step nature of Rho-dependent termination may facilitate regulation of a given coding region by multiple cytoplasmic signals.
细菌中的转录终止事件通常需要RNA解旋酶Rho。通常，Rho促进编码序列末端的终止，但它也可以在先导区域内终止转录以执行调控决策。Rho依赖性终止需要Rho的主要结合表面首先识别新生RNA上的Rho利用（rut）位点。然而，目前尚不清楚哪些因素决定转录终止的位置、RNA二级结构如何影响这一过程，以及机制差异是否区分组成型和受调控的Rho依赖性终止子。我们之前证明，鼠伤寒沙门氏菌corA基因的5'先导mRNA可以采用两种相互排斥的构象，这两种构象决定了rut位点对Rho的可及性。我们现在报告，corA先导序列还控制Rho依赖性终止的两个后续步骤。首先，呈现可及rut位点的RNA构象促进RNA聚合酶（RNAP）在下游100多个核苷酸处的单个Rho依赖性终止位点处暂停。其次，一个额外的RNA茎环促进Rho活性并控制Rho依赖性终止发生的位置，尽管它对Rho与corA先导序列的初始结合没有影响。因此，Rho依赖性终止的多步骤性质可能有助于通过多种细胞质信号对给定编码区域进行调控。
