title: RNA secondary structures regulate three steps of Rho-dependent transcription termination within a bacterial mRNA leader.
abstract: 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.
authors.affiliation: Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA.|Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Kriner
authors.affiliation: Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA eduardo.groisman@yale.edu.|Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.
authors.forename: Eduardo A
authors.initials: EA
authors.lastname: Groisman
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D027682:Cation Transport Proteins / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012234:Rho Factor / Q000378:metabolism*; D013728:Terminator Regions, Genetic
chemical_list: D001426:Bacterial Proteins; D027682:Cation Transport Proteins; C072716:CorA protein, Salmonella; D012329:RNA, Bacterial; D012333:RNA, Messenger; D012234:Rho Factor; D012321:DNA-Directed RNA Polymerases