title: RNA polymerase pausing regulates translation initiation by providing additional time for TRAP-RNA interaction.
abstract: RNA polymerase (RNAP) pause sites have been identified in several prokaryotic genes. Although the presumed biological function of RNAP pausing is to allow synchronization of RNAP position with regulatory factor binding and/or RNA folding, a direct causal link between pausing and changes in gene expression has been difficult to establish. RNAP pauses at two sites in the Bacillus subtilis trpEDCFBA operon leader. Pausing at U107 and U144 participates in transcription attenuation and trpE translation control mechanisms, respectively. Substitution of U144 caused a substantial pausing defect in vitro and in vivo. These mutations led to increased trp operon expression that was suppressed by overproduction of TRAP, indicating that pausing at U144 provides additional time for TRAP to bind to the nascent transcript and promote formation of an RNA structure that blocks translation of trpE. These results establish that pausing is capable of playing a role in regulating translation in bacteria.
authors.affiliation: Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Yakhnin
authors.forename: Helen
authors.initials: H
authors.lastname: Yakhnin
authors.forename: Paul
authors.initials: P
authors.lastname: Babitzke
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D001426:Bacterial Proteins / Q000378:metabolism*; D001665:Binding Sites; D002478:Cells, Cultured; D012321:DNA-Directed RNA Polymerases / Q000502:physiology*; D015964:Gene Expression Regulation, Bacterial; D008954:Models, Biological; D009876:Operon / Q000235:genetics; D039662:Prokaryotic Initiation Factors / Q000235:genetics* / Q000502:physiology; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism*; D013997:Time Factors; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic / Q000502:physiology*; D014364:Tryptophan / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C079092:MtrB protein, Bacteria; D039662:Prokaryotic Initiation Factors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D014364:Tryptophan; D012321:DNA-Directed RNA Polymerases