title: Complex regulation of the global regulatory gene csrA: CsrA-mediated translational repression, transcription from five promoters by Eσ⁷⁰ and Eσ(S), and indirect transcriptional activation by CsrA.
abstract: CsrA of Escherichia coli is an RNA-binding protein that globally regulates gene expression by repressing translation and/or altering the stability of target transcripts. Here we explored mechanisms that control csrA expression. Four CsrA binding sites were predicted upstream of the csrA initiation codon, one of which overlapped its Shine-Dalgarno sequence. Results from gel shift, footprint, toeprint and in vitro translation experiments indicate that CsrA binds to these four sites and represses its own translation by directly competing with 30S ribosomal subunit binding. Experiments were also performed to examine transcription of csrA. Primer extension, in vitro transcription and in vivo expression studies identified two σ⁷⁰-dependent (P2 and P5) and two σ(S) -dependent (P1 and P3) promoters that drive transcription of csrA. Additional primer extension studies identified a fifth csrA promoter (P4). Transcription from P3, which is indirectly activated by CsrA, is primarily responsible for increased csrA expression as cells transition from exponential to stationary-phase growth. Taken together, our results indicate that regulation of csrA expression occurs by a variety of mechanisms, including transcription from multiple promoters by two sigma factors, indirect activation of its own transcription, as well as direct repression of its own translation.
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Helen
authors.initials: H
authors.lastname: Yakhnin
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Yakhnin
authors.forename: Carol S
authors.initials: CS
authors.lastname: Baker
authors.forename: Elena
authors.initials: E
authors.lastname: Sineva
authors.forename: Igor
authors.initials: I
authors.lastname: Berezin
authors.forename: Tony
authors.initials: T
authors.lastname: Romeo
authors.forename: Paul
authors.initials: P
authors.lastname: Babitzke
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D004926:Escherichia coli / Q000235:genetics / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000096:biosynthesis*; D015964:Gene Expression Regulation, Bacterial; D008954:Models, Biological; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014176:Protein Biosynthesis; D016601:RNA-Binding Proteins / Q000096:biosynthesis*; D012097:Repressor Proteins / Q000096:biosynthesis*; D012808:Sigma Factor / Q000378:metabolism*; D024363:Transcription Initiation Site; D015533:Transcriptional Activation
chemical_list: D001426:Bacterial Proteins; C093587:CsrA protein, E coli; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D016601:RNA-Binding Proteins; D012097:Repressor Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases