title: Domain 1.1 of the sigma(70) subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes.
abstract: The sigma 70 (sigma(70)) subunit of Escherichia coli RNA polymerase specifies transcription from promoters that are responsible for basal gene expression during vegetative growth. When sigma(70) is present within polymerase holoenzyme, two of its domains, 2.4 and 4.2, interact with sequences within the -10 and -35 regions, respectively, of promoter DNA. However, in free sigma(70), DNA binding is prevented by domain 1.1, the N-terminal domain of the protein. Previous work has demonstrated that the presence of domain 1.1 is required for efficient transcription initiation at the lambda promoter P(R). To investigate whether this is a general property of domain 1.1, we have used five promoters to compare polymerases with and without domain 1.1 in in vitro transcription assays, and in assays assessing the formation and decay of stable, pretranscription complexes. We find that the absence of domain 1.1 does not render the polymerase defective at all of these promoters. Depending on the promoter, the absence of domain 1.1 can promote or inhibit transcription initiation by affecting the formation of stable pretranscription complexes. However, domain 1.1 does not affect the stability of these complexes once they are formed. For polymerases containing domain 1.1, the efficiency of stable complex formation correlates with how well the -10 and -35 regions of a promoter match the ideal sigma(70) recognition sequences. However, when domain 1.1 is absent, having this match becomes less important in determining how efficiently stable complexes are made. We suggest that domain 1.1 influences initiation by constraining polymerase to assess a promoter primarily by the fitness of its -10 and -35 regions to the canonical sequences.
authors.affiliation: Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 8, Room 2A-13, Bethesda, MD 20892, USA.
authors.forename: S
authors.initials: S
authors.lastname: Vuthoori
authors.forename: C W
authors.initials: CW
authors.lastname: Bowers
authors.forename: A
authors.initials: A
authors.lastname: McCracken
authors.forename: A J
authors.initials: AJ
authors.lastname: Dombroski
authors.forename: D M
authors.initials: DM
authors.lastname: Hinton
mesh_terms: D001483:Base Sequence; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D006493:Heparin / Q000378:metabolism; D020035:Holoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics; D009690:Nucleic Acid Conformation; D011196:Potassium Permanganate / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016372:RNA, Antisense / Q000235:genetics; D034741:RNA, Small Interfering; D017384:Sequence Deletion / Q000235:genetics; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D013698:Templates, Genetic; D014158:Transcription, Genetic / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D020035:Holoenzymes; D008565:Membrane Proteins; D016372:RNA, Antisense; D034741:RNA, Small Interfering; D012808:Sigma Factor; C092863:UvsX protein, Enterobacteria phage T4; D014764:Viral Proteins; D011196:Potassium Permanganate; D006493:Heparin; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases