title: Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes.
abstract: Two distinct classes of RNA polymerase sigma factors (sigma) exist in bacteria and are largely unrelated in primary amino acid sequence and their modes of transcription activation. Using tethered iron chelate (Fe-BABE) derivatives of the enhancer-dependent sigma(54), we mapped several sites of proximity to the beta and beta' subunits of the core RNA polymerase. Remarkably, most sites localized to those previously identified as close to the enhancer-independent sigma(70) and sigma(38). This indicates a common use of sets of sequences in core for interacting with the two sigma classes. Some sites chosen in sigma(54) for modification with Fe-BABE were positions, which when mutated, deregulate the sigma(54)-holoenzyme and allow activator-independent initiation and holoenzyme isomerization. We infer that these sites in sigma(54) may be involved in interactions with the core that contribute to maintenance of alternative states of the holoenzyme needed for either the stable closed promoter complex conformation or the isomerized holoenzyme conformation associated with the open promoter complex. One site of sigma(54) proximity to the core is apparently not evident with sigma(70), and may represent a specialized interaction.
authors.affiliation: Imperial College of Science, Technology and Medicine, Department of Biology, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK.
authors.forename: S R
authors.initials: SR
authors.lastname: Wigneshweraraj
authors.forename: N
authors.initials: N
authors.lastname: Fujita
authors.forename: A
authors.initials: A
authors.lastname: Ishihama
authors.forename: M
authors.initials: M
authors.lastname: Buck
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000378:metabolism; D001665:Binding Sites; D017124:Conserved Sequence; D003545:Cysteine / Q000235:genetics; D018983:DNA Footprinting; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D004492:Edetic Acid / Q000031:analogs & derivatives; D004742:Enhancer Elements, Genetic; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins; D020035:Holoenzymes; D008958:Models, Molecular; D009154:Mutation; D009942:Organometallic Compounds; D011485:Protein Binding; D051877:RNA Polymerase Sigma 54; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D020035:Holoenzymes; D009942:Organometallic Compounds; D012808:Sigma Factor; C497751:rpoN protein, E coli; C069567:sigma factor KatF protein, Bacteria; C042007:1-(4-bromoacetamidobenzyl)EDTA; D004492:Edetic Acid; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D051877:RNA Polymerase Sigma 54; D003545:Cysteine