title: Role of the spacer between the -35 and -10 regions in sigmas promoter selectivity in Escherichia coli.
abstract: In vitro, the sigma(s) subunit of RNA polymerase (RNAP), RpoS, recognizes nearly identical -35 and -10 promoter consensus sequences as the vegetative sigma70. In vivo, promoter selectivity of RNAP holoenzyme containing either sigma(s) (Esigma(s)) or sigma70 (Esigma70) seems to be achieved by the differential ability of the two holoenzymes to tolerate deviations from the promoter consensus sequence. In this study, we suggest that many natural sigma(s)-dependent promoters possess a -35 element, a feature that has been considered as not conserved among sigma(s)-dependent promoters. These -35 hexamers are mostly non-optimally spaced from the -10 region, but nevertheless functional. A +/- 2 bp deviation from the optimal spacer length of 17 bp or the complete absence of a -35 consensus sequence decreases overall promoter activity, but at the same time favours Esigma(s) in its competition with Esigma70 for promoter recognition. On the other hand, the reduction of promoter activity due to shifting of the -35 element can be counterbalanced by an activity-stimulating feature such as A/T-richness of the spacer region without compromising Esigma(s) selectivity. Based on mutational analysis of sigma(s), we suggest a role of regions 2.5 and 4 of sigma(s) in sensing sub-optimally located -35 elements.
authors.affiliation: Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Typas
authors.forename: Regine
authors.initials: R
authors.lastname: Hengge
mesh_terms: D000225:Adenine / Q000737:chemistry; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000502:physiology; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D016385:TATA Box / Q000502:physiology*; D013941:Thymine / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; C106402:RNA polymerase Esigma(38); C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases; D000225:Adenine; D013941:Thymine