title: Escherichia coli σ⁷⁰ senses sequence and conformation of the promoter spacer region.
abstract: In bacteria, promoter identification by RNA polymerase is mediated by a dissociable σ factor. The housekeeping σ(70) factor of Escherichia coli recognizes two well characterized DNA sequence elements, known as the '-10' and '-35' hexamers. These elements are separated by 'spacer' DNA, the sequence of which is generally considered unimportant. Here, we use a combination of bioinformatics, genetics and biochemistry to show that σ(70) can sense the sequence and conformation of the promoter spacer region. Our data illustrate how alterations in spacer region sequence can increase promoter activity. This stimulatory effect requires σ(70) side chain R451, which is located in close proximity to the non-template strand at promoter position -18. Conversely, R451 is not required to mediate transcriptional stimulation by improvement of the -10 element. Mutation of σ(70) residue R451, which is highly conserved, results in reduced growth rate, consistent with a central role in promoter recognition.
authors.affiliation: School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK.
authors.forename: Shivani S
authors.initials: SS
authors.lastname: Singh
authors.forename: Athanasios
authors.initials: A
authors.lastname: Typas
authors.forename: Regine
authors.initials: R
authors.lastname: Hengge
authors.forename: David C
authors.initials: DC
authors.lastname: Grainger
mesh_terms: D001483:Base Sequence; D002455:Cell Division; D004269:DNA, Bacterial / Q000737:chemistry*; D021901:DNA, Intergenic / Q000737:chemistry*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic; D029968:Escherichia coli Proteins; D012808:Sigma Factor; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases