title: Nucleotides from -16 to -12 determine specific promoter recognition by bacterial sigmaS-RNA polymerase.
abstract: The alternative sigma factor sigmaS, mainly active in stationary phase of growth, recognizes in vitro a -10 promoter sequence almost identical to the one for the main sigma factor, sigma70, thus raising the problem of how specific promoter recognition by sigmaS-RNA polymerase (EsigmaS) is achieved in vivo. We investigated the promoter features involved in selective recognition by EsigmaS at the strictly sigmaS-dependent aidB promoter. We show that the presence of a C nucleotide as first residue of the aidB -10 sequence (-12C), instead of the T nucleotide canonical for sigma70-dependent promoters, is the major determinant for selective recognition by EsigmaS. The presence of the -12C does not allow formation of an open complex fully proficient in transcription initiation by Esigma70. The role of -12C as specific determinant for promoter recognition by EsigmaS was confirmed by sequence analysis of known EsigmaS-dependent promoters as well as site-directed mutagenesis at the promoters of the csgB and sprE genes. We propose that EsigmaS, unlike Esigma70, can recognize both C and T as the first nucleotide in the -10 sequence. Additional promoter features such as the presence of a C nucleotide at position -13, contributing to open complex formation by EsigmaS, and a TG motif found at the unusual -16/-15 location, possibly contributing to initial binding to the promoter, also represent important factors for sigmaS-dependent transcription. We propose a new sequence, TG(N)0-2CCATA(c/a)T, as consensus -10 sequence for promoters exclusively recognized by EsigmaS.
authors.affiliation: Swiss Federal Institute of Environmental Technology (EAWAG), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland.
authors.forename: Stephan
authors.initials: S
authors.lastname: Lacour
authors.forename: Annie
authors.initials: A
authors.lastname: Kolb
authors.forename: Paolo
authors.initials: P
authors.lastname: Landini
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D008969:Molecular Sequence Data; D011196:Potassium Permanganate / Q000494:pharmacology; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: C090096:AidB protein, E coli; D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D011196:Potassium Permanganate; D012321:DNA-Directed RNA Polymerases