title: Sequences in the -35 region of Escherichia coli rpoS-dependent genes promote transcription by E sigma S.
abstract: sigma S is an alternate sigma factor which functions with RNA polymerase to activate transcription of genes that are involved in a number of stress responses, including stationary-phase survival and osmoprotection. The similarity of the sigma S protein to sigma D (Escherichia coli's major sigma factor) in the regions thought to recognize and bind promoter sequences suggests that sigma S- and sigma D-associated RNA polymerases recognize promoter DNA in a similar manner. However, no promoter recognition sequence for sigma S holoenzyme (E sigma S) has been identified. An apparent conservation of cytosine nucleotides was noted in the -35 region of several sigma S-dependent promoters. Site-directed mutagenesis and reporter gene fusions were used to investigate the importance of the -35 cytosine nucleotides for sigma S-dependent transcription. Substitution of cytosine nucleotides for thymidine at the -35 site of the sigma D-dependent proU promoter effectively abolished transcription by E sigma D but allowed E sigma S to direct transcription from the mutant promoter. Inclusion of the sigma D consensus -10 hexamer strengthened transcription by E sigma S, demonstrating that both E sigma D and E sigma S can recognize the same -10 sequences. Conversely, replacement of -35 site cytosine nucleotides with thymidine in the sigma S-dependent osmY promoter reduced transcription by E sigma S and increased transcription by E sigma D. Our data suggest that DNA sequences in the -35 region function as part of a discriminator mechanism to shift transcription between E sigma D and E sigma S.
authors.affiliation: Section of Microbiology, University of California, Davis 95616, USA. aawise@ucdavis.edu
authors.forename: A
authors.initials: A
authors.lastname: Wise
authors.forename: R
authors.initials: R
authors.lastname: Brems
authors.forename: V
authors.initials: V
authors.lastname: Ramakrishnan
authors.forename: M
authors.initials: M
authors.lastname: Villarejo
mesh_terms: D026905:Amino Acid Transport Systems; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D003067:Coenzymes / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins; D005798:Genes, Bacterial; D017930:Genes, Reporter; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D033902:Periplasmic Binding Proteins; D011401:Promoter Regions, Genetic; D012808:Sigma Factor / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D026905:Amino Acid Transport Systems; D001426:Bacterial Proteins; D002352:Carrier Proteins; D003067:Coenzymes; D029968:Escherichia coli Proteins; D033902:Periplasmic Binding Proteins; C060774:ProU protein, Bacteria; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; C074783:osmY protein, E coli; D012321:DNA-Directed RNA Polymerases