title: Formation of intermediate transcription initiation complexes at pfliD and pflgM by sigma(28) RNA polymerase.
abstract: The sigma subunit of prokaryotic RNA polymerase is an important factor in the control of transcription initiation. Primary sigma factors are essential for growth, while alternative sigma factors are activated in response to various stimuli. Expression of class 3 genes during flagellum biosynthesis in Salmonella enterica serovar Typhimurium is dependent on the alternative sigma factor sigma(28). Previously, a novel mechanism of transcription initiation at the fliC promoter by sigma(28) holoenzyme was proposed. Here, we have characterized the mechanism of transcription initiation by a holoenzyme carrying sigma(28) at the fliD and flgM promoters to determine if the mechanism of initiation observed at pfliC is a general phenomenon for all sigma(28)-dependent promoters. Temperature-dependent footprinting demonstrated that promoter binding properties and low-temperature open complex formation are similar for pfliC, pfliD, and pflgM. However, certain aspects of DNA strand separation and complex stability are promoter dependent. Open complexes form in a concerted manner at pflgM, while a sequential pattern of open complex formation occurs at pfliD. Open and initiated complexes formed by holoenzyme carrying sigma(28) are generally unstable to heparin challenge, with the exception of initiated complexes at pflgM, which are stable in the presence of nucleoside triphosphates.
authors.affiliation: Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas 77030, USA.
authors.forename: J R
authors.initials: JR
authors.lastname: Givens
authors.forename: C L
authors.initials: CL
authors.lastname: McGovern
authors.forename: A J
authors.initials: AJ
authors.lastname: Dombroski
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000502:physiology*; D016384:Consensus Sequence; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000378:metabolism; D005408:Flagellin / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D006493:Heparin / Q000494:pharmacology; D046911:Macromolecular Substances; D011401:Promoter Regions, Genetic; D012486:Salmonella typhimurium / Q000235:genetics; D012808:Sigma Factor / Q000502:physiology*; D013696:Temperature; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C064971:FliA protein, Bacteria; D046911:Macromolecular Substances; D012808:Sigma Factor; D005408:Flagellin; C071266:FlgM protein, Bacteria; C076733:FlaD protein, Bacteria; D006493:Heparin