title: Novel DNA Binding and Regulatory Activities for σ54(RpoN) in Salmonella enterica Serovar Typhimurium 14028s.
abstract: The variable sigma (σ) subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes.Salmonella entericaserovar Typhimurium utilizes the housekeeping σ70and five alternative sigma factors, including σ54The σ54-RNAP differs from other σ-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bacterial enhancer binding protein (bEBP) to transition to an open complex and initiate transcription. InS.Typhimurium, σ54-dependent promoters normally respond to one of 13 different bEBPs, each of which is activated under a specific growth condition. Here, we utilized a constitutively active, promiscuous bEBP to perform a genome-wide identification of σ54-RNAP DNA binding sites and the transcriptome of the σ54regulon ofS.Typhimurium. The position and context of many of the identified σ54RNAP DNA binding sites suggest regulatory roles for σ54-RNAP that connect the σ54regulon to regulons of other σ factors to provide a dynamic response to rapidly changing environmental conditions.IMPORTANCEThe alternative sigma factor σ54(RpoN) is required for expression of genes involved in processes with significance in agriculture, bioenergy production, bioremediation, and host-microbe interactions. The characterization of the σ54regulon of the versatile pathogenS.Typhimurium has expanded our understanding of the scope of the σ54regulon and how it links to other σ regulons within the complex regulatory network for gene expression in bacteria.
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia, USA.
authors.forename: Ashley C
authors.initials: AC
authors.lastname: Bono
authors.affiliation: Department of Genetics, University of Georgia, Athens, Georgia, USA.
authors.forename: Christine E
authors.initials: CE
authors.lastname: Hartman
authors.affiliation: Department of Computer Science, University of Georgia, Athens, Georgia, USA.
authors.forename: Sina
authors.initials: S
authors.lastname: Solaimanpour
authors.affiliation: Department of Statistics, University of Georgia, Athens, Georgia, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Tong
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California-Irvine School of Medicine, Irvine, California, USA.
authors.forename: Steffen
authors.initials: S
authors.lastname: Porwollik
authors.affiliation: Department of Microbiology and Molecular Genetics, University of California-Irvine School of Medicine, Irvine, California, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: McClelland
authors.affiliation: Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. Department of Agriculture, Athens, Georgia, USA.
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Frye
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia, USA.|Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Mrázek
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia, USA akarls@uga.edu.
authors.forename: Anna C
authors.initials: AC
authors.lastname: Karls
mesh_terms: D001665:Binding Sites; D004269:DNA, Bacterial / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D011485:Protein Binding; D051877:RNA Polymerase Sigma 54 / Q000378:metabolism*; D018085:Regulon; D012486:Salmonella typhimurium / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D051877:RNA Polymerase Sigma 54
keywords: RpoN; Salmonella enterica serovar Typhimurium; bEBP; promoter; regulon; σ54