title: Comprehensive mapping of the Escherichia coli flagellar regulatory network.
abstract: Flagellar synthesis is a highly regulated process in all motile bacteria. In Escherichia coli and related species, the transcription factor FlhDC is the master regulator of a multi-tiered transcription network. FlhDC activates transcription of a number of genes, including some flagellar genes and the gene encoding the alternative Sigma factor FliA. Genes whose expression is required late in flagellar assembly are primarily transcribed by FliA, imparting temporal regulation of transcription and coupling expression to flagellar assembly. In this study, we use ChIP-seq and RNA-seq to comprehensively map the E. coli FlhDC and FliA regulons. We define a surprisingly restricted FlhDC regulon, including two novel regulated targets and two binding sites not associated with detectable regulation of surrounding genes. In contrast, we greatly expand the known FliA regulon. Surprisingly, 30 of the 52 FliA binding sites are located inside genes. Two of these intragenic promoters are associated with detectable noncoding RNAs, while the others either produce highly unstable RNAs or are inactive under these conditions. Together, our data redefine the E. coli flagellar regulatory network, and provide new insight into the temporal orchestration of gene expression that coordinates the flagellar assembly process.
authors.affiliation: Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America.
authors.forename: Devon M
authors.initials: DM
authors.lastname: Fitzgerald
authors.affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.
authors.forename: Richard P
authors.initials: RP
authors.lastname: Bonocora
authors.affiliation: Department of Biomedical Sciences, University at Albany, Albany, New York, United States of America; Wadsworth Center, New York State Department of Health, Albany, New York, United States of America.
authors.forename: Joseph T
authors.initials: JT
authors.lastname: Wade
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D000939:Epitopes / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000276:immunology; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D005407:Flagella / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D009876:Operon; D011401:Promoter Regions, Genetic; D015203:Reproducibility of Results; D012808:Sigma Factor / Q000235:genetics; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism
chemical_list: D000939:Epitopes; D029968:Escherichia coli Proteins; D012808:Sigma Factor; D015534:Trans-Activators; C090552:flhC protein, E coli; C090553:flhD protein, E coli; C063202:sporulation-specific sigma factors