title: Genome amplification and promoter mutation expand the range of csgD-dependent biofilm responses in an STEC population.
abstract: Expression of the major biofilm components of E. coli, curli fimbriae and cellulose, requires the CsgD transcription factor. A complex regulatory network allows environmental control of csgD transcription and biofilm formation. However, most clinical serotype O157 : H7 strains contain prophage insertions in the csgD regulator, mlrA, or mutations in other regulators that restrict csgD expression. These barriers can be circumvented by certain compensating mutations that restore higher csgD expression. One mechanism is via csgD promoter mutations that switch sigma factor utilization. Biofilm-forming variants utilizing RpoD rather than RpoS have been identified in glycerol freezer stocks of the non-biofilm-forming food-borne outbreak strain, ATCC 43894. In this study we used whole genome sequencing and RNA-seq to study genotypic and transcriptomic differences between those strains. In addition to defining the consequences of the csgD promoter switch and identifying new csgD-controlled genes, we discovered a region of genome amplification in our laboratory stock of 43894 (designated 43894OW) that contributed to the regulation of csgD-dependent properties.
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Gaylen A
authors.initials: GA
authors.lastname: Uhlich
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Chin-Yi
authors.initials: CY
authors.lastname: Chen
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Cottrell
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Elisa
authors.initials: E
authors.lastname: Andreozzi
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Peter L
authors.initials: PL
authors.lastname: Irwin
authors.affiliation: Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 600 East Mermaid Lane, Wyndmoor, PA, USA.
authors.forename: Ly-Huong
authors.initials: LH
authors.lastname: Nguyen
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics*; D018441:Biofilms / Q000254:growth & development*; D002482:Cellulose / Q000096:biosynthesis / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D019453:Escherichia coli O157 / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D036781:Fimbriae Proteins / Q000096:biosynthesis / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012808:Sigma Factor / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; C499694:CsgD protein, E coli; D029968:Escherichia coli Proteins; C451279:MlrA protein, E coli; D012808:Sigma Factor; D015534:Trans-Activators; C069567:sigma factor KatF protein, Bacteria; D036781:Fimbriae Proteins; C077481:Crl protein, Bacteria; D002482:Cellulose; C081775:RNA polymerase sigma 70; D012321:DNA-Directed RNA Polymerases