title: The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation.
abstract: Escherichia coli O104:H4 (E. coli O104:H4), which caused a massive outbreak of acute gastroenteritis and hemolytic uremic syndrome in 2011, carries an aggregative adherence fimbriae I (AAF/I) encoding virulence plasmid, pAA. The importance of pAA in host-pathogen interaction and disease severity has been demonstrated, however, not much is known about its transcriptional organization and gene regulation. Here, we analyzed the pAA primary transcriptome using differential RNA sequencing, which allows for the high-throughput mapping of transcription start site (TSS) and non-coding RNA candidates. We identified 248 TSS candidates in the 74-kb pAA and only 21% of them could be assigned as TSS of annotated genes. We detected TSS for the majority of pAA-encoded virulence factors. Interestingly, we mapped TSS, which could allow for the transcriptional uncoupling of the AAF/I operon, and potentially regulatory antisense RNA candidates against the genes encoding dispersin and the serine protease SepA. Moreover, a computational search for transcription factor binding sites suggested for AggR-mediated activation of SepA expression, which was additionally experimentally validated. This work advances our understanding of the molecular basis of E. coli O104:H4 pathogenicity and provides a valuable resource for further characterization of pAA virulence gene regulation.
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Petya
authors.initials: P
authors.lastname: Berger
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Knödler
authors.affiliation: Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany.|Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.|Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany.
authors.forename: Konrad U
authors.initials: KU
authors.lastname: Förstner
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Berger
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Bertling
authors.affiliation: Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany.
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.affiliation: Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Helge
authors.initials: H
authors.lastname: Karch
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Dobrindt
authors.affiliation: Institute of Hygiene, University of Münster, Münster, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Mellmann
mesh_terms: D019295:Computational Biology; D000069981:Escherichia coli O104 / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics*; D010861:Fimbriae, Bacterial / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D009876:Operon; D010447:Peptide Hydrolases / Q000235:genetics*; D010957:Plasmids / Q000235:genetics*; D016372:RNA, Antisense / Q000378:metabolism; D017423:Sequence Analysis, RNA; D015534:Trans-Activators / Q000235:genetics*; D059467:Transcriptome; D014774:Virulence / Q000235:genetics*
chemical_list: C088603:AggR protein, E coli; D029968:Escherichia coli Proteins; D016372:RNA, Antisense; D015534:Trans-Activators; D010447:Peptide Hydrolases; C570452:SepA protein, E coli