title: The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system.
abstract: The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila. Genome wide transcriptome, proteome and RNA co-immunoprecipitation followed by deep sequencing of a wild type and a csrA mutant strain identified 479 RNAs with potential CsrA interaction sites located in the untranslated and/or coding regions of mRNAs or of known non-coding sRNAs. Further analyses revealed that CsrA exhibits a dual regulatory role in virulence as it affects the expression of the regulators FleQ, LqsR, LetE and RpoS but it also directly regulates the timely expression of over 40 Dot/Icm substrates. CsrA controls its own expression and the stringent response through a regulatory feedback loop as evidenced by its binding to RelA-mRNA and links it to quorum sensing and motility. CsrA is a central player in the carbon, amino acid, fatty acid metabolism and energy transfer and directly affects the biosynthesis of cofactors, vitamins and secondary metabolites. We describe the first L. pneumophila riboswitch, a thiamine pyrophosphate riboswitch whose regulatory impact is fine-tuned by CsrA, and identified a unique regulatory mode of CsrA, the active stabilization of RNA anti-terminator conformations inside a coding sequence preventing Rho-dependent termination of the gap operon through transcriptional polarity effects. This allows L. pneumophila to regulate the pentose phosphate pathway and the glycolysis combined or individually although they share genes in a single operon. Thus the L. pneumophila genome has evolved to acclimate at least five different modes of regulation by CsrA giving it a truly unique position in its life cycle.
authors.affiliation: Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France.|CNRS UMR 3525, Paris, France.
authors.forename: Tobias
authors.initials: T
authors.lastname: Sahr
authors.affiliation: Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France.|CNRS UMR 3525, Paris, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Rusniok
authors.affiliation: Institut Pasteur, Unité des Interactions Bactéries-Cellules, Inserm U604, INRA Unité sous-contrat, Paris, France.|VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium.
authors.forename: Francis
authors.initials: F
authors.lastname: Impens
authors.affiliation: Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France.|CNRS UMR 3525, Paris, France.
authors.forename: Giulia
authors.initials: G
authors.lastname: Oliva
authors.affiliation: Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, Paris, France.
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.affiliation: Institut Pasteur, Transcriptome and EpiGenome, BioMics, Center for Innovation and Technological Research, Paris, France.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppée
authors.affiliation: Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris France.|CNRS UMR 3525, Paris, France.
authors.forename: Carmen
authors.identifier: 0000-0003-3477-9190
authors.initials: C
authors.lastname: Buchrieser
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D015152:Blotting, Northern; D019143:Evolution, Molecular; D025461:Feedback, Physiological; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D006019:Glycolysis / Q000235:genetics; D054884:Host-Pathogen Interactions; D006801:Humans; D016952:Legionella pneumophila / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D007877:Legionnaires' Disease / Q000382:microbiology; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009876:Operon / Q000235:genetics; D010427:Pentose Phosphate Pathway / Q000235:genetics; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism; D058928:Riboswitch / Q000235:genetics; D053719:Tandem Mass Spectrometry; D014774:Virulence / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; C488628:CsrA protein, Legionella pneumophila; D012333:RNA, Messenger; D012097:Repressor Proteins; D058928:Riboswitch