1. Deep sequencing defines the transcriptional map ofL. pneumophilaand identifies growth phase-dependent regulated ncRNAs implicated in virulence
- Author
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Odile Sismeiro, Carmen Buchrieser, Delphine Dervins-Ravault, Tobias Sahr, Christophe Rusniok, Jean-Yves Coppée, Biologie des Bactéries intracellulaires - Biology of Intracellular Bacteria, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Transcriptome et Epigénome (PF2), Institut Pasteur [Paris] (IP), This work was supported by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS), the French Region lle-de-France (DIM MALinf) and the Institut Carnot-Pasteur MI., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]
- Subjects
Small RNA ,MESH: RNA, Bacterial/genetics ,MESH: Legionella pneumophila/pathogenicity ,Operon ,MESH: RNA, Small Untranslated/metabolism ,MESH: Base Sequence ,Legionella pneumophila ,Genome ,MESH: Sequence Analysis, RNA ,Promoter Regions, Genetic ,MESH: High-Throughput Nucleotide Sequencing ,Genetics ,Acanthamoeba castellanii ,0303 health sciences ,biology ,Chromosome Mapping ,High-Throughput Nucleotide Sequencing ,MESH: Legionella pneumophila/growth & development ,RNA, Bacterial ,MESH: Nucleic Acid Conformation ,MESH: 5' Untranslated Regions ,MESH: Transcription Initiation Site ,Transcription Initiation Site ,MESH: Gene Expression Regulation, Bacterial ,MESH: Operon ,Molecular Sequence Data ,Virulence ,MESH: Molecular Sequence Annotation ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,MESH: Bacterial Proteins/genetics ,MESH: Legionella pneumophila/genetics ,Deep sequencing ,deep sequencing ,03 medical and health sciences ,Bacterial Proteins ,Consensus Sequence ,MESH: Promoter Regions, Genetic ,MESH: Consensus Sequence ,MESH: Virulence/genetics ,Molecular Biology ,Gene ,small non-coding RNA ,030304 developmental biology ,MESH: Molecular Sequence Data ,Base Sequence ,Sequence Analysis, RNA ,030306 microbiology ,MESH: Transcriptome ,Molecular Sequence Annotation ,Promoter ,Gene Expression Regulation, Bacterial ,Cell Biology ,bacterial infections and mycoses ,biology.organism_classification ,respiratory tract diseases ,virulence ,transcriptional start site mapping ,MESH: RNA, Small Untranslated/genetics ,MESH: Acanthamoeba castellanii/microbiology ,MESH: RNA, Bacterial/metabolism ,Nucleic Acid Conformation ,RNA, Small Untranslated ,5' Untranslated Regions ,Transcriptome ,MESH: Chromosome Mapping - Abstract
International audience; The bacterium Legionella pneumophila is found ubiquitously in aquatic environments and can cause a severe pneumonia in humans called Legionnaires' disease. How this bacterium switches from intracellular to extracellular life and adapts to different hosts and environmental conditions is only partly understood. Here we used RNA deep sequencing from exponentially (replicative) and post exponentially (virulent) grown L. pneumophila to analyze the transcriptional landscape of its entire genome. We established the complete operon map and defined 2561 primary transcriptional start sites (TSS). Interestingly, 187 of the 1805 TSS of protein-coding genes contained tandem promoters of which 93 show alternative usage dependent on the growth phase. Similarly, over 60% of 713 here identified ncRNAs are phase dependently regulated. Analysis of their conservation among the seven L. pneumophila genomes sequenced revealed many strain specific differences suggesting that L. pneumophila contains a highly dynamic pool of ncRNAs. Analysis of six ncRNAs exhibiting the same expression pattern as virulence genes showed that two, Lppnc0584 and Lppnc0405 are indeed involved in intracellular growth of L. pneumophila in A. castellanii. Furthermore, L. pneumophila encodes a small RNA named RsmX that functions together with RsmY and RsmZ in the LetA-CsrA regulatory pathway, crucial for the switch to the virulent phenotype. Together our data provide new insight into the transcriptional organization of the L. pneumophila genome, identified many new ncRNAs and will provide a framework for the understanding of virulence and adaptation properties of L. pneumophila.
- Published
- 2012
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