title: Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence.
abstract: 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.
authors.affiliation: Institut Pasteur, 28, rue du Dr. Roux, Paris 75724, France.
authors.forename: Tobias
authors.initials: T
authors.lastname: Sahr
authors.forename: Christophe
authors.initials: C
authors.lastname: Rusniok
authors.forename: Delphine
authors.initials: D
authors.lastname: Dervins-Ravault
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppee
authors.forename: Carmen
authors.initials: C
authors.lastname: Buchrieser
mesh_terms: D020121:5' Untranslated Regions; D048248:Acanthamoeba castellanii / Q000382:microbiology; D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D016384:Consensus Sequence; D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D016952:Legionella pneumophila / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D059467:Transcriptome; D014774:Virulence / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D001426:Bacterial Proteins; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated