title: Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology.
abstract: The Gram-positive bacterium Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. L. monocytogenes causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. Listeriosis has one of the highest mortality rates (up to 30%) of all food-borne infections. This human pathogenic bacterium is an important model organism for biomedical research to investigate cell-mediated immunity. L. monocytogenes is also one of the best characterised bacterial systems for the molecular analysis of intracellular parasitism. Recently several transcriptomic studies have also made the ubiquitous distributed bacterium as a model to understand mechanisms of gene regulation from the environment to the infected host on the level of mRNA and non-coding RNAs (ncRNAs). We have used semiconductor sequencing technology for RNA-seq to investigate the repertoire of listerial ncRNAs under extra- and intracellular growth conditions. Furthermore, we applied a new bioinformatic analysis pipeline for detection, comparative genomics and structural conservation to identify ncRNAs. With this work, in total, 741 ncRNA locations of potential ncRNA candidates are now known for L. monocytogenes, of which 611 ncRNA candidates were identified by RNA-seq. 441 transcribed ncRNAs have never been described before. Among these, we identified novel long non-coding antisense RNAs with a length of up to 5,400 nt e.g. opposite to genes coding for internalins, methylases or a high-affinity potassium uptake system, namely the kdpABC operon, which were confirmed by qRT-PCR analysis. RNA-seq, comparative genomics and structural conservation of L. monocytogenes ncRNAs illustrate that this human pathogen uses a large number and repertoire of ncRNA including novel long antisense RNAs, which could be important for intracellular survival within the infected eukaryotic host.
authors.affiliation: Faculty of Mathematics and Computer Science, Friedrich-Schiller-University Jena, Jena, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wehner
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.
authors.forename: Gopala K
authors.initials: GK
authors.lastname: Mannala
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.
authors.forename: Xiaoxing
authors.initials: X
authors.lastname: Qing
authors.affiliation: Institute of Medical Virology, Justus-Liebig-University Giessen, Giessen, Germany.
authors.forename: Ramakanth
authors.initials: R
authors.lastname: Madhugiri
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany.
authors.forename: Trinad
authors.initials: T
authors.lastname: Chakraborty
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany.
authors.forename: Mobarak A
authors.initials: MA
authors.lastname: Mraheil
authors.affiliation: Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany; German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Giessen, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Hain
authors.affiliation: Faculty of Mathematics and Computer Science, Friedrich-Schiller-University Jena, Jena, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D056726:Genetic Association Studies; D006801:Humans; D008089:Listeria monocytogenes / Q000235:genetics*; D051379:Mice; D009876:Operon / Q000235:genetics; D016372:RNA, Antisense / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics; D015203:Reproducibility of Results; D012666:Semiconductors; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D016372:RNA, Antisense; D022661:RNA, Untranslated; D004248:DNA (Cytosine-5-)-Methyltransferases