title: Experimental identification and characterization of 97 novel npcRNA candidates in Salmonella enterica serovar Typhi.
abstract: We experimentally identified and characterized 97 novel, non-protein-coding RNA candidates (npcRNAs) from the human pathogen Salmonella enterica serovar Typhi (hereafter referred to as S. typhi). Three were specific to S. typhi, 22 were restricted to Salmonella species and 33 were differentially expressed during S. typhi growth. We also identified Salmonella Pathogenicity Island-derived npcRNAs that might be involved in regulatory mechanisms of virulence, antibiotic resistance and pathogenic specificity of S. typhi. An in-depth characterization of S. typhi StyR-3 npcRNA showed that it specifically interacts with RamR, the transcriptional repressor of the ramA gene, which is involved in the multidrug resistance (MDR) of Salmonella. StyR-3 interfered with RamR-DNA binding activity and thus potentially plays a role in regulating ramA gene expression, resulting in the MDR phenotype. Our study also revealed a large number of cis-encoded antisense npcRNA candidates, supporting previous observations of global sense-antisense regulatory networks in bacteria. Finally, at least six of the npcRNA candidates interacted with the S. typhi Hfq protein, supporting an important role of Hfq in npcRNA networks. This study points to novel functional npcRNA candidates potentially involved in various regulatory roles including the pathogenicity of S. typhi.
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Muenster, Von-Esmarch-Str. 56, 48149 Muenster, Germany.
authors.forename: Suresh V
authors.initials: SV
authors.lastname: Chinni
authors.forename: Carsten A
authors.initials: CA
authors.lastname: Raabe
authors.forename: Robaiza
authors.initials: R
authors.lastname: Zakaria
authors.forename: Gerrit
authors.initials: G
authors.lastname: Randau
authors.forename: Chee Hock
authors.initials: CH
authors.lastname: Hoe
authors.forename: Anja
authors.initials: A
authors.lastname: Zemann
authors.forename: Juergen
authors.initials: J
authors.lastname: Brosius
authors.forename: Thean-Hock
authors.initials: TH
authors.lastname: Tang
authors.forename: Timofey S
authors.initials: TS
authors.lastname: Rozhdestvensky
mesh_terms: D021901:DNA, Intergenic / Q000737:chemistry; D015723:Gene Library; D044404:Genomic Islands; D016366:Open Reading Frames; D009876:Operon; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism*; D012485:Salmonella typhi / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity
chemical_list: D021901:DNA, Intergenic; D016372:RNA, Antisense; D012329:RNA, Bacterial; D022661:RNA, Untranslated
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