title: Transcriptome-Wide Identification of Hfq-Associated RNAs in Brucella suis by Deep Sequencing.
abstract: Recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding RNAs (sRNAs) as a new important class of regulatory molecules. In prokaryotes, sRNAs are often bound to the chaperone protein Hfq, which allows them to interact with their partner mRNA(s). We screened the genome of the zoonotic and human pathogen Brucella suis 1330 for the presence of this class of RNAs. We designed a coimmunoprecipitation strategy that relies on the use of Hfq as a bait to enrich the sample with sRNAs and eventually their target mRNAs. By deep sequencing analysis of the Hfq-bound transcripts, we identified a number of mRNAs and 33 sRNA candidates associated with Hfq. The expression of 10 sRNAs in the early stationary growth phase was experimentally confirmed by Northern blotting and/or reverse transcriptase PCR.
  
  
  OBJECTIVE
  Brucella organisms are facultative intracellular pathogens that use stealth strategies to avoid host defenses. Adaptation to the host environment requires tight control of gene expression. Recently, small noncoding RNAs (sRNAs) and the sRNA chaperone Hfq have been shown to play a role in the fine-tuning of gene expression. Here we have used RNA sequencing to identify RNAs associated with the B. suis Hfq protein. We have identified a novel list of 33 sRNAs and 62 Hfq-associated mRNAs for future studies aiming to understand the intracellular lifestyle of this pathogen.
authors.affiliation: INSERM U1047, Nîmes, France Université de Montpellier, UFR Médecine, Nîmes, France.
authors.forename: Bashir
authors.initials: B
authors.lastname: Saadeh
authors.affiliation: Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA.
authors.forename: Clayton C
authors.initials: CC
authors.lastname: Caswell
authors.affiliation: Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany.
authors.forename: Yanjie
authors.identifier: http://orcid.org/0000-0002-5735-7954
authors.initials: Y
authors.lastname: Chao
authors.affiliation: INSERM U1047, Nîmes, France Université de Montpellier, UFR Médecine, Nîmes, France Université de Nîmes, Département Sciences et Arts, Nîmes, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Berta
authors.affiliation: Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.
authors.forename: Alice Rebecca
authors.initials: AR
authors.lastname: Wattam
authors.affiliation: Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA.
authors.forename: R Martin
authors.initials: RM
authors.lastname: Roop
authors.affiliation: INSERM U1047, Nîmes, France Université de Montpellier, UFR Médecine, Nîmes, France david.o-ocallaghan@umontpellier.fr.
authors.forename: David
authors.identifier: http://orcid.org/0000-0003-4350-6143
authors.initials: D
authors.lastname: O'Callaghan
mesh_terms: D000818:Animals; D041021:Brucella suis / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism*; D051379:Mice; D018832:Molecular Chaperones; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated; D059467:Transcriptome
chemical_list: D035001:Host Factor 1 Protein; D018832:Molecular Chaperones; D012329:RNA, Bacterial; D022661:RNA, Untranslated