title: Experimental identification of small non-coding regulatory RNAs in the opportunistic human pathogen Burkholderia cenocepacia J2315.
abstract: Small non-coding regulatory RNAs (sRNAs) play important roles in regulating gene expression at the post-transcriptional level and often require the RNA chaperone Hfq. The human opportunistic pathogen Burkholderia cenocepacia J2315 encodes two distinct RNA chaperones, Hfq and Hfq2. The present work describes the experimental identification and validation of 24 sRNAs from B. cenocepacia J2315, based on the co-purification of sRNAs with the bacterium Hfq protein, followed by conversion into cDNA, cloning, computational analysis of sequences and validation by Northern blot analysis. The sRNAs here reported escaped identification by previous studies based on transcriptomics or bioinformatic analyses. Results presented indicate that 3 sRNAs are exclusive to bacteria of the Burkholderia cepacia complex and have no homologues in other bacteria, while the other 21 share homology, at different extents, to sRNAs of other bacterial species.
authors.affiliation: Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, Torre Sul, Piso 6, 1049-001, Lisboa, Portugal.
authors.forename: Christian G
authors.initials: CG
authors.lastname: Ramos
authors.affiliation: Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, Torre Sul, Piso 6, 1049-001, Lisboa, Portugal.
authors.forename: André M
authors.initials: AM
authors.lastname: Grilo
authors.affiliation: Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, Torre Sul, Piso 6, 1049-001, Lisboa, Portugal.
authors.forename: Paulo J P
authors.initials: PJ
authors.lastname: da Costa
authors.affiliation: Institute for Biotechnology and Bioengineering, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, Torre Sul, Piso 6, 1049-001, Lisboa, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade Técnica de Lisboa, Av. Rovisco Pais, Torre Sul, Piso 6, 1049-001, Lisboa, Portugal. Electronic address: jorgeleitao@ist.utl.pt.
authors.forename: Jorge H
authors.initials: JH
authors.lastname: Leitão
mesh_terms: D001483:Base Sequence; D057508:Burkholderia cenocepacia / Q000235:genetics*; D003001:Cloning, Molecular; D019295:Computational Biology; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated