title: Identification of putative noncoding RNA genes in the Burkholderia cenocepacia J2315 genome.
abstract: Noncoding RNA (ncRNA) genes are not involved in the production of mRNA and proteins, but produce transcripts that function directly as structural or regulatory RNAs. In the present study, the presence of ncRNA genes in the genome of Burkholderia cenocepacia J2315 was evaluated by combining comparative genomics (alignment-based) and predicted secondary structure approaches. Two hundred and thirteen putative ncRNA genes were identified in the B. cenocepacia J2315 genome and upregulated expression of four of these could be confirmed by microarray analysis. Most of the ncRNA gene transcripts have a marked predicted secondary structure that may facilitate interaction with other molecules. Several B. cenocepacia J2315 ncRNAs seem to be related to previously characterized ncRNAs involved in regulation of various cellular processes, while the function of many others remains unknown. The presence of a large number of ncRNA genes in this organism may help to explain its complexity, phenotypic variability and ability to survive in a remarkably wide range of environments.
authors.affiliation: Laboratorium voor Microbiologie, Universiteit Gent, Gent, Belgium. tom.coenye@ugent.be
authors.forename: Tom
authors.initials: T
authors.lastname: Coenye
authors.forename: Pavel
authors.initials: P
authors.lastname: Drevinek
authors.forename: Eshwar
authors.initials: E
authors.lastname: Mahenthiralingam
authors.forename: Shiraz Ali
authors.initials: SA
authors.lastname: Shah
authors.forename: Ryan T
authors.initials: RT
authors.lastname: Gill
authors.forename: Peter
authors.initials: P
authors.lastname: Vandamme
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
mesh_terms: D001483:Base Sequence; D019117:Burkholderia / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D016680:Genome, Bacterial / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated