title: Mycoplasma non-coding RNA: identification of small RNAs and targets.
abstract: Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system.
  
  
  
  A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity.
  
  
  
  This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms.
authors: Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors: Franciele Maboni
authors: FM
authors: Siqueira
authors: Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil.
authors: Guilherme Loss
authors: GL
authors: de Morais
authors: Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.|Université Lyon 1, Villeurbanne, France.|CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
authors: Susan
authors: S
authors: Higashi
authors: Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors: Laura Scherer
authors: LS
authors: Beier
authors: Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors: Gabriela Merker
authors: GM
authors: Breyer
authors: Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil.
authors: Caio Padoan
authors: CP
authors: de Sá Godinho
authors: Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.|Université Lyon 1, Villeurbanne, France.|CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France.
authors: Marie-France
authors: MF
authors: Sagot
authors: Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
authors: Irene Silveira
authors: IS
authors: Schrank
authors: Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. zaha@cbiot.ufrgs.br.
authors: Arnaldo
authors: A
authors: Zaha
authors: Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil. atrv@lncc.br.
authors: Ana Tereza Ribeiro
authors: AT
authors: de Vasconcelos
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D009174:Mycoplasma / Q000235:genetics*; D034622:RNA Interference; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D013552:Swine
chemical_list: D022661:RNA, Untranslated
keywords: Mycoplasma flocculare; Mycoplasma hyopneumoniae; Mycoplasma hyorhinis; Porcine respiratory system; Small RNAs