title: The RNA targetome of Staphylococcus aureus non-coding RNA RsaA: impact on cell surface properties and defense mechanisms.
abstract: The virulon of Staphyloccocus aureus is controlled by intricate connections between transcriptional and post-transcriptional regulators including proteins and small non-coding RNAs (sRNAs). Many of the sRNAs regulate gene expression through base-pairings with mRNAs. However, characterization of the direct sRNA targets in Gram-positive bacteria remained a difficult challenge. Here, we have applied and adapted the MS2-affinity purification approach coupled to RNA sequencing (MAPS) to determine the targetome of RsaA sRNA of S. aureus, known to repress the synthesis of the transcriptional regulator MgrA. Several mRNAs were enriched with RsaA expanding its regulatory network. Besides mgrA, several of these mRNAs encode a family of SsaA-like enzymes involved in peptidoglycan metabolism and the secreted anti-inflammatory FLIPr protein. Using a combination of in vivo and in vitro approaches, these mRNAs were validated as direct RsaA targets. Quantitative differential proteomics of wild-type and mutant strains corroborated the MAPS results. Additionally, it revealed that RsaA indirectly activated the synthesis of surface proteins supporting previous data that RsaA stimulated biofilm formation and favoured chronic infections. All together, this study shows that MAPS could also be easily applied in Gram-positive bacteria for identification of sRNA targetome.
authors.affiliation: Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Tomasini
authors.affiliation: CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France.
authors.forename: Karen
authors.initials: K
authors.lastname: Moreau
authors.affiliation: Plateforme Protéomique IBMC, Strasbourg, France.
authors.forename: Johana
authors.initials: J
authors.lastname: Chicher
authors.affiliation: CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Geissmann
authors.affiliation: CIRI, International Center for Infectiology Research, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, University of Lyon, F-69008, Lyon, France.
authors.forename: François
authors.initials: F
authors.lastname: Vandenesch
authors.affiliation: Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Romby
authors.affiliation: Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France.
authors.forename: Stefano
authors.initials: S
authors.lastname: Marzi
authors.affiliation: Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Caldelari
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D015964:Gene Expression Regulation, Bacterial; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated / Q000502:physiology*; D013211:Staphylococcus aureus / Q000235:genetics* / Q000378:metabolism; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; D020543:Proteome; D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated