title: A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus.
abstract: We have adapted a method to map cell surface proteins and to monitor the effect of specific regulatory RNAs on the surface composition of the bacteria. This method involves direct labeling of surface proteins of living bacteria using fluorescent dyes and a subsequent separation of the crude extract by 2D gel electrophoresis. The strategy yields a substantial enrichment in surface proteins over cytoplasmic proteins. We validated this method by monitoring the effect of the regulatory RNA MicA in Escherichia coli, which regulates the synthesis of several outer membrane proteins, and highlighted the role of Staphylococcus aureus RNAIII for the maintenance of cell wall integrity.
authors.affiliation: Esplanade Proteomic Platform, Université de Strasbourg, CNRS, IBMC, 15 Rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Hammann
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Parmentier
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Cerciat
authors.affiliation: Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-75124 Uppsala, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Reimegård
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Anne-Catherine
authors.initials: AC
authors.lastname: Helfer
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Hospices Civils de Lyon, F-69008 Lyon, France.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Boisset
authors.affiliation: FRE3630 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, F-75005 Paris, France.
authors.forename: Maude
authors.initials: M
authors.lastname: Guillier
authors.affiliation: CIRI, International Center for Infectiology Research, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Hospices Civils de Lyon, F-69008 Lyon, France.
authors.forename: François
authors.initials: F
authors.lastname: Vandenesch
authors.affiliation: Department of Cell & Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-75124 Uppsala, Sweden.
authors.forename: E Gerhart H
authors.initials: EG
authors.lastname: Wagner
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Romby
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France. Electronic address: p.fechter@ibmc-cnrs.unistra.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Fechter
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D002232:Carbocyanines / Q000378:metabolism; D002462:Cell Membrane / Q000378:metabolism*; D002473:Cell Wall / Q000378:metabolism; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D018613:Microscopy, Confocal; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D015203:Reproducibility of Results; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013194:Staining and Labeling / Q000379:methods; D013211:Staphylococcus aureus / Q000235:genetics / Q000378:metabolism*
chemical_list: D001425:Bacterial Outer Membrane Proteins; D001426:Bacterial Proteins; D002232:Carbocyanines; D012329:RNA, Bacterial; C096035:RNAIII, Staphylococcus aureus; C089187:cyanine dye 3; C085321:cyanine dye 5
keywords: DIGE; Non-coding RNAs; Post-transcriptional regulation; Surface proteins