title: Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium.
abstract: Staphylococcus epidermidis is an important nosocomial agent among carriers of indwelling medical devices, due to its strong ability to form biofilms on inert surfaces. Contrary to some advances made in the transcriptomic field, proteome characterization of S. epidermidis biofilms is less developed. To highlight the relation between transcripts and proteins of S. epidermidis biofilms, we analyzed the proteomic profile obtained by two mechanical lysis methods (sonication and bead beating), associated with two distinct detergent extraction buffers, namely SDS and CHAPS. Based on gel electrophoresis-LC-MS/MS, we identified a total of 453 proteins. While lysis with glass beads provided greater amounts of protein, CHAPS extraction buffer allowed identification of a higher number of proteins compared to SDS. Our data shows the impact of different protein isolation methods in the characterization of the S. epidermidis biofilm proteome. Furthermore, the correlation between proteomic and transcriptomic profiles was evaluated. The results confirmed that proteomic and transcriptomic data should be analyzed simultaneously in order to have a comprehensive understanding of a specific microbiological condition.
authors.affiliation: CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Virginia
authors.initials: V
authors.lastname: Carvalhais
authors.affiliation: CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Angela
authors.initials: A
authors.lastname: França
authors.affiliation: Division of Infectious diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
authors.forename: Gerald B
authors.initials: GB
authors.lastname: Pier
authors.affiliation: ICBAS-Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Porto, Portugal; IBMC-Instituto de Biologia Molecular e Celular, Rua do Campo Alegre 83, Porto, Portugal.
authors.forename: Manuel
authors.initials: M
authors.lastname: Vilanova
authors.affiliation: CEB-Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
authors.forename: Nuno
authors.initials: N
authors.lastname: Cerca
authors.affiliation: QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal. Electronic address: rvitorino@ua.pt.
authors.forename: Rui
authors.initials: R
authors.lastname: Vitorino
mesh_terms: D018441:Biofilms / Q000254:growth & development*; D002458:Cell Fractionation / Q000379:methods; D002793:Cholic Acids / Q000737:chemistry; D002853:Chromatography, Liquid; D003470:Culture Media / Q000737:chemistry; D003902:Detergents / Q000737:chemistry; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D059625:Liquid-Liquid Extraction / Q000379:methods; D058977:Molecular Sequence Annotation; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D012967:Sodium Dodecyl Sulfate / Q000737:chemistry; D013010:Sonication; D013212:Staphylococcus epidermidis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D059467:Transcriptome
chemical_list: D002793:Cholic Acids; D003470:Culture Media; D003902:Detergents; D020543:Proteome; D012967:Sodium Dodecyl Sulfate; D005947:Glucose; C028213:3-((3-cholamidopropyl)dimethylammonium)-1-propanesulfonate
keywords: EmPAI; LC–MS/MS; Protein extraction methods; RNA-seq; Staphylococcus epidermidis biofilms