title: The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome.
abstract: BACKGROUND
  Pan-genomic studies aim, for instance, at defining the core, dispensable and unique genes within a species. A pan-genomics study for vaccine design tries to assess the best candidates for a vaccine against a specific pathogen. In this context, rather than studying genes predicted to be exported in a single genome, with pan-genomics it is possible to study genes present in different strains within the same species, such as virulence factors. The target organism of this pan-genomic work here presented is Corynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis (CLA) in goat and sheep, which causes significant economic losses in those herds around the world. Currently, only a few antigens against CLA are known as being the basis of commercial and still ineffective vaccines. In this regard, the here presented work analyses, in silico, five C. pseudotuberculosis genomes and gathers data to predict common exported proteins in all five genomes. These candidates were also compared to two recent C. pseudotuberculosis in vitro exoproteome results.
  
  
  RESULTS
  The complete genome of five C. pseudotuberculosis strains (1002, C231, I19, FRC41 and PAT10) were submitted to pan-genomics analysis, yielding 306, 59 and 12 gene sets, respectively, representing the core, dispensable and unique in silico predicted exported pan-genomes. These sets bear 150 genes classified as secreted (SEC) and 227 as potentially surface exposed (PSE). Our findings suggest that the main C. pseudotuberculosis in vitro exoproteome could be greater, appended by a fraction of the 35 proteins formerly predicted as making part of the variant in vitro exoproteome. These genomes were manually curated for correct methionine initiation and redeposited with a total of 1885 homogenized genes.
  
  
  CONCLUSIONS
  The in silico prediction of exported proteins has allowed to define a list of putative vaccine candidate genes present in all five complete C. pseudotuberculosis genomes. Moreover, it has also been possible to define the in silico predicted dispensable and unique C. pseudotuberculosis exported proteins. These results provide in silico evidence to further guide experiments in the areas of vaccines, diagnosis and drugs. The work here presented is the first whole C. pseudotuberculosis in silico predicted pan-exoproteome completed till today.
authors.affiliation: Molecular and Celular Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
authors.forename: Anderson R
authors.initials: AR
authors.lastname: Santos
authors.forename: Adriana
authors.initials: A
authors.lastname: Carneiro
authors.forename: Alfonso
authors.initials: A
authors.lastname: Gala-García
authors.forename: Anne
authors.initials: A
authors.lastname: Pinto
authors.forename: Debmalya
authors.initials: D
authors.lastname: Barh
authors.forename: Eudes
authors.initials: E
authors.lastname: Barbosa
authors.forename: Flávia
authors.initials: F
authors.lastname: Aburjaile
authors.forename: Fernanda
authors.initials: F
authors.lastname: Dorella
authors.forename: Flávia
authors.initials: F
authors.lastname: Rocha
authors.forename: Luis
authors.initials: L
authors.lastname: Guimarães
authors.forename: Meritxell
authors.initials: M
authors.lastname: Zurita-Turk
authors.forename: Rommel
authors.initials: R
authors.lastname: Ramos
authors.forename: Sintia
authors.initials: S
authors.lastname: Almeida
authors.forename: Siomar
authors.initials: S
authors.lastname: Soares
authors.forename: Ulisses
authors.initials: U
authors.lastname: Pereira
authors.forename: Vinícius C
authors.initials: VC
authors.lastname: Abreu
authors.forename: Artur
authors.initials: A
authors.lastname: Silva
authors.forename: Anderson
authors.initials: A
authors.lastname: Miyoshi
authors.forename: Vasco
authors.initials: V
authors.lastname: Azevedo
mesh_terms: D001428:Bacterial Vaccines / Q000235:genetics; D016925:Corynebacterium pseudotuberculosis / Q000235:genetics*; D005796:Genes / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D008565:Membrane Proteins / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D012984:Software
chemical_list: D001428:Bacterial Vaccines; D008565:Membrane Proteins; D020543:Proteome