The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome

BMC Genomics

Research

Debmalya Barh¹  Rommel Ramos²  Artur Silva²  Adriana Carneiro²  Alfonso Gala-García³  Anderson R Santos³  Ulisses Pereira³  Anderson Miyoshi³  Vasco Azevedo³  Luis Guimarães³  Siomar Soares³  Eudes Barbosa³  Flávia Rocha³  Fernanda Dorella³  Meritxell Zurita-Turk³  Sintia Almeida³  Anne Pinto³  Flávia Aburjaile³  Vinícius C Abreu³ 

[1] Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, India;DNA Polimorfism Laboratory, Universidade Federal do Pará, Campus do Guamá, Belém, PA, Brazil;Molecular and Celular Genetics Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil;

关键词: Putative Protein;    Cell Wall Thickness;    Core Genome;    Prediction Schema;    Reverse Vaccinology;   

DOI  :  10.1186/1471-2164-13-S5-S6

来源: Springer

【 摘 要 】

BackgroundPan-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.ResultsThe 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.ConclusionsThe 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.

【 授权许可】

Unknown   
© Santos et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.