The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome
Autor(a) principal: | |
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Data de Publicação: | 2012 |
Outros Autores: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFPA |
Texto Completo: | https://repositorio.ufpa.br/jspui/handle/2011/15618 |
Resumo: | 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. |
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2023-05-24T14:17:36Z2023-05-24T14:17:36Z2012ANDERSON, R. Santos et al. The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome. BMC Genomics, online, v. 13, n. S6, p. 1-12, 2012. Supl. 5. DOI: https://doi.org/10.1186/1471-2164-13-S5-S6. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15618. Acesso em:.1471-2164https://repositorio.ufpa.br/jspui/handle/2011/15618doi.org/10.1186/1471-2164-13-S5-S6Background: 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.CARNEIRO, A. R.; RAMOS, R. T. J.; SILVA, A. L. C. Universidade Federal do ParáengBioMed Central LtdReino UnidoBMC Genomicshttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccesshttps://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-S5-S6reponame:Repositório Institucional da UFPAinstname:Universidade Federal do Pará (UFPA)instacron:UFPACorynebacterium pseudotuberculosisThe Corynebacterium pseudotuberculosis in silico predicted pan-exoproteomeinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13S6112http://lattes.cnpq.br/3752226356973936http://lattes.cnpq.br/7533716053525477http://lattes.cnpq.br/9301566786212178http://lattes.cnpq.br/9968280925772857http://lattes.cnpq.br/9326996169562214http://lattes.cnpq.br/5207352332676542http://lattes.cnpq.br/2016464855117057http://lattes.cnpq.br/1504496062851809http://lattes.cnpq.br/5292717604621046http://lattes.cnpq.br/1991446268436258http://lattes.cnpq.br/3504953835113648http://lattes.cnpq.br/1274395392752454http://lattes.cnpq.br/6389878370640685http://lattes.cnpq.br/4393381414254469http://lattes.cnpq.br/1608947907609178http://lattes.cnpq.br/2484200467965399http://lattes.cnpq.br/7642043789034070http://lattes.cnpq.br/9198272608157135http://lattes.cnpq.br/1020477751003832SANTOS, Anderson Rodrigues dosCARNEIRO, Adriana RibeiroGALA-GARCÍA, AlfonsoGOMIDE, Anne Cybelle PintoBARH, DebmalyaBARBOSA, Eudes Guilherme VieiraABURJAILE, Flavia FigueiraDORELLA, Fernanda AlvesROCHA, Flávia de SouzaGUIMARÃES, Luís CarlosTURK, Meritxell ZuritaRAMOS, Rommel Thiago JucaALMEIDA, Sintia Silva deSOARES, Siomar de CastroPEREIRA, Ulisses de PáduaABREU, Vinicius Augusto Carvalho deSILVA, Artur Luiz da Costa daMIYOSHI, AndersonAZEVEDO, Vasco Ariston de Carvalhohttps://orcid.org/0000-0003-3418-0823https://orcid.org/0000-0003-1522-9871https://orcid.org/0000-0002-3934-1094https://orcid.orghttps://orcid.orghttps://orcid.orghttps://orcid.org/0000-0002-1067-1882https://orcid.org/0000-0003-1171-7106https://orcid.orghttps://orcid.orghttps://orcid.orghttps://orcid.org/0000-0002-8032-1474https://orcid.org/0000-0003-0270-9059https://orcid.org/0000-0001-7299-3724https://orcid.org/0000-0003-4868-4459https://orcid.orghttps://orcid.orghttps://orcid.orghttps://orcid.org/0000-0002-4775-2280ORIGINALArticle_CorynebacteriumPseudotuberculosisSilico.pdfArticle_CorynebacteriumPseudotuberculosisSilico.pdfapplication/pdf1209586http://repositorio.ufpa.br/oai/bitstream/2011/15618/1/Article_CorynebacteriumPseudotuberculosisSilico.pdfba6522472bb307f2937644fe194bbc3eMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; 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dc.title.pt_BR.fl_str_mv |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
title |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
spellingShingle |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome SANTOS, Anderson Rodrigues dos Corynebacterium pseudotuberculosis |
title_short |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
title_full |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
title_fullStr |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
title_full_unstemmed |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
title_sort |
The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome |
author |
SANTOS, Anderson Rodrigues dos |
author_facet |
SANTOS, Anderson Rodrigues dos CARNEIRO, Adriana Ribeiro GALA-GARCÍA, Alfonso GOMIDE, Anne Cybelle Pinto BARH, Debmalya BARBOSA, Eudes Guilherme Vieira ABURJAILE, Flavia Figueira DORELLA, Fernanda Alves ROCHA, Flávia de Souza GUIMARÃES, Luís Carlos TURK, Meritxell Zurita RAMOS, Rommel Thiago Juca ALMEIDA, Sintia Silva de SOARES, Siomar de Castro PEREIRA, Ulisses de Pádua ABREU, Vinicius Augusto Carvalho de SILVA, Artur Luiz da Costa da MIYOSHI, Anderson AZEVEDO, Vasco Ariston de Carvalho https://orcid.org/0000-0003-3418-0823 https://orcid.org/0000-0003-1522-9871 https://orcid.org/0000-0002-3934-1094 https://orcid.org https://orcid.org/0000-0002-1067-1882 https://orcid.org/0000-0003-1171-7106 https://orcid.org/0000-0002-8032-1474 https://orcid.org/0000-0003-0270-9059 https://orcid.org/0000-0001-7299-3724 https://orcid.org/0000-0003-4868-4459 https://orcid.org/0000-0002-4775-2280 |
author_role |
author |
author2 |
CARNEIRO, Adriana Ribeiro GALA-GARCÍA, Alfonso GOMIDE, Anne Cybelle Pinto BARH, Debmalya BARBOSA, Eudes Guilherme Vieira ABURJAILE, Flavia Figueira DORELLA, Fernanda Alves ROCHA, Flávia de Souza GUIMARÃES, Luís Carlos TURK, Meritxell Zurita RAMOS, Rommel Thiago Juca ALMEIDA, Sintia Silva de SOARES, Siomar de Castro PEREIRA, Ulisses de Pádua ABREU, Vinicius Augusto Carvalho de SILVA, Artur Luiz da Costa da MIYOSHI, Anderson AZEVEDO, Vasco Ariston de Carvalho https://orcid.org/0000-0003-3418-0823 https://orcid.org/0000-0003-1522-9871 https://orcid.org/0000-0002-3934-1094 https://orcid.org https://orcid.org/0000-0002-1067-1882 https://orcid.org/0000-0003-1171-7106 https://orcid.org/0000-0002-8032-1474 https://orcid.org/0000-0003-0270-9059 https://orcid.org/0000-0001-7299-3724 https://orcid.org/0000-0003-4868-4459 https://orcid.org/0000-0002-4775-2280 |
author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author author author author |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/3752226356973936 http://lattes.cnpq.br/7533716053525477 http://lattes.cnpq.br/9301566786212178 http://lattes.cnpq.br/9968280925772857 http://lattes.cnpq.br/9326996169562214 http://lattes.cnpq.br/5207352332676542 http://lattes.cnpq.br/2016464855117057 http://lattes.cnpq.br/1504496062851809 http://lattes.cnpq.br/5292717604621046 http://lattes.cnpq.br/1991446268436258 http://lattes.cnpq.br/3504953835113648 http://lattes.cnpq.br/1274395392752454 http://lattes.cnpq.br/6389878370640685 http://lattes.cnpq.br/4393381414254469 http://lattes.cnpq.br/1608947907609178 http://lattes.cnpq.br/2484200467965399 http://lattes.cnpq.br/7642043789034070 http://lattes.cnpq.br/9198272608157135 http://lattes.cnpq.br/1020477751003832 |
dc.contributor.author.fl_str_mv |
SANTOS, Anderson Rodrigues dos CARNEIRO, Adriana Ribeiro GALA-GARCÍA, Alfonso GOMIDE, Anne Cybelle Pinto BARH, Debmalya BARBOSA, Eudes Guilherme Vieira ABURJAILE, Flavia Figueira DORELLA, Fernanda Alves ROCHA, Flávia de Souza GUIMARÃES, Luís Carlos TURK, Meritxell Zurita RAMOS, Rommel Thiago Juca ALMEIDA, Sintia Silva de SOARES, Siomar de Castro PEREIRA, Ulisses de Pádua ABREU, Vinicius Augusto Carvalho de SILVA, Artur Luiz da Costa da MIYOSHI, Anderson AZEVEDO, Vasco Ariston de Carvalho https://orcid.org/0000-0003-3418-0823 https://orcid.org/0000-0003-1522-9871 https://orcid.org/0000-0002-3934-1094 https://orcid.org https://orcid.org https://orcid.org https://orcid.org/0000-0002-1067-1882 https://orcid.org/0000-0003-1171-7106 https://orcid.org https://orcid.org https://orcid.org https://orcid.org/0000-0002-8032-1474 https://orcid.org/0000-0003-0270-9059 https://orcid.org/0000-0001-7299-3724 https://orcid.org/0000-0003-4868-4459 https://orcid.org https://orcid.org https://orcid.org https://orcid.org/0000-0002-4775-2280 |
dc.subject.eng.fl_str_mv |
Corynebacterium pseudotuberculosis |
topic |
Corynebacterium pseudotuberculosis |
description |
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. |
publishDate |
2012 |
dc.date.issued.fl_str_mv |
2012 |
dc.date.accessioned.fl_str_mv |
2023-05-24T14:17:36Z |
dc.date.available.fl_str_mv |
2023-05-24T14:17:36Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
ANDERSON, R. Santos et al. The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome. BMC Genomics, online, v. 13, n. S6, p. 1-12, 2012. Supl. 5. DOI: https://doi.org/10.1186/1471-2164-13-S5-S6. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15618. Acesso em:. |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufpa.br/jspui/handle/2011/15618 |
dc.identifier.issn.pt_BR.fl_str_mv |
1471-2164 |
dc.identifier.doi.pt_BR.fl_str_mv |
doi.org/10.1186/1471-2164-13-S5-S6 |
identifier_str_mv |
ANDERSON, R. Santos et al. The Corynebacterium pseudotuberculosis in silico predicted pan-exoproteome. BMC Genomics, online, v. 13, n. S6, p. 1-12, 2012. Supl. 5. DOI: https://doi.org/10.1186/1471-2164-13-S5-S6. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15618. Acesso em:. 1471-2164 doi.org/10.1186/1471-2164-13-S5-S6 |
url |
https://repositorio.ufpa.br/jspui/handle/2011/15618 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.ispartof.pt_BR.fl_str_mv |
BMC Genomics |
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http://creativecommons.org/licenses/by-nc-nd/3.0/br/ |
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openAccess |
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BioMed Central Ltd |
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Reino Unido |
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BioMed Central Ltd |
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