Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria

Detalhes bibliográficos
Autor(a) principal: FERREIRA, Vívian D'Afonseca da Silva
Data de Publicação: 2012
Outros Autores: SOARES, Siomar de Castro, ALI, Amjad, SANTOS, Anderson Rodrigues dos, GOMIDE, Anne Cybelle Pinto, ROCHA, Aryane Aparecida Magalhães Cassiano, FARIA, Cássio de Jesus, BARBOSA, Eudes Guilherme Vieira, GUIMARÃES, Luís Carlos, ESLABÃO, Marcus Redü, ALMEIDA, Sintia Silva de, ABREU, Vinicius Augusto Carvalho de, ZERLOTINI NETO, Adhemar, CARNEIRO, Adriana Ribeiro, CERDEIRA, Louise Teixeira, RAMOS, Rommel Thiago Juca, HIRATA JÚNIOR, Raphael, GUARALDI, Ana Luiza de Mattos, TROST, Eva, TAUCH, Andreas, SILVA, Artur Luiz da Costa da, SCHNEIDER, Maria Paula Cruz, MIYOSHI, Anderson, AZEVEDO, Vasco Ariston de Carvalho, https://orcid.org/0000-0002-1685-5260, https://orcid.org/0000-0001-7299-3724, https://orcid.org, https://orcid.org/0000-0003-3418-0823, https://orcid.org/0000-0003-0270-9059, https://orcid.org/, https://orcid.org/0000-0003-1522-9871, https://orcid.org/0000-0002-4495-2615, https://orcid.org/0000-0002-8032-1474, https://orcid.org/0000-0002-2538-4827, https://orcid.org/0000-0002-4775-2280
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFPA
Texto Completo: https://repositorio.ufpa.br/jspui/handle/2011/15626
Resumo: Background: The reannotation of genomes already on file is a new approach to discovering new genetic elements and to make the genomes more descriptive and current with relevant features regarding the organism’s lifestyle. Within this approach, the present study aimed to reannotate the genome of the Gram-positive human pathogen Corynebacterium diphtheriae, which causes diphtheria. The deposit of massive amounts of information linked to other spe cies of the genus Corynebacterium has facilitated the updating of the genomic interpretation of this microorganism. Additionally, the emergence of invasive disease by nontoxigenic strains of C. diphtheriae and the reemergence of diphtheria in partially immunized populations have given impetus to new studies in relation to its structural and functional genome. Results: In relation to structural genomics, 23 coding regions (coding sequences) were deleted and 71 new genes were added to the genome annotation. Nevertheless, all the pseudogenes were validated and ten new pseudogenes were created. In relation to functional genomics, about 57% of the genome annotation was updated and became functionally more informative. The product descriptions of 41% (973 proteins) were updated. Among them, 370 that were previously annotated as “hypothetical proteins,” now have more informative descriptions. With the new annotation, the plasticity of the genome became evident, which shows improvements in the annotation of 13 pathogenicity islands already described in the literature. In addition, the large number of transposases and the presence of structural genes of bacteriophages make their genomic versatility evident. Contrasting with this reality, it also allowed the clarification of some aspects concerned with mechanisms used by C. diphtheriae to stop the invasion of the genome by bacteriophages, mediated by the clustered regularly interspaced short palindromic repeats region. Conclusion: The reannotation of the C. diphtheriae genome provided an improvement in annotation of the C. diphtheriae genome in several aspects, such as virulence characteristics and plasticity events. Moreover, the protocol used here can be extended to various other pathogens in order to improve the genomic information already on file in public databases and to minimize propagating errors. The reannotated archive and updated archive are available at: http://lgcm. icb.ufmg.br/pub/C_diphtheriae_reannotation.embl.
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spelling 2023-05-26T15:16:04Z2023-05-26T15:16:04Z2012-02D'AFONSECA, Vivian et al. Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria. Open Access Bioinformatics, online, v. 4, p. 1-13, Feb. 2012. DOI: http://dx.doi.org/10.2147/OAB.S25500. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15626. Acesso em:.1179-2701https://repositorio.ufpa.br/jspui/handle/2011/1562610.2147/OAB.S25500Background: The reannotation of genomes already on file is a new approach to discovering new genetic elements and to make the genomes more descriptive and current with relevant features regarding the organism’s lifestyle. Within this approach, the present study aimed to reannotate the genome of the Gram-positive human pathogen Corynebacterium diphtheriae, which causes diphtheria. The deposit of massive amounts of information linked to other spe cies of the genus Corynebacterium has facilitated the updating of the genomic interpretation of this microorganism. Additionally, the emergence of invasive disease by nontoxigenic strains of C. diphtheriae and the reemergence of diphtheria in partially immunized populations have given impetus to new studies in relation to its structural and functional genome. Results: In relation to structural genomics, 23 coding regions (coding sequences) were deleted and 71 new genes were added to the genome annotation. Nevertheless, all the pseudogenes were validated and ten new pseudogenes were created. In relation to functional genomics, about 57% of the genome annotation was updated and became functionally more informative. The product descriptions of 41% (973 proteins) were updated. Among them, 370 that were previously annotated as “hypothetical proteins,” now have more informative descriptions. With the new annotation, the plasticity of the genome became evident, which shows improvements in the annotation of 13 pathogenicity islands already described in the literature. In addition, the large number of transposases and the presence of structural genes of bacteriophages make their genomic versatility evident. Contrasting with this reality, it also allowed the clarification of some aspects concerned with mechanisms used by C. diphtheriae to stop the invasion of the genome by bacteriophages, mediated by the clustered regularly interspaced short palindromic repeats region. Conclusion: The reannotation of the C. diphtheriae genome provided an improvement in annotation of the C. diphtheriae genome in several aspects, such as virulence characteristics and plasticity events. Moreover, the protocol used here can be extended to various other pathogens in order to improve the genomic information already on file in public databases and to minimize propagating errors. The reannotated archive and updated archive are available at: http://lgcm. icb.ufmg.br/pub/C_diphtheriae_reannotation.embl.CARNEIRO, A. R.; CERDEIRA, L. T.; RAMOS, R. T. J.; SILVA, A. L. C.; SCHNEIDER, M. P. C. 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dc.title.pt_BR.fl_str_mv Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
title Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
spellingShingle Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
FERREIRA, Vívian D'Afonseca da Silva
Corynebacterium diphtheriae
Diphtheria
Reannotation
CRISPR
Pathogenicity islands
Genome
title_short Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
title_full Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
title_fullStr Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
title_full_unstemmed Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
title_sort Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
author FERREIRA, Vívian D'Afonseca da Silva
author_facet FERREIRA, Vívian D'Afonseca da Silva
SOARES, Siomar de Castro
ALI, Amjad
SANTOS, Anderson Rodrigues dos
GOMIDE, Anne Cybelle Pinto
ROCHA, Aryane Aparecida Magalhães Cassiano
FARIA, Cássio de Jesus
BARBOSA, Eudes Guilherme Vieira
GUIMARÃES, Luís Carlos
ESLABÃO, Marcus Redü
ALMEIDA, Sintia Silva de
ABREU, Vinicius Augusto Carvalho de
ZERLOTINI NETO, Adhemar
CARNEIRO, Adriana Ribeiro
CERDEIRA, Louise Teixeira
RAMOS, Rommel Thiago Juca
HIRATA JÚNIOR, Raphael
GUARALDI, Ana Luiza de Mattos
TROST, Eva
TAUCH, Andreas
SILVA, Artur Luiz da Costa da
SCHNEIDER, Maria Paula Cruz
MIYOSHI, Anderson
AZEVEDO, Vasco Ariston de Carvalho
https://orcid.org/0000-0002-1685-5260
https://orcid.org/0000-0001-7299-3724
https://orcid.org
https://orcid.org/0000-0003-3418-0823
https://orcid.org/0000-0003-0270-9059
https://orcid.org/
https://orcid.org/0000-0003-1522-9871
https://orcid.org/0000-0002-4495-2615
https://orcid.org/0000-0002-8032-1474
https://orcid.org/0000-0002-2538-4827
https://orcid.org/0000-0002-4775-2280
author_role author
author2 SOARES, Siomar de Castro
ALI, Amjad
SANTOS, Anderson Rodrigues dos
GOMIDE, Anne Cybelle Pinto
ROCHA, Aryane Aparecida Magalhães Cassiano
FARIA, Cássio de Jesus
BARBOSA, Eudes Guilherme Vieira
GUIMARÃES, Luís Carlos
ESLABÃO, Marcus Redü
ALMEIDA, Sintia Silva de
ABREU, Vinicius Augusto Carvalho de
ZERLOTINI NETO, Adhemar
CARNEIRO, Adriana Ribeiro
CERDEIRA, Louise Teixeira
RAMOS, Rommel Thiago Juca
HIRATA JÚNIOR, Raphael
GUARALDI, Ana Luiza de Mattos
TROST, Eva
TAUCH, Andreas
SILVA, Artur Luiz da Costa da
SCHNEIDER, Maria Paula Cruz
MIYOSHI, Anderson
AZEVEDO, Vasco Ariston de Carvalho
https://orcid.org/0000-0002-1685-5260
https://orcid.org/0000-0001-7299-3724
https://orcid.org
https://orcid.org/0000-0003-3418-0823
https://orcid.org/0000-0003-0270-9059
https://orcid.org/
https://orcid.org/0000-0003-1522-9871
https://orcid.org/0000-0002-4495-2615
https://orcid.org/0000-0002-8032-1474
https://orcid.org/0000-0002-2538-4827
https://orcid.org/0000-0002-4775-2280
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dc.contributor.author.fl_str_mv FERREIRA, Vívian D'Afonseca da Silva
SOARES, Siomar de Castro
ALI, Amjad
SANTOS, Anderson Rodrigues dos
GOMIDE, Anne Cybelle Pinto
ROCHA, Aryane Aparecida Magalhães Cassiano
FARIA, Cássio de Jesus
BARBOSA, Eudes Guilherme Vieira
GUIMARÃES, Luís Carlos
ESLABÃO, Marcus Redü
ALMEIDA, Sintia Silva de
ABREU, Vinicius Augusto Carvalho de
ZERLOTINI NETO, Adhemar
CARNEIRO, Adriana Ribeiro
CERDEIRA, Louise Teixeira
RAMOS, Rommel Thiago Juca
HIRATA JÚNIOR, Raphael
GUARALDI, Ana Luiza de Mattos
TROST, Eva
TAUCH, Andreas
SILVA, Artur Luiz da Costa da
SCHNEIDER, Maria Paula Cruz
MIYOSHI, Anderson
AZEVEDO, Vasco Ariston de Carvalho
https://orcid.org/0000-0002-1685-5260
https://orcid.org/0000-0001-7299-3724
https://orcid.org
https://orcid.org/0000-0003-3418-0823
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dc.subject.eng.fl_str_mv Corynebacterium diphtheriae
Diphtheria
Reannotation
CRISPR
Pathogenicity islands
Genome
topic Corynebacterium diphtheriae
Diphtheria
Reannotation
CRISPR
Pathogenicity islands
Genome
description Background: The reannotation of genomes already on file is a new approach to discovering new genetic elements and to make the genomes more descriptive and current with relevant features regarding the organism’s lifestyle. Within this approach, the present study aimed to reannotate the genome of the Gram-positive human pathogen Corynebacterium diphtheriae, which causes diphtheria. The deposit of massive amounts of information linked to other spe cies of the genus Corynebacterium has facilitated the updating of the genomic interpretation of this microorganism. Additionally, the emergence of invasive disease by nontoxigenic strains of C. diphtheriae and the reemergence of diphtheria in partially immunized populations have given impetus to new studies in relation to its structural and functional genome. Results: In relation to structural genomics, 23 coding regions (coding sequences) were deleted and 71 new genes were added to the genome annotation. Nevertheless, all the pseudogenes were validated and ten new pseudogenes were created. In relation to functional genomics, about 57% of the genome annotation was updated and became functionally more informative. The product descriptions of 41% (973 proteins) were updated. Among them, 370 that were previously annotated as “hypothetical proteins,” now have more informative descriptions. With the new annotation, the plasticity of the genome became evident, which shows improvements in the annotation of 13 pathogenicity islands already described in the literature. In addition, the large number of transposases and the presence of structural genes of bacteriophages make their genomic versatility evident. Contrasting with this reality, it also allowed the clarification of some aspects concerned with mechanisms used by C. diphtheriae to stop the invasion of the genome by bacteriophages, mediated by the clustered regularly interspaced short palindromic repeats region. Conclusion: The reannotation of the C. diphtheriae genome provided an improvement in annotation of the C. diphtheriae genome in several aspects, such as virulence characteristics and plasticity events. Moreover, the protocol used here can be extended to various other pathogens in order to improve the genomic information already on file in public databases and to minimize propagating errors. The reannotated archive and updated archive are available at: http://lgcm. icb.ufmg.br/pub/C_diphtheriae_reannotation.embl.
publishDate 2012
dc.date.issued.fl_str_mv 2012-02
dc.date.accessioned.fl_str_mv 2023-05-26T15:16:04Z
dc.date.available.fl_str_mv 2023-05-26T15:16:04Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
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dc.identifier.citation.fl_str_mv D'AFONSECA, Vivian et al. Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria. Open Access Bioinformatics, online, v. 4, p. 1-13, Feb. 2012. DOI: http://dx.doi.org/10.2147/OAB.S25500. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15626. Acesso em:.
dc.identifier.uri.fl_str_mv https://repositorio.ufpa.br/jspui/handle/2011/15626
dc.identifier.issn.pt_BR.fl_str_mv 1179-2701
dc.identifier.doi.pt_BR.fl_str_mv 10.2147/OAB.S25500
identifier_str_mv D'AFONSECA, Vivian et al. Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria. Open Access Bioinformatics, online, v. 4, p. 1-13, Feb. 2012. DOI: http://dx.doi.org/10.2147/OAB.S25500. Disponível em: http://repositorio.ufpa.br/jspui/handle/2011/15626. Acesso em:.
1179-2701
10.2147/OAB.S25500
url https://repositorio.ufpa.br/jspui/handle/2011/15626
dc.language.iso.fl_str_mv eng
language eng
dc.relation.ispartof.pt_BR.fl_str_mv Open Access Bioinformatics
dc.rights.driver.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/3.0/br/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/3.0/br/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Dove Medical Press
dc.publisher.country.fl_str_mv Nova Zelândia
publisher.none.fl_str_mv Dove Medical Press
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFPA
instname:Universidade Federal do Pará (UFPA)
instacron:UFPA
instname_str Universidade Federal do Pará (UFPA)
instacron_str UFPA
institution UFPA
reponame_str Repositório Institucional da UFPA
collection Repositório Institucional da UFPA
dc.source.uri.pt_BR.fl_str_mv https://www.dovepress.com/reannotation-of-the-corynebacterium-diphtheriae-nctc13129-genome-as-a--peer-reviewed-fulltext-article-OAB
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repository.name.fl_str_mv Repositório Institucional da UFPA - Universidade Federal do Pará (UFPA)
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