Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria
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 o...
| Autor principal: | FERREIRA, Vívian D'Afonseca da Silva |
|---|---|
| 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 |
| Grau: | Artigo |
| Idioma: | eng |
| Publicado em: |
Dove Medical Press
2023
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| Assuntos: | |
| Acesso em linha: |
https://repositorio.ufpa.br/jspui/handle/2011/15626 |
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ir-2011-15626 |
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ir-2011-156262023-05-26T15:20:33Z 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 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 Corynebacterium diphtheriae Diphtheria Reannotation CRISPR Pathogenicity islands Genome 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. CARNEIRO, A. R.; CERDEIRA, L. T.; RAMOS, R. T. J.; SILVA, A. L. C.; SCHNEIDER, M. P. C. Universidade Federal do Pará 2023-05-26T15:16:04Z 2023-05-26T15:16:04Z 2012-02 Artigo de Periódico 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 https://repositorio.ufpa.br/jspui/handle/2011/15626 10.2147/OAB.S25500 eng Open Access Bioinformatics Acesso Aberto http://creativecommons.org/licenses/by-nc-nd/3.0/br/ application/pdf Dove Medical Press Nova Zelândia https://www.dovepress.com/reannotation-of-the-corynebacterium-diphtheriae-nctc13129-genome-as-a--peer-reviewed-fulltext-article-OAB |
| institution |
Repositório Institucional - Universidade Federal do Pará |
| collection |
RI-UFPA |
| language |
eng |
| topic |
Corynebacterium diphtheriae Diphtheria Reannotation CRISPR Pathogenicity islands Genome |
| spellingShingle |
Corynebacterium diphtheriae Diphtheria Reannotation CRISPR Pathogenicity islands Genome FERREIRA, Vívian D'Afonseca da Silva Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria |
| topic_facet |
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. |
| format |
Artigo |
| author |
FERREIRA, Vívian D'Afonseca da Silva |
| 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 |
| author2Str |
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 |
| title |
Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria |
| 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 |
| publisher |
Dove Medical Press |
| publishDate |
2023 |
| url |
https://repositorio.ufpa.br/jspui/handle/2011/15626 |
| _version_ |
1787148312142413824 |
| score |
11.755432 |