In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes
Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic marke...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-09-01
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| Series: | Frontiers in Bioinformatics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2022.931583/full |
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| author | Kenny da Costa Pinheiro Bruna Verônica Azevedo Gois Wylerson Guimarães Nogueira Fabrício Almeida Araújo Ana Lídia Cavalcante Queiroz Oscar Cardenas-Alegria Artur Luiz da Costa da Silva Antônio Márcio Gomes Martins Júnior Rommel Thiago Jucá Ramos |
| author_facet | Kenny da Costa Pinheiro Bruna Verônica Azevedo Gois Wylerson Guimarães Nogueira Fabrício Almeida Araújo Ana Lídia Cavalcante Queiroz Oscar Cardenas-Alegria Artur Luiz da Costa da Silva Antônio Márcio Gomes Martins Júnior Rommel Thiago Jucá Ramos |
| author_sort | Kenny da Costa Pinheiro |
| collection | DOAJ |
| description | Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite groups belonging to equi and ovis biovars have a significance of 0.006 (p-value) in similarity, thus indicating them as good biomarker candidates for C. pseudotuberculosis. |
| first_indexed | 2024-12-10T10:33:17Z |
| format | Article |
| id | doaj.art-2a204b0b845d4e5992c5f7f0e3f32a93 |
| institution | Directory Open Access Journal |
| issn | 2673-7647 |
| language | English |
| last_indexed | 2024-12-10T10:33:17Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Bioinformatics |
| spelling | doaj.art-2a204b0b845d4e5992c5f7f0e3f32a932022-12-22T01:52:30ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472022-09-01210.3389/fbinf.2022.931583931583In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomesKenny da Costa Pinheiro0Bruna Verônica Azevedo Gois1Wylerson Guimarães Nogueira2Fabrício Almeida Araújo3Ana Lídia Cavalcante Queiroz4Oscar Cardenas-Alegria5Artur Luiz da Costa da Silva6Antônio Márcio Gomes Martins Júnior7Rommel Thiago Jucá Ramos8Institute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilInstitute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilDepartment of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, BrazilInstitute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilInstitute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilInstitute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilLaboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, BrazilLaboratory of Genetics, Evolution and Bioinformatics, Federal Institute of Pará, Tucuruí, Pará, BrazilInstitute of Biological Sciences, Federal University of Pará, Belém, Pará, BrazilCorynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite groups belonging to equi and ovis biovars have a significance of 0.006 (p-value) in similarity, thus indicating them as good biomarker candidates for C. pseudotuberculosis.https://www.frontiersin.org/articles/10.3389/fbinf.2022.931583/fullCorynebacterium pseudotuberculosiscaseous lymphadenitisbiomarkersmicrosatellitesvirulence factors (VFs)simple sequence repeats (SSRs) |
| spellingShingle | Kenny da Costa Pinheiro Bruna Verônica Azevedo Gois Wylerson Guimarães Nogueira Fabrício Almeida Araújo Ana Lídia Cavalcante Queiroz Oscar Cardenas-Alegria Artur Luiz da Costa da Silva Antônio Márcio Gomes Martins Júnior Rommel Thiago Jucá Ramos In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes Frontiers in Bioinformatics Corynebacterium pseudotuberculosis caseous lymphadenitis biomarkers microsatellites virulence factors (VFs) simple sequence repeats (SSRs) |
| title | In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes |
| title_full | In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes |
| title_fullStr | In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes |
| title_full_unstemmed | In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes |
| title_short | In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes |
| title_sort | in silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of corynebacterium pseudotuberculosis genomes |
| topic | Corynebacterium pseudotuberculosis caseous lymphadenitis biomarkers microsatellites virulence factors (VFs) simple sequence repeats (SSRs) |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2022.931583/full |
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