Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei
Abstract Background The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement to...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-03-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43141-022-00324-5 |
| _version_ | 1827280950769221632 |
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| author | Amit Joshi Sunil Krishnan Vikas Kaushik |
| author_facet | Amit Joshi Sunil Krishnan Vikas Kaushik |
| author_sort | Amit Joshi |
| collection | DOAJ |
| description | Abstract Background The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement tools were deployed to detect the rare, very rare codons, and also synonymous codons usage. The higher effective number of codon usage values indicates the low codon usage bias in T. whipplei and also in the 23S and 16S ribosomal RNA genes. Results In T. whipplei, it was found to hold low codon biasness in genomic sets. The synonymous codons possess the base content in 3rd position that was calculated as A3S% (24.47 and 22.88), C3S% (20.99 and 22.88), T3S% (21.47 and 19.53), and G3S% (33.08 and 34.71) for 23s and 16s rRNA, respectively. Conclusion Amino acids like valine, aspartate, leucine, and phenylalanine hold high codon usage frequency and also found to be present in epitopes KPSYLSALSAHLNDK and FKSFNYNVAIGVRQP that were screened from proteins excinuclease ABC subunit UvrC and 3-oxoacyl-ACP reductase FabG, respectively. This method opens novel ways to determine epitope-based peptide vaccines against different pathogenic organisms. |
| first_indexed | 2024-04-24T08:49:49Z |
| format | Article |
| id | doaj.art-6b6fff1676d14e2784ba761541abea9b |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-04-24T08:49:49Z |
| publishDate | 2022-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-6b6fff1676d14e2784ba761541abea9b2024-04-16T12:04:12ZengElsevierJournal of Genetic Engineering and Biotechnology2090-59202022-03-0120111210.1186/s43141-022-00324-5Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whippleiAmit Joshi0Sunil Krishnan1Vikas Kaushik2School of Bioengineering and Biosciences, Lovely Professional UniversitySchool of Bioengineering and Biosciences, Lovely Professional UniversitySchool of Bioengineering and Biosciences, Lovely Professional UniversityAbstract Background The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement tools were deployed to detect the rare, very rare codons, and also synonymous codons usage. The higher effective number of codon usage values indicates the low codon usage bias in T. whipplei and also in the 23S and 16S ribosomal RNA genes. Results In T. whipplei, it was found to hold low codon biasness in genomic sets. The synonymous codons possess the base content in 3rd position that was calculated as A3S% (24.47 and 22.88), C3S% (20.99 and 22.88), T3S% (21.47 and 19.53), and G3S% (33.08 and 34.71) for 23s and 16s rRNA, respectively. Conclusion Amino acids like valine, aspartate, leucine, and phenylalanine hold high codon usage frequency and also found to be present in epitopes KPSYLSALSAHLNDK and FKSFNYNVAIGVRQP that were screened from proteins excinuclease ABC subunit UvrC and 3-oxoacyl-ACP reductase FabG, respectively. This method opens novel ways to determine epitope-based peptide vaccines against different pathogenic organisms.https://doi.org/10.1186/s43141-022-00324-5Tropheryma whippleiSynonymous codonsRibosomal RNAGastroenteritis and codon usage |
| spellingShingle | Amit Joshi Sunil Krishnan Vikas Kaushik Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei Journal of Genetic Engineering and Biotechnology Tropheryma whipplei Synonymous codons Ribosomal RNA Gastroenteritis and codon usage |
| title | Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei |
| title_full | Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei |
| title_fullStr | Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei |
| title_full_unstemmed | Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei |
| title_short | Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei |
| title_sort | codon usage studies and epitope based peptide vaccine prediction against tropheryma whipplei |
| topic | Tropheryma whipplei Synonymous codons Ribosomal RNA Gastroenteritis and codon usage |
| url | https://doi.org/10.1186/s43141-022-00324-5 |
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