Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

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...

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Bibliographic Details
Published in:Journal of Genetic Engineering and Biotechnology 2022-03, Vol.20 (1), p.41-12, Article 41
Main Authors: Joshi, Amit, Krishnan, Sunil, Kaushik, Vikas
Format: Article
Language:English
Subjects:
Antigenic determinants
aspartic acid
biotechnology
Care and treatment
Codon
codon usage
disease progression
epitopes
Gastroenteritis
Gastroenteritis and codon usage
genomics
Homeopathy
leucine
Materia medica and therapeutics
Medical research
Medicine, Experimental
neurons
oxidoreductases
peptides
Phenylalanine
prediction
Proteins
Ribosomal RNA
Synonymous codons
Therapeutics
Tropheryma
Tropheryma whipplei
Vaccines
valine
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Summary: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. 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. 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.
ISSN:1687-157X
2090-5920
DOI:10.1186/s43141-022-00324-5