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Dash M, Meher P, Aditya Kumar, Satapathy SS, Namsa ND. High frequency of transition to transversion ratio in the stem region of RNA secondary structure of untranslated region of SARS-CoV-2. PeerJ 2024; 12:e16962. [PMID: 38666080 PMCID: PMC11044879 DOI: 10.7717/peerj.16962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/26/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction The propensity of nucleotide bases to form pairs, causes folding and the formation of secondary structure in the RNA. Therefore, purine (R): pyrimidine (Y) base-pairing is vital to maintain uniform lateral dimension in RNA secondary structure. Transversions or base substitutions between R and Y bases, are more detrimental to the stability of RNA secondary structure, than transitions derived from substitutions between A and G or C and T. The study of transversion and transition base substitutions is important to understand evolutionary mechanisms of RNA secondary structure in the 5' and 3' untranslated (UTR) regions of SARS-CoV-2. In this work, we carried out comparative analysis of transition and transversion base substitutions in the stem and loop regions of RNA secondary structure of SARS-CoV-2. Methods We have considered the experimentally determined and well documented stem and loop regions of 5' and 3' UTR regions of SARS-CoV-2 for base substitution analysis. The secondary structure comprising of stem and loop regions were visualized using the RNAfold web server. The GISAID repository was used to extract base sequence alignment of the UTR regions. Python scripts were developed for comparative analysis of transversion and transition frequencies in the stem and the loop regions. Results The results of base substitution analysis revealed a higher transition (ti) to transversion (tv) ratio (ti/tv) in the stem region of UTR of RNA secondary structure of SARS-CoV-2 reported during the early stage of the pandemic. The higher ti/tv ratio in the stem region suggested the influence of secondary structure in selecting the pattern of base substitutions. This differential pattern of ti/tv values between stem and loop regions was not observed among the Delta and Omicron variants that dominated the later stage of the pandemic. It is noteworthy that the ti/tv values in the stem and loop regions were similar among the later dominant Delta and Omicron variant strains which is to be investigated to understand the rapid evolution and global adaptation of SARS-CoV-2. Conclusion Our findings implicate the lower frequency of transversions than the transitions in the stem regions of UTRs of SARS-CoV-2. The RNA secondary structures are associated with replication, translation, and packaging, further investigations are needed to understand these base substitutions across different variants of SARS-CoV-2.
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Affiliation(s)
- Madhusmita Dash
- Department of Electronics and Communication Engineering, National Institute of Technology Arunachal Pradesh, Jote, Arunachal Pradesh, India
| | - Preetisudha Meher
- Department of Electronics and Communication Engineering, National Institute of Technology Arunachal Pradesh, Jote, Arunachal Pradesh, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
| | | | - Nima D. Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India
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Beura PK, Sen P, Aziz R, Satapathy SS, Ray SK. Transcribed intergenic regions exhibit a lower frequency of nucleotide polymorphism than the untranscribed intergenic regions in the genomes of Escherichia coli and Salmonella enterica. J Genet 2023. [DOI: 10.1007/s12041-023-01418-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Aziz R, Sen P, Beura PK, Das S, Tula D, Dash M, Namsa ND, Deka RC, Feil EJ, Satapathy SS, Ray SK. Incorporation of transition to transversion ratio and nonsense mutations, improves the estimation of the number of synonymous and non-synonymous sites in codons. DNA Res 2022; 29:6654588. [PMID: 35920776 PMCID: PMC9358017 DOI: 10.1093/dnares/dsac023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
A common approach to estimate the strength and direction of selection acting on protein coding sequences is to calculate the dN/dS ratio. The method to calculate dN/dS has been widely used by many researchers and many critical reviews have been made on its application after the proposition by Nei and Gojobori in 1986. However, the method is still evolving considering the non-uniform substitution rates and pretermination codons. In our study of SNPs in 586 genes across 156 Escherichia coli strains, synonymous polymorphism in 2-fold degenerate codons were higher in comparison to that in 4-fold degenerate codons, which could be attributed to the difference between transition (Ti) and transversion (Tv) substitution rates where the average rate of a transition is four times more than that of a transversion in general. We considered both the Ti/Tv ratio, and nonsense mutation in pretermination codons, to improve estimates of synonymous (S) and non-synonymous (NS) sites. The accuracy of estimating dN/dS has been improved by considering the Ti/Tv ratio and nonsense substitutions in pretermination codons. We showed that applying the modified approach based on Ti/Tv ratio and pretermination codons results in higher values of dN/dS in 29 common genes of equal reading-frames between E. coli and Salmonella enterica. This study emphasizes the robustness of amino acid composition with varying codon degeneracy, as well as the pretermination codons when calculating dN/dS values.
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Affiliation(s)
- Ruksana Aziz
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Piyali Sen
- Department of Computer Science and Engineering, Tezpur University , Tezpur, 784028 Assam, India
| | - Pratyush Kumar Beura
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Saurav Das
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
| | - Debapriya Tula
- TCS Innovation, Tata Consultancy Services , Hyderabad, 500081 Telangana, India
| | - Madhusmita Dash
- Department of Electronics and Communication Engineering, NIT , Papum Pare, 791113 Arunachal Pradesh, India
| | - Nima Dondu Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
| | - Ramesh Chandra Deka
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
- Department of Chemical Sciences, Tezpur University , Tezpur, 784028 Assam, India
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath , Bath BA2 7AY, UK
| | - Siddhartha Sankar Satapathy
- Department of Computer Science and Engineering, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
| | - Suvendra Kumar Ray
- Department of Molecular Biology and Biotechnology, Tezpur University , Tezpur, 784028 Assam, India
- Center for Multidisciplinary Research, Tezpur University , Tezpur, 784028 Assam, India
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