Bioinformatics study of reverse transcriptase sequence in viruses

Karimi, Samira; Pouresmaeil, Mahin

doi:10.30473/cb.2023.69786.1933

Bioinformatics study of reverse transcriptase sequence in viruses

Document Type : Research Paper

Authors

Samira Karimi ¹
Mahin Pouresmaeil ²

¹ M.Sc. Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran.

² Post Doctoral Researcher, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili

10.30473/cb.2023.69786.1933

Abstract

Bioinformatics is an interdisciplinary science that utilizes information technologies to organize and analyze biological data. This science enables researchers to perform comprehensive and documented investigations on various biological problems without the need for expensive and time-consuming laboratory experiments .In this study, we acquired the reverse transcriptase (RT) sequence of eight virus strains from NCBI with the following accession numbers: NC_001497.2, NC_001648.1, NC_001839.2, NC_003977.2, AF053008.1, EF428979.1, NC_001802.1. We investigated the structural and functional characteristics, domains, and motifs. The analysis revealed that the proteins from the eight virus strains, belonging to different families, exhibited distinct properties that set them apart from one another. The analysis also showed that these proteins are found in the membrane, cytoplasm, and periplasm, and all of them contain at least one specific domain of the reverse transcriptase enzyme. Based on all the analyses performed, Cauliflower mosaic virus, Cassava vein mosaic virus, and Soybean chlorotic mottle virus, all belonging to the Caulimoviridae family, were suitable for producing RT enzymes. The ability of these viruses to adapt to different plant hosts could potentially lead to the development of more efficient and cost-effective methods for producing RT enzymes. This adaptability could also open up new possibilities for genetic engineering and biotechnology, enabling the development of more effective enzymes.

Keywords

Main Subjects

Bioinformatics

References

Allahi, S., Sohani, M. M., & Hasani Kumleh, H. (2017). In silico identification of the pld gene family and analysis of their expression pattern in response to salt stress in medicago truncatula. Genetic Engineering and Biosafety Journal, 6(1), 143-156. Auslander, N., Gussow, A. B., & Koonin, E. V. (2021). Incorporating machine learning into established bioinformatics frameworks. International journal of molecular sciences, 22(6), 2903. Bhagavan, N., & Ha, C.-E. (2015). DNA replication, repair, and mutagenesis. Essentials of Medical Biochemistry, 2, 401-417. Brown, T. A. (2020). Gene cloning and DNA analysis: An introduction: John Wiley & Sons. Coffin, J. M., & Fan, H. (2016). The discovery of reverse transcriptase. Annual review of virology, 3, 29-51. Ellefson, J. W., Gollihar, J., Shroff, R., Shivram, H., Iyer, V. R., & Ellington, A. D. (2016). Synthetic evolutionary origin of a proofreading reverse transcriptase. Science, 352(6293), 1590-1593. Gauthier, J., Vincent, A. T., Charette, S. J., & Derome, N. (2019). A brief history of bioinformatics. Briefings in bioinformatics, 20(6), 1981-1996. Gupta, A., Gangotia, D., & Mani, I. (2021). Bioinformatics tools and software. Advances in Bioinformatics, 15-35. Haddad, F., & Baldwin, K. M. (2010). Reverse transcription of the ribonucleic acid: The first step in rt-pcr assay. RT-PCR Protocols: Second Edition, 261-270. Harper, D. (2011). Viruses: Biology, applications, and control: Garland Science. Hufsky, F., Abecasis, A., Agudelo-Romero, P., Bletsa, M., Brown, K., Claus, C., ... Gismondi, M. I. (2022). Women in the european virus bioinformatics center. Viruses, 14(7), 1522. Kaiser, F., Eisold, A., & Labudde, D. (2015). A novel algorithm for enhanced structural motif matching in proteins. Journal of Computational Biology, 22(7), 698-713. Kozlowski, L. P. (2017). Proteome-pi: Proteome isoelectric point database. Nucleic acids research, 45(D1), D1112-D1116. Krupovic, M., Blomberg, J., Coffin, J. M., Dasgupta, I., Fan, H., Geering, A. D., . . . Johnson, W. (2018). Ortervirales: New virus order unifying five families of reverse-transcribing viruses. Journal of virology, 92(12), 10.1128/jvi. 00515-00518. Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). Mega x: Molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution, 35(6), 1547. Kuznetsov, A., & Bollin, C. J. (2021). Ncbi genome workbench: Desktop software for comparative genomics, visualization, and genbank data submission. Multiple Sequence Alignment: Methods and Protocols, 261-295. Leonetti, P., Miesen, P., van Rij, R. P., & Pantaleo, V. (2020). Viral and subviral derived small rnas as pathogenic determinants in plants and insects. Advances in Virus Research, 107, 1-36. Llorens, C., Soriano, B., Krupovic, M., & Consortium, I. R. (2021). Ictv virus taxonomy profile: Pseudoviridae. Journal of General Virology, 102(3), 001563. Magnius, L., Mason, W. S., Taylor, J., Kann, M., Glebe, D., Dény, P., ... Consortium, I. R. (2020). Ictv virus taxonomy profile: Hepadnaviridae. Journal of General Virology, 101(6), 571-572. Menéndez-Arias, L., & Delgado, R. (2022). Update and latest advances in antiretroviral therapy. Trends in pharmacological sciences, 43(1), 16-29. Menéndez-Arias, L., Sebastián-Martín, A., & Álvarez, M. (2017). Viral reverse transcriptases. Virus research, 234, 153-176. Naznin, F., Sarker, R., & Essam, D. (2011). Vertical decomposition with genetic algorithm for multiple sequence alignment. BMC bioinformatics, 12(1), 1-26. Passos, D. O., Li, M., Craigie, R., & Lyumkis, D. (2021). Retroviral integrase: Structure, mechanism, and inhibition. In The enzymes (Vol. 50, pp. 249-300): Elsevier. Rhee, S. Y., Dickerson, J., & Xu, D. (2006). Bioinformatics and its applications in plant biology. Annu. Rev. Plant Biol., 57, 335-360. Schoelz, J. E., & Adhab, M. (2021). Caulimoviruses (caulimoviridae). Sluis-Cremer, N. (2021). Retroviral reverse transcriptase: Structure, function and inhibition. In The enzymes (Vol. 50, pp. 179-194): Elsevier. Sobhy, H. (2016). A review of functional motifs utilized by viruses. Proteomes, 4(1), 3. Teycheney, P.-Y., Geering, A. D., Dasgupta, I., Hull, R., Kreuze, J. F., Lockhart, B., . . . Pooggin, M. M. (2020). Ictv virus taxonomy profile: Caulimoviridae. Journal of General Virology, 101(10), 1025-1026. Vogel, C., Berzuini, C., Bashton, M., Gough, J., & Teichmann, S. A. (2004). Supra-domains: Evolutionary units larger than single protein domains. Journal of molecular biology, 336(3), 809-823. Zhang, Y., Zhang, Q., Zhou, J., & Zou, Q. (2022). A survey on the algorithm and development of multiple sequence alignment. Briefings in bioinformatics, 23(3), bbac069.