A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications
Abstract Background The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an endangered group. To understand the probable...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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SpringerOpen
2023-08-01
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| Series: | Journal of Genetic Engineering and Biotechnology |
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| Online Access: | https://doi.org/10.1186/s43141-023-00534-5 |
| _version_ | 1797743976811331584 |
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| author | Shahla Yasmin Sushant Kumar Gajendra Kumar Azad |
| author_facet | Shahla Yasmin Sushant Kumar Gajendra Kumar Azad |
| author_sort | Shahla Yasmin |
| collection | DOAJ |
| description | Abstract Background The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an endangered group. To understand the probable genetic factors associated with the decline of P. muticus, we compared the mitogenome-encoded proteins (13 proteins) between these two species. Results Our data revealed that the most frequent variant between these two species was mtND1, which had an alteration in 9.57% residues, followed by mtND5 and mtATP6. We extended our study on the rest of the proteins and observed that cytochrome c oxidase subunits 1, 2, and 3 do not have any change. The 3-dimensional structure of all 13 proteins was modeled using the Phyre2 programme. Our data show that most of the proteins are alpha helical, and the variations observed in P. muticus reside on the surface of the respective proteins. The effect of variation on protein function was also predicted, and our results show that amino acid substitution in mtND1 at 14 sites could be deleterious. Similarly, destabilising changes were observed in mtND1, 2, 3, 4, 5, and 6 and mtATP6–8 due to amino acid substitution in P. muticus. Furthermore, protein disorder scores were considerably altered in mtND1, 2, and 5 of P. muticus. Conclusions The results presented here strongly suggest that variations in mitogenome-encoded proteins of P. cristatus and P. muticus may alter their structure and functions. Subsequently, these variations could alter energy production and may correlate with the decline in the population of P. muticus. |
| first_indexed | 2024-03-12T15:03:14Z |
| format | Article |
| id | doaj.art-310b9ef3c6dd42149a95b513513a08c9 |
| institution | Directory Open Access Journal |
| issn | 2090-5920 |
| language | English |
| last_indexed | 2024-03-12T15:03:14Z |
| publishDate | 2023-08-01 |
| publisher | SpringerOpen |
| record_format | Article |
| series | Journal of Genetic Engineering and Biotechnology |
| spelling | doaj.art-310b9ef3c6dd42149a95b513513a08c92023-08-13T11:20:14ZengSpringerOpenJournal of Genetic Engineering and Biotechnology2090-59202023-08-0121111110.1186/s43141-023-00534-5A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implicationsShahla Yasmin0Sushant Kumar1Gajendra Kumar Azad2Department of Zoology, Patna UniversityMolecular Biology Laboratory, Department of Zoology, Patna UniversityMolecular Biology Laboratory, Department of Zoology, Patna UniversityAbstract Background The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an endangered group. To understand the probable genetic factors associated with the decline of P. muticus, we compared the mitogenome-encoded proteins (13 proteins) between these two species. Results Our data revealed that the most frequent variant between these two species was mtND1, which had an alteration in 9.57% residues, followed by mtND5 and mtATP6. We extended our study on the rest of the proteins and observed that cytochrome c oxidase subunits 1, 2, and 3 do not have any change. The 3-dimensional structure of all 13 proteins was modeled using the Phyre2 programme. Our data show that most of the proteins are alpha helical, and the variations observed in P. muticus reside on the surface of the respective proteins. The effect of variation on protein function was also predicted, and our results show that amino acid substitution in mtND1 at 14 sites could be deleterious. Similarly, destabilising changes were observed in mtND1, 2, 3, 4, 5, and 6 and mtATP6–8 due to amino acid substitution in P. muticus. Furthermore, protein disorder scores were considerably altered in mtND1, 2, and 5 of P. muticus. Conclusions The results presented here strongly suggest that variations in mitogenome-encoded proteins of P. cristatus and P. muticus may alter their structure and functions. Subsequently, these variations could alter energy production and may correlate with the decline in the population of P. muticus.https://doi.org/10.1186/s43141-023-00534-5Pavo muticusPavo cristatusMitogenomeProtein-coding genesIntrinsic protein disorderVariations; Stability |
| spellingShingle | Shahla Yasmin Sushant Kumar Gajendra Kumar Azad A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications Journal of Genetic Engineering and Biotechnology Pavo muticus Pavo cristatus Mitogenome Protein-coding genes Intrinsic protein disorder Variations; Stability |
| title | A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications |
| title_full | A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications |
| title_fullStr | A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications |
| title_full_unstemmed | A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications |
| title_short | A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications |
| title_sort | computational study on mitogenome encoded proteins of pavo cristatus and pavo muticus identifies key genetic variations with functional implications |
| topic | Pavo muticus Pavo cristatus Mitogenome Protein-coding genes Intrinsic protein disorder Variations; Stability |
| url | https://doi.org/10.1186/s43141-023-00534-5 |
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