Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses
The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm <i>Duplodnaviria</i>, which include tailed bacteriophages, head-tailed archaea...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/1/110 |
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| author | Peter Evseev Daria Gutnik Mikhail Shneider Konstantin Miroshnikov |
| author_facet | Peter Evseev Daria Gutnik Mikhail Shneider Konstantin Miroshnikov |
| author_sort | Peter Evseev |
| collection | DOAJ |
| description | The evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm <i>Duplodnaviria</i>, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of <i>Duplodnaviria</i> taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified <i>Duplodnaviria</i> families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal <i>Duplodnaviria</i> groups, and problems relating to the taxonomic classification of <i>Duplodnaviria</i> have been discussed. |
| first_indexed | 2024-03-09T13:26:55Z |
| format | Article |
| id | doaj.art-103607a386f741c6807f7c619f1a1188 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T13:26:55Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-103607a386f741c6807f7c619f1a11882023-11-30T21:22:55ZengMDPI AGBiomolecules2218-273X2023-01-0113111010.3390/biom13010110Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> VirusesPeter Evseev0Daria Gutnik1Mikhail Shneider2Konstantin Miroshnikov3Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, RussiaLimnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 117997 Moscow, RussiaThe evaluation of the evolutionary relationships is exceptionally important for the taxonomy of viruses, which is a rapidly expanding area of research. The classification of viral groups belonging to the realm <i>Duplodnaviria</i>, which include tailed bacteriophages, head-tailed archaeal viruses and herpesviruses, has undergone many changes in recent years and continues to improve. One of the challenging tasks of <i>Duplodnaviria</i> taxonomy is the classification of high-ranked taxa, including families and orders. At the moment, only 17 of 50 families have been assigned to orders. The evaluation of the evolutionary relationships between viruses is complicated by the high level of divergence of viral proteins. However, the development of structure prediction algorithms, including the award-winning AlphaFold, encourages the use of the results of structural predictions to clarify the evolutionary history of viral proteins. In this study, the evolutionary relationships of two conserved viral proteins, the major capsid protein and terminase, representing different viruses, including all classified <i>Duplodnaviria</i> families, have been analysed using AlphaFold modelling. This analysis has been undertaken using structural comparisons and different phylogenetic methods. The results of the analyses mainly indicated the high quality of AlphaFold modelling and the possibility of using the AlphaFold predictions, together with other methods, for the reconstruction of the evolutionary relationships between distant viral groups. Based on the results of this integrated approach, assumptions have been made about refining the taxonomic classification of bacterial and archaeal <i>Duplodnaviria</i> groups, and problems relating to the taxonomic classification of <i>Duplodnaviria</i> have been discussed.https://www.mdpi.com/2218-273X/13/1/110viral taxonomyevolution of virusesAlphaFoldmajor capsid proteinterminaseprotein structure comparison |
| spellingShingle | Peter Evseev Daria Gutnik Mikhail Shneider Konstantin Miroshnikov Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses Biomolecules viral taxonomy evolution of viruses AlphaFold major capsid protein terminase protein structure comparison |
| title | Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses |
| title_full | Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses |
| title_fullStr | Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses |
| title_full_unstemmed | Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses |
| title_short | Use of an Integrated Approach Involving AlphaFold Predictions for the Evolutionary Taxonomy of <i>Duplodnaviria</i> Viruses |
| title_sort | use of an integrated approach involving alphafold predictions for the evolutionary taxonomy of i duplodnaviria i viruses |
| topic | viral taxonomy evolution of viruses AlphaFold major capsid protein terminase protein structure comparison |
| url | https://www.mdpi.com/2218-273X/13/1/110 |
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