Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins
Abstract Background Tospoviruses (genus Tospovirus, family Peribunyaviridae, order Bunyavirales) cause significant losses to a wide range of agronomic and horticultural crops worldwide. Identification and characterization of specific sequences and motifs that are critical for virus infection and pat...
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | Virology Journal |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12985-018-1106-4 |
| _version_ | 1818110189324206080 |
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| author | Cristian Olaya Badri Adhikari Gaurav Raikhy Jianlin Cheng Hanu R. Pappu |
| author_facet | Cristian Olaya Badri Adhikari Gaurav Raikhy Jianlin Cheng Hanu R. Pappu |
| author_sort | Cristian Olaya |
| collection | DOAJ |
| description | Abstract Background Tospoviruses (genus Tospovirus, family Peribunyaviridae, order Bunyavirales) cause significant losses to a wide range of agronomic and horticultural crops worldwide. Identification and characterization of specific sequences and motifs that are critical for virus infection and pathogenicity could provide useful insights and targets for engineering virus resistance that is potentially both broad spectrum and durable. Tomato spotted wilt virus (TSWV), the most prolific member of the group, was used to better understand the structure-function relationships of the nucleocapsid gene (N), and the silencing suppressor gene (NSs), coded by the TSWV small RNA. Methods Using a global collection of orthotospoviral sequences, several amino acids that were conserved across the genus and the potential location of these conserved amino acid motifs in these proteins was determined. We used state of the art 3D modeling algorithms, MULTICOM-CLUSTER, MULTICOM-CONSTRUCT, MULTICOM-NOVEL, I-TASSER, ROSETTA and CONFOLD to predict the secondary and tertiary structures of the N and the NSs proteins. Results We identified nine amino acid residues in the N protein among 31 known tospoviral species, and ten amino acid residues in NSs protein among 27 tospoviral species that were conserved across the genus. For the N protein, all three algorithms gave nearly identical tertiary models. While the conserved residues were distributed throughout the protein on a linear scale, at the tertiary level, three residues were consistently located in the coil in all the models. For NSs protein models, there was no agreement among the three algorithms. However, with respect to the localization of the conserved motifs, G18 was consistently located in coil, while H115 was localized in the coil in three models. Conclusions This is the first report of predicting the 3D structure of any tospoviral NSs protein and revealed a consistent location for two of the ten conserved residues. The modelers used gave accurate prediction for N protein allowing the localization of the conserved residues. Results form the basis for further work on the structure-function relationships of tospoviral proteins and could be useful in developing novel virus control strategies targeting the conserved residues. |
| first_indexed | 2024-12-11T02:43:11Z |
| format | Article |
| id | doaj.art-eab4964e13df4f98a0e62390d3e644f2 |
| institution | Directory Open Access Journal |
| issn | 1743-422X |
| language | English |
| last_indexed | 2024-12-11T02:43:11Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Virology Journal |
| spelling | doaj.art-eab4964e13df4f98a0e62390d3e644f22022-12-22T01:23:31ZengBMCVirology Journal1743-422X2019-01-0116111510.1186/s12985-018-1106-4Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteinsCristian Olaya0Badri Adhikari1Gaurav Raikhy2Jianlin Cheng3Hanu R. Pappu4Department of Plant Pathology, Washington State UniversityDepartment of Mathematics and Computer Science, University of MissouriDepartment of Microbiology and Immunology, Louisiana State UniversityDepartment of Electrical Engineering and Computer Science, University of MissouriDepartment of Plant Pathology, Washington State UniversityAbstract Background Tospoviruses (genus Tospovirus, family Peribunyaviridae, order Bunyavirales) cause significant losses to a wide range of agronomic and horticultural crops worldwide. Identification and characterization of specific sequences and motifs that are critical for virus infection and pathogenicity could provide useful insights and targets for engineering virus resistance that is potentially both broad spectrum and durable. Tomato spotted wilt virus (TSWV), the most prolific member of the group, was used to better understand the structure-function relationships of the nucleocapsid gene (N), and the silencing suppressor gene (NSs), coded by the TSWV small RNA. Methods Using a global collection of orthotospoviral sequences, several amino acids that were conserved across the genus and the potential location of these conserved amino acid motifs in these proteins was determined. We used state of the art 3D modeling algorithms, MULTICOM-CLUSTER, MULTICOM-CONSTRUCT, MULTICOM-NOVEL, I-TASSER, ROSETTA and CONFOLD to predict the secondary and tertiary structures of the N and the NSs proteins. Results We identified nine amino acid residues in the N protein among 31 known tospoviral species, and ten amino acid residues in NSs protein among 27 tospoviral species that were conserved across the genus. For the N protein, all three algorithms gave nearly identical tertiary models. While the conserved residues were distributed throughout the protein on a linear scale, at the tertiary level, three residues were consistently located in the coil in all the models. For NSs protein models, there was no agreement among the three algorithms. However, with respect to the localization of the conserved motifs, G18 was consistently located in coil, while H115 was localized in the coil in three models. Conclusions This is the first report of predicting the 3D structure of any tospoviral NSs protein and revealed a consistent location for two of the ten conserved residues. The modelers used gave accurate prediction for N protein allowing the localization of the conserved residues. Results form the basis for further work on the structure-function relationships of tospoviral proteins and could be useful in developing novel virus control strategies targeting the conserved residues.http://link.springer.com/article/10.1186/s12985-018-1106-4Conserved amino acidsTospovirusNucleoproteinSilencing suppressorThree-dimensional protein structure |
| spellingShingle | Cristian Olaya Badri Adhikari Gaurav Raikhy Jianlin Cheng Hanu R. Pappu Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins Virology Journal Conserved amino acids Tospovirus Nucleoprotein Silencing suppressor Three-dimensional protein structure |
| title | Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins |
| title_full | Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins |
| title_fullStr | Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins |
| title_full_unstemmed | Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins |
| title_short | Identification and localization of Tospovirus genus-wide conserved residues in 3D models of the nucleocapsid and the silencing suppressor proteins |
| title_sort | identification and localization of tospovirus genus wide conserved residues in 3d models of the nucleocapsid and the silencing suppressor proteins |
| topic | Conserved amino acids Tospovirus Nucleoprotein Silencing suppressor Three-dimensional protein structure |
| url | http://link.springer.com/article/10.1186/s12985-018-1106-4 |
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