Modelling the three-dimensional structure of the right-terminal domain of pospiviroids
Abstract Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding p...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2017-04-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-017-00764-x |
| _version_ | 1818856098576203776 |
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| author | Gerhard Steger |
| author_facet | Gerhard Steger |
| author_sort | Gerhard Steger |
| collection | DOAJ |
| description | Abstract Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain. |
| first_indexed | 2024-12-19T08:19:06Z |
| format | Article |
| id | doaj.art-322cbcbc72874fdfa94051309152e4a2 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T08:19:06Z |
| publishDate | 2017-04-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-322cbcbc72874fdfa94051309152e4a22022-12-21T20:29:26ZengNature PortfolioScientific Reports2045-23222017-04-017111210.1038/s41598-017-00764-xModelling the three-dimensional structure of the right-terminal domain of pospiviroidsGerhard Steger0Institut für Physikalische Biologie, Heinrich-Heine-University DüsseldorfAbstract Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain.https://doi.org/10.1038/s41598-017-00764-x |
| spellingShingle | Gerhard Steger Modelling the three-dimensional structure of the right-terminal domain of pospiviroids Scientific Reports |
| title | Modelling the three-dimensional structure of the right-terminal domain of pospiviroids |
| title_full | Modelling the three-dimensional structure of the right-terminal domain of pospiviroids |
| title_fullStr | Modelling the three-dimensional structure of the right-terminal domain of pospiviroids |
| title_full_unstemmed | Modelling the three-dimensional structure of the right-terminal domain of pospiviroids |
| title_short | Modelling the three-dimensional structure of the right-terminal domain of pospiviroids |
| title_sort | modelling the three dimensional structure of the right terminal domain of pospiviroids |
| url | https://doi.org/10.1038/s41598-017-00764-x |
| work_keys_str_mv | AT gerhardsteger modellingthethreedimensionalstructureoftherightterminaldomainofpospiviroids |