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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Autor principal:	Gerhard Steger
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/322cbcbc72874fdfa94051309152e4a2
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spelling	oai:doaj.org-article:322cbcbc72874fdfa94051309152e4a22021-12-02T16:08:24ZModelling the three-dimensional structure of the right-terminal domain of pospiviroids10.1038/s41598-017-00764-x2045-2322https://doaj.org/article/322cbcbc72874fdfa94051309152e4a22017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00764-xhttps://doaj.org/toc/2045-2322Abstract 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.Gerhard StegerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Gerhard Steger Modelling the three-dimensional structure of the right-terminal domain of pospiviroids
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.
format	article
author	Gerhard Steger
author_facet	Gerhard Steger
author_sort	Gerhard Steger
title	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_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_sort	modelling the three-dimensional structure of the right-terminal domain of pospiviroids
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/322cbcbc72874fdfa94051309152e4a2
work_keys_str_mv	AT gerhardsteger modellingthethreedimensionalstructureoftherightterminaldomainofpospiviroids
_version_	1718384520344895488

Modelling the three-dimensional structure of the right-terminal domain of pospiviroids

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