Parsimonious scenario for the emergence of viroid-like replicons de novo

Catalan Fernandez, Pablo; Elena, Santiago F.; Cuesta, José A.; Manrubia, Susanna C.

Publication:
Parsimonious scenario for the emergence of viroid-like replicons de novo

dc.affiliation.dpto	UC3M. Departamento de Matemáticas	es
dc.affiliation.grupoinv	UC3M. Grupo de Investigación: Interdisciplinar de Sistemas Complejos (GISC)	es
dc.contributor.author	Catalan Fernandez, Pablo
dc.contributor.author	Elena, Santiago F.
dc.contributor.author	Cuesta, José A.
dc.contributor.author	Manrubia, Susanna C.
dc.contributor.funder	Ministerio de Ciencia, Innovación y Universidades (España)	es
dc.date.accessioned	2022-02-02T09:38:24Z
dc.date.available	2022-02-02T09:38:24Z
dc.date.issued	2019-05
dc.description	This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs.	en
dc.description.abstract	Viroids are small, non-coding, circular RNA molecules that infect plants. Different hypotheses for their evolutionary origin have been put forward, such as an early emergence in a precellular RNA World or several de novo independent evolutionary origins in plants. Here, we discuss the plausibility of de novo emergence of viroid-like replicons by giving theoretical support to the likelihood of different steps along a parsimonious evolutionary pathway. While Avsunviroidae-like structures are relatively easy to obtain through evolution of a population of random RNA sequences of fixed length, rod-like structures typical of Pospiviroidae are difficult to fix. Using different quantitative approaches, we evaluated the likelihood that RNA sequences fold into a rod-like structure and bear specific sequence motifs facilitating interactions with other molecules, e.g., RNA polymerases, RNases, and ligases. By means of numerical simulations, we show that circular RNA replicons analogous to Pospiviroidae emerge if evolution is seeded with minimal circular RNAs that grow through the gradual addition of nucleotides. Further, these rod-like replicons often maintain their structure if independent functional modules are acquired that impose selective constraints. The evolutionary scenario we propose here is consistent with the structural and biochemical properties of viroids described to date.	en
dc.description.sponsorship	P.C. is supported by a Ramón Areces Foundation Postdoctoral Fellowship. The Spanish Ministerio de Ciencia, Innovación y Universidades-FEDER funds of the European Union support Projects BASIC (PGC2018-098186-B-I00, J.A.C. and P.C.), MiMevo (FIS2017-89773-P, S.M.), and EvolSysVir (BFU2015-65037-P, S.F.E.).	en
dc.format.extent	20
dc.identifier.bibliographicCitation	Catalán, P., Elena, S. F., Cuesta, J. A. & Manrubia, S. (2019). Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo. Viruses, 11(5), 425.	en
dc.identifier.doi	https://doi.org//10.3390/v11050425
dc.identifier.issn	1999-4915
dc.identifier.publicationfirstpage	425
dc.identifier.publicationissue	5
dc.identifier.publicationtitle	Viruses	en
dc.identifier.publicationvolume	11
dc.identifier.uri	https://hdl.handle.net/10016/34010
dc.identifier.uxxi	AR/0000025464
dc.language.iso	eng	en
dc.publisher	MDPI	en
dc.relation.projectID	Gobierno de España. PGC2018-098186-B-I00	es
dc.relation.projectID	Gobierno de España. FIS2017-89773-P	es
dc.relation.projectID	Gobierno de España. BFU2015-65037-P	es
dc.rights	© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.	en
dc.rights	Atribución 3.0 España	*
dc.rights.accessRights	open access	en
dc.rights.uri	http://creativecommons.org/licenses/by/3.0/es/	*
dc.subject.eciencia	Biología y Biomedicina	es
dc.subject.eciencia	Matemáticas	es
dc.subject.other	Computational simulations	en
dc.subject.other	Modular evolution	en
dc.subject.other	Population dynamics	en
dc.subject.other	RNA secondary structure	en
dc.subject.other	Simple replicators	en
dc.subject.other	Structure enumeration	en
dc.subject.other	Viroid	en
dc.title	Parsimonious scenario for the emergence of viroid-like replicons de novo	en
dc.type	research article	*
dc.type.hasVersion	VoR	*
dspace.entity.type	Publication