Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
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 o...
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doaj-ea28c9efb1b54ebcab7487dd370d6b972020-11-25T01:38:42ZengMDPI AGViruses1999-49152019-05-0111542510.3390/v11050425v11050425Parsimonious Scenario for the Emergence of Viroid-Like Replicons De NovoPablo Catalán0Santiago F. Elena1José A. Cuesta2Susanna Manrubia3Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UKInstituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Paterna, 46980 València, SpainGrupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, SpainGrupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, SpainViroids 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.https://www.mdpi.com/1999-4915/11/5/425viroidRNA secondary structurepopulation dynamicscomputational simulationsstructure enumerationsimple replicatorsmodular evolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Pablo Catalán Santiago F. Elena José A. Cuesta Susanna Manrubia |
spellingShingle |
Pablo Catalán Santiago F. Elena José A. Cuesta Susanna Manrubia Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo Viruses viroid RNA secondary structure population dynamics computational simulations structure enumeration simple replicators modular evolution |
author_facet |
Pablo Catalán Santiago F. Elena José A. Cuesta Susanna Manrubia |
author_sort |
Pablo Catalán |
title |
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo |
title_short |
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo |
title_full |
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo |
title_fullStr |
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo |
title_full_unstemmed |
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo |
title_sort |
parsimonious scenario for the emergence of viroid-like replicons de novo |
publisher |
MDPI AG |
series |
Viruses |
issn |
1999-4915 |
publishDate |
2019-05-01 |
description |
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. |
topic |
viroid RNA secondary structure population dynamics computational simulations structure enumeration simple replicators modular evolution |
url |
https://www.mdpi.com/1999-4915/11/5/425 |
work_keys_str_mv |
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