Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
| Autor: | José A. Cuesta, Susanna C. Manrubia, Pablo Catalán, Santiago F. Elena |
|---|---|
| Přispěvatelé: | Ministerio de Ciencia, Innovación y Universidades (España) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Population dynamics Viroid Matemáticas viruses Population Pospiviroidae lcsh:QR1-502 Computational biology computational simulations Virus Replication lcsh:Microbiology Article Nucleic acid secondary structure Evolution Molecular Viral Proteins 03 medical and health sciences 0302 clinical medicine Circular RNA Virology population dynamics Modular evolution Replicon education Polymerase Biología y Biomedicina Simple replicators Computational simulations education.field_of_study structure enumeration biology simple replicators viroid Structure enumeration RNA RNA Circular biology.organism_classification RNA secondary structure Viroids 030104 developmental biology Infectious Diseases biology.protein Nucleic Acid Conformation RNA Viral modular evolution 030217 neurology & neurosurgery |
| Zdroj: | Viruses Volume 11 Issue 5 e-Archivo. Repositorio Institucional de la Universidad Carlos III de Madrid instname Viruses, Vol 11, Iss 5, p 425 (2019) |
| ISSN: | 1999-4915 |
| DOI: | 10.3390/v11050425 |
| Popis: | This article belongs to the Special Issue Viroid-2018: International Conference on Viroids and Viroid-Like RNAs. 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. 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.). |
| Databáze: | OpenAIRE |
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