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MBE Advance Access published online on May 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl005
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted May 1, 2006

Research Article

In Silico Predicted Robustness of Viroids RNA Secondary Structures. I. The effect of single mutations

Rafael Sanjuán 1, Javier Forment 2, and Santiago F. Elena 2 *

1 Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los naranjos s/n, 46022 València, Spain; Temporary address: Section of Integrative Biology, University of Texas, Austin TX 78712, USA
2 Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los naranjos s/n, 46022 València, Spain

* To whom correspondence should be addressed.
Santiago F. Elena, E-mail: sfelena{at}ibmcp.upv.es


  Abstract

Viroids are plant subviral pathogens whose genomes are constituted by a singlestranded and covalently closed small RNA molecule which does not encode for any protein. Despite this genomic simplicity, they are able of inducing devastating symptoms in susceptible plants. Most of the 29 described viroid species fold into a rod-like or quasi-rod-like structure, whereas a few of them fold as branched structures. The shape of these RNA structures is perhaps one of the most characteristic properties of viroids and sometimes is considered their only phenotype. Here we use RNA thermodynamic secondary structure prediction algorithms to compare the mutational robustness of all viroid species. After characterizing the statistical properties of the distribution of mutational effects on structure stability and the wideness of neutral neighborhood for each viroid species, we show an evolutionary trend towards increased structural robustness during viroid radiation, giving support to the adaptive value of robustness. Differences in robustness among the two viroid families can be explained by the larger fragility of branched structures compared with the rod-like ones. We also show that genomic redundancy can contribute to the robustness of these simple RNA genomes.

Keywords: mutational robustness; neutrality; plant pathogens; RNA folding; viroids.
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