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Open Access Research article

Describing the structural robustness landscape of bacterial small RNAs

Guillermo Rodrigo13* and Mario A Fares12

Author affiliations

1 Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain

2 Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

3 Institute of Systems and Synthetic Biology, Genopole, Université d' Évry Val d' Essonne, CNRS, 91034 Évry Paris, France

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Citation and License

BMC Evolutionary Biology 2012, 12:52  doi:10.1186/1471-2148-12-52

Published: 13 April 2012

Abstract

Background

The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes.

Results

Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs) encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity.

Conclusion

Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.

Keywords:
Evolution; Evolvability; Plasticity; RNA structure; Robustness; Small RNA; Thermodynamics