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Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families

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  • Anuj Srivastava
  • Liming Cai
  • Jan Mrázek
  • Russell L Malmberg

Abstract

The goal of this work was to study mutational patterns in the evolution of RNA secondary structure. We analyzed bacterial tmRNA, RNaseP and eukaryotic telomerase RNA secondary structures, mapping structural variability onto phylogenetic trees constructed primarily from rRNA sequences. We found that secondary structures evolve both by whole stem insertion/deletion, and by mutations that create or disrupt stem base pairing. We analyzed the evolution of stem lengths and constructed substitution matrices describing the changes responsible for the variation in the RNA stem length. In addition, we used principal component analysis of the stem length data to determine the most variable stems in different families of RNA. This data provides new insights into the evolution of RNA secondary structures and patterns of variation in the lengths of double helical regions of RNA molecules. Our findings will facilitate design of improved mutational models for RNA structure evolution.

Suggested Citation

  • Anuj Srivastava & Liming Cai & Jan Mrázek & Russell L Malmberg, 2011. "Mutational Patterns in RNA Secondary Structure Evolution Examined in Three RNA Families," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    • Handle: RePEc:plo:pone00:0020484
    DOI: 10.1371/journal.pone.0020484
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    References listed on IDEAS

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    4. Robert K Bradley & Ian Holmes, 2009. "Evolutionary Triplet Models of Structured RNA," PLOS Computational Biology, Public Library of Science, vol. 5(8), pages 1-20, August.
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