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Related Experiment Videos

Multiple coding and the evolutionary properties of RNA secondary structure

M A Huynen1, D A Konings, P Hogeweg

  • 1Bioinformatics Group, University of Utrecht, The Netherlands.

Journal of Theoretical Biology
|November 21, 1993
PubMed
Summary

Conserving protein codes in RNA sequences limits their evolution towards specific secondary structures. While some large-scale adaptations are possible, small-scale changes are hindered, with insertions/deletions having minimal impact.

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Bioinformatics

Background:

  • RNA molecules fold into specific secondary structures crucial for their function.
  • The interplay between RNA sequence, protein-coding constraints, and secondary structure evolution is complex.

Purpose of the Study:

  • To investigate how protein-coding constraints affect RNA's ability to evolve secondary structures.
  • To analyze the impact of restricted mutations (point mutations, insertions, deletions) on RNA evolution.

Main Methods:

  • Simulated evolutionary search processes.
  • Analysis of sequence space accessibility and connectivity.
  • Examination of fitness landscape ruggedness and epistatic interactions.

Main Results:

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  • Protein-coding constraints restrict RNA sequence space, limiting small-scale adaptations but allowing some large-scale topological changes.
  • Abolishing insertions and deletions had minimal effect on evolutionary search outcomes.
  • Evolutionary search converged to subspaces with high similarity between secondary structures of neighboring sequences.
  • Evidence suggests selection for RNA secondary structure can influence amino acid sequences (e.g., in lentiviral RRE).

Conclusions:

  • Fitness landscapes for RNA secondary structure evolution exhibit ruggedness due to epistasis.
  • Understanding these constraints is vital for both biological evolution and computational optimization processes.