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Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA
Nan Cheng1, Yuanhui Mao, Youyi Shi
1StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China.
Plos One
|September 14, 2012
Summary
Intra-molecular coevolution in 5S ribosomal RNA (rRNA) reveals significant positive selection driven by structural and functional integrity. Compensatory evolution mechanisms maintain molecular structure and function.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Biochemistry
Background:
- Intra-molecular coevolution provides insights into molecular structure, function, and interactions.
- Understanding selective constraints on molecular evolution is crucial for predicting molecular behavior.
- 5S ribosomal RNA (rRNA) serves as a model system for studying RNA evolution.
Purpose of the Study:
- To investigate the role of selective constraints in shaping 5S rRNA evolution.
- To identify mechanisms of compensatory evolution in 5S rRNA.
- To understand the relationship between sequence coevolution and molecular integrity.
Main Methods:
- Phylogenetic analysis of 5S rRNA sequences.
- Identification of paired differences and evolutionary rates.
- Calculation of TIR scores to assess selection pressures.
Main Results:
- Observed nonrandom paired differences and high rates of compensatory evolution in 5S rRNA.
- Identified significant positive selection driving 5S rRNA evolution, indicated by high TIR scores.
- Discovered three compensatory evolution mechanisms: Watson-Crick interactions, multi-site stem interactions, and stem-loop interplay.
- Coevolutionary interactions are context-dependent, often occurring in structurally important regions near loops or bulges.
Conclusions:
- Sequence coevolution in 5S rRNA is a direct consequence of maintaining optimal structural and functional integrity.
- Selective constraints play a significant role in the evolutionary trajectory of RNA molecules.
- Compensatory evolution mechanisms are essential for preserving molecular function under evolutionary pressure.
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