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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Ambush hypothesis revisited: Evidences for phylogenetic trends
Tiratha Raj Singh1, Kamal Raj Pardasani
1Department of Zoology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel. tiratharaj@gmail.com
Computational Biology and Chemistry
|May 29, 2009
Summary
Recoding events, like frame-shifting, reprogram mRNA translation. This study reveals ancient adaptive selection for "hidden stops" that prevent wasted energy on non-functional proteins, especially in viruses and bacteria.
Area of Science:
- Molecular Biology
- Genomics
- Evolutionary Biology
Background:
- Recoding events alter standard mRNA translation rules at specific sites.
- Frame-shifting is a recoding type where translation starts at non-standard nucleotide positions within a codon.
- Frame-shifted sequences contain numerous 'hidden stops' (off-frame stop codons).
Purpose of the Study:
- To investigate the adaptive significance of hidden stops in frame-shifted sequences.
- To explore the evolutionary selection of codons that form hidden stops.
- To analyze the prevalence and impact of this mechanism across different taxonomic groups.
Main Methods:
- Analysis of nuclear and mitochondrial genomic data.
- Phylogenomic analysis to identify selection patterns.
- Correlation analysis between codon usage frequencies and hidden stop contributions.
Main Results:
- A positive correlation exists across all taxonomic groups between codon usage and their contribution to hidden stops.
- Genomic data revealed phylogenomic selection for this 'ambush mechanism'.
- The strongest impact of hidden stop selection was observed in viruses and bacteria.
Conclusions:
- The findings support the hypothesis of an ancient adaptive event favoring codons that form hidden stops.
- This mechanism likely evolved to prevent energy and resource waste on non-functional proteins.
- The ambush mechanism appears to be an ancient evolutionary strategy, particularly significant in early life forms like viruses and bacteria.
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