Consequences of stop codon reassignment on protein evolution in ciliates with alternative genetic codes
Karen Lee Ring1, Andre R O Cavalcanti
1Biology Department, Pomona College, Claremont, California, USA.
Molecular Biology and Evolution
|November 3, 2007
Summary
Ciliate species like Tetrahymena thermophila and Paramecium tetraurelia reassign genetic code stop codons to glutamine. This codon reassignment significantly impacts protein evolution, even in distantly related proteins, affecting evolutionary studies and protein alignments.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Genetics
Background:
- Tetrahymena thermophila and Paramecium tetraurelia are ciliates known to reassign TAA and TAG codons from stop signals to glutamine.
- Limited genomic data previously hindered comprehensive analysis of codon reassignment's impact on protein evolution.
Purpose of the Study:
- To investigate the effects of genetic code reassignment on amino acid substitution patterns in ciliates.
- To evaluate the influence of codon reassignment on protein evolution across varying divergence levels.
- To assess the implications of altered substitution patterns for evolutionary analyses and protein alignment.
Main Methods:
- Utilized recently sequenced genomes of Tetrahymena thermophila and Paramecium tetraurelia.
- Analyzed patterns of amino acid substitution in proteins from these ciliate species.
- Compared substitution patterns with those expected from the standard genetic code.
Main Results:
- Codon reassignment significantly impacts amino acid substitutions in both closely and distantly related proteins.
- The influence of codon reassignment persists even in highly diverged protein sequences.
- Glutamine usage is elevated in ciliates, consistent with the two newly assigned codons, suggesting neutral processes shape proteome amino acid frequencies.
Conclusions:
- Codon reassignment has a profound and lasting effect on protein evolution in ciliates.
- Previous methods for genetic code minimization using substitution data may be tautological due to persistent code influence.
- Altered substitution patterns in ciliates necessitate adjustments in protein alignment algorithms that rely on standard genetic code substitution matrices.
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