Consequences of Stop Codon Reassignment on Protein Evolution in Ciliates with Alternative Genetic Codes

Tetrahymena thermophila and Paramecium tetraurelia are ciliates that reassign TAA and TAG from stop codons to glutamine codons. Because of the lack of full genome sequences, few studies have concentrated on analyzing the effects of codon reassignment in protein evolution. We used the recently sequen...

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Bibliographic Details
Published in:Molecular biology and evolution 2008-01, Vol.25 (1), p.179-186
Main Authors: Ring, Karen Lee, Cavalcanti, Andre R. O.
Format: Article
Language:English
Subjects:
Amino Acid Substitution
Amino acids
Animals
Codon - genetics
Evolution, Molecular
Evolutionary biology
Genome, Protozoan
Genomics
Molecular biology
Paramecium tetraurelia
Paramecium tetraurelia - genetics
Proteins
Protozoan Proteins - genetics
Species Specificity
Tetrahymena thermophila
Tetrahymena thermophila - genetics
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Summary:Tetrahymena thermophila and Paramecium tetraurelia are ciliates that reassign TAA and TAG from stop codons to glutamine codons. Because of the lack of full genome sequences, few studies have concentrated on analyzing the effects of codon reassignment in protein evolution. We used the recently sequenced genome of these species to analyze the patterns of amino acid substitution in ciliates that reassign the code. We show that, as expected, the codon reassignment has a large impact on amino acid substitutions in closely related proteins; however, contrary to expectations, these effects also hold for very diverged proteins. Previous studies have used amino acid substitution data to calculate the minimization of the genetic code; our results show that because of the lasting influence of the code in the patterns of substitution, such studies are tautological. These different substitution patterns might affect alignment of ciliate proteins, as alignment programs use scoring matrices based on substitution patterns of organisms that use the standard code. We also show that glutamine is used more frequently in ciliates than in other species, as often as expected based on the presence of the 2 new reassigned codons, indicating that the frequencies of amino acids in proteomes is mostly determined by neutral processes based on their number of codons.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/msm237