Journal Article

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

Karen Lee Ring and Andre R. O. Cavalcanti

in Molecular Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 25, issue 1, pages 179-186
Published in print January 2008 | ISSN: 0737-4038
Published online November 2007 | e-ISSN: 1537-1719 | DOI: http://dx.doi.org/10.1093/molbev/msm237
Consequences of Stop Codon Reassignment on Protein Evolution in Ciliates with Alternative Genetic Codes

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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.

Keywords: scoring matrix; substitution matrix; genetic code; Tetrahymena; Paramecium

Journal Article.  5503 words.  Illustrated.

Subjects: Evolutionary Biology ; Molecular and Cell Biology

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