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MBE Advance Access published online on November 1, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm237
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

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

Karen Lee Ring and Andre R O Cavalcanti*

Biology Department, Pomona College, Claremont, CA. 91711

* Corresponding author: 175 w 6th street, Biology Department, Pomona College, Claremont, CA. 91711, e-mail: aroc{at}pomona.edu

Received for publication July 22, 2007. Revision received October 22, 2007. Accepted for publication October 27, 2007.

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 two new reassigned codons, indicating that the frequencies of amino acids in proteomes is mostly determined by neutral processes based on their number of codons.

Key Words: Scoring matrix • substitution matrix • genetic code • Tetrahymena • Paramecium


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