Journal Article

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in <i>Condylostoma magnum</i>

Stephen M. Heaphy, Marco Mariotti, Vadim N. Gladyshev, John F. Atkins and Pavel V. Baranov

in Molecular Biology and Evolution

Volume 33, issue 11, pages 2885-2889
Published in print November 2016 | ISSN: 0737-4038
Published online August 2016 | e-ISSN: 1537-1719 | DOI: http://dx.doi.org/10.1093/molbev/msw166

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mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3′ end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state.

Keywords: the genetic code; ciliates; translation termination; stop codon reassignment; alternative genetic decoding

Journal Article.  3601 words.  Illustrated.

Subjects: Evolutionary Biology ; Molecular and Cell Biology

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