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

Mol Biol Evol. 2016 Nov;33(11):2885-2889. doi: 10.1093/molbev/msw166. Epub 2016 Aug 8.


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

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Alveolata / genetics
  • Amino Acid Sequence
  • Ciliophora / genetics*
  • Codon
  • Codon, Terminator*
  • Genetic Code
  • Genetic Variation / genetics
  • Open Reading Frames
  • Peptide Termination Factors / genetics
  • Protein Biosynthesis
  • Sequence Alignment / methods


  • Codon
  • Codon, Terminator
  • Peptide Termination Factors