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

Abstract

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.

Fig. 1

Classification of ciliate stop codons. Stop codon densities (axis y) in protein coding sequences are indicated for each species (bottom). Rectangles specify stop codons of the organisms used for defining a threshold (gray area) for discriminating reassigned codons (above gray area) from those that retained their function as signals for termination (below gray area). The phylogenetic tree constructed with 18S rRNA sequences above indicates the relatedness of each species. The histogram on the right shows distribution of stop codon densities.

Fig. 2

Identification of amino acid specifications of the reassigned codons. Each row corresponds to a single reassigned codon. The organism, the codon identity and the total number of occurrences at highly conserved positions of aligned sequences are indicated on the left. The normalized frequencies of amino acid substitutions are shown as heatmaps.

Fig. 3

Frequency of codons relative to expected positions (zero on axis x) of translation termination in Condylostoma. Top panel—frequency of each out of 64 codons (stop codons are highlighted). Bottom panel—total number of codons found at corresponding location. The total number differs due to variance in transcript and CDS lengths and also due to presence of ambiguous nucleotides (codons with ambiguous nucleotides were ignored).