[Contexts of the suppressive terminal codons of translation in genes RNA-containing plant viruses]

A computer search of the suppressive terminal codons of translation (STCT) of plant virus genes in genetic banks and a comparative analysis of their suppression contexts were performed. Using "readthrough" and "transl_except" as key words STCT were found in replicase and coat protein genes in 118 strains of ssRNA plant viruses, belonging to 68 species from 13 genera. It was established that in genomes of plant viruses the most frequent suppressive termination codon is UAG (167 from 211, 79.1%), less frequent--UGA (37 from 211, 17.5%) and rare--UAA (7 from 211, 3.3%). The most of weak suppressive terminal codons contain in +4 position caauua, cgguuu, gggugc, ggaggc or guagac, the hexanucleotide sites that are believed to be important (consensus) elements of leaky stop codons in positive-sense ssRNA viruses of plants, animals and microorganisms. At the same time one can observe great variability of consensus nucleotide sites in many viral genes as well as additional positions of hexanucleotide sites in different reading frames and at different distances from terminal codons. Availability of clasters of identical nucleotide sites, in different virus genera, located as far as some hundred bases from terminal codons is a characteristic feature of suppressive terminal codons. Results obtained support a hypothesis that the translation termination efficiency as well as stop codon readthrough may be determinated at genome or gene level rather than by a short nucleotide context surrounding stop codons.