A high percentage of Euplotes genes require a +1 translational frameshift for expression

Abstract

A previous survey of Euplotes genes available in GenBank indicated that >5% required a +1 translational frameshift for expression, much higher than observed in other organisms. Because this sample of sequences was non‐random and biased towards highly expressed genes, we have randomly selected and sequenced 25 Euplotes crassus macronuclear DNA molecules to more accurately assess the frequency of frameshifting. Three new +1 frameshift genes were identified, and all have sequence features similar to the previously postulated frameshift sites. The results indicate that the frequency of Euplotes+1 frameshift genes is indeed high, and likely >10%. We have also examined the evolution of one of two frameshift sites present in the telomerase reverse transcriptase (TERT) genes of E. crassus. TERT gene segments were isolated from five additional Euplotes species. FS2 was found only in E. crassus and the closely related E. vannus, and phylogenetic analyses indicate that the site arose late in the evolution of the Euplotes group. Moreover, a novel frameshift site (FS3) was identified solely in the TERT gene of E. minuta. These results indicate that frameshift sites have arisen within genes during the recent history of Euplotes, and that it may be an ongoing process. Overall, the data suggest to us that the appearance of a frameshift site in a Euplotes gene is selectively neutral, or near‐neutral. This would require an efficient mechanism of frameshifting in Euplotes. A model will be presented linking frequent frameshifting to a second unusual genetic feature of Euplotes, stop codon reassignment.