We continue to study the mechanism by which frameshifting occurs, especially at the poorly understood Euplotes frameshift sites. We have, however, extended our work to use the programmed frameshift sites as probes of the basic error correction mechanism of the ribosome.
Very recently, we broadened our focus by beginning a set of experiments aimed at characterizing the phenomenon of missense errors in both the bacteria E. coli and in yeast. That work has shown that a major determinant of missense error rate is the availability of the correct (cognate) tRNA that competes with the tRNA responsible for the error. Limiting the availability of the cognate tRNA causes increased error. Availability is not the only determinant, though. We find significant error only by near-cognate tRNAs (those that make no more than one base pair mismatch with the mRNA codon). We see no striking preference for tRNAs that are mismatched at the first two codon positions. Mismatching at the third or wobble position, however, does appear to produce a much higher frequency of error.
We are also interested in the evolution of programmed frameshifting in the budding yeast. Three genes from the yeast Saccharomyces cerevisiae use +1 programmed frameshifting in their expression. EST3 and ABP140 use frameshift signals related to the frameshift signals of the Ty family of retrotransposons in yeast that our laboratory has studied for the last 25 years. The third, OAZ1, uses a mechanism termed a shifty stop that is related to the frameshift at the E. coli prfB gene. We studied the evolution of the EST3 and ABP140 genes and showed that their programmed frameshift mechanism evolved approximately 150 million years ago. The fact that the frameshift has been preserved for such a long time argues that it frameshifting per se is essential to the proper functioning of these genes. We are interested in determining what essential function frameshifting provides.