Most retroviruses and retrotransposons express their pol gene as a translational fusion to the upstream gag gene, often involving translational frameshifting. We describe here an unusual translational frameshift event occurring between the GAG3 and POL3 genes of the retrotransposon Ty3 of yeast. A +1 frameshift occurs within the sequence GCG AGU U (shown as codons of GAG3), encoding alanine-valine (GCG A GUU). Unlike other programed translational frameshifts described, this event does not require tRNA slippage between cognate or near-cognate codons in the mRNA. Two features distal to the GCG codon stimulate frameshifting. The low availability of the tRNA specific for the "hungry" serine codon, AGU, induces a translational pause required for frameshifting. A sequence of 12 nt distal to the AGU codon (termed the Ty3 "context") also stimulates the event.

Recently we described an unusual programmed +1 frameshift event in yeast retrotransposon Ty3.Frameshifting depends on the presence of peptidyl-tRNA " on the GCG codon in the ribosomal P site and on a translational pause stimulated by the slowly decoded AGU codon. Frameshifting occurs on the sequence GCG-AGU-U by out-of-frame binding of a valyl-tRNA to GUU without slippage of peptidyl-tRNAV&. This mechanism challenges the conventional understanding that frameshift efficiency must correlate with the ability of mRNA-bound tRNA to slip between cognate or near-cognate codons. Though frameshifting does not require slippery tRNAs, it does require special peptidyl-tRNAs. We show that overproducing a second isoacceptor whose anticodon had been changed to CGC eliminated frameshifting; peptidyl-tRNAVZ' must have a special capacity to induce +1 frameshifting in the adjacent ribosomal A site. In order to identify other special peptidyl-tRNAs, we tested the ability of each of the other 63 codons to replace GCG in the P site. We found no correlation between the ability to stimulate + 1 frameshifting and the ability of the cognate tRNA to slip on the mRNA-several codons predicted to slip efficiently do not stimulate frameshifting, while several predicted not to slip do stimulate frameshifting. By inducing a severe translational pause, we identified eight tRNAs capable of inducing measurable +1 frameshifting, only four of which are predicted to slip on the mRNA. We conclude that in Saccharomyces cerevisiae, special peptidyl-tRNAs can induce frameshifting dependent on some characteristic(s) other than the ability to slip on the mRNA.Protein synthesis produces a low frequency of errors: both missense errors and processivity errors (those leading to premature termination). However, spontaneous frameshift errors are extremely infrequent (34). This means that the translational machinery must much more efficiently avoid changes in frame than it does other errors. Some genes have evolved sequences which manipulate this machinery to allow very high levels of frameshifting, with efficiencies from a few to nearly 100% (2, 22, 28). All such sequences, termed programmed frameshift sites, consist of two elements: the actual site at which the frame shifts, termed the recoding site (22), and sequences which increase the probability that the ribosome will slip, termed stimulators (2).In all but one case, the recoding site is a sequence which allows slippage of one or more tRNAs between cognate or near-cognate codons and thus is termed a slippery site. Frameshifts occur in either the upstream, or leftward, direction (e.g., -1 frameshift) or in the downstream, or rightward direction (e.g., +1 frameshifting). In -1 simultaneous slippage frameshifting, common in retroviruses but found in other viruses and one chromosomal gene, the slippery site is a heptamer of the form X-XXY-YYZ. Frameshifting occurs by the simultaneous slippage of two tRNAs from XXY-YYZ to 46). Mutational changes which decrease the likelihood of the slip tend to decrease or elimi...

Programmed translational frameshifts efficiently alter a translational reading frame by shifting the reading frame during translation. A +1 frameshift has two simultaneous requirements: a translational pause which occurs when either an inefficiently recognized sense or termination codon occupies the A site, and the presence of a special peptidyl-tRNA occupying the P site during the pause. The special nature of the peptidyl-tRNA reflects its ability to slip +1 on the mRNA or to facilitate binding of an incoming aminoacyl-tRNA out of frame in the A site. This second mechanism suggested that in some cases the first +1 frame tRNA could have an active role in frameshifting. We found that overproducing this tRNA can drive frameshifting, surprisingly regardless of whether frameshifting occurs by peptidyl-tRNA slippage or out-of-frame binding of aminoacyl-tRNA. This finding suggests that in both cases, the shift in reading frame occurs coincident with formation of a cognate codon-anticodon interaction in the shifted frame.

includes a site recognized by the product of a gene, STE12, required for expression of haploid-specific genes, including Tyl elements (7, 12); its binding site is termed a sterile responsive element, SRE (7). Tyl and Ty2 elements include a second downstream region which represses transcription of the element (8, 15); they may be analogous to transcriptional silencers (4), since they repress transcription at a distance. The maximal level of Ty transcription presumably depends upon the interplay between positively and negatively acting transcription factors bound to the various sites.Many genes other than STE12 have been identified genetically as suppressors of Ty and 8 LTR insertions into the promoters of various genes; the genes identified are termed SPT (16,36,37). Few of these have been shown to interact directly with the element; an exception is the product of the SPT15 gene, the TATA-binding factor TFIID of S. cerevisiae (11). The products of several of the genes, SPT3, SPT7, SPT8, and SPT15, are required for normal Ty transcription (11,37,38). Many SPT gene products have a global role in regulation of transcription, as indicated by their pleiotropic phenotypic effects, including defects in sporulation and mating (36,38). Several SPT mutation genes also regulate SUC2 transcription (reference 23 and references therein); correspondingly, some SUC2 regulators (SNF and SSN genes) also alter the effect of Ty promoter insertions. The connection among these genes is underscored by genetic interactions among SPT and SNFISSN mutations. This connection could reflect alteration of chromatin structure and its effect on transcription (32). Alteration of chromatin structure is known to affect Tyl transcription. SPT11 and SPT12 encode histones H2A and H2B; mutations in these genes alter dosage of histones affecting Ty-regulated transcription (6). The SPT2ISINI, SPT4, SPT5, and SPT6ISSN6 genes may act to establish an appropriate chromatin context for regulation of transcription by gene-specific activators (32).

No abstract