Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

Atkins, John F.; Loughran, Gary; Bhatt, Pramod R.; Firth, Andrew E.; Baranov, Pavel V.

While the S. cerevisiae Ty3 shift site (GCG AGU U) also features a slow-to-decode A-site codon, AGU U is less effective than its Ty1 counterpart and the 5 -adjacent codon in Ty3 is GCG instead of CUU (214,414) ( Figure 8 ). As discussed in relation to Ty3 frameshifting (415) , S. cerevisiae is unusual in lacking a tRNA Ala (anticodon CGC) that provides a good match with codon GCG which is instead decoded by tRNA Ala (anticodon 3 CGI 5 ). While inosine pairs strongly with U and C, its apposition with A allows weaker decoding (416, 417) and its purine:purine apposition with G is surely relevant to the frameshifting. Discussion of potential relevance of I pairing through its Watson-Crick side with the Hoogsteen face of A with the A base in the syn conformation with respect to the ribose, and counterpart I:G pairing (418) has been revived (387,419) and may be pertinent. (The IS1222 frameshifting mentioned at the start of this section also involves wobble position I:A apposition.) Unlike Ty1, with Ty3 the peptidy-tRNA does not have realistic standard pairing to the +1 frame codon as C:C, G:G, I:A would be involved. One interpretation is that slippage is not involved but there is some level of occlusion of the 3 base, A, facilitating incoming aminoacyl-tRNA pairing with GUU rather than AGU (214, 414) . Alternatively, there may be peptidyl-tRNA dissociation but not re-pairing to mRNA following slippage (420) . [The dif- (241, 421) .] Regardless, it is clear that Ty3 frameshifting yields Ala Val (422) . Surprisingly S. cerevisiae antizyme frameshifting (shift site GCG UGA C (273)) also shows +1 frameshifting even though there is -2 re-pairing potential (423) . In Kluyveromyces waltii yeast, which unlike S. cerevisiae does have tRNA Ala (anticodon CGC), the shift site is CCG UGA C. However, it lacks a corresponding tRNA Pro (anticodon 3 GGC 5 ) (423). Despite S. cerevisiae Ty3 and antizyme shift sites both having GCG, when both are tested in the same reporter system, and extrapolated from measurements in the absence of Ty or antizyme context effects, the intrinsic shiftiness of GCG UGA C (antizyme) is 37% and GCG AGU U (Ty3) is 2%, showing the greater effectiveness of the stop codon (214, 414) . [For comparison the shiftiness of CUU AGG C (Ty1 and ABP140) is 43%.] Correspondingly, as considered below, in its natural yeast context antizyme has inhibitory modulators while Ty3 has a stimulatory modulator.