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.

Two-thirds of the way through the E. coli dnaX coding sequence, 50% of the ribosomes shift to the −1 frame and terminate one codon later to synthesize ␥ (320-322). In many fewer bacteria, the product derived from ribosomal frameshifting seems to be reversed with being derived from frameshifting and the termination codon for ␥ being in the zero frame directly after the frameshift site (198) . One of these candidates that has potential stimulatory signals similar to E. coli dnaX, is Chlorobium phaeobacteroids (S. Heaphy, J.F.A. and P.V.B., unpublished). Though the expression of Thermus thermophilus dnaX is also not like its E. coli counterpart, its longer product, , is encoded in a single ORF as in E. coli. Transcriptional slippage results in a population of mRNAs with extra bases. As there are nearby stop codons in both non-zero frames (with respect to the template DNA), standard translation of those with non-multiples of three extra bases, yields ␥ , which is again synthesized in a 1:1 ratio to (323). In E. coli, the shift site involved is highly shift-prone (94,320-322) due to the pairing of the sole tRNA Lys with the second shift-site codon involved being relatively weak (324). However, in Thermus thermophilus there are two lysine tRNAs one for each of the two lysine codons, AAA and AAG. As one of these is expected to tightly pair, and so poorly dissociate from AAG, this may be relevant to T. thermophilus utilization of RNA polymerase slippage rather than the ribosomal frameshifting used to generate its E. coli counterpart.