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.

Antizyme mRNAs with the CCC UGA shift site have naturally emerged in evolution but are in a tiny minority as only two were known at the time of an extensive survey (270, 293) . For the substantial majority of antizyme genes the +1 shift site is UCC UGA. When CCC UGA was tested in place of UCC UGA in a specific cassette in mammalian cells, significantly reduced frameshifting was monitored (465) . Of greater interest is nascent peptide relevance. As just discussed, the S. cerevisiae antizyme shift site GCG UGA C, is anomalously shift-prone. When accompanied by its flanking sequence the frameshifting level of 65% has been measured (268) . In contrast to organisms other than budding yeast, dynamic regulation is achieved by controlled reduction of the frameshifting level instead of controlled enhancement. As the discoveries on S. cerevisiae antizyme regulation by Dohmen and colleagues (268) are not only intriguing in their own right, their implications for the mechanism in other organisms make it desirable to consider first (Figure 10 ). At low polyamine levels inactivation of the frameshift inhibitory signals leads to a 20-fold increase in antizyme synthesis. A crucial inhibitory component is a nascent peptide encoded near the end of the coding sequence and only synthesized by a ribosome that frameshifted 669 nts (223 codons) upstream. At low polyamine levels, this nascent peptide interacts with the ribosome peptide exit tunnel to stall the ribosome. This blocks progression of following ribosomes and so of antizyme synthesis. However, at high levels polyamines bind Figure 10 . Scheme for S. cerevisiae antizyme mRNA +1 frameshifting. The top box represents low cellular polyamine concentrations, where ribosomes pause at the frameshifting site (RFS) with the ORF1 stop codon in the ribosomal A-site. Some terminate, while others continue translation in the +1 frame. An inhibitory element near the N-terminus of the nascent peptide, encoded near the start of ORF1, keeps frameshifting rates low. When a ribosome approaches the 3 end of ORF2, a newly synthesized part of the nascent peptide, causes this ribosome (pink) to stall. Following translating ribosomes (green) encounter the stalled ribosome and their movement is also blocked (line 2 with multiple pink ribosomes). When polyamine levels are high (lower panel) the nascent peptide encoded near the 3 end of ORF2, binds polyamines and is then unable to cause stalling. This allows the ribosome containing it to proceed to termination and release of functional antizyme. Reprinted by permission from Macmillan Publishers Ltd: Kurian,L., Palanimurugan,R., Godderz,D. and Dohmen,R.J. (2011) Polyamine sensing by nascent ornithine decarboxylase antizyme stimulates decoding of its mRNA. Nature, 477, 490-494. to the nascent peptide precluding it from causing a stall. For the leading ribosome to stall at low polyamine levels, there has to be adequate distance from the following ribosome and the frameshifting provides a partial 'choke' to decrease ribosome density and increase the spacing. [An additional more mysterious larger structural element specified upstream of this inhibitory signal but downstream of the frameshift site is also relevant.] A second inhibitory element is also a nascent peptide sequence, but it is encoded so far upstream of the frameshift site that it is expected to be well outside the ribosome at the time of its modulatory action. Changing the Ile encoded by codon 5 to Phe had a major effect