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 role of the Shine Dalgarno sequence in this case is relatively unimportant, internal Shine Dalgarno-like sequences are of major importance for bacterial single nucleotide frameshifting both −1 and +1. The number of nucleotides between frameshift stimulatory Shine Dalgarno sequences and the shift site at which it exerts its effect, depends on the directionality of the shift. For +1 frameshifting, it is 3 nts (54,490) and for −1 frameshifting it is 9-14 nts (491). It was known since 1975 (492) , that 30S ribosomal subunit recognition of Shine Dalgano sequences to position initiation was due to pairing of a sequnce near the 3 end of 16S rRNA. However, it was not suspected that this 'anti-Shine Dalgarno' sequence in translating 70S ribosomes scanned mRNA being decoding for potential complementarity. The finding of Shine Dalgarno-like stimulators for frameshifting showed that such scanning must occur (54, 493) . [It has also been recently shown for threadingmediated 70S-scanning initiation (494) , and is also likely important for translational coupling where the Shine Dalgarno sequence for initiation of a 3 adjacent gene is before the terminator of the 5 gene.] The −1 frameshifting assays led to the deduction that, after formation, the hybrid stays intact as the ribosome translates 5-7 nts and only then does it rupture (491) . Consistent with this, and the need for the anti-Shine Dalgano to be available to pair with its frameshift stimulatory complement and not be sequestered by pairing to a 5 counterpart, the sequence directly 5 of the stimulatory Shine Dalgarno lacks potential competitor Shine Dalgarno sequences (394) (Figure 12 ). Direct supportive evidence for hybrid maintenance for several translation cycles comes from the extended number of nucleotides protected from ribonuclease digestion, at internal Shine Dalgarno containing sites revealed by a ribosome profiling/footprinting study (495) .