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.

ing. Multiple features of 3 intra-mRNA structural stimulators may influence frameshifting including thermodynamic stability, stem and loop lengths, torsional resistance, susceptibility or not to a protonated dependent switch and specific three-dimensional structures. The involvement of pseudoknots as frameshift stimulators was first shown for the coronavirus, infectious bronchitis virus (526) ( Figure 13C ) and predicted to be widespread (527,528) ∼4 years after the discovery of retroviral frameshifting. The great majority are H (hairpin)type pseudoknots meaning that a sequence of nucleotides within a hairpin loop base-pairs with a complementary region external to the hairpin. All H-type pseudoknots contain two helical stems, S1 and S2, and two non-equivalent loops, L1 and L2. Some also contain a third loop, L3. The IBV frameshift stimulatory pseudoknot features a long stem 1 which cannot be functionally reduced to less than 11 base pairs, significantly equivalent to one turn of an RNA A-form helix (106) , and other pseudoknots such as those in the alphavirus, western equine encephalitis virus also have long stems (140) . In contrast, the MMTV gagpro frameshift stimulatory pseudoknot (529), features an unpaired intercalated 'wedge' adenosine between two short stems of similar length ( Figure 13D ). This frameshift stimulatory pseudoknot was the first to be characterized by NMR (530) . Thermodynamic and structural insights into the role divalent metal ions play in stabilizing the structure followed (531,532). The intercalated, or 'wedge' A gives a bent, 'kinked', structure that is important for function (533, 534) , though it contributes only modestly to stability (532) . A wedge A base is also present in several other frameshift stimulatory pseudoknots (85, 86, 227) including the related simian retrovirus-1 gag-pro pseudoknot (535, 536) where, despite the wedge A, NMR analysis highlighted the importance of stem coaxial stacking and loop L2-stem S1 interactions (537) . Other studies focused on the importance of the triple helical feature and several interactions (538, 539) .