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.

When the hexanucleotide motif is extended to become a heptanucleotide so that the tRNA decoding the 5 codon of the pair of adjacent codons also has the potential of repairing to mRNA in the −1 frame, then the frameshifting propensity substantially increases. This was discovered in retroviral frameshifting studies (102) . The motif has the form X XXY YYZ. While XXX often represents any three identical nucleotides, there are intermediates with the hexanucleotide situation just described; e.g. X XX is G GU in phage T7 gene 10 decoded by bacterial ribosomes (397), cardioviruses, e.g. encephalomyocarditis virus (58) and some luteoviruses; G GA in many insect specific flaviviruses (119, 123, 124) , some umbraviruses and dianthoviruses and in mesoniviruses (398); G UU(A) in equine arteritis virus (104, 134) ; C CA(A) in IS3 (399) and U CC in some members of the Japanese encephalitis serogroup of flaviviruses (70, 124) . Initial studies in the contexts of retroviral frameshifting and coronaviral frameshifting showed that among the most shifty −1 heptanucleotide sequences with mammalian cytoplasmic ribosomes are A AAA AAC, G GGA AAC, U UUA AAC and G GGU UUU (62, 104) . Following on from the shiftiness described in the last paragraph for A AAG in E. coli, further work with synthetic constructs, also in E. coli showed that A AAA AAG is much more shiftprone than A AAA AAC, A AAA AAA, U UUU UUA or U UUU UUU (94) . Shortly afterward A AAA AAG was found to be the naturally utilized shift site for E. coli dnaX frameshifting (320-322). Approximately half of known bacteria including E. coli, have just one lysine tRNA for decoding both AAA and AAG. Its wobble position, base 34, S, which pairs with the third codon base, is U hypermodified with 5-methylaminomethyl-2-thiouridine. While the conserved base 3 adjacent to the anticodon, N6threonylcarbamoyladenosine (t 6 A), is critical for recognition of codons with first position A, it is the modification of U34 which is important for discrimination against asparagine codons, AAC and AAU, and also AUA, (400) and refs therein. NMR studies showed that these two modifications remodel an otherwise dynamic loop (401) . X-ray crystallographic studies with 70S ribosomes and long mRNA revealed a novel type of base-pairing interaction with third codon base G that broadens known wobble position geometries. In it the modified U is moved toward the minor groove in contrast to standard Crick-proposed wobble geometry in which the pyrimidine is displaced toward the major groove of the codon:anticodon minihelix (400) . This work highlights the role of the larger subunit, in E. coli ribosomes helix 69, for positioning and stabilization of the anticodon loop (helix 69 forms intersubunit bridge B2a relevant to regulation of groove monitor A1492 (402)). Further, the work is regarded as important evidence for their proposi-Nucleic Acids Research, 2016, Vol. 44, No. 15 7033 tion that steric complementarity is predominant over the number of hydrogen bonds for third base discrimination (400) . As the degree of stability of third codon position pairing is highly relevant to the codon:anticodon dissociation central to at least most frameshifting, several earlier discussions about frameshift sites and in particular the less restrictive third codon position, were likely overly focused on hydrogen bonding.