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.

A bioinformatic analysis of higher eukaryotic LTR retrotransposons in 2003 showed that 28 of 51 animal retroelements surveyed had their pol in the −1 frame relative to gag and many had appropriately positioned classical heptanucleotide tandem shift sites. Most were in D. melanogaster and none were in C. elegans. Only 2 of the 51 had pol in the +1 frame whereas in fungi the proportion using +1 compared to −1 was less skewed. At that time just two different types of plant elements were found to have gag and pol in separate frames and in both pol was in the +1 frame. One has a gag pol overlap of 310 nts. The other type is a set of sirevirus retrotransposons that comprise two sub-sets, one of which has a simple gag pol overlap. However, the second sub-set has a conserved UAG in the pol frame 10 nts 3 of the gag terminator. Both sub-sets from both monocots, and dicots have a conserved sequence motif of 27 nts that can form an 11-bp stem containing covariant nucleotides and capped by a 4-nt loop (217) . Puzzles awaiting resolution abound.