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.

The word 'spacer' is most commonly used to describe the nt distance between the shift site and a 3 structural stimulator, but is more generally used to signify the distance between a recoding signal and the site at which a non-standard event occurs, e.g. between a 5 stimulatory Shine Dalgarno sequence and the shift site. However, especially for nucleotides between the shift site and a recognized 3 stimulator, 'spacer' nt identity has to be treated carefully since it may be significant (405) . This has been explored systematically in E. coli (192) with attention being paid to stacking potential of spacer nucleotides. That study used an A AAA AAG shift site. Independent of utilization for frameshifting, AAA is used ∼3 times more commonly than AAG except when the 3 adjacent base is C when AAG is preferred (507) . However, in the frameshifting study though 3 adjacent CC was the most shift-prone of the dincleotides, 3 C was in general more shift-prone than U (192) . Spacer nucleotide effects has also been studied with a variety of cassettes to a lesser extent in eukaryotes (104, 508) where in some cases an initially unrecognized 'lower' part of an identified structure, was thought to be 'spacer' nts, and, as just described, potential to interact directly with ribosomal components is a comparable issue.