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.

Frameshifting at the last codon of the leader peptide encoding sequence, pheL, of an E. coli K12 mRNA central for phenylalanine biosynthesis occurs at 15%. However, shifting at the site involved, CCC UGA, only occurs at 1.9% in Salmonella enterica -possible reasons for the difference are discussed in the original publication (19) . In E. coli K12, not only is peptidyl-tRNA Pro relevant to the level of frameshifting, the identity of the penultimate amino acid, phenylalaine, is significant and that of the amino acid encoded 10 codons 5 is also relevant. So specific amino acid effects occur not just at the time of polymerization but well within the ribosome peptide exit tunnel. The frameshifting in this case appears an incidental accompaniment of features important for transcription attenuation. Still it is interesting that when tested in E. coli K12, the nascent peptide signal utilized to promote the efficient bypassing of 50 nucleotides in decoding phage T4 gene 60 (considered below) stimulated 60% +1 frameshifting at the CCC UGA (19) . Though CCC UGA is not known to be utilized for frameshifting in E. coli, it is not under-represented in K-12 with 19 genes terminating with it and in half of them the frameshifting occurs at more than 1% (464) .