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 genomic RNA of phage MS2, and that of its close relatives R17 and f2, was used as a model mRNA for many early ground-breaking protein synthesis studies and it was also the first genome to be sequenced. It is a levivirus. Though members of this genus are not as small as the mitochondrial-infecting mitoviruses and other members of the family Narnaviridae, their genomes are among the smallest for RNA viruses. The replicase of both the single-stranded phages MS2 and Q␤ is composed of three host translational components and one viral encoded component often termed synthetase. Synthetase is encoded by the gene closest to the 3 end of the positive-sense genomes that acts as mRNA. The termination codon of the gene for the 66 kDa Q␤ synthetase is substantially closer than its MS2 counterpart to the 3 end from which replicase commences synthesis of the negative strand. Though there is minimal space between MS2 genes, the termination codon for its 62 kDa MS2 synthetase product is 174 nt from the 3 end of its genome. Functional MS2 replicase likely assembles from components of the translation apparatus terminating synthesis of the synthetase and acts in cis on the nearby 3 end of the RNA -unlike its Q␤ counterpart it cannot be isolated in a functional state free from its RNA. Cell free protein synthesis studies revealed that −1 frameshifting yields a small proportion of MS2 synthetase of similar size as its Q␤ counterpart due to termination 63-61 nts from the 3 end of MS2 RNA (73, 75) . Product of this size has not been detected in vivo whether for lability or other reasons. It has not been determined whether the frameshifting has functional significance, but because of the short generation time and large progeny yield, the intense selection could have favored even very subtle effects.