Ribosomal Frameshifting and Transcriptional Slippage: from Genetic Steganography and Cryptography to Adventitious Use John F
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Published online 19 July 2016 Nucleic Acids Research, 2016, Vol. 44, No. 15 7007–7078 doi: 10.1093/nar/gkw530 SURVEY AND SUMMARY Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use John F. Atkins1,2,3,*, Gary Loughran1, Pramod R. Bhatt1, Andrew E. Firth4 and Pavel V. Baranov1 1School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland, 2School of Microbiology, University College Cork, Cork, Ireland, 3Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA and 4Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK Received March 21, 2016; Revised May 20, 2016; Accepted May 26, 2016 ABSTRACT INTRODUCTION Genetic decoding is not ‘frozen’ as was earlier AUG. Doubtless applicability of the word ‘steganography’ thought, but dynamic. One facet of this is frameshift- to certain forms of genetic recoding and frameshifting in ing that often results in synthesis of a C-terminal re- particular, was not envisaged when it was first used in 1499 gion encoded by a new frame. Ribosomal frameshift- to mean an intended secret message that does not attract ing is utilized for the synthesis of additional prod- attention in contrast to cryptography where just the con- tents of the hidden message is protected and not its ex- ucts, for regulatory purposes and for translational istence. Nevertheless, its use in connection with produc- ‘correction’ of problem or ‘savior’ indels. Utilization tively utilized frameshifting by Patrick Moore (1) highlights for synthesis of additional products occurs promi- the extra N-terminally coincident product(s) whose syn- nently in the decoding of mobile chromosomal el- thesis involves a switch from the frame set at initiation to ement and viral genomes. One class of regulatory one of the two alternative reading frames (registers) inher- frameshifting of stable chromosomal genes governs ent with standard non-overlapping triplet decoding (Fig- cellular polyamine levels from yeasts to humans. ure 1). The frameshift-derived product is generally quite In many cases of productively utilized frameshift- different in both length and sequence from the product ing, the proportion of ribosomes that frameshift at of standard decoding. It is not only ribosomal frameshift- a shift-prone site is enhanced by specific nascent ing that can yield a trans-frame encoded protein, but also peptide or mRNA context features. Such mRNA sig- where the RNA polymerase ‘slips’ to yield mRNA lacking or containing one or more extra bases (that are not 3 nt or nals, which can be 5 or 3 of the shift site or both, can multiples thereof). Such ‘transcriptional frameshifting’ also act by pairing with ribosomal RNA or as stem loops yields products that are trans-frame specified with respect to or pseudoknots even with one component being 4 sequence present in the encoding DNA (or RNA in the case kb 3 from the shift site. Transcriptional realignment of some viruses). at slippage-prone sequences also generates produc- To commemorate this year the 50th anniversary of the tively utilized products encoded trans-frame with re- full-deciphering of the genetic code and the 100th anniver- spect to the genomic sequence. This too can be en- sary of Crick’s birth, we provide an overview of knowledge hanced by nucleic acid structure. Together with dy- gained since then on the aspects of the dynamic nature of namic codon redefinition, frameshifting is one of the both mRNA generation and code readout gained by study- forms of recoding that enriches gene expression. ing frameshifting, especially ribosomal frameshifting. For space reasons, other features of the ‘extra layer’ in code readout, including dynamic codon redefinition and other processes that yield a trans-frame encoded product with re- spect to the DNA will generally be omitted (even though *To whom correspondence should be addressed. Tel: +1 353 21 4205420; Fax: +1 353 21 4205462; Email: [email protected] C The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 7008 Nucleic Acids Research, 2016, Vol. 44, No. 15 Figure 1. Genetic ‘Bletchley-ism’: As illustrated with three letter words, the framing of genetic informational readout can be modified to convey meaning from genetic ‘hieroglyphs’ (cryptography) or additional and hidden meaning (steganography). Embellishing the old adage ‘From tapes to shapes’ (proteins), in several cases this involves ‘shapes-in-the-tapes’ unlike counterparts in many human languages. The process is dynamic, and the competition yields products from both standard reading and frameshifted reading. The relative proportions of the products from each are case dependent. Examples of genetic cryptography involving translational bypassing are in the decoding of phage T4 gene 60 and the mitochondrial genome of the yeast Magnusiomyces capitatus (56,65,158) and another type is in decoding the mitochondrial genome of glass sponges (252). The latter is a WT translation component counterpart of the suppression of frameshift mutants by suppressor mutants of translational components. Examples of genetic steganography involving transcriptional realignment are in the gene expression of paramyxoviruses, potyviruses and the bacterial insertion sequence Roseiflexus IS630 (42,99,617); examples of genetic steganography involving ribosomal frameshifting are in the decoding of influenza A virus expression (125,270) and D. melanogaster APC (46). While standard expression of most bacterial release factor 2 genes, and also probably eukaryotic antizyme genes except for antizyme 3, yields a product that is non-functional on its own, the +1 frameshifting required for productive expression has been positively selected. The representation was inspired in part by a genetic framing garden ‘rebus’ (812), a slide by V.N. Gladyshev and a recent publication (1). Nucleic Acids Research, 2016, Vol. 44, No. 15 7009 certain RNA processing (2) involves a ribosome/nascent form and ribosomal frameshifting associated with it (11– chain complex, indel editing can have similar consequences 13) that may have survival value under stressful conditions to RNA polymerase slippage, and of course splicing is of and create the opportunity for a later mutational change major importance). However, tmRNA which has been re- to genetically fix the newly advantageous trait (14–16). In- cently reviewed (3,4) will be treated minimally. triguingly, [PSI+] induces synthesis of a substantial amount Many cases of utilized frameshifting are phylogenetically of a trans-frame encoded variant from the gene for eIF1, conserved, thereby facilitating their identification bioinfor- and specific other translation initiation, tRNA maturation matically though this is most feasible when the ribosomes and amino acid metabolism genes (13). In other cases, even that shift frame do not encounter a stop immediately in when high level, frameshifting can be effectively inconse- the new frame but continue translating in the new frame to quential. In some, the signals promoting the high level were synthesize an extensive C-terminal protein segment. While selected for a different purpose, and efficiency of degrada- increasing sequence information has of course helped, im- tion of ‘dangling tail’ C-terminal extensions is also relevant provements in bioinformatics software has been crucial, es- (17–19). pecially in its application to RNA viruses. Productive frameshifting is generally in competition with standard decoding. At the functional level there are three mRNA stabilization and destabilization broad classes. In many cases the proportion of ribosomes that shift frame, or of polymerases that slip with conse- Frameshifting selected due to productive utilization of its quent frameshifting with respect to their template, is con- derived protein product generally results in a proportion of stant (though in some cases this may reflect our ignorance of ribosomes terminating on sequence on which ribosomes in a relevant regulatory condition). This is often termed ‘set ra- another frame are continuing downstream translation. To tio’ frameshifting and the function is commonly generation an unknown extent, selection has presumably operated to of an extra N-terminally coincident product. In a second generate features for avoidance of mRNA instability associ- class, frameshift efficiency is responsive to the level of ini- ated with the terminator in either of the utilized frames that tiation or a trans-acting factor. In this class the frameshift- is closest to the start codon. Avoidance is likely most rele- ing acts as a sensor and effector for regulatory purposes, ei- vant when the great majority of ribosomes are in the frame ther via synthesis of a functional trans-frame encoded prod- that leads to termination at the first terminator in either uct, mRNA half-life or new frame ribosome movement af- frame. Given the complexity of mRNA degradation and fecting translation of a downstream ORF, e.g. by affecting difference between the major classes of organisms, there is mRNA structure and initiation site accessibility. A third probably a diversity of answers with cytoplasmic transcrip- functional class is ‘corrective’