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 number of other coronaviruses utilize a different type of pseudoknot termed 'elaborated pseudoknot' or 'kissing stem loops'. Initially found for human coronavirus 229E (109) , it is also utilized by viruses such as transmissible gastroenteritis virus and porcine epidemic diarrhea virus (543) . The pairing involves apical loops, and counterpart pairing involving an internal loop on one or other of the stems is described in the next paragraph. In contrast, the pseudoknot of the coronavirus that mediates SARS disease is an H-type pseudoknot, like that of infectious bronchitis virus. However, that of SARS virus differs in having part of its counterpart of loop 3 folded into a stem loop (543) (544) (545) (546) . This is involved in intermolecular kissing loop: loop pairing that functions in viral genomic RNA dimerization that in turn affects frameshift efficiency with likely regulatory consequences (547) . A pseudoknot stem 3 is also known to be significant for Rous sarcoma virus gag-pol frameshifting (548, 549) . An additional sub-structure between the main stem loops known as an 'Interstem Element' was characterized in the Visna-Maedi retrovirus frameshift stimulatory pseudoknot where it unusually comprises a 7-nt loop between the two stems and is essential for frameshifting promotion (550) . This pseudoknot features a long loop 1 (550) . By extrapolation an interstem element of 3 nts also occurs in the pseudoknot of the 1a/1b frameshift stimulator of the arterivirus lactate dehydrogenase-elevating virus (550, 551) .