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.

[This is just one of the types of regulatory events that can come from RNA polymerase: nascent RNA structure interactions, with RNA polymerase progression involving a 'rugged kinetic landscape' (614) .] This programmed unidirectional specific slippage occurs uniquely at the C4 position of the T5C5 motif. Inviability of more than one rU:dG and even one rC:dA mismatch prevents a two-base deletion and any insertions, respectively, making it quite distinct from the slippage on 9 Ts in T. thermophilus dnaX. While transient realignment occurs on a broad variety of heteropolymeric sequences, rapid reversal prevents deletions and insertions in the mRNA unless additional sequence elements that inhibit the reversal are present. S. cerevisiae RNA polymerase can also slip on a cassette with the same T5C5 sequence (99) . The proposed mechanical model involving the RNAP translocation state differs from that proposed for Paramyxovirinae 'programmed transcriptional frameshifting', where, following random movement, efficiency is mainly dependent on the stability of the new realigned hybrid. The Sendai virus slippage sequence is 3 (Uug)UUUUUUCCC 5 and 30% of the mRNA synthesized from the P-gene has an additional G residue that causes ribosomes, by standard translation, to enter the coding sequence for the host-defense inactivating V protein. This is the sole Sendai virus alternative product to P, an essential viral polymerase co-factor, for synthesis that initiates with the P-gene start site (615) . However, with parainfluenza virus type 3 there is an additional product due to the realignment within its P-gene yielding separate RNAs that permit standard translational access to both alternative ORFs. This realignment involves 1 to 6 Gs being added with approximately equal frequency. Most of the relevant features are in its (Uaa)U 6 C 3 slippage sequence and when Sendai's UugU 6 C 3 is replaced within the Sendai virus context by UaaU 6 C 3 , the slippage becomes parainfluenza virus type 3-like. The relevant context feature is the phasing of the binding of multiple nucleocapsid proteins (N) that sheath the genomic negative-strand (and positivestrand antigenome) of these viruses. Such binding prevents complementary progeny positive-strand mRNAs from annealing with the genomic RNA. Each adjacent N protein binds precisely 6 nts of genomic RNA (615) , and adjusting the phasing of hexamer binding to two particular phases, causes the pattern of G inserts in progeny RNA to revert to the Sendai-virus pattern. Even when N is displaced from the genomic RNA by polymerase, it apparently remains closely associated with the polymerase and its hexamer phasing is thought to influence polymerase pausing at the slippage site with realignment consequences (616, 163) . The genome length is such that there is full phasing coverage and for the different species their respective phasing number is coordinated with that required for realignment by the relevant polymerase ( Figure 19 ). N binding is also relevant to avoidance of G insertion genomic fixation, with deleterious consequences for P protein synthesis, as only genomes with length an exact multiple of 6 nts are efficiently replicated (616) . A few paramyxoviruses, including Nipah virus, a member of the less well known Henipavirus genus, exhibit hyper transcriptional slippage, with some unresolved mechanistic issues (617, 618) .