The Highly Conserved Codon following the Slippery Sequence Supports -1 Frameshift Efficiency at the HIV-1 Frameshift Site

Mathew, Suneeth F.; Crowe-McAuliffe, Caillan; Graves, Ryan; Cardno, Tony S.; McKinney, Cushla; Poole, Elizabeth S.; Tate, Warren P.

PRF utilises a specific cis-element within the mRNA sequence where the change in reading frame occurs. In HIV-1 this sequence is a heptanucleotide string termed the 'slippery sequence' U UUU UUA (spaces separate codons in the 0 frame). Frameshift sites often contain additional RNA structural elements 3´of the slippery sequence that further stimulate frameshifting; in most viruses the downstream structure is a pseudoknot, although stem-loops and protein binding sites can also be used [14] [15] [16] [17] . For most strains of HIV-1, however, this structure is atypical and has been shown by NMR studies to be a stem-loop of two parts with an internal purine bulge, although recently it has been proposed that a network of pseudoknots exists in equilibrium with the widely accepted stem-loop structure [18] [19] [20] [21] . While slippage can occur using a minimal 25-nucleotide sequence containing only a 'slippery' element [22] , the downstream structure further stimulates the event to give frameshift efficiencies in the order of 5-10% dependent on the assay system used [23] . In vivo, the RNA helicase DDX17 modulates −1 PRF in HIV-1 [24] . The nucleotides immediately upstream of the slippery sequence, as well as distal elements of the HIV-1 RNA that affect the ribosomal density along the HIV-1 mRNA by modulating the rate of translation initiation, can also affect the efficiency of −1 PRF [25] [26] [27] [28] . However, the frameshift efficiency measured in vitro with the element alone placed between different bicistronic reporter systems is surprisingly similar to the in vivo rate [29] .