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.

In common with the nucleotides at or downstream of the −1 PRF slippage site, the intercodon encodes amino acids in two reading frames (GGG in the 0 frame and AGG in the −1 frame) and is at the very beginning of the extended stem-loop structure forming part of a structured RNA element. Our examination of the sequence downstream of the intercodon corresponding to the extended stem-loop showed it is not as highly conserved as the intercodon that forms the start of the stem-loop (Fig. 1C) . The higher degree of conservation of the nucleotides of the intercodon compared to the other nucleotides of the downstream stem-loop led us to hypothesise that the intercodon might be directly involved in the translational frameshifting process.