Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance

Abstract

A hallmark of translation in human immunodeficiency virus type 1 (HIV-1) is a –1 programmed ribosome frameshifting event that produces the Gag-Pol fusion polyprotein. The constant Gag to Gag-Pol ratio is essential for the virion structure and infectivity. Here we show that the frameshifting efficiency is modulated by Leu-tRNA Leu that reads the UUA codon at the mRNA slippery site. This tRNA Leu isoacceptor is particularly rare in human cell lines derived from T-lymphocytes, the cells that are targeted by HIV-1. When UUA decoding is delayed, the frameshifting follows an alternative route, which maintains the Gag to Gag-Pol ratio constant. A second potential slippery site downstream of the first one is normally inefficient but can also support –1-frameshifting when altered by a compensatory resistance mutation in response to current antiviral drug therapy. Together these different regimes allow the virus to maintain a constant –1-frameshifting efficiency to ensure successful virus propagation.

mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding

“…(i) slippage of the single P-site tRNA when the A site remains vacant, or (ii) frameshifting of both P-site and A-site tRNAs when two tRNAs are bound to the ribosome (Caliskan et al, 2017;Korniy et al, 2019). Our finding that the dnaX FSS slows the rate of ribosome translocation by ~10-fold is also in excellent agreement with a number of previous reports (Caliskan et al, 2017;Chen et al, 2014;Choi et al, 2020;Kim et al, 2014;Kim and Tinoco, 2017).…”

“…1) that in combination with the slippery sequence UUUUUUA, induces -1 PRF with 5-10% efficiency to produce the Gag-Pol polyprotein. mRNAs containing the slippery sequence and HIV FSS undergo frameshifting in bacterial (E. coli) ribosomes in vitro and in vivo at frequencies comparable to those observed for HIV frameshifting in eukaryotic translation systems (Brunelle et al, 1999;Korniy et al, 2019;Leger et al, 2004;Mazauric et al, 2009). The FSS from HIV can be studied in E. coli, analogous to -1 PRF on mRNA derived from another eukaryotic virus (avian infectious bronchitis virus, IBV) that could also be reconstituted in the E. coli translation system (Caliskan et al, 2014) suggesting a common mechanism of frameshifting and ribosomal stalling induced by FSS in bacteria and eukaryotes.…”

Mechanisms and biomedical implications of –1 programmed ribosome frameshifting on viral and bacterial mRNAs

“…Kinetic analysis shows that -1PRF in HIV-1 proceeds via the same two routes as previously described for IBV 1a/1b and E. coli dnaX mRNAs (Fig. 2) [69]. Intriguingly, we found that the two routes depend on the availability of Leu-tRNA Leu(UAA) to read the UUA codon of the SS1 (Fig.…”

“…When SS1 is functional and pSS2 harbors the C 5 U mutation, the overall -1 frameshifting efficiency remains unchanged but a significant amount of -2 frameshifting is observed. Most importantly, when SS1 is dysfunctional, the C 5 U mutation in pSS2 can restore about 70% of the wildtype -1PRF efficiency, which might be enough to sustain the viral lifecycle [69]. Interestingly, HIV-1 is not the only virus which develops an alternative slippery site in response to antiviral treatment.…”

High-throughput interrogation of programmed ribosomal frameshifting in human cells

“…Ribosome stalling due to limited tRNA availability has the potential to lead to slippage of the ribosome 82,83 and contributes to nonprogrammed frameshifting in huntingtin 84 . Availability of tRNAs decoding slippery site codons have been shown to influence HIV gag-pol frameshifting efficiency 85 , and HIV-1 itself has the ability to modulate the tRNA pool of the host cell 86 . Our observation that limited tRNA availability in the codons leading up to the slippery site progressively contributes to PRF efficiency is in line with these data and expands the notion of an influence of the tRNA pool on frameshifting beyond the slippery site codons and individual PRF events.…”