Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity

• Published in: Journal of virology 2016-08, Vol.90 (15), p.6906-6917
• Main Authors: Garcia-Miranda, Pablo, Becker, Jordan T, Benner, Bayleigh E, Blume, Alexander, Sherer, Nathan M, Butcher, Samuel E
• Format: Article
• Language: English
• Subjects: Base Pairing; Base Sequence; Frameshift Mutation - genetics; Frameshifting, Ribosomal - genetics; Fusion Proteins, gag-pol - metabolism; Gene Expression Regulation, Viral; HEK293 Cells; HIV Infections - genetics; HIV Infections - virology; HIV-1 - chemistry; HIV-1 - genetics; HIV-1 - metabolism; Human immunodeficiency virus; Human immunodeficiency virus 1; Humans; Lentivirus; Nucleic Acid Conformation; Retrovirus; RNA Stability; RNA, Viral - chemistry; RNA, Viral - genetics; RNA, Viral - metabolism; Structure and Assembly; Virion - physiology; Virus Assembly; Virus Replication
• ISSN: 0022-538X; 1098-5514
• DOI: 10.1128/JVI.00149-16

Human immunodeficiency virus (HIV) replication is strongly dependent upon a programmed ribosomal frameshift. Here we investigate the relationships between the thermodynamic stability of the HIV type 1 (HIV-1) RNA frameshift site stem-loop, frameshift efficiency, and infectivity, using pseudotyped HIV-1 and HEK293T cells. The data reveal a strong correlation between frameshift efficiency and local, but not overall, RNA thermodynamic stability. Mutations that modestly increase the local stability of the frameshift site RNA stem-loop structure increase frameshift efficiency 2-fold to 3-fold in cells. Thus, frameshift efficiency is determined by the strength of the thermodynamic barrier encountered by the ribosome. These data agree with previous in vitro measurements, suggesting that there are no virus- or host-specific factors that modulate frameshifting. The data also indicate that there are no sequence-specific requirements for the frameshift site stem-loop. A linear correlation between Gag-polymerase (Gag-Pol) levels in cells and levels in virions supports the idea of a stochastic virion assembly mechanism. We further demonstrate that the surrounding genomic RNA secondary structure influences frameshift efficiency and that a mutation that commonly arises in response to protease inhibitor therapy creates a functional but inefficient secondary slippery site. Finally, HIV-1 mutants with enhanced frameshift efficiencies are significantly less infectious, suggesting that compounds that increase frameshift efficiency by as little as 2-fold may be effective at suppressing HIV-1 replication. HIV, like many retroviruses, utilizes a -1 programmed ribosomal frameshift to generate viral enzymes in the form of a Gag-Pol polyprotein precursor. Thus, frameshifting is essential for viral replication. Here, we utilized a panel of mutant HIV strains to demonstrate that in cells, frameshifting efficiency is correlated with the stability of the local thermodynamic barrier to ribosomal translocation. Increasing the stability of the frameshift site RNA increases the frameshift efficiency 2-fold to 3-fold. Mutant viruses with increased frameshift efficiencies have significantly reduced infectivity. These data suggest that this effect might be exploited in the development of novel antiviral strategies.