Influence of Viral Nucleocapsid Protein and Genomic RNA Structural Intricacies on the Mechanism of HIV Recombination

Internal strand transfers involve template switching during retroviral replication, within internal regions of the viral genome. Such transfers are a major source of genetic variability in retroviruses like HIV-1. An in vitro strand transfer assay that mimicked recombinational events occurring during reverse transcription in HIV-1 was used to assess the role of nucleocapsid protein (NC) and structural intricacies of genomic RNA in strand transfer. Transfers in highly structured templates from the U3 3' LTR, gag-pol frameshift region, and Rev response element (RRE) were strongly enhanced by NC. In contrast, weakly structured templates from the env and pol-vif regions transferred well without NC and showed lower enhancement. Assays conducted using NC zinc finger mutants supported a differential role for the two fingers in strand transfer with finger one (N-terminal) being more important on highly structured RNAs. The lack of strong polymerase pause sites in the weakly structured templates from the env and pol-vif regions demonstrated that non-pause driven mechanisms could also promote transfer. Mapping assays were conducted on high and low structured templates from the gag-pol and the env regions respectively (called GagPol and Env templates), to locate the point(s) of transfer in each case. The majority of transfers were located near a major pause site in the gag-pol region; in contrast, in the env region, most transfers were located towards the end of the homologous region between donor and acceptor templates. Various truncated/mutant GagPol acceptor templates were analyzed with wild type GagPol donor templates in strand transfer assays. Results indicated that destabilized acceptor templates enhance the level of transfer and cause a highly efficient 'chasing' of the pause site into transfer products. The outcome of these experiments also suggested that strand transfer in the GagPol templates is via a pause induced 'donor dissociation' method. In the Env template the mechanism of transfer was proposed to occur by a pause independent, 'acceptor invasion' method. This knowledge about the interplay of RNA structure and NC protein on recombination could help in designing antiviral vaccines and drug inhibitors