The roles of five conserved lentiviral RNA structures in HIV-1 replication

The HIV-1 RNA genome contains complex structures with many structural elements playing regulatory roles during viral replication. A recent study has identified multiple RNA structures with unknown functions that are conserved among HIV-1 and two simian immunodeficiency viruses. To explore the roles of these conserved RNA structures, we introduced synonymous mutations into the HIV-1 genome to disrupt each structure. These mutants exhibited similar particle production, viral infectivity, and replication kinetics relative to the parent NL4-3 virus. However, when replicating in direct competition with the wild-type NL4-3 virus, mutations of RNA structures at inter-protein domain junctions can cause fitness defects. These findings reveal the ability of HIV-1 to tolerate changes in its sequences, even in apparently highly conserved structures, which permits high genetic diversity in HIV-1 population. Our results also suggest that some conserved RNA structures may function to fine-tune viral replication. •We analyzed three conserved HIV-1 RNA structures in inter-protein domain junctions.•These conserved RNA structures are not essential for HIV-1 replication.•Altering some RNA structures with synonymous mutations caused fitness defects.•The conserved RNA structures can be altered, illustrating HIV-1 genome flexibility.•We suggest that conserved RNA structures may play a role in fine-tuning replication.