Understanding Retroviral Reverse Transcription, Recombination, and Replication

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

HIV-1 uses multiple transcription start sites and generates several unspliced RNA species including two major transcripts known as 1G RNA and 3G RNA. We have previously shown that co-expression of both RNAs is important for HIV-1 replication fitness. To understand the regulation of HIV-1 RNA functions, we passaged the plusAC virus, which predominantly expresses 3G RNA and have a replication fitness defect, and characterized the changes near the transcription start sites. We found that the mutant virus improved its replication kinetics after passaging, indicating adaptation. Our analyses showed that, through mutations occurring during DNA synthesis, multiple revertants arose rapidly to replace the input mutant virus. The major revertants regained the ability to generate more than one major transcript and preferentially package 1G RNA. These results highlight the importance of expressing HIV-1 RNA species that serve distinct functions and the ability of HIV-1 to adapt through mutations in the genome. This study was published in Journal of Virology in 2025. In collaboration with Dr. Vinay Pathak, we have assisted in determining the regulatory factor of HIV-1 uncoating. The genome of HIV-1 is encapsidated in the core of an infectious virus. In an infection event, HIV-1 releases the core into the cells, DNA synthesis is initiated in the cytoplasm and completed after the core is imported into the nucleus. HIV-1 core must uncoat at the appropriate time, if it occurs too early, the replication complex can dissociate preventing the completion of DNA synthesis. If the core does not uncoat, DNA cannot assess and integrate into host chromosome, which is essential for replication. However, the mechanism that regulates HIV-1 core uncoating was unknown. Dr. Pathak's group has shown that the synthesis of long double-stranded DNA is the key for core uncoating. These findings also explained how HIV-1 controls the timing and location of uncoating to maximize the successful completion of HIV-1 replication. These studies are published in Science Advances in 2024. In addition, we have assisted Dr. Pathak's group in determining the mechanism of action for lenacapavir, the first-in-class antiviral against HIV-1 capsid. This study demonstrated that lenacapvir stabilizes the capsid core lattice, leading to breakage and prevents nuclear import. This study is published in PNAS in 2025.