Retroviral RNA Trafficking, RNA Packaging, Virus Assembly, and Replication
We study how retroviruses transfer genetic information to the next generation. HIV-1 packages two copies of full-length viral RNA into a particle. Upon infecting a new host cell, virion RNA is used as the template to generate viral DNA, which integrates into the host chromosome to form a provirus. We study several aspects of the viral replication cycles that affect the transfer of viral genetic information, including the transport and trafficking of the viral RNA, packaging of the viral RNA genome, virus assembly, and reverse transcription. We use molecular biology and biochemical approaches in combination with state-of-the-art microscopy techniques to study these topics.
Retroviral RNA packaging and virus assembly. In order to generate infectious viruses, HIV-1 must encapsidate full-length unspliced RNAs into its particle. To study HIV-1 RNA packaging, we have developed a novel assay to directly visualize viral RNA in the particles at single-RNA-molecule sensitivity. This assay reveals that most HIV-1 particles contain two copies of full-length viral RNA. Although it is known that retroviral RNAs that are packaged into particles are dimeric, standard biochemical assays cannot determine the number of RNA molecules in one particle; our results provide evidence to support the long-standing assumption that two RNA molecules (one dimer) are packaged into a particle. To better understand the mechanisms of RNA packaging, we have performed genetic, biochemical, and imaging analyses to show that HIV-1 RNA uses base-pairing of the dimerization initiation signal sequence to select its copackaged RNA partner, and this process occurs in the producer cell prior to RNA packaging into particles. We study the mechanisms that HIV-1 uses to regulate which and how many RNAs are packaged. Additionally, we study the interactions between viral Gag protein and full-length RNA that lead to the encapsidation of the viral genome during virus assembly.
Retroviral RNA trafficking. Full-length HIV-1 RNA needs to traffic to specific subcellular locations to carry out its functions, including serving as a template for Gag/Gag-Pol translation and as a genome in the newly assembled virion. The functions of the viral RNA and the translated proteins can be affected when RNA is targeted to incorrect locations in the cells. Using our newly developed imaging tools and live-cell imaging techniques, we study HIV-1 RNA transport and its relation to the function of viral RNAs. These experiments will provide an understanding of aspects of HIV-1 replication that we currently know very little about and will allow us to better understand how HIV-1 uses the cellular machinery to traffic its macromolecules.
Reverse transcription and recombination. Recombination plays an important role in HIV replication and evolution. For example, many of the primary isolates of HIV are recombinants, and recombination can assort mutations to generate variants that escape host immune responses or are resistant to multidrug treatment protocols. Recombination of HIV-1 occurs during reverse transcription, using information in the two RNAs to produce a hybrid DNA. Therefore, phenotypically different recombinants are generated from viruses containing two copies of different RNAs. Only cells that are doubly infected can produce virions containing two different RNAs. To better understand interactions in HIV-1 populations, we study the dynamics of double infection, the frequency of recombination, and the mechanism of reverse transcription.
- Chen J, Liu Y, Wu B, Nikolaitchik OA, Mohan PR, Chen J, Pathak VK, Hu WS. Visualizing the translation and packaging of HIV-1 full-length RNA. Proc Natl Acad Sci U S A. 2020;117(11):6145-6155.
- Rawson JMO, Nikolaitchik OA, Keele BF, Pathak VK, Hu WS. Recombination is required for efficient HIV-1 replication and the maintenance of viral genome integrity. Nucleic Acids Res. 2018;46(20):10535-10545.
- Chen J, Rahman SA, Nikolaitchik OA, Grunwald D, Sardo L, Burdick RC, Plisov S, Liang E, Tai S, Pathak VK, Hu WS. HIV-1 RNA genome dimerizes on the plasma membrane in the presence of Gag protein. Proc Natl Acad Sci U S A. 2016;113(2):E201-8.
- Chen J, Grunwald D, Sardo L, Galli A, Plisov S, Nikolaitchik OA, Chen D, Lockett S, Larson DR, Pathak VK, Hu WS. Cytoplasmic HIV-1 RNA is mainly transported by diffusion in the presence or absence of Gag protein. Proc Natl Acad Sci U S A. 2014;111(48):E5205-13.
- Nikolaitchik OA, Dilley KA, Fu W, Gorelick RJ, Tai SH, Soheilian F, Ptak RG, Nagashima K, Pathak VK, Hu WS. Dimeric RNA recognition regulates HIV-1 genome packaging. PLoS Pathog. 2013;9(3):e1003249.
Related Scientific Focus Areas
Microbiology and Infectious Diseases
Molecular Biology and Biochemistry
This page was last updated on Tuesday, April 5, 2022