In silico mutagenesis of RNA splicing in HIV-1

Nucleolar Localization of HIV-1 Rev Is Required, Yet Insufficient for Production of Infectious Viral Particles

Combination antiretroviral therapy fails in complete suppression of HIV-1 due to drug resistance and persistent latency. Novel therapeutic intervention requires knowledge of intracellular pathways responsible for viral replication, specifically those untargeted by antiretroviral drugs. An understudied phenomenon is the nucleolar localization of Rev phosphoprotein, which completes nucleocytoplasmic transport of unspliced/partially spliced HIV mRNA through multimerization with intronic cis-acting targets-the Rev-response element (RRE). Rev contains a nucleolar localization signal (NoLS) comprising the COOH terminus of the arginine-rich motif for accumulation within nucleoli-speculated as the interaction ground for Rev with cellular proteins mediating mRNA-independent nuclear export and splicing. Functionality of Rev nucleolar access during HIV-1 production and infection was investigated in the context of deletion and single-point mutations within Rev-NoLS. Mutations induced upon Rev-NoLS are hypothesized to inactivate the HIV-1 infectious cycle. HIV-1_HXB2 replication ceased with Rev mutations lacking nucleolar access due to loss or replacement of multiple arginine residues. Rev mutations missing single arginine residues remained strictly nucleolar in pattern and participated in proviral production, however, with reduced efficiency. Viral RNA packaging also decreased in efficiency after expression of nucleolar-localizing mutations. These results were observed during propagation of variant HIV-1_NL4-3 containing nucleolar-localizing mutations within the viral backbone (M4, M5, and M6). Lentiviral particles produced with Rev single-point mutations were transducible at extremely low frequency. Similarly, HIV-1_NL4-3 Rev-NoLS variants lost infectivity, unlike virulent WT (wild type) HIV-1_NL4-3. HIV-1_NL4-3 variants were capable of CD4⁺ host entry and reverse transcription as WT HIV-1_NL4-3, but lacked ability to complete a full infectious cycle. We currently reveal that viral integration is deregulated in the presence of Rev-NoLS mutations.

Kinetic Modeling of Virus Growth in Cells

When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular environment. For a large number of virus types, much has been learned about the molecular mechanisms and rates of the various steps. However, in only relatively few cases during the last 50 years has an attempt been made-using mathematical modeling-to account for how the different steps contribute to the overall timing and productivity of the infection cycle in a cell. Here we review the initial case studies, which include studies of the one-step growth behavior of viruses that infect bacteria (Qβ, T7, and M13), human immunodeficiency virus, influenza A virus, poliovirus, vesicular stomatitis virus, baculovirus, hepatitis B and C viruses, and herpes simplex virus. Further, we consider how such models enable one to explore how cellular resources are utilized and how antiviral strategies might be designed to resist escape. Finally, we highlight challenges and opportunities at the frontiers of cell-level modeling of virus infections.

A stochastic spatio-temporal (SST) model to study cell-to-cell variability in HIV-1 infection

Although HIV viremia in infected patients proceeds in a manner that may be accounted for by deterministic mathematical models, single virus-cell encounters following initial HIV exposure result in a variety of outcomes, only one of which results in a productive infection. The development of single molecule tracking techniques in living cells allows studies of intracellular transport of HIV, but it remains less clear what its impact may be on viral integration efficiency. Here, we present a stochastic intracellular mathematical model of HIV replication that incorporates microtubule transport of viral components. Using this model, we could study single round infections and observe how viruses entering cells reach one of three potential fates - degradation of the viral RNA genome, formation of LTR circles, or successful integration and establishment of a provirus. Our model predicts global trafficking properties, such as the probability and the mean time for a HIV viral particle to reach the nuclear pore. Interestingly, our model predicts that trafficking determines neither the probability or time of provirus establishment - instead, they are a function of vRNA degradation and reverse transcription reactions. Thus, our spatio-temporal model provides novel insights into the HIV infection process and may constitute a useful tool for the identification of promising drug targets.