The roles of five conserved lentiviral RNA structures in HIV-1 replication
Many viral RNA genomes have complex structures that serve regulatory roles. Comparisons of the RNA genomes from HIV-1 and two simian immunodeficiency viruses revealed multiple conserved RNA structures. In addition to structures with known functions, our collaborators identified five highly conserved structures with unknown functions among these lentiviruses. To explore the roles of these conserved structures in viral replication, we mutated each RNA structure in HIV-1 without changing the encoded viral protein and found all the mutants have infectivities similar to thate of wild-type HIV-1. We then performed competition experiments by infecting cells with both wild-type and mutant HIV-1, allowing multiple-round of viral replication, and analyzing the kinetics of viral replication. We found that the wild-type HIV-1 outcompeted two of the mutant viruses in the spreading infections, indicating that these mutants have defects in replication fitness. We hypothesize that these RNA structures exert subtle effects that regulate HIV-1 gene expression and replication.
The idea of examining these RNA structures arose from our collaborators’ studies of lentiviral RNA structures. Dr. Kevin Weeks discussed these structures with us; we were impressed with the striking conservation and intrigued by their potential roles in viral replication. One of the structures is located downstream of the gag stop codon, at a location similar to the recently described Rous sarcoma virus RNA stability element, leading us to hypothesize that it may regulate HIV-1 expression. However, altering this structure does not affect HIV-1 production, infectivity, or replication fitness. Furthermore, none of the five RNA structures is absolutely required for viral replication. However, two mutants have replication fitness defects, which suggest that these elements may play subtle roles in regulating viral replication. The biggest surprise for us is the finding that although these five structures were highly conserved, HIV-1 can tolerate synonymous changes in each of these regions to generate infectious viruses and the mutant viruses can carry out spreading infection. These observations clearly illustrate that HIV-1 genome has great flexibility and can tolerate extensive changes. We believe that this flexibility lays the foundation for this human pathogen to achieve high diversity in viral population, which allows HIV-1 to escape challenges in the environment such as drug treatment and/or host immune response. Therefore, despite decades of research efforts, drug-resistant HIV-1 variants remain a challenge in treating HIV-1 infection and an effective HIV-1 vaccine has not been obtained for the prevention of this pathogen.
Fig. 1. Five conserved RNA structures in the HIV-1 genome. The approximate locations and the predicted RNA structures are shown; for clarity, the HIV-1 genome in DNA form is shown.
About the Author
Yang Liu is a postdoctoral fellow in the Viral Recombination Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, NIH.
About the research
The roles of five conserved lentiviral RNA structures in HIV-1 replication
Virology, Volume 514, 15 January 2018, Pages 1-8
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