Structure and Function of Lentiviral Genomic and Messenger RNA Public Deposited

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  • March 21, 2019
  • Pollom, Elizabeth Grace
    • Affiliation: School of Medicine, Department of Biochemistry and Biophysics
  • The positive sense lentiviral RNA genome is packaged within the virus as a dimer of two single strands. The RNA of primate lentiviruses human immunodeficiency virus (HIV-1) and simian immunodeficiency virus (SIVmac239) are distantly related and the secondary structures of these viral RNAs share many known biological functions. Using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE), I present an analysis of the secondary structure of ex virio genomic SIVmac239 RNA in relation to that of HIV-1 as well as an investigation into the secondary structure of the various in vitro mRNA species of HIV-1 resolved using the SHAPE technique. First, I describe a SHAPE-derived model of SIVmac239 genomic RNA structure. When compared to that of HIV-1, I find very few conserved structural regions outside the previously studied functional structures. I observe that this is due to the flexible nature of the adenosine-rich lentiviral genome. The structures that are conserved are located in regions with high guanosine concentration, forming more stable pairing interactions. These results suggest that lentiviral genomic RNA structure is flexible and metastable unless held by stronger pairing interactions that seem to persist through the course of viral evolution. The lentiviral genomic RNA structures that I have studied do share a few common base pairs, including a small stem-loop at the site of the first splice acceptor (SA1). In the second part, I describe the effect of mutating this structure on viral replication and on the splicing profile of the viral mRNA. To further investigate viral splicing regulation, I determined the SHAPE-derived structures of the most abundant mRNA variants for all of the protein products of HIV-1. Results reveal local interactions that form at regulatory regions in the viral transcripts. Because RNA is an important feature throughout the lentiviral replication cycle, a greater understanding into the role of RNA in various aspects of viral replication will increase comprehension toward the complex biology of infection. This analysis provides insight into evolutionary conservation of RNA structures that play functional roles and may be possible targets for novel factors as part of a broad spectrum of viral inhibitory agents.
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  • In Copyright
  • Swanstrom, Ronald
  • Doctor of Philosophy
Degree granting institution
  • University of North Carolina at Chapel Hill
Graduation year
  • 2012

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