Interdisciplinary Initiatives Program Round 10 - 2020

Joseph Puglisi, Structural Biology
Robert Shafer, Medicine (Infectious Diseases)

Viruses often use ribonucleic acids as their genetic material. Upon infecting a cell, viruses replicate by hijacking host components. Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immunodeficiency Syndrome (AIDS), and is a retrovirus, meaning that its RNA genome is copied to DNA, which then integrates into the infected host cell’s DNA. This copying process occurs immediately upon the virus entry into a cell, within a protein cone called a capsid. The virus brings all the enzymes and factors needed to start the process; this is called initiation, and the main enzyme that performs the copying of genetic material is reverse transcriptase (RT). RT initiates at a complex RNA structure formed between a host tRNA and the 5’ end of the genome; the copying during initiation is slow, as the enzyme must navigate through a highly structured RNA, and then jump from one end of the viral RNA to the other to continue reverse transcription. Because initiation is slow, it is vulnerable to drug intervention; in fact, many HIV drugs target reverse transcription. Here we combine the Puglisi lab’s ability to create molecular movies through structural snapshots and direct dynamic methods to understand the how RT and RNA collaborate during reverse transcriptase initiation, and how drugs block this process. We will merge imaging using cryoelectron microscopy and tomography to determine how this RNA-protein assembly changes and how RT works inside a capsid shell. We will use state of the art sequencing methods from the Shafer lab on paired patient samples to understand how RNA sequences and protein sequences are linked in the confines of a virus, and how drug resistance can be caused by mutational changes outside of the RT. The results of this deeply interdisciplinary work will show the importance of both RNA-protein sequence and structures in targeting RNA assemblies for therapy.