Retroviruses are serious pathogens that cause immune deficiency syndromes, cancer, and neurological disease in humans. Conversely, retroviruses are highly useful for directing beneficial genes into human cells. Well characterized retroviral proteins can often be targeted by drugs or be manipulated genetically to achieve important biomedical advances. In strong contrast, retroviruses have RNA genomes and very little is known regarding RNA structures that play critical roles in retroviral infection and morbidity. One compelling example is that retroviral RNA genomes both enter and leave a targeted cell as a stable dimer. The two strands of a retroviral RNA genome are linked at their 5'ends by a precise, but poorly understood, three-dimensional structure. Understanding the mechanism of retroviral dimerization at a molecular level therefore represents opportunities both to disrupt the infectivity of pathogenic viruses and to enhance the function of therapeutic vectors. This work thus extends from basic mechanistic insights to potential clinical applications. Our team of virologists and chemical biologists will tackle the following Aims: (1) Refine a three-dimensional model for the dimerization domain of Moloney murine sarcoma virus. Analysis of this model will provide important new information regarding the RNA conformational changes that accompany dimerization and will facilitate identification of structural targets for anti-retroviral agents. (2) Determine the folding pathway for the Moloney murine leukemia virus (MuLV) RNA dimerization at nucleotide resolution in the presence and absence of the viral Gag protein. We will explore the hypothesis that dimerization progresses by highly specific sequential interactions involving distinct RNA domains and that this step-wise assembly is crucial for the ability of the virus to package its genomic RNA with such extraordinary specificity. (3) Use high-throughput RNA structure analysis technology, invented in our laboratory, to analyze (i) the structure of the dimerization domain and (ii) protein-RNA interactions inside authentic MuLV virions. This information will then be used to define, and genetically validate, the packaging signal of MuLV in vivo at single nucleotide resolution. (4) Initiate a program to determine the structure of the dimerization domain and sites of specific viral protein binding in HTLV-1.
This Aim further extends our successful invention, in collaboration with retrovirologists, of direct approaches for analyzing retroviral RNA structure ex virio and in virio that circumvent the requirement for laborious and notoriously inefficient manipulation and transfection of HTLV-1. Experimental innovations developed in this Aim will be broadly useful to the virology community for analyzing any RNA structure in any RNA virus.

Public Health Relevance

This work will advance significantly our understanding of the structure and function of the RNA genomes of retroviruses. This project makes use of multiple, innovative, advances in technology and involves a distinctive and close collaboration between chemical biologists and virologists. Over the long term, improved, molecular quality, information about retroviral genome structure has significant potential to provide a framework for designing new anti-retroviral therapeutics and for engineering better gene therapy vectors for introducing corrective genes into human cells.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM064803-08
Application #
8106205
Study Section
Virology - A Study Section (VIRA)
Program Officer
Sakalian, Michael
Project Start
2002-04-01
Project End
2012-06-30
Budget Start
2011-07-01
Budget End
2012-06-30
Support Year
8
Fiscal Year
2011
Total Cost
$276,945
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Shobair, Mahmoud; Popov, Konstantin I; Dang, Yan L et al. (2018) Mapping allosteric linkage to channel gating by extracellular domains in the human epithelial sodium channel. J Biol Chem 293:3675-3684
Li, Bo; Tunc-Ozdemir, Meral; Urano, Daisuke et al. (2018) Tyrosine phosphorylation switching of a G protein. J Biol Chem 293:4752-4766
Dagliyan, Onur; Krokhotin, Andrey; Ozkan-Dagliyan, Irem et al. (2018) Computational design of chemogenetic and optogenetic split proteins. Nat Commun 9:4042
Han, Qingjian; Liu, Di; Convertino, Marino et al. (2018) miRNA-711 Binds and Activates TRPA1 Extracellularly to Evoke Acute and Chronic Pruritus. Neuron 99:449-463.e6
Zhang, Yuliang; Hashemi, Mohtadin; Lv, Zhengjian et al. (2018) High-speed atomic force microscopy reveals structural dynamics of ?-synuclein monomers and dimers. J Chem Phys 148:123322
Williams 2nd, Benfeard; Convertino, Marino; Das, Jhuma et al. (2017) Molecular Mechanisms of the R61T Mutation in Apolipoprotein E4: A Dynamic Rescue. Biophys J 113:2192-2198
Woods, Chanin T; Lackey, Lela; Williams, Benfeard et al. (2017) Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J 113:290-301
Dakal, Tikam Chand; Kala, Deepak; Dhiman, Gourav et al. (2017) Predicting the functional consequences of non-synonymous single nucleotide polymorphisms in IL8 gene. Sci Rep 7:6525
Krokhotin, Andrey; Mustoe, Anthony M; Weeks, Kevin M et al. (2017) Direct identification of base-paired RNA nucleotides by correlated chemical probing. RNA 23:6-13
Larman, Bridget C; Dethoff, Elizabeth A; Weeks, Kevin M (2017) Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States. Biochemistry 56:2175-2183

Showing the most recent 10 out of 56 publications