Translational recoding is the process by which ribosomes are directed into an alternate reading frame of an mRNA to synthesize a different protein. Most retroviruses, and some coronaviruses, utilize translational recoding in the form of an RNA programmed -1 frameshift, which increases the viral genomic coding capacity and regulates expression of essential genes. It is also now becoming clear that translational recoding regulates cellular gene expression in many organisms, including humans. This proposal will examine RNA structures from viruses and cellular mRNAs that recode the reading frame, thus providing insights into the fundamental strategies of how RNA structures direct translational recoding in cells. We will measure for the first time the thermodynamic relationship between HIV-1 mRNA structure and frameshift efficiency in vivo. We will explore how novel, high affinity compounds bind to the HIV-1 frameshift site, stimulate frameshifting, and inhibit HIV replication. Using the tools we have developed for HIV, we will investigate the structure and function of the human CCR5 mRNA frameshift site, which regulates expression of the HIV co-receptor and is stimulated by microRNAs through an unknown mechanism. Finally, we will determine the structural basis for +1 frame recoding, using the well-studied Israeli Acute Paralysis Virus internal ribosome entry site as a model system. These studies will significantly advance our understanding of how mRNAs program translational recoding in human cells, and may eventually lead to the development of novel antiviral therapies.

Public Health Relevance

We aim to broadly understand how viral and cellular mRNA structures program translational recoding events in the form of -1 and +1 frameshifts. This project has direct relevance to public health because it will elucidate the molecular basis of HIV-1 frameshifting and how this process can be targeted with small molecules that inhibit viral replication.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM072447-09
Application #
8961619
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter
Project Start
2005-04-01
Project End
2019-04-30
Budget Start
2015-09-01
Budget End
2016-04-30
Support Year
9
Fiscal Year
2015
Total Cost
$291,757
Indirect Cost
$92,796
Name
University of Wisconsin Madison
Department
Biochemistry
Type
Schools of Earth Sciences/Natur
DUNS #
161202122
City
Madison
State
WI
Country
United States
Zip Code
53715
Butcher, Samuel E; Jan, Eric (2016) tRNA-mimicry in IRES-mediated translation and recoding. RNA Biol 13:1068-1074
Garcia-Miranda, Pablo; Becker, Jordan T; Benner, Bayleigh E et al. (2016) Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity. J Virol 90:6906-6917
Vander Meulen, Kirk A; Horowitz, Scott; Trievel, Raymond C et al. (2016) Measuring the Kinetics of Molecular Association by Isothermal Titration Calorimetry. Methods Enzymol 567:181-213
Hilimire, Thomas A; Bennett, Ryan P; Stewart, Ryan A et al. (2016) N-Methylation as a Strategy for Enhancing the Affinity and Selectivity of RNA-binding Peptides: Application to the HIV-1 Frameshift-Stimulating RNA. ACS Chem Biol 11:88-94
Mouzakis, Kathryn D; Dethoff, Elizabeth A; Tonelli, Marco et al. (2015) Dynamic motions of the HIV-1 frameshift site RNA. Biophys J 108:644-54
Au, Hilda H; Cornilescu, Gabriel; Mouzakis, Kathryn D et al. (2015) Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci U S A 112:E6446-55
Low, Justin T; Garcia-Miranda, Pablo; Mouzakis, Kathryn D et al. (2014) Structure and dynamics of the HIV-1 frameshift element RNA. Biochemistry 53:4282-91
Yin, Kaifeng; Hacia, Joseph G; Zhong, Zhe et al. (2014) Genome-wide analysis of miRNA and mRNA transcriptomes during amelogenesis. BMC Genomics 15:998
Moser, Ann B; Hey, Jody; Dranchak, Patricia K et al. (2013) Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells. Lipids Health Dis 12:10
Mouzakis, Kathryn D; Lang, Andrew L; Vander Meulen, Kirk A et al. (2013) HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome. Nucleic Acids Res 41:1901-13

Showing the most recent 10 out of 29 publications