This is an application for renewal of a grant to study to the mechanism and fidelity of nucleotide incorporation by the replicative polymerase of RNA viruses, the RNA-dependent RNA polymerase (RdRp). Over the past ten years, the world has witnessed the emergence of SARS, the spread of West Nile encephalitis, and the fear of a global flu pandemic. These diseases are caused by RNA viruses. In addition, the threat of intentional release of RNA viruses as weapons or agents of terror has increased substantially. The long-term goal of this research program is to develop strategies to treat and/or prevent RNA virus infection by targeting the RdRp. Our program has employed a prototypical RNA virus, poliovirus (PV), and its RdRp (3Dpol) as our model system. The previous funding period was devoted to the interrogation of the chemical mechanism for 3Dpol- catalyzed nucleotidyl transfer, elucidation of the structural basis for 3Dpol incorporation fidelity, and development of the tools to solve a crystal structure for 3Dpol in complex with primed template and nucleotide. We have made outstanding progress towards completion of all our aims. We have obtained new insight into the chemical mechanism for nucleotidyl transfer. We discovered a link between RdRp incorporation fidelity and pathogenesis. We discovered a connection between RdRp dynamics and incorporation fidelity. Together, our studies lead to the very provocative hypothesis that RdRp incorporation fidelity is a target for antiviral and vaccine development that will be elaborated during the next funding period. We will pursue the following specific aims: (1) Elucidate additional roles for the general acid in polymerase function;(2) Identify novel determinants and mechanisms of polymerase fidelity;and (3) Establish dynamics-function relationships for the RdRp.

Public Health Relevance

RNA viruses represent an existing and emerging threat to US public health. Achievement of the goals of the application will provide novel targets and mechanisms for development of vaccines and inhibitors to prevent and to treat infections by RNA viruses.

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Project (R01)
Project #
2R01AI045818-11
Application #
7751941
Study Section
Special Emphasis Panel (ZRG1-GGG-J (02))
Program Officer
Park, Eun-Chung
Project Start
1999-07-01
Project End
2014-06-30
Budget Start
2009-07-01
Budget End
2010-06-30
Support Year
11
Fiscal Year
2009
Total Cost
$343,120
Indirect Cost
Name
Pennsylvania State University
Department
Biochemistry
Type
Schools of Arts and Sciences
DUNS #
003403953
City
University Park
State
PA
Country
United States
Zip Code
16802
Li, Chen; Wang, Haiwei; Yuan, Tiangang et al. (2018) Foot-and-mouth disease virus type O specific mutations determine RNA-dependent RNA polymerase fidelity and virus attenuation. Virology 518:87-94
Fitzsimmons, William J; Woods, Robert J; McCrone, John T et al. (2018) A speed-fidelity trade-off determines the mutation rate and virulence of an RNA virus. PLoS Biol 16:e2006459
Gizzi, Anthony S; Grove, Tyler L; Arnold, Jamie J et al. (2018) A naturally occurring antiviral ribonucleotide encoded by the human genome. Nature 558:610-614
Dulin, David; Arnold, Jamie J; van Laar, Theo et al. (2017) Signatures of Nucleotide Analog Incorporation by an RNA-Dependent RNA Polymerase Revealed Using High-Throughput Magnetic Tweezers. Cell Rep 21:1063-1076
Yang, Xiaorong; Liu, Xinran; Musser, Derek M et al. (2017) Triphosphate Reorientation of the Incoming Nucleotide as a Fidelity Checkpoint in Viral RNA-dependent RNA Polymerases. J Biol Chem 292:3810-3826
Li, Sixing; Ma, Fen; Bachman, Hunter et al. (2017) Acoustofluidic bacteria separation. J Micromech Microeng 27:
Li, Sixing; Ren, Liqiang; Huang, Po-Hsun et al. (2016) Acoustofluidic Transfer of Inflammatory Cells from Human Sputum Samples. Anal Chem 88:5655-61
Cameron, C E; Moustafa, I M; Arnold, J J (2016) Fidelity of Nucleotide Incorporation by the RNA-Dependent RNA Polymerase from Poliovirus. Enzymes 39:293-323
Lee, Cheri A; August, Avery; Arnold, Jamie J et al. (2016) Polymerase Mechanism-Based Method of Viral Attenuation. Methods Mol Biol 1349:83-104
Woodman, Andrew; Arnold, Jamie J; Cameron, Craig E et al. (2016) Biochemical and genetic analysis of the role of the viral polymerase in enterovirus recombination. Nucleic Acids Res 44:6883-95

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