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Research Associate Professor
Cell Biology & Physiology
8332 MBRB

Viral RNA-dependent RNA polymerases and replicases


Central to the multiplication of positive-strand RNA viruses is the virus-encoded RNA-dependent RNA polymerase (RdRp). This enzyme, therefore, represents an attractive target for the development of antivirals.  To gain a better understanding of this class of polymerase, over the past several years we have developed novel strategies that provide information on the kinetic, thermodynamic, and structural basis for fidelity of nucleotide incorporation.  This has allowed us to obtain key insights into the chemical mechanism for nucleotidyl transfer, discovery of a link between RdRp incorporation fidelity and pathogenesis, uncovering of a connection between RdRp dynamics and incorporation fidelity; identifying a correlation between RdRp infidelity and the frequency of RNA recombination; and discovery of novel mechanisms of RdRp inhibition critical to the development of antiviral ribonucleotides. Our initial focus was on viruses that encode a single-subunit RdRp, we are now including viruses that have more complex multi-subunit viral replicases-this includes flaviviruses, alphaviruses and coronaviruses.

The world is currently in the midst of a global pandemic caused by the second severe acute respiratory syndrome coronavirus (SARS2). In spite of the foreshadowing of such a pandemic by the emergence of SARS1 in 2002 and Middle East respiratory syndrome coronavirus (MERS) in 2012, we were ill equipped to address this scourge. Our laboratory is pledging a sustained commitment to elucidation of the fundamental enzymology and corresponding mechanisms of coronavirus genome replication. The SARS2 replisome has emerged as a clinically tractable target for development antiviral therapeutics and will therefore require a quantitative, mechanistic perspective of the SARS2 replisome. Such a perspective will be essential to elucidation of the mechanism of drug action and the mechanism of drug resistance. We are committed to elucidating the principles governing the dynamics and function of the SARS2 core replicase using state-of-the-art ensemble and single-molecule approaches.

Selected Publications

Gizzi, A. S., Grove, T. L., Arnold, J. J., Jose, J., Jangra, R. K., Garforth, S. J., Du, Q., Cahill, S. M., Dulyaninova, N. G., Love, J. D., Chandran, K., Bresnick, A. R., Cameron, C. E. and Almo, S. C. (2018). A naturally occurring antiviral ribonucleotide encoded by the human genome. Nature 558: 610-614. PMC6026066

Dulin D., Arnold, J.J., van Laar, T., Oh, H.S., Lee, C., Perkins, A.L., Harki, D.A., Depken, M., Cameron, C.E., Dekker, N.H. (2017). Signatures of nucleotide analog incorporation by an RNA-Dependent RNA polymerase revealed using high-throughput magnetic tweezers. Cell Reports. 21, 1063-1076. PMC5670035.

Arnold, J.J., Sharma, S.D., Feng, J.Y., Ray, A.S., Smidansky, E.D., Kireeva, M.L., Cho, A., Perry, J., Vela, J., Park, Y., Xu, Y., Tian, Y., Babusis, D., Barauskus, O., Peterson, B.R., Gnatt, A., Kashlev, M., Zhong, W. and Cameron, C.E. (2012). Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides. PLoS Pathog. 8, PMC3499576

Weeks, S.A., Lee, C.A., Zhao, Y., Smidansky, E.D., August, A., Arnold, J.J. and Cameron, C.E. (2012). A polymerase mechanism-based strategy for viral attenuation and vaccine development. Biol. Chem. 287, 31618-22. PMCID: PMC3442494

Arnold, J.J., Vignuzzi, J.K. Stone, R. Andino and C.E. Cameron (2005) Remote Site Control of an Active Site Fidelity Checkpoint in a Viral RNA-dependent RNA polymerase. J. Biol. Chem. 280, 25706-25716.

Link to My Bibliography

Jamie Arnold