Parris, Deborah S.
Department of Molecular Virology, Immunology, and Medical Genetics
Department of Molecular Genetics
2198 Graves Hall
333 W. 10th Avenue
Columbus, Oh. 43210
Ph. (614) 292-0735
2167E & G Graves Hall
333 W. 10th Avenue
Columbus, Oh. 43210
Ph. (614) 292-0846
Herpes simplex virus (HSV) is one of the most complex of the animal viruses encoding more than 85 different genes. Despite its complexity, it is the easiest member of the herpes virus family with which to work and has proven to be a good model system to study functions related to viral replication and mechanisms of DNA synthesis.
HSV DNA Replication
In my laboratory, we are studying the process of HSV DNA replication for two reasons: 1) This process represents an excellent target for the development of antiviral compounds against this important family of viruses; and 2) The virus encodes many of the genes involved in DNA replication and, therefore, is a good model system for studying this process in eukaryotes. My research in this area covers 2 areas—coordination of lagging strand DNA synthesis and mechanisms of HSV polymerase fidelity.
Coordination of lagging strand DNA synthesis:
Seven HSV encoded proteins have been shown to be required for viral DNA synthesis, yet no in vitro system exists that emulates the process. Six of these essential proteins can carry out leading strand synthesis, but attempts to obtain coordinated leading and lagging strand synthesis have largely failed. We hypothesize that some cellular proteins and perhaps additional viral proteins are involved in this process. Using purified proteins, we determined that human flap-endonuclease 1 and DNA ligase I activities can coordinate with HSV DNA polymerase to carry out most of the processes required to process Okazaki fragments, important intermediates in lagging strand synthesis. Moreover, we have shown that these human proteins relocalize to areas of viral DNA synthesis upon infection by HSV. We are in the process of identifying additional components involved in lagging strand synthesis using a proteomics approach. In addition, we are using biochemical and molecular approaches to understand the requirements for polymerase cycling during lagging strand synthesis and the coordination of the primase and polymerase activities. A long term goal of these studies is to determine the requirements for the assembly of a functional replisome capable of coordinated leading and lagging strand synthesis.
Mechanisms of HSV DNA polymerase fidelity:
The HSV DNA polymerase (pol) is the central enzyme involved in all aspects of viral DNA replication and is the ultimate target for the only antiviral drugs currently in use against this virus—acyclovir and foscarnet. Although similar in many ways to the major replicative DNA polymerases in mammalian cells, the HSV pol has a unique processivity factor, UL42, with which it forms a stable heterodimer. Unlike the eukaryotic polymerase processivity factor, PCNA, UL42 does not require a loading factor or ATP for assembly onto DNA, and does not form a toroid. We are interested in understanding the apparently unique mechanisms by which UL42 increases pol processivity. In addition, we wish to determine the general means by which processivity factors contribute to fidelity of the polymerases. Recently we demonstrated that the inherent base misincorporation frequency for the HSV pol is one of the highest for a replicative polymerases—1 in 300 events. Yet, the overall mutation frequency of the HSV pol is orders of magnitude lower. We have used pre-steady-state kinetics to determine that the processivity factor increases the fidelity of the polymerase without affecting the catalylic activity of the polymerizing or exonuclease domains. Our results suggest that the processivity factor alters the equilibrium between the association of template with each of these domains. Our current work in this area extends to the involvement of the HSV pol in the bypass and/or repair of lesions, such as abasic or oxidized sites. Our results suggest that abasic sites occur at least once per genome, but the polymerase is unable to extend past such a site. These results suggest other mechanisms are necessary for the polymerase to bypass such lesions, such as recombination and/or repair.
Suppression of RNA Silencing by HSV:
The role of RNA silencing in mammals as an innate response to virus infection is unknown, although RNA silencing is well-established as an antiviral defense mechanism in plants, insects, and nematodes. Current work in my laboratory and in collaboration with Dr. Dave Bisaro’s lab has revealed that HSV can suppress RNA silencing that is transiently induced in mammalian cells. Silencing suppression is achieved by increasing the stability of the target mRNA, resulting in up to a 5-fold increase in steady-state mRNA levels. Recently we utilized an established plant assay to demonstrate that a structural component of herpes virions can suppress RNA silencing in plants, independent of other HSV proteins. The mechanism by which this protein achieves silencing is under investigation. Long-term goals of this project are 1) to identify other herpes-encoded silencing suppressors; 2) to examine the role of cellular RNA silencing on virus replication and yields; 3) to create mutant viruses deficient in RNA silencing suppression and to examine the pathogenicity of these mutants in cell culture and in animals; 4) to determine the cross-communication that occurs between several innate response pathways, including those involved in silencing and RNA-activated protein kinase activation and function; and 5) to determine the impact of silencing suppression on expression of viral encoded microRNAs.
For current publications please visit The National Center for Biotechnology Information's PubMed website at http://www.ncbi.nlm.nih.gov/pubmed?term=parris%2C%20Deborah
Wu, Z., Cherukuri, N.C., Buckley, K., Crary, M., Jackel, J.N. , Bisaro, D.M., and Parris, D.S. Identification of a herpes simplex virus type 1-encoded RNA silencing suppressor that functions in plants and in mammalian cells. In preparation.
Wang, J.B., Zhu, Y., McVoy, M.A., and Parris, D.S. Changes in subcellular localization reveal interactions between human cytomegalovirus terminase subunits, currently in revision.
Kuchta, A.L., Parikh, H., Zhu, Y., Kellogg, G.E., Parris, D.S., and McVoy, M.A. Structural modelling and mutagenesis of human cytomegalovirus alkaline nuclease UL98. J. Gen. Virol., 93:130-138, 2012.
Zhu, Y., Cherukuri, N.C , Jackel, J.N., Wu, Z., Crary, M., Buckley, K.J., Bisaro, D.M., and Parris, D.S. Characterization of the RNA silencing suppression activity of the Ebola virus VP35 protein in plants and mammalian cells. J. Virol. 86: 3038-3049, 2012.
Zhu, Y., Stroud, J., Song, L., and Parris, D.S. Kinetic approaches to understanding the mechanisms of fidelity of the herpes simplex virus type 1 DNA polymerase. J. Nucleic Acids, Vol. 2010, Article ID 631595, 15 pages, 2010. doi:10.4061/2010/631595.
Zhu, Y., Wu, Z., Cardosa, M.C., and Parris, D.S. Processing of lagging strand intermediates in vitro by herpes simplex virus type 1 DNA polymerase. J. Virol. 84: 7459-7472, 2010.
Wu, Z., Zhu, Y., Bisaro, D.M., and Parris, D.S. Herpes simplex virus type 1 suppresses RNA-induced gene silencing in mammalian cells. J. Virol. 83: 6652-6663, 2009.
Zhu, Y., Song, L., Stroud, J., and Parris, D.S. Mechanisms by which herpes simplex virus DNA polymerase limits translesion synthesis through abasic sites. DNA Repair 7: 95-107, 2008.
Hanes, J.W., Zhu, Y., Parris, D.S., and Johnson, K.A. Enzymatic therapeutic index of acyclovir: viral versus human polymerase specificity. J. Biol. Chem. 282: 25159-25167, 2007.
Trego, K.S., Zhu, Y., and Parris, D.S. The herpes simplex virus type 1 DNA polymerase processivity factor, UL42, does not alter the catalytic activity of the UL9 origin-binding protein but facilitates its loading onto DNA. Nuc. Acids Res. 33: 536-545, 2005.
Song, L., Chaudhuri, M., Knopf, C.W., and Parris, D.S. Contribution of the 3’ to 5’ exonuclease activity of herpes simplex virus type 1 DNA polymerase to fidelity of DNA synthesis. J. Biol. Chem. 279: 18535-18543, 2004.
Arana, M.E., Song, L., Tanguy Le Gac, N., Parris, D.S., Villani, G., and Boehmer, P.E. On the role of proofreading exonuclease in bypass of a bulky 1,2d(GpG) cisplatin adduct by the herpes simplex virus-1 DNA polymerase. DNA Repair 3: 659-669, 2004.
Trego, K.S., and Parris, D.S. Functional interaction between the herpes simplex virus type 1 polymerase processivity factor and origin-binding proteins: Enhancement of UL9 helicase activity. J. Virol. 77: 12646-12659, 2003.
Zhu, Y., Trego, K.S., Song, L., and Parris, D.S. The 3’ to 5’ exonuclease activity of herpes simplex virus type 1 DNA polymerase modulates its strand displacement activity. J. Virol. 77: 10147-10153, 2003.
Chaudhuri, M., Song, L., and Parris, D.S. The herpes simplex virus type 1 DNA polymerase processivity factor increases fidelity without altering pre-steady-state rate constants for polymerization or excision. J. Biol. Chem. 278: 8996-9004, 2003.
National Institutes of Health (NIGMS) R01 GM073832-01A2, “Coordination of HSV Lagging Strand Synthesis”, 8/1/06-7/31/10; Direct Costs: $210,500/year
National Institutes of Health (NIAID) R21 AI 062837-02; “Suppression of RNA Interference by Herpes Simplex Virus”, 7/1/05-6/30/07; Direct costs (year 2): $146,475