This is an application to renew a grant to study RNA synthesis in minus-strand RNA viruses. Nonsegmented negative-strand (NNS) RNA viruses include some of the most significant human pathogens that are a major ongoing threat to US public health. To combat those agents, we need a combination of antiviral drugs and vaccines. Our long-term objective is to understand the mechanisms by which the replication machinery of vesicular stomatitis virus (VSV), a prototype of the NNS RNA viruses, functions. VSV is the ideal choice for such studies because it is the only NNS RNA virus for which robust transcription can be reconstituted in vitro from purified recombinant components. The catalytic core of the RNA synthesis machinery is a 241 kDa large polymerase protein (L) that contains an RNA dependent RNA polymerase (RdRP), a polyribonucleotidyltransferase (PRNTase) that caps the mRNA, and a dual specificity mRNA cap methyltransferase (MTase). During mRNA synthesis, those activities are coordinated so that the nascent mRNA is capped, methylated and polyadenylated. Although L contains all the enzymatic activities for RNA synthesis, it requires a 29 kDa phosphoprotein (P) that bridges interactions between L and the nucleocapsid protein (N) that completely coats the genomic RNA template. In the last grant period, we developed in vitro assays to separately study each of the steps of mRNA cap addition independent of ongoing transcription. Those assays, combined with a powerful reverse genetic system allow mechanistic analysis of lethal mutations in the viral RNA synthesis machinery. We have used those assays to provide a map of where the different enzymatic activities for each step of mRNA cap addition are localized within L. Those studies lead us to the hypothesis that L contains independent functional domains whose activities are coordinated by the assembly of L into the RNA synthesis machine of the L-P complex with the N-RNA template. A major gap to understanding the mechanisms by which the RNA synthesis machinery of NNS RNA viruses function is the absence of structural information for L. During the next funding period, we will use electron microscopy, X-ray crystallography and in vitro assays of polymerase function to provide unique structural and functional insights into the RNA synthesis machinery of VSV. We will: (i) determine the functional organization of the VSV polymerase complex;(ii) determine the three dimensional structure of the VSV polymerase, and (iii) probe the relationship between the mRNA capping and RNA synthesis activities of L. The successful completion of this study will provide a structure of the polymerase of an NNS RNA virus as well as new mechanistic insights into the function of this RNA synthesis machine that may help in the rational design of antiviral therapeutics and candidate vaccines.

Public Health Relevance

The L polymerase protein of nonsegmented negative-strand (NNS) RNA viruses contains an RNA dependent RNA polymerization activity as well as a set of highly conserved and unusual enzymatic activities that add an mRNA cap structure. Understanding how those activities are controlled to ensure that the viral genome is expressed is of intrinsic interest and has the potential to impact the development of antiviral drugs and live attenuated vaccines. Here we will obtain structural and functional insights into this protein for a prototype NNS RNA virus, vesicular stomatitis virus.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Virology - B Study Section (VIRB)
Program Officer
Cassetti, Cristina
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Harvard University
Schools of Medicine
United States
Zip Code
Morin, Benjamin; Liang, Bo; Gardner, Erica et al. (2017) An In Vitro RNA Synthesis Assay for Rabies Virus Defines Ribonucleoprotein Interactions Critical for Polymerase Activity. J Virol 91:
Wang, Bingyin; Yang, Chen; Tekes, Gergely et al. (2015) Recoding of the vesicular stomatitis virus L gene by computer-aided design provides a live, attenuated vaccine candidate. MBio 6:
Liang, Bo; Li, Zongli; Jenni, Simon et al. (2015) Structure of the L Protein of Vesicular Stomatitis Virus from Electron Cryomicroscopy. Cell 162:314-327
Lee, Amy Si-Ying; Burdeinick-Kerr, Rebeca; Whelan, Sean P J (2014) A genome-wide small interfering RNA screen identifies host factors required for vesicular stomatitis virus infection. J Virol 88:8355-60
Morin, Benjamin; Whelan, Sean P J (2014) Sensitivity of the polymerase of vesicular stomatitis virus to 2' substitutions in the template and nucleotide triphosphate during initiation and elongation. J Biol Chem 289:9961-9
Ma, Yuanmei; Wei, Yongwei; Zhang, Xiaodong et al. (2014) mRNA cap methylation influences pathogenesis of vesicular stomatitis virus in vivo. J Virol 88:2913-26
Morin, Benjamin; Kranzusch, Philip J; Rahmeh, Amal A et al. (2013) The polymerase of negative-stranded RNA viruses. Curr Opin Virol 3:103-10
Semler, Bert L; Whelan, Sean P J (2013) Methods to study RNA virus molecular biology. Methods 59:165-6
Lee, Amy Si-Ying; Burdeinick-Kerr, Rebeca; Whelan, Sean P J (2013) A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs. Proc Natl Acad Sci U S A 110:324-9
Kranzusch, Philip J; Whelan, Sean P J (2012) Architecture and regulation of negative-strand viral enzymatic machinery. RNA Biol 9:941-8

Showing the most recent 10 out of 33 publications