Hepatitis C virus (HCV) infects approximately 2% of the world's population and is the primary cause of liver transplants in the United States. Based on lessons learned from diseases such as AIDS, HCV RNA replication is a promising target for antiviral development. However, the replication of all viruses with plus-strand RNA genomes is poorly understood, especially at the biochemical level. The overall goal of the research in the Kao lab is to understand mechanism of RNA virus replication. The goal for this project is to build knowledge about the subunits of the HCV replication complex, with emphasis on protein-RNA, and protein-protein interactions. This is an extension of the past six years of research in the Kao lab, where a number of basic properties of the HCV polymerase and the HCV protease-helicase have been examined using biochemical, biophysical, and cell-based methods. The research can be partitioned into several related subaims that will: 1. Identify and validate the biological importance of the residues in the HCV RdRp that interacts with the substrate NTPs, the template RNA, and during different stages of HCV RNA synthesis. 2. Elucidate the interactions between the HCV RdRp and the nascent RNA and identify and characterize the nascent RNA exit channel. 3. Examine the protein-protein and protein-RNA interactions with other replicase- associated subunits of the HCV replicase and examine effects of the interactions on HCV replicase formation in cells. 4. Obtain images of the protein complexes using electron microscopy and reconstruct their structures. Results from this proposal will advance the understanding of the mechanism of viral RNA-dependent RNA synthesis for ALL positive-strand RNA viruses. The knowledge can also be used to compare the mechanisms of action of all template-dependent (both viral and cellular) polymerases.

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
Koshy, Rajen
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Indiana University Bloomington
Schools of Arts and Sciences
United States
Zip Code
Wen, Y; Cheng Kao, C (2014) The hepatitis C virus core protein can modulate RNA-dependent RNA synthesis by the 2a polymerase. Virus Res 189:165-76
Yamane, Daisuke; McGivern, David R; Wauthier, Eliane et al. (2014) Regulation of the hepatitis C virus RNA replicase by endogenous lipid peroxidation. Nat Med 20:927-35
Yi, Guanghui; Deval, Jerome; Fan, Baochang et al. (2012) Biochemical study of the comparative inhibition of hepatitis C virus RNA polymerase by VX-222 and filibuvir. Antimicrob Agents Chemother 56:830-7
Lu, Cheng; Ranjith-Kumar, C T; Hao, Lujiang et al. (2011) Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate. Nucleic Acids Res 39:1565-75
Ranjith-Kumar, C T; Wen, Yahong; Baxter, Nielson et al. (2011) A cell-based assay for RNA synthesis by the HCV polymerase reveals new insights on mechanism of polymerase inhibitors and modulation by NS5A. PLoS One 6:e22575
Lai, Yvonne; Yi, Guanghui; Chen, Alice et al. (2011) Viral double-strand RNA-binding proteins can enhance innate immune signaling by toll-like Receptor 3. PLoS One 6:e25837
Subba-Reddy, Chennareddy V; Goodfellow, Ian; Kao, C Cheng (2011) VPg-primed RNA synthesis of norovirus RNA-dependent RNA polymerases by using a novel cell-based assay. J Virol 85:13027-37
Lu, Cheng; Xu, Hengyu; Ranjith-Kumar, C T et al. (2010) The structural basis of 5' triphosphate double-stranded RNA recognition by RIG-I C-terminal domain. Structure 18:1032-43
Chinnaswamy, S; Murali, A; Li, P et al. (2010) Regulation of de novo-initiated RNA synthesis in hepatitis C virus RNA-dependent RNA polymerase by intermolecular interactions. J Virol 84:5923-35
Hwang, Jungwook; Huang, Luyun; Cordek, Daniel G et al. (2010) Hepatitis C virus nonstructural protein 5A: biochemical characterization of a novel structural class of RNA-binding proteins. J Virol 84:12480-91

Showing the most recent 10 out of 16 publications