Viral capsid proteins are important regulators of viral processes from translation, to RNA replication, to RNA packaging, and the modulation of cellular innate immune responses. In viruses with segmented genomes that are packaged into separate virions, the capsid protein must coordinate the activities for each of the RNAs. The overall goal of this project is to better understand the early steps in an RNA virus infection. That is, how does the capsid interact with the viral RNAs within the virion and facilitate entry into cells? Brome mosaic virus (BMV) will be the model virus for this study. BMV is a nonenveloped segmented positive-strand RNA virus that has served as a model system with notable contributions to the cis- and trans-acting factors, the formation of the replicase complex, and the mechanism of viral RNA-dependent RNA synthesis. Preliminary results showed that an arginine-rich motif of the BMV capsid contributes to the selective encapsidation of BMV RNAs and acts as a cell-penetration signal. The latter set of observations led to the hypothesis that plant viruses gain entry into cells through a protein transduction mechanism. This project contains two aims, the first will seek to understand the architecture of the virion through a combination of cryoelectron microscopy and single particle reconstruction, biochemical mapping of RNA conformation and RNA-capsid interaction, and a molecular genetic analysis of how the interactions will influence the infection process.
The second aim seeks to elucidate the mechanism of cell entry of the cell-penetration peptides and the viral capsid using fluorescently-labeled peptides and viruses, confocal microscopy and electron microscopy. The work will lead to improved understanding of the viral infection process.

Public Health Relevance

Viral capsid proteins have many essential roles during a virus infection, from the regulation of translation to the protection of the viral genome against cellular innate immune detection. This proposal contains a comprehensive set of experiments to examine how the capsid protein of a plant-infecting RNA virus interacts with the viral RNA, reconfigures the shape of the RNA during encapsidation, and mediates entry into cells. The information gained from the proposed studies will contribute new insights to virus architecture, protein-RNA interactions, and how viruses gain entry into the cell.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
Project #
Application #
Study Section
Virology - A Study Section (VIRA)
Program Officer
Park, Eun-Chung
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
Fan, Baochang; Ni, Peng; Kao, C Cheng (2015) Mapping RNA interactions to proteins in virions using CLIP-Seq. Methods Mol Biol 1297:213-24
Rao, A L N; Cheng Kao, C (2015) The brome mosaic virus 3' untranslated sequence regulates RNA replication, recombination, and virion assembly. Virus Res 206:46-52
Vaughan, Robert C; Kao, C Cheng (2015) Mapping protein-RNA interactions by RCAP, RNA-cross-linking and peptide fingerprinting. Methods Mol Biol 1297:225-36
Wang, Zhao; Hryc, Corey F; Bammes, Benjamin et al. (2014) An atomic model of brome mosaic virus using direct electron detection and real-space optimization. Nat Commun 5:4808
Kao, C Cheng; Peersen, Olve B (2014) Editorial overview: Virus replication in animals and plants. Curr Opin Virol 9:iv-v
Zhao, Huiying; Yang, Yuedong; Janga, Sarath Chandra et al. (2014) Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome. Proteins 82:640-7
Ni, Peng; Vaughan, Robert C; Tragesser, Brady et al. (2014) The plant host can affect the encapsidation of brome mosaic virus (BMV) RNA: BMV virions are surprisingly heterogeneous. J Mol Biol 426:1061-76
Kao, C Cheng; Chuang, Ella; Ford, James et al. (2014) Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions. Bio Protoc 7:
PĂ©rez-Vargas, Jimena; Vaughan, Robert C; Houser, Carolyn et al. (2014) Isolation and characterization of the DNA and protein binding activities of adenovirus core protein V. J Virol 88:9287-96
Vaughan, Robert; Tragesser, Brady; Ni, Peng et al. (2014) The tripartite virions of the brome mosaic virus have distinct physical properties that affect the timing of the infection process. J Virol 88:6483-91

Showing the most recent 10 out of 20 publications