Research

Our lab studies the different stages of alphavirus assembly and spread. We are interested in the viral and host factors that mediate and regulate virus assembly.

How do the glycoprotein spikes assemble and incorporate into a virus particle?

The viral spikes on the surface of the virus particle are absolutely required for cell entry. Misassembled spikes can mean a less infectious virus. In addition, the spikes interact directly with the internal core suggesting a role in particle stability. We want to know the molecular steps necessary to assembly a spike.

Some questions we are asking:

  • What are the different conformations of the glycoproteins during spike assembly?
  • When and where do the spikes interact with the capsid proteins?
  • How does polyprotein translation and topology affect spike assembly?

Recent papers:

  1. Ren, S. C., Qazi, S. A, Towell, B., Wang, C-Y, and Mukhopadhyay, S. (2022) Mutations at the Alphavirus E2/E1 inter-dimer interface have host-specific phenotypes. Virol. 96:e02149-21.
  2. Harrington, H. R., Zimmer, M. H., Chamness, L. M., Nash, V., Penn, W. D., Miller III, T. F. Mukhopadhyay, S., and Schlebach, J. S. (2020) Cotranslational Folding Stimulates Programmed Ribosomal Frameshiting in the Alphavirus Structural Prolyprotein. J. Biol. Chem.  295(20):6798-6808.
  3. Zeng, X., Mukhopadhyay, S., and Brooks III, C. L. (2015) Residue level resolution of alphavirus envelope protein interactions in pH dependent fusion. Proc. Natl. Acad. Sci. USA. 112(7):2034-9.

How does the capsid protein self-assemble into the nucleocapsid core?

The core must balance between protecting the viral genome during transmission and then in response to the proper trigger releasing the genome to initiate an infection. We want to know how the core maintains this balance of function and can we use identified interactions to modulate core function.

Some questions we are asking

  • How do the capsid proteins select viral RNA to encapsidate?
  • What else is in the core and why is it packaged?
  • What are the assembly subunits for building a core?
  • Are all cores icosahedral and is that is necessary for function?

Recent papers:

  1. Button, J. M. and Mukhopadhyay, S. (2021) Capsid-E2 interactions rescue core assembly in viruses that cannot form cytoplasmic nucleocapsid cores. J. Virol. 95:e01062-21.
  2. Button, J.M. and Mukhopadhyay, S. (2020) Removing the Polyanionic Cargo Requirement for Assembly of Alphavirus Core-Like Particles to Make an Empty Alphavirus Core. Viruses, 12:846
  3. Rayaprolu, V., Moore, A., Wang, C-Y, Goh, B. C., Perilla, J. R., Zlotnick, A., and Mukhopadhyay, S. (2017) Length of encapsidated cargo impacts stability and structure of in vitro assembled Alphavirus core-like particles. Phys.: Condens. Matter. 29(48):484003

What is this little protein, TF, and what does it do?

The protein TF is made about 10-15% of the time, a result of a programmed ribosomal frameshifting event. Palmitoylation of TF is necessary for it’s localization to the plasma membrane and incorporation into the virus particle.  TF also antagonizes cellular IFN levels. How does TF do all these functions and what regulates it?

Some questions we are asking:

  • How does TF modulate IFN-beta levels in the cell?
  • What regulates TF palmitoylation?
  • What are the functions of 6K and TF during assembly, budding and spread?

Recent papers:

  1. Roger, K.J., Jones-Burrage, S. E., Maury, W., and Mukhopadhyay, S. (2020) TF protein of Sindbis virus antagonizes host type I interferon responses in a palmitoylation-dependent manner. Virology. 542:63-70.
  2. Ramsey, J., Chavez, M., and Mukhopadhyay, S. (2019) Domains of the TF protein important in regulating its own palmitoylation. Virology  531:31-39.
  3. Ramsey, J., Renzi, E. C., Arnold, R. J., Trinidad, J. C., and Mukhopadhyay, S. (2016) Palmitoylation of Sindbis virus TF protein regulates its plasma membrane localization and subsequent incorporation into virions. J Virol. 91(3). pii: e02000-16.

How does one virus with one set of “instructions” know what to do in various cell types?

Arboviruses infect arthropods and vertebrates and present a different pathology and disease state in each organism. We want to determine the molecular interactions that occur in different hosts to find evolutionary conserved mechanisms.

 

 

Some questions we are asking:

  • What proteins initiate alphavirus budding?
  • How do the glycoproteins contact the nucleocapsid core and where does this occur in the cell?
  • What the different host factors required for assembly and are these conserved?
  • Where in the cell do different lifecycle stages occur and how are these coordinated?

Recent papers:

  1. Chen, R., Plante, J. A., Plante, K. S., Yun, R., Mirchandani, D., Liu, J, Haller, S., Mukhopadhyay, S., and Weaver, S. W. (2021) Lineage Divergence and Vector-Specific Adaptation Have Driven Chikungunya Virus onto Multiple Adaptive Landscapes. mBio. Nov 9:e02738-21.
  2. Dunbar, C.A., Rayaprolu, V., Wang, J.C., Brown, C.J., Leishman, E., Jones-Burrage, S., Trinidad, J.C., Bradshaw, H.B., Clemmer, D.E., Mukhopadhyay, S., and Jarrold, M.F. (2019) Dissecting the Components of Sindbis Virus from Arthropod and Vertebrate Hosts: Implications for Infectivity Differences. ACS Infect. Dis. Apr 15. doi: 10.1021/acsinfecdis.8b00356.
  3. Lazaro, G.R., Mukhopadhyay, S, and Hagan M.F. (2017) Why enveloped viruses need cores—the contribution of a nucleocapsid core to viral budding. Biophys J. 114(3):619-630.