Research Area
Viruses and Bacteriophage Biology. Bacteriophages and viruses are the most abundant and widely distributed “organisms” on Earth. We study bacteriophage T4, a tailed virus containing ~170-kb double stranded DNA genome, to elucidate the basic mechanisms of virus assembly, genome packaging, and infection. Our approaches are multidisciplinary, including biochemistry, molecular genetics, structure, and biophysics. We have teased out the functional motifs, determined the atomic structures, and analyzed the viral genome packaging machine at single molecule level to understand how this nanomachine works. Some of this basic knowledge is translated into platforms for vaccine delivery, gene therapy, and stem cell therapy. Our current focus is to integrate CRISPR genome editing into bacteriophage research to create new ways to design future vaccines and gene therapeutics.
Team Description
Our laboratory consists of post-doctoral fellows, graduate students, undergraduate students, and high school students working together in small teams. We also have collaborators across the country playing key roles in our research. Our team’s current focus is to develop bacteriophage T4 into a universal vaccine platform by CRISPR genome engineering that allows rapid design of multi-component vaccines against pandemics pathogens. We have designed an anthrax-plague dual vaccine that can confer protection against both the biothreats. A phage T4-COVID vaccine has been designed and successfully tested in animal models and is being transitioned to Phase 1 clinical trial. In parallel, we are developing phage T4 nanoparticles that can deliver large gene and protein cargos into human cells for genetic therapies.
Team Members
Team Show
Publications
1. Zhu, J., Ananthaswamy, N., Jain, S., Batra, H., Tang, W-C., Lewry, D. A., Richards, M. L., David, S. A., Kilgore, P. A., Sha, J., Drelich, A., Tseng, C-T., Chopra, A. K., and Rao, V. B., A Universal Bacteriophage T4 Nanoparticle Platform to Design Multiplex SARS-CoV-2 Vaccine Candidates by CRISPR Engineering (in review). https://www.biorxiv.org/content/10.1101/2021.01.19.427310v1
2. Tao, P., Wu, X. and Rao, V.B. (2018) Unexpected evolutionary benefit to phages imparted by bacterial CRISPR-Cas9. Science Advances Vol. 4, no. 2, eaar4134.
3. Tao P, Wu X, Tang WC, Zhu J, Rao V. (2017) Engineering of Bacteriophage T4 Genome Using CRISPR-Cas9. ACS Synth Biol. 2017 6(10):1952-1961.
4. Fang Q, Tang WC, Tao P, Mahalingam M, Fokine A, Rossmann MG, Rao VB. (2020). Structural morphing in a symmetry-mismatched viral vertex. Nature Communications 2020 11(1):1713.
5. Zhu, J., Tao, P., Mahalingam, M., Sha, J., Kilgore, P., Chopra, A. K. and Rao, V. (2019) A prokaryotic eukaryotic hybrid viral vector for delivery of large cargos of genes and proteins into human cells. Science Advances 5, eaax0064.
6. Tao, P., Zhu, J., Mahalingam, M., Batra, H. and Rao, V.B. (2019) Bacteriophage T4 nanoparticles for vaccine delivery against infectious diseases. Advances in Drug Delivery Reviews 145:57-72.
7. Tao P, Mahalingam M, Zhu J, Moayeri M, Sha J, Lawrence WS, Leppla SH, Chopra AK, Rao VB. (2018) A Bacteriophage T4 Nanoparticle-Based Dual Vaccine against Anthrax and Plague. mBio 9(5): e01926-18.
8. Islam MZ, Fokine A, Mahalingam M, Zhang Z, Garcia-Doval C, van Raaij MJ, Rossmann MG, Rao VB. (2019) Molecular anatomy of the receptor binding module of a bacteriophage long tail fiber. PLoS Pathogens 15(12):e1008193.
9. Ananthaswamy, N., Fang, Q., AlSalmi,W., Jain, S., Chen, Z., Klose, T., Sun, Y., Liu, Y., Mahalingam, M., Chand, S., Tovanabutra, S., Robb, M., Rossmann, M.and Rao, V. B. (2019) A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer. Nature Communications 10(1):873.
10. Ordyan, M., Alam, I., Mahalingam, M., Rao, V. B. and Smith, D. E. (2018) Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor. Nature Communications 9(1):5434.
11. Lin, S., Alam, T.I., Kottadiel, V., VanGessel, C.J., Tang, W-C., Chemla, Y.R. and Rao, V.B. (2017) Altering the speed of a DNA packaging motor from bacteriophage T4. Nucleic Acids Research 45(19):11437-11448.
12. Chen Z, Sun L, Zhang Z, Fokine A, Padilla-Sanchez V, Hanein D, Jiang W, Rossmann MG, Rao VB. (2017) Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses. Proc Natl Acad Sci U S A. 114:E8184-8193.
13. Rao, V.B. and Feiss, M. (2015) Mechanisms of DNA Packaging in Large Double Stranded DNA Viruses. Ann. Rev. Virology 2(1):351-78.
14. Sun, L., Zhang, X., Gao S., Rao, P.A., Padilla-Sanchez V., Chen, Z., Sun, S., Xiang, Y., Subramaniam S., Rao, V.B. & Rossmann, M.G. (2015) Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Nature Communications 6:7548.
15. Vafabakhsh, R., Kondabagil, K., Earnest, T. M., Lee, K. S., Zhang, Z., Dai, L., Dahmen, K. A., Rao, V. B. and Ha, T. (2014) Single-molecule packaging initiation in real time by a viral DNA packaging machine from bacteriophage T4. Proc. Natl. Acad. Sci. USA 111(42):15096-15101.
16. Migliori, A. D., Kellera, N., Alam, T. I., Mahalingam, M., Rao, V. B., Arya, G., and Smith, D. E. (2014) Evidence for an electrostatic mechanism of force generation by the bacteriophage T4 DNA packaging motor. Nature Communications 5: 4173.
17. Tao, P., Mahalingham, M., Kirtley, M., van Lier, C. J., Sha, J., Yeager, L. A., Chopra, A. K. and Rao, V. B. (2013). Mutated and bacteriophage T4 nanoparticle arrayed F1-V immunogens from Yersenia pestis as next generation plague vaccines. PLOS Pathogens 9(7): e1003495.
18. Tao, P., Mahalingham, M., Marasa, B., Chopra, A. and Rao, V. B. (2013). In vitro and in vivo delivery of genes and proteins using the bacteriophage T4 DNA packaging machine. Proc. Natl. Acad. Sci. USA 110:5846-5851.
19. Kottadiel VI, Rao VB, Chemla YR. (2012) The dynamic pause-unpackaging state, an off-translocation recovery state of a DNA packaging motor from bacteriophage T4. Proc. Natl. Acad. Sci. U S A. 109:20000-20005.
20. Black, L.W. and Rao, V.B. (2012) Structure, Assembly, and DNA packaging of bacteriophage T4 head Adv. Virus Res. 82:119-153.
21. Sun S, Gao S, Kondabagil K, Xiang Y, Rossmann MG, Rao VB. (2012) Structure and function of the small terminase component of the DNA packaging machine in T4-like bacteriophages. Proc Natl Acad Sci U S A. 109(3):817-22.
22. Kondabagil, K., Draper, B., Rao, V.B. (2012). Adenine recognition is a key checkpoint in the energy release mechanism of phage T4 DNA packaging motor. J. Mol. Biol. 415(2):329-42.
23. Zhang, Z., Kottadiel, V., Vafabakhsh, R., Li, Dai, Chemla,Y.R., Ha, T.J. and Rao, V.B. (2011) A promiscuous DNA packaging machine from bacteriophage T4. PLOS Biology 9:e1000592, 1-11.
24. Rao, M., Peachman, K., Li, Q., Matyas, G., Shivachandra, S., Borschel, R., Morthole, V.I., Fernandez-Prada, C. R., Alving, C. and Rao, V.B. (2011) Highly effective generic adjuvant systems for orphan or poverty-related vaccines. Vaccine 29:873-877.
25. Sun, S., Rao, V.B. and Rossmann, M. Genome packaging in viruses. (2010) Curr. Opin. Struct. Biol. 20 (1):114-120.
26. Rao, V. B. (2009) A virus DNA gate: zipping and unzipping the packed viral genome. Proc. Natl. Acad. Sci. USA 106: 8403-8404.
27. Sun, S, Kondabagil, K., Draper, B., Alam, I.T., Baumann, V., Zhang, Z., Hegde., Fokine, A., Rossmann, M.G., and Rao, V.B. (2008) The atomic structure of bacteriophage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135:1251-1262. This paper was featured as a "LEADING EDGE" article; Williams, R.S., Williams, G.J. and Tainer, J.A. Cell 135:1169-71.
28. Rao, V.B. and Feiss, M. The bacteriophage DNA packaging motor. (2008). Ann. Rev. Genetics 42:642-681.
29. Fuller, D. N., Raymer, D. M., Kottadiel, V. I., Rao, V. B. and Smith, D. E. (2007). Single Phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability. Proc. Natl. Acad. Sci. U.S.A. 104:16868-16873.
30. Sun S, Kondabagil K, Gentz PM, Rossmann MG, and Rao V. B. (2007). The Structure of the ATPase that Powers DNA Packaging into Bacteriophage T4 Procapsids. Mol. Cell. 25(6):943-949.