Vidhyadhar Nandana

Vidhyadhar Nandana

Research interest(s)/area of expertise

Biochemical and biophysical characterization of protein-protein interactions, protein-RNA interactions, ribonucleoprotein complexes and biomolecular condensates in eukaryotic and bacterial gene regulation processes.

Research

Proteomic investigation of Bacterial Ribonucleoprotein body (BR-body):
Rationale: BR-bodies are biomolecular condensates that organize mRNA decay in bacteria by concentrating main endonuclease RNase E and the DEAD-box ATPase RhlB. In contrast, their eukaryotic counterparts, P-bodies and stress granules, contain hundreds of proteins. Are BR-bodies simple compartments, or do they exhibit a complexity similar to that of eukaryotic condensates?
Outcome and significance: Employing mass-spectrometry, in vitro and in vivo reconstitutions and microscopy techniques, we found that BR-bodies are enriched with about 111 proteins, and they are regulated by a complex network of protein-protein and protein-RNA interactions. The finding that client proteins can regulate BR-body assembly in the cells may help to design strategies to manipulate their assembly, thereby providing an opportunity to enhance/disrupt key biochemical processes within those condensates in bacteria including pathogenic bacteria.

Nandana, V., Rathnayaka-Mudiyanselage, I.W., Muthunayake, N.S., Hatami, A. Mousseau, C.B., Ortiz-Rodríguez, L.A., Vaishnav, J., Collins, M., Gega, A., Mallikaarachchi, K.S., Yassine, H., Ghosh,A., Biteen, J.S., Zhu, Y., Champion, M.M., Childers, W.S., Schrader, J.M. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions (2023). https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01241-X

Reconstitution of multiprotein-RNA condensates for biochemical and structural analyses:
Rationale and significance: RNA binding proteins containing intrinsically disordered regions play a key role in both bacterial and eukaryotic RNA metabolisms. Such proteins are often shown to form condensates in the cell. Reconstituting functional ribonucleoprotein condensates in vitro provides opportunity to investigate condensate microenvironment mediated regulation of macromolecular interactions and as well as the enzymatic activity of nucleases, ATPases and other associated enzymes. These reconstituted condensates serve as ideal samples for structural determination using cryo-electron microscopy, and the insights gained can be used to better understand and target condensates within living cells.

Nandana, V., Al-Husini, N., Vaishnav, A., Dilrangi, K.H., and Schrader, J.M. Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness (2024). https://www.molbiolcell.org/doi/full/10.1091/mbc.E23-12-0493

Collins M, Tomares D, Nandana V, Schrader J.M, Childers S.W. RNase E biomolecular condensates stimulate PNPase activity (2023). https://www.nature.com/articles/s41598-023-39565-w

Education

News mentions

 https://clas.wayne.edu/biology/news/vidhyadhar-nandana-awarded-wsu-postdoctoral-research-award-56805

Selected publications

• Luis A. Ortiz-Rodríguez, Hadi Yassine, Vidhyadhar Nandana, Christopher A. Azaldegui, Jiayu Cheng, Jared M. Schrader, Julie S. Biteen. Stress Changes the Bacterial Biomolecular Condensate
  Material State and Shift Function from mRNA Decay to Storage. Preprint: https://www.biorxiv.org/content/10.1101/2024.11.12.623272v1
  
• Nandana, V., Al-Husini, N., Vaishnav, A., Dilrangi, K.H., and Schrader, J.M. (2024). Caulobacter crescentus RNase E condensation contributes to autoregulation and fitness. MBoC, mbc.E23-12-0493
• Rathnayaka-Mudiyanselage, I.W, Nandana V, Schrader, J.M. Proteomic comparison of eukaryotic and bacterial RNA decay condensates suggests convergent evolution. Current Opinion in Microbiology 2024, 79:102467
• Nandana, V., Rathnayaka-Mudiyanselage, I.W., Muthunayake, N.S., Hatami, A. Mousseau, C.B., Ortiz-Rodríguez, L.A., Vaishnav, J., Collins, M., Gega, A., Mallikaarachchi, K.S., Yassine, H., Ghosh, A., Biteen, J.S., Zhu, Y., Champion, M.M., Childers, W.S., Schrader, J.M. The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions. Cell Reports 2023, 42 (10), 113229
• Collins M, Tomares D, Nandana V, Schrader J.M, Childers S.W. RNase E biomolecular condensates stimulate PNPase activity. Sci Rep 13, 12937 (2023).
• Ghosh A, Bharmal M.H, Ghaleb A, Nandana V, Schrader J.M. Initiator AUGs are discriminated from elongator AUGs predominantly through mRNA accessibility in C. crescentus. Journal of Bacteriology 2023, Vol. 205, No. 5.
• Nandana V, Schrader J.M. Roles of liquid–liquid phase separation in bacterial RNA metabolism. Current Opinion in Microbiology 2021, 61:91–98
• Nandana V, Singh S, Singh AN, Dubey VK. Procerain B, a cysteine protease from Calotropis procera, requires N-terminus pro-region for activity: cDNA cloning and expression with pro- sequence. Protein Expr Purif. 2014;103: 16–22.

Citation index

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