Protein synthesis in pathogenic microbes & structure-based drug design

Our research focuses on protein synthesis and ribosome assembly in pathogenic microbes, mainly Mycobacterium tuberculosis (Mtb), which causes the deadliest disease, tuberculosis, and Entamoeba histolytic (Eth), which causes amoebiasis. Protein synthesis is a fundamental cellular process that consumes nearly half of the cell's resources, and ~ 40% of the known antibiotics target the protein synthesis machinery, the ribosome. The research aims to find how pathogens survive under stresses by regulating translation machinery and exploit these features for novel inhibitor design.

In Mtb, the research focuses on understanding how the pathogen survives for decades in the hostile environment of the host macrophage in a dormant state. It is also believed that nearly one-third of the world’s population possesses the dormant Mtb, which serves as a huge reservoir for tuberculosis infection. We have reported a cryo-EM structure M. smegmatis ribosome, in complex with RafH protein at 2.8 Å resolution in Nature Communication . RafH is a hypoxia stress induced ribosome hibernation promotion factor. In the near future, we would like to understand mycobacterial survival under nutrition starvation and multiple stresses.

In Eth, our laboratory has reported the cryo- EM structure of its ribosome at 2.8 Å resolution, preprint available in bioRxive. This study reveals several unique features such as rRNA triple helix and helical assembly of Eth ribosome. In future we would like to determine its functional complexes, and understand the structural based of helical assembly.

Ribosomes, the mega Dalton sizes complexes, must assemble accurately to perform error-free translation. Defects in ribosome assembly, are associated with diseases such as cancer, age-related degenerative diseases, and aging. We aim to understand the ribosome assembly process by depleting the ribosome assembly factors such as GTPase, EngA, RhlE and DeaD, and trapping ribosomes in an assembly intermediate stage. Ultimately determining the cryo-EM structure of assembly intermediates.

• EMSI Excellence in Microscopy Award (2023)
• EMBL Corporate Partnership Programme Fellowship (2023)
• DST-SERB Early Career Research Award (2019)

Highly motivated researchers interested in structural biology, particularly, in Cryo- electron microscopy (Cryo- EM) and X-ray crystallography are requested to contact directly to the PI.

• Niraj Kumar
  Senior Research Fellow

• Ankita Arora
  Senior Research Fellow

• Shivani Sharma
  Senior Research Fellow

• Soumen Ta
  Junior Research Fellow

• Tajamul Islam
  Integrated MS-PhD student

• Ruchika Kumari
  Junior Research Fellow (Project)

• Tejas Nimkar
  Junior Research Fellow (project)

• Parthasarathi Behera
  Junior Research Fellow (project)

1. Sharma S, Mishra S, Gourinath S, Kaushal PS (2024). Cryo- EM structure of ribosome from pathogenic protozoa Entamoeba histolytica, reveals unique features of its architecture. BioRxiv https://doi.org/10.1101/2024.04.29.591517;15(1):638.
2. Kumar N, Sharma S, Kaushal PS. Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Nat Commun. 2024 Jan 20;15(1):638. doi: 10.1038/s41467-024-44879-y
3. Prajapat SK, Mishra L, Khera S, Owusu SD, Ahuja K, Sharma P, Choudhary E, Chhabra S, Kumar N, Singh R, Kaushal PS, Mahajan D, Banerjee A, Motiani RK, Vrati S, Kalia M. Methotrimeprazine is a neuroprotective antiviral in JEV infection via adaptive ER stress and autophagy. EMBO Mol Med. 2024 Jan;16(1):185-217. doi: 10.1038/s44321-023-00014-w. Epub 2024
4. Arora A, Kaushal PS (2023). Cryo-EM in the study of ribosome biogenesis. Cryo- Electron Microscopy in Structural Biology. CRC Press Taylor & Francis Group. (Accepted)
5. Kumar N, Sharma S, Kaushal PS (2023). Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH, reveals the unique mode of mycobacterial ribosome hibernation. BioRxiv https://doi.org/10.1101/2023.04.18.537051.
6. Pal P, Khan MY, Sharma S, Kumar Y, Mangla N, Kaushal PS, Agarwal N.ResR/McdR-regulated protein translation machinery contributes to drug resilience in Mycobacterium tuberculosis. Commun Biol. 2023 Jul 11;6(1):708. doi: 10.1038/s42003-023-05059-8. PMID: 37433855
7. Agarwal N, Sharma S, Pal P, Kaushal PS, Kumar N. (2022) Era, a GTPase-like protein of the Ras family, does not control ribosome assembly in Mycobacterium tuberculosis. Microbiology (Reading). 2022 Aug;168(8). doi: 10.1099/mic.0.001200. PMID: 35917161.
8. Kumar N, Sharma S & Kaushal PS. (2021) Protein synthesis in Mycobacterium tuberculosis as a potential target for therapeutic interventions. Molecular Aspects of Medicine, https://doi.org/10.1016/j.mam.2021.101002.
9. Koripella RK, Sharma MR, Bhargava K, Datta PP, Kaushal PS, Keshavan P, Spremulli LL, Banavali NK & Agrawal RK. (2020) Structures of the human mitochondrial ribosome bound to EF-G1 reveal distinct features of mitochondrial translation elongation. Nat Commun 11, 3830 https://doi.org/10.1038/s41467-020-17715-2.
10. Li Y, Sharma MR, Koripella RK, Yong Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, & Ojha AK. (2018)Zinc depletion induces ribosome hibernation in mycobacteria. Proceedings of the National Academy of Sciences USA (PNAS) 115:8191-6.
11. Qu G *, Kaushal PS*, Wang J*, Shigematsu H, Piazza CL, Agrawal RK, Belfort M & Wang HW. Structure of group II intron complexed with its transcriptase. (2016) Nature Structure and Molecular Biology (NSMB) 23, 549-57. (*equal contributions). Highlighted as the News and Views in NSMB 23, 507-9 and a follow up review in RNA BIOLOGY 13, 1218-22.
12. Kaushal PS, Sharma MR and Agrawal RK. (2015) The 55S mammalian mitochondrial ribosome and its tRNA-exit region. Biochimie. 114, 119-26.
13. Kaushal PS*, Sharma MR*, Booth TM, Haque E, Tung C, Sanbonmatsu KY, Spremulli LL and Agrawal R K. (2014) Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome. Proceedings of the National Academy of Sciences USA (PNAS) 111(20), 7284-9 (*equal contributions).
14. Sharma MR, Kaushal PS, Gupta M, Banavali N K, & Agrawal RK. (2013) Insights into structural basis of mammalian mitochondrial translation. In Translation in Mitochondria and Other Organelles, Duchene, A.M. ed. (Springer-Verlag, Berlin/ Heidelberg), pp. 1-28
15. Ahmad MF, Kaushal PS, Wan, Q, Wijeratna SR, An X, Huang M & Dealwis CD. (2012) Role of arginine-293 and glutamine-288 in communication between catalytic and allosteric sites in yeast ribonucleotide reductase. Journal of Molecular Biology 419, 315-29.
16. Kaushal PS, Wan Q, Faber C, & Dealwis C. (2012) Crystal dehydration Technique. In Crystallography: Research, Technology and Applications, Hokkaido, M. and Nagano, E. ed. (Nova Science Publishers, Inc.), pp. 91-104.
17. Wijerathna SR, Ahmad MF, Xu H, Fairman JW, Zhang A, Kaushal PS, Wan Q, Kiser J & Dealwis CG. (2011) Targeting the Large Subunit of Human Ribonucleotide Reductase for Cancer Chemotherapy. Pharmaceuticals, 4(10),1328-54.
18. Kaushal PS, Singh P, Sharma A, Muniyappa K & Vijayan M. (2010) X-ray and molecular dynamics studies on Mycobacterium leprae single-stranded DNA binding protein and comparison with other eubacterial SSB structures. Acta Crystallographica D66, 1048-58.
19. Kaushal PS, Talawar RK, Varshney U & Vijayan M. (2010) Structure of uracil-DNA glycosylase from Mycobacterium tuberculosis. Insights into interactions with ligands. Acta Crystallographica F66, 887-92 (cover illustration).
20. Kaushal PS, Talawar RK, Krishna PD, Varshney U & Vijayan M. (2008). Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources.Acta Crystallographica D64, 551-560.
21. Kaushal PS, Sankaranarayanan R & Vijayan M. (2008) Water-mediated variability in the structure of relaxed-state haemoglobin. Acta Crystallographica F64, 463-9.
22. Singh P, Talawar RK, Krishna PD, Varshney U & Vijayan M. (2006) Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor. Acta Crystallographica F62, 1231-4.