# Valakunja Nagaraja
**Valakunja Nagaraja** (born 1954) is an Indian molecular biologist known for work on protein-nucleic acid interactions, restriction-modification systems, DNA topology, and the molecular biology of *Mycobacterium tuberculosis*, the bacterium that causes tuberculosis.[1](https://ssbprize.gov.in/Content/Detail.aspx?AID=205) • [2](https://fellows.ias.ac.in/profile/v/FL1999012) His laboratory at the [Indian Institute of Science](https://www.edgepedia.org/indian-institute-of-science) (IISc) in [Bangalore](https://www.edgepedia.org/bangalore) studies DNA topoisomerases and nucleoid-associated proteins of *M. tuberculosis* using genetics, biochemistry, structural biology, and cell biology.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) The IISc Microbiology and Cell Biology department page lists him as Honorary Professor.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja)
| Key fact | Detail |
|---|---|
| Field | Molecular biology: protein-nucleic acid interactions, restriction-modification systems, mycobacterial gene regulation[2](https://fellows.ias.ac.in/profile/v/FL1999012) |
| Born | 1954[1](https://ssbprize.gov.in/Content/Detail.aspx?AID=205) |
| Career record | became President of JNCASR[4](https://orcid.org/0000-0002-3298-8741) |
| Signature work | Targeting *M. tuberculosis* nucleoid-associated protein HU with structure-based inhibitors (*Nature Communications*, 2014)[6](https://doi.org/10.1038/ncomms5124) |
| Major honors | Shanti Swarup Bhatnagar Prize (1999, Biological Sciences); TWAS Prize in Biology (2011)[1](https://ssbprize.gov.in/Content/Detail.aspx?AID=205) • [7](https://twas.org/directory/nagaraja-valakunja) |
| Fellowships | Fellow of the Indian Academy of Sciences (1999); FNA, FNASc, FTWAS[2](https://fellows.ias.ac.in/profile/v/FL1999012) |
## Education and career
According to a 1985 *Journal of Molecular Biology* paper on two type I restriction enzymes from *Salmonella*, with Thomas A. Bickle as corresponding author, he carried a University of Basel affiliation, corroborating the Basel period.[8](https://doi.org/10.1016/0022-2836(85)90243-8)
His ORCID record lists him as President of JNCASR, Bengaluru, and Professor of Microbiology and Cell Biology at IISc.[4](https://orcid.org/0000-0002-3298-8741) According to IBAB, he is also a Professor at the Institute of Bioinformatics and Applied Biotechnology (IBAB) alongside his IISc professorship.[5](https://www.ibab.ac.in/prof-v-nagaraja/)
## Research
His laboratory works on how the bacterial genome, which is supercoiled and compacted into a nucleoid, is organized by the combined action of topoisomerases and nucleoid-associated proteins (NAPs), studied in *M. tuberculosis* with genetics, biochemistry, structural, and cell biology approaches.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) A 2004 *Current Science* review by Nagaraja explains that the contrasting activities of DNA topoisomerase I and [DNA gyrase](https://www.edgepedia.org/dna-gyrase) maintain topological homeostasis in mycobacteria, and that many aspects of their organization and regulation differ from *Escherichia coli*.[9](https://repository.ias.ac.in/26993/)
On DNA gyrase, the group demonstrated the enzyme's dual role in supercoiling and decatenation, showed that the molecular basis of the switch between the two activities is binding of a second DNA to the GyrB subunit, and developed peptide inhibitors specific to mycobacterial gyrase with a novel mechanism of action.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) The group also established the mechanism of autoregulation of gyrase and topoisomerase I expression, and reported transcription-facilitated genome-wide recruitment of topoisomerase I and DNA gyrase in a 2017 *PLoS Genetics* paper.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) Earlier work on restriction-modification included a 2012 PNAS study showing that promiscuous restriction is a cellular defense strategy conferring a fitness advantage to bacteria.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja)
## Representative work
His 2014 *Nature Communications* paper, "Targeting *Mycobacterium tuberculosis* nucleoid-associated protein HU with structure-based inhibitors", reported small-molecule inhibitors of the HU protein designed from structure. The inhibitors bind the DNA-binding cleft, displace DNA, de-compact the nucleoid, and inhibit *M. tuberculosis* growth.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) • [6](https://doi.org/10.1038/ncomms5124) The laboratory cloned, expressed, and purified the HU protein, deciphered its three-dimensional structure, and identified small molecules that bind a key pocket in the protein; an IISc feature notes this was the first time proteins of this class had been targeted for inhibition from any organism.[10](http://www.iisc.ac.in/wp-content/uploads/2016/03/Nagaraja_Ramakumar_Final.pdf)
## Tuberculosis drug discovery
The laboratory's drug-discovery program targets essential mycobacterial proteins through an approach of understanding pathogen biology to develop inhibitors that kill the pathogen; the group has either developed inhibitors that curtail bacterial growth or constructed knock-down strains to down-regulate expression of essential proteins and disturb cellular function.[11](https://www.icts.res.in/colloquium/2025-02-18/valakunja-nagaraja) A 2016 *Drug Discovery Today* review co-authored by Nagaraja framed the rationale: tuberculosis is the deadliest bacterial disease in the world, DNA gyrase has been extensively targeted, including the clinically successful fluoroquinolones used in TB therapy, while bacterial topoisomerase I has yet to be exploited as a target for clinical antibiotics.[12](https://doi.org/10.1016/j.drudis.2016.11.006) His group's work on gyrase peptide inhibitors and HU small molecules addresses the exploited target in that framing.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja)
A 2023 *Nature Communications* paper with Nagaraja as corresponding author showed that *M. tuberculosis* secretes the methyltransferase Rv2067c into macrophages, trimethylating histone H3K79 in a non-nucleosomal context. Rv2067c downregulates the host methyltransferase DOT1L, decreasing H3K79me3 on pro-inflammatory response genes, inhibiting caspase-8-dependent apoptosis, and enhancing RIPK3-mediated necrosis, which increases pathogenesis; the paper also provided structures of Rv2067c and DOT1L explaining how their action on H3K79 is spatially and temporally separated.[13](https://doi.org/10.1038/s41467-023-43940-6)
## Honors and recognition
Nagaraja received the Shanti Swarup Bhatnagar Prize in 1999 in Biological Sciences; the citation credits his work on mycobacterial topoisomerases as laying the basis for new drug discovery.[1](https://ssbprize.gov.in/Content/Detail.aspx?AID=205) He received the TWAS Prize in Biology in 2011.[7](https://twas.org/directory/nagaraja-valakunja) His other awards include the J C Bose Fellowship of the Department of Science and Technology, the J C Bose Medal of the Indian National Science Academy, and the IISc Alumni Award for Excellence in Research; he is a Fellow of all the Science Academies in India and of TWAS (FNA, FNASc, FTWAS).[5](https://www.ibab.ac.in/prof-v-nagaraja/) • [2](https://fellows.ias.ac.in/profile/v/FL1999012) He was elected Fellow of the Indian Academy of Sciences in 1999 under the General Biology section and served on its Council from 2019 to 2024.[2](https://fellows.ias.ac.in/profile/v/FL1999012)
## Recent developments
Nagaraja has remained active as corresponding author from JNCASR. In June 2024 he was corresponding author, from JNCASR, of a *Molecular Microbiology* review on the nucleoid-associated proteins of mycobacteria, and in November 2024 a *Trends in Microbiology* review on epigenetic maneuvering as an emerging strategy for mycobacterial intracellular survival.[14](https://doi.org/10.1111/mmi.15287) • [15](https://doi.org/10.1016/j.tim.2024.10.007) On 18 February 2025 he gave an ICTS colloquium in Bengaluru, listed with his IISc affiliation, titled on how to tackle resurgent drug-resistant tuberculosis, describing his group's inhibitor and knock-down strain approaches.[11](https://www.icts.res.in/colloquium/2025-02-18/valakunja-nagaraja) The IISc department page lists him as Honorary Professor in [Microbiology](https://www.edgepedia.org/microbiology) and Cell Biology, while his ORCID record and IBAB profile list him as Professor.[3](https://mcb.iisc.ac.in/research-single/prof-v-nagaraja) • [4](https://orcid.org/0000-0002-3298-8741)
## References
1. Awardee Details: Shanti Swarup Bhatnagar Prize. https://ssbprize.gov.in/Content/Detail.aspx?AID=205
2. Prof. Valakunja Nagaraja, Indian Academy of Sciences fellowship record. https://fellows.ias.ac.in/profile/v/FL1999012
3. Research Themes, Prof. V Nagaraja, Department of Microbiology and Cell Biology, IISc. https://mcb.iisc.ac.in/research-single/prof-v-nagaraja
4. Valakunja Nagaraja (0000-0002-3298-8741), ORCID. https://orcid.org/0000-0002-3298-8741
5. Prof. V. Nagaraja, Institute of Bioinformatics and Applied Biotechnology. https://www.ibab.ac.in/prof-v-nagaraja/
6. Targeting *Mycobacterium tuberculosis* nucleoid-associated protein HU with structure-based inhibitors, *Nature Communications* (2014). https://doi.org/10.1038/ncomms5124
7. Nagaraja, Valakunja, TWAS directory. https://twas.org/directory/nagaraja-valakunja
8. https://doi.org/10.1016/0022-2836(85)90243-8
9. Nagaraja, V. (2004) Regulation of DNA topology in mycobacteria, *Current Science* 86(1):135-140. https://repository.ias.ac.in/26993/
10. Combating tuberculosis, IISc Connect feature. http://www.iisc.ac.in/wp-content/uploads/2016/03/Nagaraja_Ramakumar_Final.pdf
11. How do we tackle the resurgent drug-resistant tuberculosis? ICTS colloquium, 18 February 2025. https://www.icts.res.in/colloquium/2025-02-18/valakunja-nagaraja
12. DNA topoisomerase I and DNA gyrase as targets for TB therapy, *Drug Discovery Today* (2016). https://doi.org/10.1016/j.drudis.2016.11.006
13. The *Mycobacterium tuberculosis* methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival, *Nature Communications* (2023). https://doi.org/10.1038/s41467-023-43940-6
14. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor, *Molecular Microbiology* (2024). https://doi.org/10.1111/mmi.15287
15. Epigenetic maneuvering: an emerging strategy for mycobacterial intracellular survival, *Trends in Microbiology* (2024). https://doi.org/10.1016/j.tim.2024.10.007
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in immunology, microbiology, and virology*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026 · Edited: Sep 25, 2026; Oct 12, 2026; Oct 15, 2026 · Last review: Sep 25, 2026*
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