Molecular determinants of genomic integrity and plasticity

The blueprint of life is resident in the genome of every organism. For all cellular processes to function optimally, the integrity of the genome has to be maintained. Conversely, plasticity in the genome can relieve selection pressure imposed by an adverse environment. These two conflicting requirements have led to the presence of molecules and pathways that either prevent or facilitate changes in the genome. The antagonistic action of these two different sets of molecules probably ensures that genomic plasticity is calibrated to endow adaptive capability without severely compromising genetic viability. We aim to unearth the mechanism utilized by these molecular throttles of evolution to achieve function. These studies will provide valuable insights into how organisms evolve and adapt to the environment.

The biological processes under scrutiny in the laboratory currently are (i) DNA replication, (ii) DNA Mismatch Repair, (iii) Genome replication in RNA viruses, (iv) Stress-Induced Mutagenesis, and (v) Transposition. The first two processes ensure that the integrity of the information resident within the genome is maintained. The last two processes are responsible for enhancing phenotypic diversity to allow the presentation of multiple phenotypes for natural selection and thus drastically heighten the probability of adaptation. The third process- replication of RNA viruses- may be accurate and error-prone during different stages of genome duplication.

Using structural tools in conjunction with relevant biochemical methods and allied biophysical techniques, we aim to provide structural insight into the mechanism of action of enzymes and their functional complexes that are critical in each of these processes. Through ongoing and new collaborative efforts, we aim to shed more light on the relationship between the structure, biochemistry, and biological function of molecules under scrutiny. A clear mechanistic understanding of the activity of these molecules will provide deep insight into how these molecules impact the ability of an organism to survive and propagate in diverse environments.

More than 150 years ago, Darwin postulated that new species arise through natural selection of genetic variations. Through studies on molecules that influence the appearance of these variations, we aim to contribute towards developing a deeper and more fundamental understanding of how biological organisms evolve and adapt. Also, the information derived from our studies can be exploited to identify inhibitors that can be developed into novel drugs against pathogenic bacteria and viruses.

• Dr. Tuleshwori Sapam
  Project Staff
• Patterson Clement
  PhD Student
• Dalchand Sharma
  PhD Student
• AbhayDeep Pandey
  PhD Student
• V. Thangaraj
  PhD Student
• Bhawna Mawri
  PhD Student
• Vaibhav Joshi
  PhD Student
• Ritika
  PhD Student
• Dhiraj Kumar
  PhD Student
• Dr. Namadurai Sivakumar
  Project Staff
• Amith Babu
  Project Staff
• Amit Rathore
  Project Staff
• Abhishek Kumar
  Shared Laboratory Attendant

• Shanti Swarup Bhatnagar Prize in Life Sciences (CSIR)
• National Bioscience Award for Career Development (Department of Biotechnology)
• Ramanujan Fellowship (Department of Science & Technology) 2008-2013
• Member, Guha Research Conference
• Fellow of the Indian National Science Academy, New Delhi.

1. Clement, P. C., Sapam, T, and Nair, D. T. § (2024) A conserved polar residue plays a critical role in mismatch detection in A-family DNA polymerases. Int J Biol Macromol. 131965. doi: 10.1016/j.ijbiomac.2024.131965. PMID: 38697428.
2. Parray, H. A., Narayanan, N., Garg, S., Rizvi, Z. A., Shrivastava, T, Kushwaha, S., Singh, J., Murugavelu, P., Anantharaj, A., Mehdi, F., Raj, N., Singh, S., Dandotiya, J., Lukose, A., Jamwal, D., Kumar, S., Chiranjivi, A. K., Dhyani, S., Mishra, N., Kumar, S., Jakhar, K., Sonar, S., Panchal, A. K., Tripathy, M. R., Chowdhury, S. R., Ahmed, S., Samal, S., Mani, S., Bhattacharyya, S., Das, S., Sinha, S., Luthra, K., Batra, G., Sehgal, D., Medigeshi, G. R., Sharma, C., Awasthi, A., and Garg, P. K.§, Nair, D. T.§, Kumar R§. (2022) A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern. PLoS Pathog. 18(12):e1010994. doi: 10.1371/journal.ppat.1010994.
3. Jaiswal, D., Verma, S., Nair, D. T., and Salunke, D. M. (2022) Antibody multispecificity: A necessary evil? Mol Immunol. 152:153-161. doi: 10.1016/j.molimm.2022.10.012.
4. Sharma, M., and Nair, D. T.§ (2022) Pfprex from Plasmodium falciparum can bypass oxidative stress-induced DNA lesions. FEBS J. doi: 10.1111/febs.16414.
5. Bhatia, S., Narayanan, N., Nagpal, S., and Nair, D. T. § (2021) Antiviral therapeutics directed against RNA dependent RNA polymerases from positive-sense viruses. Mol. Aspects. Med. 81:101005.
6. Nagpal, S. and Nair, D. T. § (2021) The PHP domain of PolX from Staphylococcus aureus aids high fidelity DNA synthesis through the removal of misincorporated deoxyribo-, ribo- and oxidized nucleotides. Sci. Rep. 11:4178.
7. Narayanan, N. and Nair, D. T. § (2020) Ritonavir may inhibit exoribonuclease activity of nsp14 from the SARS-CoV-2 virus and potentiate the activity of chain terminating drugs. Int. J. Biol Macromol. 168:272-278.
8. Narayanan, N. and Nair, D. T. § (2020) Vitamin B12 May Inhibit RNA-Dependent-RNA Polymerase Activity of nsp12 from the SARS-CoV-2 Virus. IUBMB Life 72:2112-2120.
9. Sharma, M., Narayanan, N. and Nair, D. T. § (2020) The proofreading activity of Pfprex from Plasmodium falciparum can prevent mutagenesis of the apicoplast genome by oxidized nucleotides. Sci. Rep. 10:11157.
10. Jain, A., Kumar, A., Shikhi, M., Kumar, A., Nair, D. T. and Salunke, D. M. (2020) The structure of MP-4 from Mucuna pruriens at 2.22 Å resolution. Acta Crystallogr F Struct Biol Commun. 76:47-57.
11. Narayanan, N., Banerjee, A., Jain, D., Kulkarni, D. S., Sharma, R., Nirwal, S., Rao, D. N. and Nair, D. T. § (2020) Tetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress. J. Mol. Biol. 432:324-342.
12. Johnson, M. K., Kottur, J., and Nair, D. T. § (2019) A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res. 47:10693-10705.
13. Ghodke, P. P., Bommisetti, P., Nair, D. T.§, and Pradeepkumar, P. I.§ (2019) Synthesis of N(2)-Deoxyguanosine Modified DNAs and the Studies on Their Translesion Synthesis by the E. coli DNA Polymerase IV. J Org Chem. 84:1734-1747.
14. Shikhi, M., Nair, D. T., and Salunke, D. M. Structure-guided identification of function: role of Capsicum annuum vicilin during oxidative stress. (2018) Biochem J. 475:3057-3071.
15. Kottur, J., and Nair, D. T. § (2018) Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res. 46:5875-5885.
16. Sharma, R., Nirwal, S., Narayanan, N., and Nair, D. T. § (2018) Dimerization through the RING-Finger Domain Attenuates Excision Activity of the piggyBac Transposase. Biochemistry. 57:2913-2922.
17. Kumar, A., Kaur, H., Jain, A., Nair, D. T., and Salunke, D. M. (2018) Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens. Sci Rep. 8:689.
18. Nirwal, S., Kulkarni, D. S., Sharma, A., Rao, D. N. and Nair, D. T. § (2018) Mechanism of formation of a toroid around DNA by the Mismatch Sensor protein. Nucleic Acids Res. 46:256-266.
19. Salunke, D. M.§, Nair, D. T.§ (2017) Macromolecular structures: Quality assessment and biological interpretation. IUBMB Life. 69:563-571.
20. Kumar, A., Gupta, C., Nair, D. T. §, Salunke, D. M. § (2016) MP-4 Contributes to Snake Venom Neutralization by Mucuna pruriens Seeds through an Indirect Antibody-mediated Mechanism. J Biol Chem. 291:11373-84.
21. Kottur, J. and Nair, D. T.§ (2016) Reactive Oxygen Species Play an Important Role in the Bactericidal Activity of Quinolone Antibiotics. Angew Chem Int Ed Engl. 55:2397.
22. Ghodke, P. P., Gore, K. R., Harikrishna, S., Samanta, B., Kottur, J., Nair, D. T. § and Pradeepkumar, P. I. § (2016) The N(2)-Furfuryl-deoxyguanosine Adduct does not alter the structure of B-DNA. J. Org. Chem. 81:502.
23. Jain, D., Narayanan, N. and Nair, D. T.§ (2016) Plasticity in repressor-DNA interactions neutralizes loss of symmetry in bipartite operators. J. Biol. Chem. 291:1235.
24. Nair, D. T.§, Kottur, J. and Sharma, R. (2015) A rescue act: Translesion DNA synthesis past N(2)-deoxyguanosine adducts. IUBMB Life. 67:564.
25. Kottur, J., Sharma, A., Gore, K. R., Narayanan, N., Samanta, B., Pradeepkumar, P. I. and Nair, D. T.§ (2014) Unique Structural Features in DNA Polymerase IV enable efficient bypass of the N2-Adduct induced by the Nitrofurazone antibiotic. Structure 23:56.
26. Weinert, T., Olieric, V., Waltersperger, S., Panepucci, E., Chen, L., Zhang, H., Zhou, D., Rose, J., Ebihara, A., Kuramitsu, S., Li, D., Howe, N., Schnapp, G., Pautsch, A., Bargsten, K., Prota, A. E., Surana, P., Kottur, J., Nair, D. T., Basilico, F., Cecatiello, V., Pasqualato, S., Boland, A., Weichenrieder, O., Wang, B. C., Steinmetz, M. O., Caffrey, M. and Wang, M. (2014) Fast native-SAD phasing for routine macromolecular structure determination. Nat Methods. 12:131.
27. Surana, P., Vijaya, S. and Nair, D. T.§ (2014) RNA-dependent RNA polymerase of Japanese Encephalitis Virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. Nucleic Acids Res. 42:2758.
28. Sharma A., Kottur, J., Narayanan, N. and Nair, D. T.§ (2013) A strategically located serine residue is critical for the mutator activity of DNA Polymerase IV from Escherichia coli. Nucleic Acids Res. 41:5104
29. Jain, D. and Nair, D. T§ (2013) Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators. Nucleic Acids Research. 41:639.
30. Sharma, A., Subramanian, V. and Nair, D. T.§ (2012) The PAD region in the mycobacterial dinB homolog MsPolIV exhibits positional heterogeneity. Acta Crystallogr D Biol Crystallogr. 68:960.
31. Sharma, A. and Nair, D. T.§ (2012) MsDpo4—a DinB Homolog from Mycobacterium smegmatis—is an Error-Prone DNA Polymerase that can Promote G:T and T:G Mismatches. Journal of Nucleic Acids, vol. 2012, Article ID 285481.
32. Sharma A. and Nair, D. T.§ (2011) Cloning, expression, purification, crystallization and preliminary crystallographic analysis of MsDpo4: a Y-family DNA polymerase from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 67:812.
33. Namadurai, S., Jain, D., Kulkarni, D. S., Tabib, C. R., Friedhoff, P., Rao, D. N. and Nair, D. T.§. (2010) The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. PLoS One. 5:e13726.
34. Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S. and Aggarwal, A. K. (2011) DNA Synthesis across an Abasic Lesion by Yeast Rev1 DNA Polymerase. J Mol Biol. 406:18.
35. Jain, R., Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009) Replication across template T/U by human DNA polymerase-iota. Structure. 17:974.
36. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2009) DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure. 17:530.
37. Gupta, Y.K., Nair, D.T., Wharton, R. P., and Aggarwal, A. K. (2008). Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity. Structure. 16:549.
38. Nair, D.T.*, Johnson, R. E.*, Prakash, S., Prakash, L. and Aggarwal, A. K. (2008) Protein-template directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA Polymerase. Structure. 16:239.
39. Lone, S.*, Townson, S. A.*, Uljon, S. N.*, Johnson, R. E., Brahma, A., Nair, D.T., Prakash, S., Prakash, L. and Aggarwal, A. K. (2007) Human DNA Polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Mol. Cell. 25:601.
40. Nair, D.T.*, Johnson, R. E.*, Prakash, S., Prakash, L. and Aggarwal, A. K. (2006) Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA Polymerase iota. Nat. Struct. Mol. Biol. 13:619.
41. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2006) Incoming nucleotide imposes a syn conformation on templating purine in the human DNA polymerase –ι active site. Structure (Camb). 14:749
42. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2005) Human DNA Polymerase iota incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure (Camb). 13:1569.
43. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science. 309:2219
44. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2005) Hoogsteen base-pairing in DNA replication? (reply) Nature 437, E7.
45. Nair, D.T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2004) Replication by human DNA polymerase-iota occurs by Hoogsteen base- pairing. Nature. 430:377
46. Nair, D.T., Kaur, K. J., Singh, K., Mukherjee, P., Rajagopal, D., George, A., Bal, V., Rath, S., Rao, K. V. and Salunke, D. M. (2003) Mimicry of native peptide antigens by the corresponding retro-inverso analogs is dependent on their intrinsic structure and interaction propensities. J. Immunol. 170:1362
47. Nair, D.T., Singh, K., Siddiqui, Z., Nayak, B. P., Rao, K. V. S. and Salunke, D. M. (2002) Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. J. Immunol. 168:2371.
48. Nayak, S.K., Bagga, S., Gaur, D., Nair, D.T., Salunke, D.M. and Batra, J.K. Mechanism of specific target recognition and RNA hydrolysis by ribonucleolytictoxin restrictocin. (2001) Biochemistry. 40:9115.
49. *Jain, D., *Nair, D.T., Swaminathan, G. J., Abraham, E.G., Nagaraju, J. and Salunke, D.M. (2001) Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antherea mylitta: Implications to molecular evolution. J. Biol. Chem. 276:41377.
50. 50. Nair, D.T., Singh, K., Shahu, N., Rao, K. V. S. and Salunke, D. M. (2000). Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition. J. Immunol. 165:6949.

(*Equal contribution, §= corresponding author)