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) Stress- Induced mutagenesis (ii) Stress- induced epigenetic modifications (iii) Transposition (iv) Mechanism and fidelity of replication of the RNA genome of the Japanese Encephalitis Virus (JEV) (v) Nucleotide Excision Repair (vi) DNA Mismatch Repair (vii) Regulation of recombination frequency. The first three processes are responsible to enhancing phenotypic diversity to allow presentation of multiple phenotypes for natural selection and thus drastically heighten the probability of adaptation. The last three processes ensure that the integrity of the information resident within the genome is maintained. The fourth process- replication of the JEV genome- may be accurate and error-prone during different stages of genome duplication.

Using X-ray crystallography as the primary tool in conjunction with relevant biochemical methods and allied biophysical techniques, we aim to provide structural insight into the mechanism of action of enzymes/enzyme-complexes that are critical in each of these processes. Through ongoing and new collaborative efforts, we aim to shed more light on the relation between biochemical and structural properties of these enzymes and their observed and predicted roles in physiology. 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. About 155 years ago, Darwin had 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 organisms evolve and adapt.

• Dr. Sunil Kumar Yadav
  Project Scientist II
  
• Dr. Aditya Sharma
  Project Scientist I
  
• Minakshi Sharma
  Senior Research Fellow
• 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
• Amith Babu
  Project Assistant
• Amit Rathore
  Laboratory Attendant
• Abhishek Kumar
  Shared Laboratory Attendant

• Shanti Swarup Bhatnagar Prize in Life Sciences (CSIR), 2017
• National Bioscience Award for Career Development (Department of Biotechnology) 2014
• Ramanujan Fellowship (Department of Science & Technology) 2008-2013
• Member, Guha Research Conference (2013 onwards)
• Fellow of the Indian National Science Academy (2023 onwards)

1. Jaiswal, D., Verma, S., Nair, D. T. & Salunke, D. M. (2022) Antibody multispecificity: A necessary evil? Mol. Immunol. 152:153-161.
2. Sharma M, and Nair DT. (2022) Pfprex from Plasmodium falciparum can bypass oxidative stress-induced DNA lesions. FEBS J, doi: 10.1111/febs.16414
3. 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. (in press) DOI: https://doi.org/10.1016/j.mam.2021.101005
4. 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.
5. Narayanan, N. and Nair, D. T. (2021) 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.
6. Narayanan N and Nair DT (2020) Vitamin B12 May Inhibit RNA-Dependent-RNA Polymerase Activity of nsp12 from the SARS-CoV-2 Virus. IUBMB Life, Doi: 10.1002/iub.2359
7. 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
8. 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.
9. Narayanan N, Banerjee A, Jain D, Kulkarni D.S., Sharma R, Nirwal S, Rao D.N, Nair D.T (2019) Tetramerization at low pH licenses DNA methylation activity of M.HpyAXI in the presence of acid stress. Journal of Molecular Biology | Doi.org/10.1016/j.jmb.2019.10.001
10. Johnson MK, Kottur J, Nair DT. (2019) A polar filter in DNA polymerases preventsribonucleotide incorporation. Nucleic Acids Res. (in press)
11. Ghodke PP, Bommisetti P, Nair DT, Pradeepkumar PI. (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
12. Shikhi M, Nair DT, Salunke DM. (2018) Structure-guided identification of function: role of Capsicum annuum vicilin during oxidative stress. Biochem J. | 475:3057.
13. Kottur J, Nair DT. (2018) Pyrophosphate hydrolysis is an intrinsic and critical step of the DNA synthesis reaction. Nucleic Acids Res. | 46:5875.
14. Nirwal S, Kulkarni D, Sharma A, Rao DN, Nair DT. (2018) Mechanism of formation of a toroid around DNA by the mismatch sensor protein. Nucleic Acids Res. 46:266
15. Sharma R, Nirwal S, Narayanan N, Nair DT (2018) Dimerization through the RING-Finger Domain Attenuates Excision Activity of the piggyBac Transposase. Biochemistry. 57:2922
16. Salunke DM, Nair DT. (2017) Macromolecular structures: Quality assessment and biological interpretation. IUBMB Life 69:571
17. Nirwal S, Kulkarni DS, Sharma A, Rao DN, Nair DT (2017) Mechanism of formation of a toroid around DNA by the mismatch sensor protein Nucleic Acids Research (In Press)
18. Kumar A, Gupta C, Nair DT, Salunke DM. (2016) MP-4 contributes to snake venom neutralization by Mucuna pruriens seeds through an indirect antibody-mediated mechanism. J Biol Chem. pii: jbc.M115.699173. [Epub ahead of print] PubMed PMID: 26987900.
19. Kottur J. & Nair DT (2016) Reactive oxygen species play an important role in bactericidal activity of quinolone antibiotics. Angewandte Chemie 55: 2397
20. Ghodke PP, Gore KR, Harikrishna S, Samanta B, Kottur J, Nair DT, Pradeepkumar PI.(2015)  The N2-Furfuryl-Deoxyguanosine (fdG) Adduct Does Not Alter the Structure of B-DNA. J Org Chem. 81:502
21. Jain D, Narayanan N, Nair DT. (2015) Plasticity in repressor-DNA interactions neutralizes loss of symmetry in bipartite operators. J Biol Chem. (in press).
22. Nair DT, Kottur J, Sharma R (2015)  A rescue act: Translesion DNA synthesis past N2 -deoxyguanosine adducts. IUBMB Life 67:564.
23. Kottur J, Sharma A, Gore KR, Narayanan N, Samanta B, Pradeepkumar PI, Nair DT. (2015) Unique Structural Features in DNA Polymerase IV Enable Efficient Bypass of the N(2) Adduct Induced by the Nitrofurazone Antibiotic. Structure 23:56.
24. 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 AE, Surana P, Kottur J, Nair DT, Basilico F, Cecatiello V, Pasqualato S, Boland A, Weichenrieder O, Wang BC, Steinmetz MO, Caffrey M, Wang M. (2015) Fast native-SAD phasing for routine macromolecular structure determination. Nat Methods 12:131.
25. Surana P, Vijaya S, Nair DT. (2014) RNA-dependent RNA polymerase of Japanese Encephalitis Virus binds the initiator nucleotide GTP to form a mechanistically important pre-initiation state. Nucleic Acids Research 42:2758.
26. Sharma A, Kottur J, Narayanan N, Nair DT. (2013) A strategically located serine residue is critical for the mutator activity of DNA Polymerase IV from Escherichia coli. Nucleic Acids Research 41:5104.
27. Jain D, Nair DT. (2013) Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators. Nucleic Acids Research 41:639.
28. Sharma A, Subramanian V, Nair DT. (2012) The PAD region in the mycobacterial dinB homolog MsPolIV exhibits positional heterogeneity. Acta Crystallogr D Biol Crystallogr 68:960.
29. Sharma A, Nair DT. (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 2012:285481.
30. Sharma A, Nair DT. (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.
31. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK. (2011) DNA Synthesis across an Abasic Lesion by Yeast Rev1 DNA Polymerase. J Mol Biol 406:18.
32. Namadurai S, Jain D, Kulkarni DS, Tabib CR, Friedhoff P, Rao DN, Nair DT. (2010) The C-terminal domain of the MutL homolog from Neisseria gonorrhoeae forms an inverted homodimer. PLoS One 5:e13726.
33. Jain R, Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2009) Replication across template T/U by human DNA polymerase-iota. Structure 17:974.
34. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2009) DNA synthesis across an abasic lesion by human DNA polymerase iota. Structure 17:530.
35. Gupta YK, Nair DT, Wharton RP, Aggarwal AK. (2008) Structures of Human Pumilio with Noncognate RNAs Reveal Molecular Mechanisms for Binding Promiscuity. Structure. 16:549.
36. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2008) Protein-template directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA Polymerase. Structure 16:239. 
37. Lone S, Townson, SA, Uljon SN, Johnson RE, Brahma A, Nair DT, Prakash S, Prakash L, Aggarwal AK. (2007) Human DNA Polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Mol Cell 25:601.
38. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2006) Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA Polymerase iota. Nat Struct Mol Biol 13:619.
39. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2006) Incoming nucleotide imposes a syn conformation on templating purine in the human DNA polymerase -? active site. Structure (Camb) 14:749.
40. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2005) Human DNA Polymerase iota incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure (Camb). 13:1569.
41. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science. 309:2219.
42. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK. (2004) Replication by human DNA polymerase-iota occurs by Hoogsteen base- pairing. Nature 430:377.
43. Nair DT, Kaur KJ, Singh K, Mukherjee P, Rajagopal D, George A, Bal V, Rath S, Rao KV, Salunke DM. (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.
44. Nair DT, Singh K, Siddiqui Z, Nayak BP, Rao KVS, Salunke DM. (2002) Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response. J Immunol 168:2371
45. Nayak SK, Bagga S, Gaur D, Nair DT, Salunke DM, Batra JK. (2001) Mechanism of specific target recognition and RNA hydrolysis by ribonucleolytictoxin restrictocin. Biochemistry 40:9115.
46. Jain D, Nair DT, Swaminathan GJ, Abraham EG, Nagaraju J, Salunke DM. (2001) Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antherea mylitta: Implications to molecular evolution. J Biol Chem 276:41377.
47. Nair DT, Singh K, Shahu N, Rao KVS, Salunke DM. (2000) Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition. J Immunol 165:6949.