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Dr. Deepti Jain

Associate Professor
E-mail: deepti at rcb dot res dot in

  • PhD 2000, National Institute of Immunology, Delhi
  • Postdoc at Rockefeller University, NYC, USA
  • Visiting Fellow, NCBS, Bangalore
  • Associate Professor

Transcription Regulation: Structure and Mechanism

Resistance to antibiotics represents an escalating challenge in the treatment of bacterial infections. Pathogenic bacteria are known to switch phenotype such as planktonic to biofilms, to reduce sensitivity towards antimicrobial agents. These phenotypic transitions are generally regulated at the level of transcription which is an essential process for modulating gene expression profiles in bacteria. The molecular events that underlie transcription regulation include interaction of regulators with promoters and RNA polymerase (RNAP). RNAP and associated factors are conserved across the bacterial domain and serve as excellent targets for broad-spectrum antibacterial therapy.

We employ an integrated approach, involving structural tools, biophysical techniques, biochemical methods and functional in vivo assays to investigate the molecular mechanisms of transcription regulation.

The mechanistic insights obtained using this approach are exploited for the development of novel therapeutic agents against pathogenic bacteria. In addition, knowledge of transcription modulation is utilized to develop inducible expression systems that are sensitive to the presence of small molecules.


Transcription regulation of flagellar and biofilm gene network in Pseudomonas aeruginosa

Pseudomonas aeruoginosa is an opportunistic pathogen and is a primary cause for nosocomial infections.Motility in Pseudomonasis mediated by the action of flagella that are complex dynamic structures composed of numerous proteins. In addition, flagella play a crucial role in adhesion to substrate, biofilm formation and colonization. The regulation of flagellar and biofilm genes is brought about primarily at the transcription level through the action of a number of dedicated regulatory proteins. The research in our lab focuses on structural studies of macromolecular complexes involved in regulation of genesresponsible for biofilm and flagella expression in Pseudomonas.

Allosteric mechanism utilized by transcription factors responsive towards small metabolites

Allostery has been defined as the fundamental process wherein the binding of a ligand or the effector molecule alters the activity of the protein at a distant site. In the case of transcription modulators, effector binding can either increase (activation) or decrease its affinity to the DNA (derepression) thereby altering the gene expression. Thus, transcription modulators serve as molecular switches, turning on and off the expression of genes. Through our structural work on transcription repressor AraR, we have provided essential insights into long-standing fundamental questions in the field of regulation of gene expression and uncovered the mechanistic details of the diverse approaches utilized by transcription modulators to bind different DNA sequences without compromise on specificity and affinity thereby regulating gene expression to different extents at different promoters.

Opportunities:

Inquiries from prospective students, graduate trainees, postdocs with an interest in structural biology are welcome. Please write to deepti at rcb dot res dot in explaining your interests.

2016-2019  SERB Early Career Award, DST
2012-2016  Innovative Young Biotechnologist Award, DBT.
2009-2012  FAST track grant for Young Investigators, DST.
2003-2006  Jane Coffin Child Memorial Fellowship for medical research, New Haven, CT, USA
2002-2003  Charles Revson Foundation Post Doctoral Fellowship, USA
1995  University Medal IIT Roorkee
1994  Dr. G. Pande medal IIT Roorkee
  • Aruna Rani
    Reasearch Associate
  • Vineet Kumar
    DBT-RA
  • Chanchal
    Senior research fellow
  • Priyajit Banerjee
    Senior Research Fellow
  • Pankaj Kumar Sahoo
    Junior research fellow
  • Shikha Raghav
    Junior research fellow
  • Keshav Gupta
    Junior Research Fellow
  • Sheenu
    Junior Research Fellow
  • Deepika Choubey
    Project Assistant
  • Sumit Kumar
    Project JRF
  1. Banerjee, P, Chanchal, Jain, D.* (2019) Sensor I regulated ATPase activity of FleQ is essential for motility to biofilm transition in Pseudomonas aeruginosa. ACS Chemical Biology | 14:1515-1527
  2. Jain D*, Salunke DM (2019) Antibody specificity and promiscuity. Biochem J |476: 433-447
  3. Naskar T, Faruq M, Banerjee P, Khan M, Midha R, Kumari R, Devasenapathi R, Prajapati B, Sengupta S,  Jain D, Mukerji M, Singh NC, Sinha S (2018) Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family. EBioMedicine 28:179
  4. Chanchal, Banerjee P. and Jain D* (2017) ATP-Induced Structural Remodeling in the Antiactivator FleN Enables Formation of the Functional Dimeric Form. Structure 25:252
  5. Harshita, Chanchal and Jain D* (2016)  Cloning, expression, purification, crystallization and initial crystallographic analysis of FleN from Pseudomonas aeruginosa. Acta Cryst. F72, 135
  6. Jain D*, Naveen N, Nair DT (2015)   Plasticity in repressor-DNA interactions neutralizes loss of symmetry in bipartite operators Journal of Biological Chemistry 10.1074/jbc.M115.689695
  7. Jain D* (2015)  Allosteric control of transcription in GntR family of transcription regulators: A structural overview. IUBMB Life 67:556.
  8. Jain D, Nair DT. (2013) Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators. Nucleic Acid Research, 41:639.
  9. Twist, KA., Husnain, SI, Franke JD, Jain D, Campbell EA, Nickels, B.E Thomas, MS, Darst SA, Westblade LF (2011) A novel method for the production of in vivo-assembled, recombinant Escherichia coli RNA polymerase lacking the C- terminal domain Protein Science. 20:986.
  10. Jain D, Lamour V. (2010) Computational tools in protein crystallography. Methods in Molecular Biology 673:129.
  11. 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. PlosOne 5(10):e13726.
  12. Jain D, Kim, Y, Maxwell, K.L, Beasley S, Zhang R, Gussin GN, Edwards A, Darst SA. (2005) Crystal Structure of Bacteriophage lambda cII and its DNA complex. Molecular Cell 19:259.
  13. Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. (2004) Structure of a Ternary Transcription Activation Complex. Molecular Cell 13:45.
  14. Nagpal S, Kaur KJ, Jain D, Salunke DM. (2002) Plasticity in structure and interactions is critical for the action of indolicidin, an antibacterial peptide of innate immune origin
  15. Chakraborty S, Chakraborty N, Jain D, Salunke DM, Datta A. (2002) Active site geometry of oxalate decarboxylase from Collybia velutipes: Role of histidine coordinated copper in substrate recognition Protein Science 11:2138.
  16. Jain D, Nair DT, Swaminathan GJ, Abraham EG, Nagaraju J, Salunke DM. (2001) Structure of the Induced Antibacterial Protein from Tasar Silkworm, Antheraea mylitta: Implications to molecular evolution. J Biol Chem 276:41377.
  17. Jain, D, Kaur KJ, Salunke DM. (2001). Plasticity in Protein-Peptide Recognition: Crystal Structures of Two Different Peptides Bound to Concanavalin A Biophys. J 80:2912.
  18. Jain D, Kaur KJ, Salunke DM. (2001) Enhanced Binding of a Rationally Designed Peptide Ligand of Concanavalin A Arises From Improved Geometrical Complementarity. Biochemistry 40:12059.
  19. Goel M, Jain D, Kaur KJ, Kenoth R, Maiya BG, Swamy MJ, Salunke DM. (2001) Functional equality in the absence of structural similarity: An added dimension to molecular mimicry. J Biol Chem 276:39277.
  20. Kaur K, Jain D, Goel M, Salunke DM. (2001) Immunological Implications of Structural Mimicry between a Dodecapeptide and a Carbohydrate moiety Vaccine. 19:3124.
  21. Jain D, Kaur K, Goel M, Salunke DM. (2000) Structural Basis of Functional Mimicry between Carbohydrate and Peptide Ligands of ConA. Biochem. Biophys. Res. Commun. 272:843.
  22. Jain D, Kaur K, Sundaravadivel B, Salunke DM. (2000) Structural and Functional Consequences of Peptide-Carbohydrate Mimicry: Crystal Structure of a Carbohydrate-Mimicking Peptide Bound to Concanavalin. J Biol Chem 275:16098.

Dr. Deepti Jain
Associate Professor
Regional Centre for Biotechnology
NCR Biotech Science Cluster
3rd Milestone, Faridabad-Gurgaon Expressway
P.O. Box No. 3, Faridabad - 121 001
Haryana (NCR Delhi), India
E-mail: deepti at rcb dot res dot in
Phone: 91 129-2848839

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