Jayanta Mukhopadhyay Ph.D (Dept. of Biochemistry, Bose Institute) Jadavpur University, 2000

Associate Professor,
 Department of Chemistry/ Structural Biology Group


Contact: Email: jayanta@jcbose.ac.in

PH:  91-33-2303-1143

Fax: 91-33-2303-6790

Research interest
Transcription is the first step in gene expression where most regulation occurs. RNAP core enzyme together with sigma factor(s) and/or numerous regulator(s) orchestrates the gene expression in bacteria. Our lab seeks to characterize the interactions among RNAP, sigma factors, and regulators required for various gene expressions in prokaryote, e.g. Escherichia coli, Bacillus subtilis and Mycobacterium tuberculosis. The proposed work will use integrated biophysical, biochemical and genetic approaches, along with a recombinant in vitro transcription system to address the following specific aims:
  1. Mechanism of gene regulation by various transcriptional factors and sigma factors in prokaryote.
  2. Study `sigma cycle' paradigm in prokaryote
  3. Identify and characterize inhibitors of M. tuberculosis gene expression.


Ph. D Scholars:

  1. Rajdeep Banerjee (2009-2014); Ph. D Awarded 2014, current position: Post-doctoral fellow at Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health

  2. Paulami Rudra (2009-2015);Ph.D awarded 2016

  3. Ranjit  Kumar Prajapati (2009-2015) Ph.D awarded 2016, current position: Post-doctoral fellow at Department of Biochemistry and Food Chemistry, University of Turku, Finland

  4. Shreya Sengupta (2009-2015)

  5. Arkajyoti Dutta  (2013-

 Research Associate:

  1. Sangeeta Majumdar  (2011-2013)

(Interested candidates with NET fellowships may contact us for Ph.D admission)

Related publications:

Review Articles:

  1. New target for inhibition of bacterial RNA polymerase: 'switch region'. Srivastava A, Talaue M, Liu S, Degen D, Ebright RY, Sineva E, Chakraborty A, Druzhinin SY, Chatterjee S, Mukhopadhyay J, Ebright YW, Zozula A, Shen J, Sengupta S, Niedfeldt RR, Xin C, Kaneko T, Irschik H, Jansen R, Donadio S, Connell N, Ebright RH. Curr Opin Microbiol. (2011),14: 532-43.

  2. Book chapter in `Recent Trends in Gene Expression and Regulation' Mechanism of transcription in prokaryote. Mukhopadhyay J and Sur R. (2013) Nova science publishers, Inc, Hauppauge, NY, USA.

Research Publications:

  1. Prajapati RK, Sur R, Mukhopadhyay J.  A Novel function of d factor from Bacillus subtilis as a transcriptional repressor (2016) J Biol Chem. (in press) doi:10.1074/jbc.M116.746065

  2. Datta A, Yadav V, Ghosh A, Choi J, Bhattacharyya D,. Kar R K, Ilyas H, Dutta A, An E, Mukhopadhyay J, Lee D, Sanyal K, Ramamoorthy A, and Bhunia A. Mode of Action of a Designed Antimicrobial Peptide:High Potency Against Cryptococcus neoformans. (2016) Biophysical Journal 111: 1724–1737

  3. Roy A, Dutta A, Roy D, Ganguly P, Ghosh R, Kar RK, Bhunia A, Mukhopadhyay J, and Chaudhuri S. Deciphering the role of the AT-rich interaction domain and the HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana. (2106) Plant Molecular Biology (in press) DOI: 10.1007/s11103-016-0519-y

  4. Prajapati RK, Sengupta S, Rudra P, Mukhopadhyay J. Bacillus subtilis δ Factor Functions as a Transcriptional Regulator by Facilitating the Open Complex Formation. (2016) J Biol Chem. 291(3):1064-75.

  5. Promoter escape with bacterial two-component sigma factor suggests retention of sigma region two in the elongation complex. Sengupta S, Prajapati RK, and Mukhopadhyay J. (2015) J Biol Chem. 290(47):28575-83.

  6. Rudra P, Prajapati RK, Banerjee R, Sengupta S, and Mukhopadhyay J. Novel mechanism of gene regulation: the protein Rv1222 of Mycobacterium tuberculosis inhibits transcription by anchoring the RNA polymerase onto DNA. (2015Nucleic Acid Research, 43: 5855-67.

  7. Saha A, Mukhopadhyay J, Datta AB, Parrack P. Revisiting the mechanism of activation of cyclic AMP receptor protein (CRP) by cAMP in Escherichia coli: Lessons from a subunit-crosslinked form of CRP. (2015)  FEBS Letters 589: 358–363.

  8. Sharma AK, Chatterjee A, Gupta S, Banerjee R, Mandal S, Mukhopadhyay J, Basu J, Kundu M. MtrA, an essential response regulator of the MtrAB two component system regulates the  transcription of resuscitation promoting factor B (RpfB) of Mycobacterium tuberculosis. (2015) Microbiology 161(6):1271-81.

  9. Banerjee R, Rudra ., Saha A, and Mukhopadhyay J. Recombinant Reporter Assay Using Transcriptional Machinery of Mycobacterium tuberculosis. (2015) Journal of bacteriology 197, 646-653.

  10. Banerjee R, Rudra P, Prajapati, RK, Sengupta S., and Mukhopadhyay J. Optimization of recombinant Mycobacterium tuberculosis RNA polymerase expression and purification. (2014) Tuberculosis (Edinb) 94:397-404.

  11. Polyphosphate kinase 1, a central node in the stress response network of Mycobacterium tuberculosis, connects the two-component systems MprAB, SenX3-Reg X3 and the extra-cytoplasmic function sigma factor, Sigma E. Sanyal S, Banerjee, S K Banerjee, R, Mukhopadhyay J,  Kundu, M. (2013) Microbiology 159: 2074-86.

  12. Mukhopadhyay J, Das K, Ismail S, Koppstein D, Jang M,  Sarafianos St, Tuske S, Hudson B, Patel J, Jansen R, Höfle G, Arnold E, and Ebright RH (2008).The RNA polymerase "switch region" is a target for inhibitors. Cell, 135: 295-305.

  13. Pavlova O, Mukhopadhyay J, Sineva E, Ebright RH, Severinov K. (2008) Structure-activity  analysis of Microcin J25. J Biol Chem., 283: 25589- 95.

  14. Mukhopadhyay J, Sineva E, Knight J, Levy RL, and Ebright RH (2004) Antibacterial peptide microcin J25 (MccJ25) inhibits transcription by binding within, and obstructing, the RNA polymerase secondary channel. Mol Cell, 14, 739-751.

  15. Mukhopadhyay J, Mekler V, Kortkhonjia E, Kapanidis AN, Ebright YW, Ebright RH (2003) Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function. Methods Enzymol, 371, 144-159.

  16. Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell, 108, 599-614.

  17. Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH (2001) Translocation of 70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell, 106, 453-63.