Ph.D (Dept. of Biochemistry, Bose Institute) Jadavpur
Department of Chemistry/ Structural Biology Group
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:
gene regulation by various transcriptional factors and sigma
factors in prokaryote.
Study `sigma cycle' paradigm in prokaryote
characterize inhibitors of M. tuberculosis gene
Ph. D Scholars:
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
Paulami Rudra (2009-2015);Ph.D awarded 2016
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
Shreya Sengupta (2009-2015)
Arkajyoti Dutta (2013-
Sangeeta Majumdar (2011-2013)
with NET fellowships may contact us for Ph.D admission)
New target for inhibition of bacterial RNA polymerase: 'switch
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.
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.
Prajapati RK, Sur R, Mukhopadhyay J. A Novel function of
factor from Bacillus subtilis as a transcriptional repressor
(2016) J Biol Chem. (in press) doi:10.1074/jbc.M116.746065
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:
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:
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.
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.
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. (2015)
Nucleic Acid Research, 43: 5855-67.
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.
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
Banerjee R, Rudra ., Saha A, and Mukhopadhyay J.
Recombinant Reporter Assay Using Transcriptional Machinery of
Mycobacterium tuberculosis. (2015) Journal
of bacteriology 197, 646-653.
Banerjee R, Rudra P, Prajapati, RK, Sengupta S., and
Mukhopadhyay J. Optimization of recombinant Mycobacterium
tuberculosis RNA polymerase expression and purification.
(2014) Tuberculosis (Edinb)
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.
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.
Pavlova O, Mukhopadhyay J, Sineva E, Ebright RH,
Severinov K. (2008) Structure-activity analysis of
Microcin J25. J Biol Chem., 283: 25589- 95.
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,
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.
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.
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.