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.

• Pankaj Kumar Sahoo
  Project Associate II
• Shikha Raghav
  Senior research fellow
  
• Sheenu
  Senior Research Fellow
• Moumita Ghosh
  Senior Research Fellow
• Puja Ghosh
  Junior Research Fellow
• Swagatam Maity
  Integrated MSc-PhD student
• Rohit Prajapati
  Integrated MSc-PhD student
• Gulshan Maurya
  Junior Research Fellow
• Devendra Sharma
  Junior Research Fellow
• Kavery Mohela
  Project JRF

Alumni

1. Sahoo, P.K., Sheenu and Jain D.* (2023) REC domain is essential for stabilization of the heptamer of σ54 dependent transcription factor, FleR from Pseudomonas aeruginosa iScience doi:10.1016/j.isci.2023.108397
2. Ghosh, M., Raghav, S., Ghosh, P., Maity, S., Mohela, K., Jain, D.* (2023) Structural analysis of novel drug targets for mitigation of Pseudomonas aeruginosa biofilms FEMS Microbiology Reviews doi: 10.1093/femsre/fuad054.
3. Ruhal, R.#, Ghosh, M.#, Kumar, V., and Jain D.* (2023) Mutation of putative glycosyl transferases PslC and PslI confers susceptibility to antibiotics and leads to a drastic reduction in biofilm formation in Pseudomonas aeruginosa Microbiology doi:10.1099/mic.0.001392
4. Goel N, Ghosh M, Jain D, Sinha R, Khare SK (2023) Inhibition and Eradication of Pseudomonas aeruginosa biofilms by secondary metabolites of Nocardiposis lucentensis EMB25 RSC Medicinal Chemistry doi.org/10.1039/D2MD00439A
5. Sahoo PK, Kumar R, Rani A, Yadav SK, Jha G*, Jain D.* (2022) N-Terminus Plays a Critical Role for Stabilizing the Filamentous Assembly and the Antifungal Activity of Bg_9562 Microbiology Spectrum doi: 10.1128/spectrum.01607-22.PMID: 36005835
6. Chanchal, Banerjee P, Raghav S, Goswami HN, Jain D^*. (2021) The antiactivator FleN uses an allosteric mechanism to regulate σ⁵⁴-dependent expression of flagellar genes in Pseudomonas aeruginosa. Science Advances, doi: 10.1126/sciadv.abj1792
7. Adhikary A, Bansal T, Gupta P, Jain D, Anand P, Gupta R, Virdi JS, Marwah RG. (2021) Draft Genome Sequence of a Poly-γ-Glutamic Acid-Producing Isolate, Bacillus paralicheniformis Strain bcasdu2018/01. Microbiol Resour Announc, 46:e0101321
8. Banerjee, P., Sahoo, P.K., Sheenu, Adhikary, A., Ruhal, R. and Jain, D.* (2021) Molecular and structural facets of c-di-GMP signalling associated with biofilm formation in Pseudomonas aeruginosa. Molecular Aspects of Medicine doi.org/10.1016/j.mam.2021.101001
9. Gupta, M, Dubey S, Jain D, and Chandran D (2021) The Medicago truncatula sugar transport protein 13 and Its Lr67res-like variant confer powdery mildew resistance in legumes via defense modulation. Plant and Cell Physiology doi.org/10.1093/pcp/pcab021
10. Yadav, AK, Sahoo, PK, Goswami, HN and Jain D* (2019) Transcriptional fidelity of mitochondrial RNA polymerase RpoTm from Arabidopsis thaliana | doi.org/10.1016/j.jmb.2019.08.022
11. 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
12. Sharma G, Aminedi R, Saxena D, Gupta A, Banerjee P, Jain D, Chandran D (2019) Effector mining from the Erysiphe pisi haustorial transcriptome identifies novel candidates involved in pea powdery mildew pathogenesis Mol. Plant Pathol. | doi.org/10.1111/mpp.12862
13. 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
14. Jain D*, Salunke DM (2019) Antibody specificity and promiscuity. Biochem J |476: 433-447
15. 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
16. 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
17. Harshita, Chanchal and Jain D* (2016)  Cloning, expression, purification, crystallization and initial crystallographic analysis of FleN from Pseudomonas aeruginosa. Acta Cryst. F72, 135
18. 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
19. Jain D* (2015)  Allosteric control of transcription in GntR family of transcription regulators: A structural overview. IUBMB Life 67:556.
20. Jain D, Nair DT. (2013) Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators. Nucleic Acid Research, 41:639.
21. 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.
22. Jain D, Lamour V. (2010) Computational tools in protein crystallography. Methods in Molecular Biology 673:129.
23. 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.
24. 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.
25. Jain D, Nickels BE, Sun L, Hochschild A, Darst SA. (2004) Structure of a Ternary Transcription Activation Complex. Molecular Cell 13:45.
26. 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
27. 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.
28. 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.
29. 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.
30. 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.
31. 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.
32. Kaur K, Jain D, Goel M, Salunke DM. (2001) Immunological Implications of Structural Mimicry between a Dodecapeptide and a Carbohydrate moiety Vaccine. 19:3124.
33. 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.
34. 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.