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Dr. Ranjan Sen
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Current Research Interests

Laboratory of transcription is engaged in understanding the mechanism of transcription termination and antitermination in prokaryotes. A wide range of techniques from biophysics (spectroscopy, thermodynamics, fast kinetics etc.), biochemistry (protein purification, chemical and enzymatic foot-printing of protein and nucleic acids, cross-linking etc.), molecular biology (recombinant DNA techniques, site-directed mutagenesis), bacterial genetics and genomics are used in the laboratory to solve these intellectually challenging problems.

Projects:

  1. Mechanism of transcription termination by transcription termination factor Rho.
  2. Mechanism of Rho-NusG interaction in vivo and in vitro.
  3. In vivo nature of Rho-dependent terminators.
  4. Physiological roles of Rho-dependent terminations.
  5. Super-resolution microscopy of the transcription machineries.
  6. Fast-kinetics approach to study the transcription termination processes.
  7. Isolation of myco-bacteriophage derived inhibitors of the Mycobacterium sp.
  8. Design of antimicrobial peptides from bacteriophage proteins.

Research Highlights

The Rho-dependent transcription termination regulates broad-spectrum antibiotic sensitivity in Escherichia coli (submitted, 2020).

One of the major ways of acquiring multidrug resistance in bacteria is via drug–influx and -efflux pathways. Here, we show that E.coli with compromised Rho-dependent transcription termination function have a broad-spectrum antibiotic sensitivity, which arises from the inefficient TolC-efflux process and enhanced permeability of the outer membrane. Log-phase cells of the Rho mutants have altered cell surface decorated with glycocalyx and increased level of lipopolysaccharide in their outer membrane rendering the membrane-embedded TolC pumps inefficient. These alterations are due to the upregulations of the poly-N-acetyl-glucosamine and lipopolysaccharide synthesis operons because of inefficient Rho functions. The metabolomics of these strains revealed the presence of high level of unusual metabolites, and they are also capable of growing on various di-peptides and carbohydrate sources unlike their WT counterpart. Di-peptides uptake arises from the upregulations of the di-peptide permease operon in these mutants. The accumulation of unusual metabolites in these Rho mutants might clog the TolC-pumps that further reduced their efficiency. We concluded that the Rho regulates broad-spectrum antibiotic sensitivity of E.coli through multipartite pathways in a TolC-dependent manner. Involvement of Rho-dependent termination in multiple pathways led us to propose that the antibiotic treatment regime should include specific Rho-inhibitors together with other antibiotics.


A mycobacteriophage genomics approach to identify novel mycobacteriophage proteins having Mycobactericidal properties (Microbiology 2019).

The Mycobacteriophages specific to mycobacteria are the sources of varieties of effector proteins capable of eliciting bactericidal responses. We describe a genomics approach combining with bioinformatics to identify mycobacteriophage proteins that are toxic to mycobacteria upon expression. A genomic library made from the collections of phage genomes is screened for the clones capable of killing the M. smegmatis strain mc2155. We identified four unique clones; clones 45 and 12N (from the mycobacteriophage D29), clones 66 and 85 (from the mycobacteriophage Che12). The gene products from the clones 66 and 45 were identified as Gp49 of Che12 phage and Gp34 of D29 phage, respectively. The gene products of the other two clones, 85 and 12N, utilized novel ORFs coding for synthetic proteins. These four clones (clone 45, 66, 85 and 12N) upon expression caused growth defects in M. smegmatis and M. bovis. Clones having Gp49 and Gp34 also induced growth defects in E. coli indicating that they target conserved host-machineries. Their expressions induced various morphological changes indicating that they affected DNA replication and cell division steps. We predicted Gp34 to be a Xis protein required in phage DNA excision from the bacterial chromosome. Gp49 is predicted to have a HTH motif having DNA-bending/twisting properties. We suggest that this methodology is useful to identify new phage proteins having desired properties without laboriously characterizing the individual phages. It is universal and could be applied to other bacteria-phage systems. We speculate that the existence of virtually “unlimited” number of phages and their unique gene products could offer cheaper and less hazardous alternative to explore new antimicrobial molecules.


Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions (Nature Communications, 2019).

In bacteria, transcription-coupled repair of DNA lesions initiates after the Mfd protein removes RNA polymerases (RNAPs) stalled at the lesions. The bacterial RNA helicase, Rho, is a transcription termination protein that dislodges the elongation complexes. Here, we show that Rho dislodges the stalled RNAPs at DNA lesions. Strains defective in both Rho and Mfd are susceptible to DNA-damaging agents and are inefficient in repairing or propagating UV damaged DNA. In vitro transcription assays show that Rho dissociates the stalled elongation complexes at the DNA lesions. We conclude that Rho-dependent termination recycles stalled RNAPs, which might facilitate DNA repair and other DNA-dependent processes essential for bacterial cell survival. We surmise that Rho might compete with, or augment, the Mfd function.

Projects in progress:

  1. Characterization of NusG dependent terminators.
  2. Understanding the physiological consequences of Rho-dependent termination.
  3. Understanding the role of omega subunit of RNAP in Rho-dependent termination.
  4. In vivo localization of Rho and NusG by super-resolution microscopy.
  5. Identification Rho-RNAP interaction domain.
  6. Isolation and characterization of anti-mycobacterial proteins from mycobacteriophages.
  7. Constructions of antiterminator peptides from Psu protein.
  8. Computational approaches to understand the conformational changes of Rho and NusG during the termination process.

Extramural Funding:

  1. Indo-German ICMR grant (2020-2023).
  2. DST Grant (2020-2023).
  3. Tata Innovation Fellowship (2019-2022).
  4. DBT grant (2019-2022).
  5. Grant from DBT COE on "Microbial Physiology" (2014-2020).

Awards/Recognition:

  1. 2002-2007: GRIP research grant award from NIH, USA.
  2. 2003-2008: Wellcome Trust, UK, Senior Research Fellowship.
  3. 2007: DBT Bioscience carrier development award.
  4. 2007: Elected member of GRC.
  5. 2008: DST Swarnajayanti Research Fellowship.
  6. 2011: Elected fellow of NASI, Allahabad.
  7. 2015: Member DST- SERB, task force.
  8. 2018: Elected Fellow INSA, New Delhi.
  9. 2018: Elected fellow IASc, Bangalore. 2018: Fellow of Telengana Academy of Sciences.
  10. 2019: DBT TATA Innovation Fellowship.

Reviewer of Journals/grants:

  1. Nature Communications, TIBS, Journal of Molecular Biology, Molecular Microbiology, Journal of Bacteriology, Science Reports, Microbiology, PLOS one, Indian Journal of Biophysics and Biochemistry, Journal of Bioscience etc.
  2. Reviewer of grants for different granting agencies like DBT, DST etc.
Contact Information
Email: rsen<at>cdfd.org.in
Phone: +91-40-27216103
Fax: +91-40-27216006
Last updated on : Wednesday, 15th April, 2020.

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