CDFD :: Transcription :: Publications

Chhakchhuak, P. I. R. and Sen, R. (2022). In vivo regulation of bacterial Rho-dependent transcription termination by the nascent RNA. Journal of Biological Chemistry, accepted.

Hafeezunnisa, M., Chhakchhuak, P. I. R., Krishnakumar, J. and Sen, R. (2021) E. coli cryptic prophage expressions are controlled by Rho-dependent transcription termination primarily to regulate their toxin-antitoxin modules. FEBS Letters, 595, 2057-2067.

Ghosh, G., Sharma, P. V., Kumar, A., Jain, S. and Sen, R. (2021). Design of novel peptide - inhibitors against the conserved bacterial transcription terminator, Rho. Journal of Biological Chemistry, Apr 9:100653. doi: 10.1016/j.jbc.2021.100653.

Said, N., Hilal, T., Sunday, N. D., Khatri, A., Bürger, J., Mielke, T. Belogurov, G. A., Loll, B., Sen, R., Artsimovitch, I. and Wahl, M. C. (2021). Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase ?. Science, Jan 1;371(6524): eabd1673.

Hafeezaunnisa, M. and Sen, R. (2020). The Rho-Dependent Transcription Termination Is Involved in Broad-Spectrum Antibiotic Susceptibility in Escherichia coli. Front. Microbiol. 11:605305. doi: 10.3389/fmicb.2020.605305.

Pal, K., Yadav, M., Jain, S., Ghosh, B., Sen, R. and Sen, U. (2019). Vibrio cholerae YaeO is a structural homologue of RNA chaperone Hfq that inhibits Rho-dependent transcription termination by dissociating its hexameric state. Journal of Molecular Biology, 431(24), 4749-4766.

Wahl, M. and Sen, R. (2019). Exploiting phage strategies to modulate bacterial transcription. Transcription, Oct 30:1-9.

Singh, S., Godavarthi, S., Kumar, A. and Sen, R. (2019). A genomics approach to identify novel mycobacteriophage proteins having mycobactericidal properties. Microbiology, Jul;165(7):722-736.

Jain, S., Gupta, R, and Sen, R. (2019) Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at the DNA lesions. Nature Communications, Mar 14; 10(1):1207.doi: 10.1038/s41467-019-09146-5.

Chhakchhuak, P.I.R., Khatri, A. and Sen, R. (2019) Mechanism of action of bacterial transcription terminator Rho. Proc Indian Natn Sci Acad. 85, 157-168; DOI: 10.16943/ptinsa/2018/49436

Ghosh, G., Reddy, J. Sambhare, S. and Sen, R. (2018) A bacteriophage capsid protein is an inhibitor of a conserved transcription terminator of various bacterial pathogens. Journal of Bacteriology, 200(1): e00380-17, 1-16.

Mitra, P., Ghosh, G., Hafeezunnisa, M. and Sen, R. (2017). Rho protein: mechanism and action. Annual Review of Microbiology, 71, 687-709.

Takada, H., Shimada, T., Dey, D, Quyuum, MZ, Nakano, N., I Ishiguro, A., Yoshida, A., Yamamoto, K., Sen, R. and Ishihama, A.(2016) *Differential regulation of rRNA and tRNA transcription from the rRNA-tRNA composite operon in Escherichia coli. Plos one. Dec 22; 11(12):e0163057.

Vishalini, V., Agarawal, S. and Sen, R. (2016). Molecular basis of NusG-mediated regulation of Rho-dependent transcription termination in bacteria. Journal of Biological Chemistry. 291 (43), 22386-22403

Qayyum M. Z., Dey D. and Sen, R. (2016). Transcription elongation factor NusA is a negative regulator of Rho-dependent termination. Journal of Biological Chemistry, 291(15), 8090-8108.

Mishra, S. and Sen, R. (2015). N protein from lambdoid phages transform NusA into an antiterminator by modulating NusA-RNA polymerase flap domain interactions. Nucleic Acids Research. 43(12):5744-58.

Kalyani, B. S., Kunamneni, R., Wal, M., Ranjan, A. and Sen, R. (2015). A NusG paralogue from Mycobacterium tuberculosis, Rv0639, has evolved to interact with ribosomal protein S10 (Rv0700) but not to function as a transcription elongation-termination factor. Microbiology, 161, 67-83.

Sen, R., Chalissery, J., Qayyum, M.Z., Vishalini, V. Muteeb, G. (2014). Nus factors of Escherichia coli., EcoSal plus, ASM Press, doi:10.1128 /ecosalplus.ESP-0008-2013.

Shashni, R., Qayyum, M. Z., Vishalini, V., Dey, D. and Sen, R. (2014). Redundancy of primary RNA-binding functions of the bacterial transcription terminator, Rho. Nucleic Acids Research, 42(15):9677-90.

Mishra, S., Mohan, S., Godavarthi, S. and Sen, R. (2013). The interaction surface of a bacterial transcription elongation factor required for complex formation with an antiterminator during transcription antitermination. Journal of Biological Chemistry, 288 (39), 28089–28103.

Ranjan, A., Banerjee, R., Pani, B., Sen, U. and Sen, R. (2013). The moonlighting function of bacteriophage P4 capsid protein, Psu, as a transcription antiterminator. Bacteriophage 3:2, e25657.

Ranjan, A., Banerjee, R., Sharma, S., Sen, U. and Sen, R. (2013). Structural and mechanistic basis of antitermination of Rho-dependent transcription termination by a bacteriophage capsid protein. Nucleic Acids Research, 41 (14):6839-6856.

Banerjee, R., Nath, S., Ranjan, A., Khamrui, K., Pani, B. Sen, R. and Sen, U. (2012). The first structure of Polarity Suppression protein, Psu from Enterobacteria phage P4, reveals a novel fold and a knotted dimer. Journal of Biological Chemistry. 287(53), 44667–44675.

Muteeb, G., Dey, D., Mishra, S. and Sen, R. (2012). A multi-pronged strategy by an antiterminator to overcome Rho-dependent termination. Nucleic Acids Research, 40(22), 11213-11228.

Shashni, R., Mishra, S., Kalayani, B. S. and Sen. R. (2012). Suppression of in vivo Rho-dependent transcription termination defects: evidence for kinetically controlled steps. Microbiology, 158:1468 - 1481.

Kalyani, B. S., Muteeb, G., Qayyum, M. Z. and Sen, R. (2011). Interaction with the nascent RNA is a pre-requisite for the recruitment of Rho to the transcription elongation complex in vitro. Journal of Molecular Biology, 413, 548-560.

Swapna, G., Chakraborty A, Kumari, V., Sen, R. and Nagaraja, V. (2011). Mutations in ' subunit of E.coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance. Molecular Microbiology, 80(5):1169-85.

Chalissery, J., Muteeb, G., Nisha C. K., Mohan, S. Jisha, V and Sen, R. (2011). Interaction surface of the transcription terminator Rho required to form a complex with the C-terminal domain of the antiterminator NusG. Journal of Molecular Biology, 405, 49-64.

Muteeb, G. and Sen, R. (2010). Random mutagenesis using mutator strain. Methods in Molecular Biology, 634, 411-419.

Khamurai, S., Ranjan, A., Pani, B., Sen, R. and Sen, U. (2010) Crystallization and preliminary X-Ray analysis of Psu, an inhibitor of bacterial transcription terminator, Rho. Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 2), 204-6.

Nisha, C. K., Ranjan, A., Kalyani, B. S., Wal, M. and Sen, R. (2010). A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function. Journal of Molecular Biology, 395, 966-982.

Pani, B., Ranjan, A. and Sen, R. (2009). Interaction surface of bacteriophage P4 protein Psu required for the complex formation with the transcription terminator Rho. Journal of Molecular Biology. 389. 647-660.

Komissarova, N., Velikodvorskaya, T., Sen, R . King, R. A., Banik-Maiti, S. and Weisberg, R. A. (2008). Inhibition of a Transcriptional Pause by RNA Anchoring to RNA polymerase. Molecular Cell, 31, 683-694.

Dutta, D., Chalissery, J. and Sen, R. (2008). Transcription termination factor Rho prefers catalytically active elongation complex for releasing RNA. Journal of Biological Chemistry, 283(29), 20243-20251.

Sen, R., J. Chalissery, and G. Muteeb. 18 January 2008, posting date. Chapter 4.5.3.1, Nus Factors of Escherichia coli. In A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, T. Nyström, J. M. Slauch, and C. L. Squires (ed.), EcoSal - Escherichia coli and Salmonella: cellular and molecular biology. http://www.ecosal.org. ASM Press, Washington, D.C.

Cheeran, A., Kolli, N. and Sen, R. (2007). The Site of Action of the Antiterminator Protein N from the Lambdoid Phage H-19B. Journal of Biological Chemistry, 282(42), 30997-31007.

Chalissery, J., Banerjee, S., Bandey, I. and Sen, R. (2007). Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complex. Journal of Molecular Biology. 371, 855-872.

Pani, B., Banerjee, S., Chalissery, J., Abhishek, M., Ramya, M. L., Suganthan, R. and Sen, R. (2006). Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu. Journal of Biological Chemistry. 281 (36), 26491-26500.

Banerjee, S., Chalissery, J., Bandey, I and Sen, R. (2006). Rho-dependent transcription termination. More questions than answers. Journal of Microbiology, 44(1):11-22.

Viswanathan, S., Qmra, R. Burma, C., Sen, R., and Mande, S.C. (2006) Cation-mediated interplay of loops in Mycobacterium tuberculosis Chaperonin-10. Journal of Biophysical and structural Dynamics, 23(4), 365-376.

Cheeran, A., Suganthan, R., Swapna, G., Bandey, I., Acharya, S., Nagarajaram, H. A. and Sen, R. (2005) E.coli RNA polymerase mutations impaired for H19B N specific transcription antitermination are located close to the upstream edge of RNA:DNA hybrid and beginning of RNA exit channel of elongation complex. Journal of Molecular Biology, 252, 28-43.

King, R.A., Markov, D., Sen, R., Severinov, K. and Weisberg, R. A. (2004) A conserved Zinc binding site in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complex. Journal of Molecular Biology, 342(4): 1143-54.

Sen, R. and Dasgupta, D. (2003) Simple fluorescence assays probing conformational changes of Escherichia coli RNA polymerase during transcription initiation. Methods in Enzymology. 370:598-605.

King R.A., Sen, R. and Weisberg, R. A. (2003) Using a lac repressor roadblock to analyze the E. coli transcription elongation complex. Methods in Enzymology. 371:207-18.

Sen, R., King, R.A., Mzhavia, N., Madsen, P. and Weisberg, RW (2002). Sequence specific interaction of nascent antiterminator RNA with the Zn-finger motif of E.coli RNA polymerase. Molecular Microbiology, 46(1):215-22.

Susa, M., Sen R. and Shimamoto, N. (2002) Generality of the Branched Pathway in Transcription Initiation by Escherichia coli RNA Polymerase. Journal of Biological Chemistry. 3; 277(18): 15407-12.

Sen, R. , King, R. and Weisberg, R. W. (2001). Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA. Molecular Cell. 7(5): 993-1001.

Sen, R. , Nagai, H and Shimamoto, N. (2001). Conformational switching of the E.coli RNA polymerase-promoter binary complex is facilitated by elongation factors GreA/B. Genes to Cell, 6(5), 389-402.

Sen, R. , Nagai, H. and Shimamoto, N. (2000). RNA Polymerase-arrest at Lambda PR promoter during transcription initiation Journal of Biological Chemistry. 275(15), 10899-10904.

Sen, R. , Nagai, H., Hernandez VJ and Shimamoto, N. (1998). Reduction in abortive transcription from the Lambda PR promoter by mutations in region 3 of the sigma-70 subunit of Escherichia coli RNA polymerase. Journal of Biological Chemistry. 273(16), 9872-9877.

Majee, S., Sen, R. , Guha, S., Bhattacharyya, D. and Dasgupta, D. (1997). Differential interaction of the Mg+2 complexes of chromomycin A3 and mithramycin with poly(dG-dC).poly(dC-dG) and poly(dG).poly(dC). Biochemistry, 36(8), 2291-2299.

Sen, R. and Dasgupta, D. (1996). Conformational changes of E.coli RNA polymerase during transcription initiation. Biophysical Chemistry. 57(2-3), 269-278.

Sen, R. and Dasgupta, D. (1994). Intrinsic fluorescence of E.coli RNA polymerase as a probe for its conformational changes during transcription initiation. Biochemical Biophysical Research. Communication. 201(2), 820-828

Sen, R. and Dasgupta, D. (1993). Interaction of ribonucleotides with T7 RNA polymerase: probable role of GTP in transcription initiation. Biochemical Biophysical Research Communicaton. 195(2), 616-622.

Dasgupta, D., Aich, P., Sen, R. and Bhattacharya, K. (1992). Characterization of interaction of an antitumor antibiotic, Chromomycin A3 with synthetic DNA, poly(dC-dC).poly(dG-dC)-- a spectroscopic study. Proceedings of Indian National Science Academy. B58, 311-320.

Aich, P., Sen, R. and Dasgupta D. (1992). Interaction between antitumour antibiotic chromomycin A3 and Mg+2: Evidence for the formation of two types of chromomycin A3-Mg+2 complexes. Chemico- Biological Interaction. 83(1), 22-33.

Aich, P., Sen, R. and Dasgupta D. (1992). Role of magnesium ion in the interaction between chromomycin A3 and DNA: binding of chromomycin A3-Mg+2 complexes with DNA. Biochemistry, 31(11), 2988-2997.