Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho

Nucleic Acids Research

Volumn 42, Issue 15, 2014, Pages 9677-9690

  Shashni, Rajesh ^a   Qayyum, M Zuhaib ^a   Vishalini, V ^a   Dey, Debashish ^a   Sen, Ranjan ^a  

^a Center for DNA Fingerprinting and Diagnostics   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MESSENGER RNA; NUSG PROTEIN; RHO FACTOR; UNCLASSIFIED DRUG; ADENOSINE TRIPHOSPHATE; ELONGATION FACTOR; ESCHERICHIA COLI PROTEIN; NUSG PROTEIN, E COLI; RNA BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARTICLE; BACTERIAL VIABILITY; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; IN VITRO STUDY; IN VIVO STUDY; ISOMERIZATION; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NONHUMAN; PRIMARY RNA BINDING SITE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN RNA BINDING; SECONDARY RNA BINDING SITE; SEQUENCE ANALYSIS; CHEMISTRY; GENETICS; METABOLISM; MUTATION; PROPHAGE; TRANSCRIPTION TERMINATION;

ADENOSINE TRIPHOSPHATE; BINDING SITES; ESCHERICHIA COLI PROTEINS; MUTATION; PEPTIDE ELONGATION FACTORS; PROPHAGES; RHO FACTOR; RNA, MESSENGER; RNA-BINDING PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION TERMINATION, GENETIC; TRANSCRIPTOME;

EID: 84920890032     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku690     Document Type: Article

References (29)

1. Banerjee, S., Chalissery, J., Bandey, I. and Sen, R. (2006) Rho-dependent transcription termination: more questions than answers. J. Microbiol., 44, 11-22.
2. Peters, J.M., Vangeloff, A.D. and Landick, R. (2011) Bacterial transcription terminators: the RNA 3'-end chronicles. J. Mol. Biol, 412, 793-813.
3. Peters, J.M., Mooney, R.A., Grass, J.A., Jessen, E.D., Tran, F. and Landick, R. (2012) Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev., 26, 2621-2633.
4. Hollands, K., Proshkin, S., Sklyarova, S., Epshtein, V, Mironov, A., Nudler, E. and Groisman, E.A. (2012) Riboswitch control of Rho-dependent transcription termination. Proc. Natl. Acad. Sci. U.S.A., 109, 5376-5381.
5. Bossi, L., Schwartz, A., Guillemardet, B., Boudvillain, M. and Figueroa-Bossi, N. (2012) A role for Rho-dependent polarity in gene regulation by a noncoding small RNA. Genes Dev., 26, 1864-1873.
6. Cardinale, C.J., Washburn, R.S., Tadigotla, VR., Brown, L.M., Gottesman, M.E. and Nudler, E. (2008) Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science, 320, 935-938.
7. Menouni, R., Champ, S., Espinosa, L., Boudvillain, M. and Ansaldi, M. (2013) Transcription termination controls prophage maintenance in Escherichia coli genomes. Proc. Natl. Acad. Sci. U.S.A., 110, 14414-14419.
8. Harinarayanan, R. and Gowrishankar, J. (2003) Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli. J. Mol. Biol., 332, 31-46.
9. Tomar, S.K. and Artsimovitch, I. (2013) NusG-Spt5 proteins-universal tools for transcription modification and communication. Chem. Rev., 113, 8604-8619.
10. Burns, C.M., Nowatzke, W.L. and Richardson, J.P. (1999) Activation of Rho-dependent transcription termination by NusG. Dependence on terminator location and acceleration of RNA release. J. Biol. Chem., 274, 5245-5251.
11. 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. J. Mol. Biol., 371, 855-872.
12. Chalissery, J., Muteeb, G, Kalarickal, NC, 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. J. Mol. Biol, 405, 49-64.
13. Mooney, R.A., Davis, S.E., Peters, J.M., Rowland, J.L., Ansari, A.Z. and Landick, R. (2009) Regulator trafficking on bacterial transcription units in vivo. Mol. Cell, 33, 97-108.
14. Epshtein, V, Dutta, D, Wade, J. and Nudler, E. (2010) An allosteric mechanism of Rho-dependent transcription termination. Nature, 463, 245-249.
15. Kalyani, B.S., Muteeb, G, Qayyum, M.Z. and Sen, R. (2011) Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro. J. Mol. Biol., 413, 548-560.
16. Saxena, S. and Gowrishankar, J. (2011) Modulation of Rho-dependent transcription termination in Escherichia coli by the H-NS family of proteins. Journal of bacteriology, 193 3832-3841.
17. Cheeran, A., Suganthan, R.B., Swapna, G, Bandey, I., Achary, M.S., Nagarajaram, H.A. and Sen, R. (2005) Escherichia coli RNA polymerase mutations located near the upstream edge of an RNA: DNA hybrid and the beginning of the RNA-exit channel are defective for transcription antitermination by the N protein from lambdoid phage H-19B. Journal of molecular biology, 352, 28-43.
18. Pani, B., Banerjee, S., Chalissery, J., Muralimohan, A., Loganathan, R.M., Suganthan, R.B. and Sen, R. (2006) Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein Psu. J. Biol. Chem., 281, 26491-26500.
19. 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.
20. Dutta, D, Chalissery, J. and Sen, R. (2008) Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA. J. Biol. Chem., 283, 20243-20251.
21. Cherepanov, PP and Wackernagel, W. (1995) Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene, 158, 9-14.
22. Muteeb, G., Dey, D., Mishra, S. and Sen, R. (2012) A multipronged strategy of an anti-terminator protein to overcome Rho-dependent transcription termination. Nucleic Acids Res., 40, 11213-11228.
23. Martinez, A., Opperman, T. and Richardson, J.P. (1996) Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor Rho. J. Mol. Biol., 257, 895-908.
24. Barik, S., Bhattacharya, P. and Das, A. (1985) Autogenous regulation of transcription termination factor Rho. J. Mol. Biol., 182, 495-508.
25. Skordalakes, E. and Berger, J.M. (2006) Structural insights into RNA-dependent ring closure and ATPase activation by the Rho termination factor. Cell, 127, 553-564.
26. Thomsen, N.D. and Berger, J.M. (2009) Running in reverse: the structural basis for translocation polarity in hexameric helicases. Cell, 139, 523-534.
27. Ciampi, M.S. (2006) Rho-dependent terminators and transcription termination. Microbiology, 152, 2515-2528.
28. Burmann, B.M. and Rosch, P. (2011) The role of E. coli Nus-factors in transcription regulation and transcription: translation coupling: from structure to mechanism. Transcription, 2, 130-134.
29. Epshtein, V., Kamarthapu, V., McGary, K., Svetlov, V., Ueberheide, B., Proshkin, S., Mironov, A. and Nudler, E. (2014) UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature, 505, 372-377.