Structural and functional analysis of the transcriptional regulator Rv3066 of Mycobacterium tuberculosis

Nucleic Acids Research

Volumn 40, Issue 18, 2012, Pages 9340-9355

  Bolla, Jani Reddy ^a   Do, Sylvia V ^a   Long, Feng ^a   Dai, Lei ^a   Su, Chih Chia ^a   Lei, Hsiang Ting ^a   Chen, Xiao ^a   Gerkey, Jillian E ^a   Murphy, Daniel C ^a   Rajashankar, Kanagalaghatta R ^b   Zhang, Qijing ^a   Yu, Edward W ^a  

^a IOWA STATE UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DEOXYRIBONUCLEASE I; ETHIDIUM; HOMODIMER; MICROORGANISM PROTEIN; PROTEIN MMR; PROTEIN RV3066; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA STRUCTURE; ELECTROPHORETIC MOBILITY; FLUORESCENCE POLARIZATION; GEL FILTRATION; IN VITRO STUDY; INVERTED REPEAT; LIGAND BINDING; MOLECULAR CLONING; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR RECOGNITION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; PROMOTER REGION; RESIDUE ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; BINDING SITES; CHROMATOGRAPHY, GEL; DNA FOOTPRINTING; DNA-BINDING PROTEINS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ETHIDIUM; FLUORESCENCE POLARIZATION; INVERTED REPEAT SEQUENCES; MEMBRANE TRANSPORT PROTEINS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; PROMOTER REGIONS, GENETIC; PROTEIN CONFORMATION; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84867551562     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks677     Document Type: Article

References (43)

1. World Health Organization. (2010) Fact sheet no. 104: tuberculosis. 2. Goldman, R. C., Plumley, K. V. and Laughon, B. E. (2007) The evolution of extensively drug resistant tuberculosis (XDR-TB): history, status and issues for global control. Infect. Disord. Drug Targets, 7, 73-91.
2. Iseman, M. D. (1993) Treatment of multidrug-resistant tuberculosis. N. Engl. J. Med, 329, 784-791.
3. Frieden, T. R., Sterling, T., Pablos-Mendez, A., Kilburn, J. O., Cauthen, G. M. and Dooley, S. W. (1993) The emergence of drug-resistant tuberculosis in New York City. N. Engl. J. Med, 328, 521-556.
4. Pillay, M. and Sturm, A. W. (2007) Evolution of the extensively drug-resistant F15/LAM4/KZN strain of Mycobacterium tuberculosis in KwaZulu-Natal, South Africa. Clin. Infect. Dis., 45, 1409-1414. (Pubitemid 351411867)
5. Udwadia, Z. F., Amale, R. A. and Rodrigues, C. (2012) Totally drug-resistant tuberculosis in India. Clin. Infect. Dis., 54, 579-581.
6. Nikaido, H. (2001) Preventing drug access to targets: cell surface permeability barriers and active efflux in bacteria. Semin. Cell. Dev. Biol., 12, 215-223.
7. Li, X. Z. and Nikaido, H. (2004) Efflux-mediated drug resistance in bacteria. Drugs, 64, 159-204. (Pubitemid 38186964)
8. De Rossi, E., Ainsa, J. A. and Riccardi, G. (2006) Role of mycobacterial efflux transporters in drug resistance: an unresolved question. FEMS Microbiol. Rev., 30, 36-52.
9. Danilchanka, O., Mailaender, C. and Niederweis, M. (2008) Identification of a novel multidrug efflux pump of mycobacterium tuberculosis. Antimicrob. Agents Chemother., 52, 2503-2511. (Pubitemid 351915682)
10. De Rossi, E., Branzoni, M., Cantoni, R., Milano, A., Riccardi, G. and Ciferri, O. (1998) mmr, a Mycobacterium tuberculosis gene conferring resistance to small cationic dyes and inhibitors. J. Bacteriol., 180, 6068-6071. (Pubitemid 28514231)
11. Dutta, N. K., Mehra, S. and Kaushal, D. (2010) A Mycobacterium tuberculosis sigma factor network responds to cell-envelope damage by the promising anti-mycobacterial thioridazine. PLoS One, 5,-e10069.
12. Grkovic, S., Brown, M. H. and Skurray, R. A. (2002) Regulation of bacterial drug export systems. Microbiol. Mol. Biol. Rev., 66, 671-701. (Pubitemid 35425113)
13. Ramos, J. L., Martinez-Bueno, M., Molina-Henares, A. J., Teran, W., Watanabe, K., Zhang, X. D., Gallegos, M. T., Brennan, R. and Tobes, R. (2005) The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev., 69, 326-356. (Pubitemid 40847943)
14. Yu, Z., Reichheld, S. E., Savchenko, A., Parkinson, J. and Davidson, A. R. (2010) A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators. J. Mol. Biol., 400, 847-864.
15. Otwinowski, Z. and Minor, M. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326. (Pubitemid 27085611)
16. Schneider, T. R. and Sheldrick, G. M. (2002) Substructure solution with SHELX D. Acta Crystallogr., D58, 1772-1779.
17. Pape, T. and Schneider, T. R. (2004) HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J. Appl. Crystallogr., 37, 843-844.
18. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. and Read, R. J. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674. (Pubitemid 47080256)
19. Cowtan, K. (2010) Recent developments in classical density modification. Acta Crystallogr., D66, 470-478.
20. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R., McCroy, A. J., Moriarty, N. W. et al. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr., 58, 1948-1954. (Pubitemid 35337293)
21. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr., D60, 2126.
22. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr., D54, 905-921.
23. Alekshun, M. N., Kim, Y. S. and Levy, S. B. (2000) Mutational analysis of MarR, the negative regulator of marRAB expression in Escherichia coli, suggests the presence of two regions required for DNA binding. Mol. Microbiol., 35, 1394-1404. (Pubitemid 30175515)
24. Zianni, M., Tessanne, K., Merighi, M., Laguna, R. and Tabita, F. R. (2006) Identification of the DNA bases of a DNase I footprint by the use of dye primer sequencing on an automated capillary DNA analysis instrument. J. Biomol. Techniques, 17, 103-113.
25. Jacobs, W. R. Jr, Kalpana, G. V., Cirillo, J. D., Pascopella, L., Snapper, S. B., Udani, R. A., Jones, W. D. Jr, Barletta, R. G. and Bloom, B. R. (1991) Genetic systems for mycobacteria. Methods Enzymol, 204, 537-555.
26. Li, X. Z., Zhang, L. and Nikaido, H. (2004) Efflux pump-mediated intrinsic drug resistance. Mycobacterium smegmatis. Antimicrob. Agents Chemother, 48, 2415-2423. (Pubitemid 38823405)
27. Livak, K. J. and Schmittgen, T. D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods, 25, 402-408. (Pubitemid 34164012)
28. Trott, O. and Olson, A. J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function,-efficient optimization, and multithreading. J. Comp. Chem, 31, 455-461.
29. Bellinzoni, M., Buroni, S., Schaeffer, F., Riccardi, G., De Rossi, E. and Alzari, P. M. (2009) Structural plasticity and distinct drug-binding modes of LfrR, a mycobacterial efflux pump regulator. J. Bacteriol., 191, 7531-7537.
30. Hinrichs, W., Kisker, C., Duvel, M., Muller, A., Tovar, K., Hillen, W. and Saenger, W. (1994) Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science, 264, 418-420. (Pubitemid 24178904)
31. Orth, P., Schnappinger, D., Hillen, W., Saenger, W. and Hinrichs, W. (2000) Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat. Struct. Biol., 7, 215-219. (Pubitemid 30140767)
32. Schumacher, M. A., Miller, M. C., Grkovic, S., Brown, M. H., Skurray, R. A. and Brennan, R. G. (2001) Structural mechanisms of QacR induction and multidrug recognition. Science, 294, 2158-2163. (Pubitemid 33150671)
33. Schumacher, M. A., Miller, M. C., Grkovic, S., Brown, M. H., Skurray, R. A. and Brennan, R. G. (2002) Structural basis for cooperative DNA binding by two dimers of the multidrug-binding protein Qac R. EMBO J., 21, 1210-1218. (Pubitemid 34206194)
34. Natsume, R., Ohnishi, Y., Senda, T. and Horinouchi, S. (2003) Crystal structure of a g-butyrolactone autoregulator receptor protein in Streptomyces coelicolor A3(2). J. Mol. Biol., 336, 409-419. (Pubitemid 38147636)
35. Dover, L. G., Corsino, P. E., Daniels, I. R., Cocklin, S. L., Tatituri, V., Besra, G. S. and Futterer, K. (2004) Crystal structure of the TetR/ CamR family repressor Mycobacterium tuberculosis EthR implicated in ethionamide resistance. J. Mol. Biol., 340, 1095-1105. (Pubitemid 38968703)
36. Frenois, F.,-engohang-Ndong, J., Locht, C., Baulard, A. R. and Villeret, V. (2004) Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis. Mol. Cell, 16, 301-307. (Pubitemid 39388844)
37. Gu, R., Su, C.-C., Shi, F., Li, M., McDermott, G., Zhang, Q. and Yu, E. W. (2007) Crystal Structure of the transcriptional regulator CmeR from Campylobacter jejuni. J. Mol. Biol., 372, 583-593. (Pubitemid 47313482)
38. Li, M., Gu, R., Su, C.-C., Routh, M. D., Harris, K. C., Jewell, E. S., McDermott, G. and Yu, E. W. (2007) Crystal structure of the transcriptional regulator AcrR from Escherichia coli. J. Mol. Biol., 374, 591-603. (Pubitemid 350018769)
39. Herná ndez, A., Maté, M. J., Sá nchez-Díaz, P. C., Romero, A., Rojo, F. and Martínez, J. L. (2009) Structural and functional analysis of SmeT, the repressor of the Stenotrophomonas maltophilia multidrug efflux pump SmeDE F. J. Biol. Chem., 284, 14428-14438.
40. Amaral, L., Boeree, M. J., Gillespie, S. H., Udwadia, Z. F. and van Soolingen, D. (2010) Thioridazine cures extensively drug-resistant tuberculosis (XDR-TB) and the need for global trials is now! Int. J. Antimicrob. Agents, 35, 524-526.
41. Hoffmann, K. M., Williams, D., Shafer, W. M. and Brennan, R. G. (2005) Characterization of the multiple transferable resistance repressor, MtrR, from Neisseria gonorrhoeae. J. Bacteriol., 187, 5008-5012. (Pubitemid 40962220)
42. Le, T. B. K., Schumacher, M. A., Lawson, D. M., Brennan, R. G. and Buttner, M. J. (2011) The crystal structure of the TetR family transcriptional repressor SimR bound to DNA and the role of a flexible N-terminal extension in minor groove binding. Nucleic Acids Res., 39, 9443-9447.
43. Alguel, Y., Meng, C., Terá n, W., Krell, T., Ramos, J. L., Gallegos, M.-T. and Zhang, X. (2007) Crystal structures of multidrug binding protein TtgR in complex with antibiotics and plant antimicrobials. J. Mol. Biol., 369, 829-840. (Pubitemid 46709926)