Characterization of the ligand and DNA binding properties of a putative archaeal regulator ST1710

Biochemistry

Volumn 48, Issue 10, 2009, Pages 2099-2108

  Yu, Linliang ^a   Fang, Jun ^a   Wei, Yinan ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

[CARBONYL; ANTIBIOTIC RESISTANCES; ARCHAEAL; ARCHAEON; BINDING AFFINITIES; CONFORMATIONAL CHANGES; DISSOCIATION CONSTANTS; DNA-BINDING PROPERTIES; DNA-BINDING SITES; ETHIDIUM; FLUORESCENCE POLARIZATION METHODS; LIGAND BINDINGS; LIGAND-BINDING SITES; LIVING CONDITIONS; MOLECULAR LEVELS; RECOGNITION SITES; SULFOLOBUS TOKODAII; TEMPERATURE SENSITIVES;

BACTERIOLOGY; BINDING ENERGY; BIOCHEMISTRY; CYANIDES; DISSOCIATION; DNA; GENES; LIGANDS; NUCLEIC ACIDS;

BINDING SITES;

ANTIBIOTIC AGENT; CARBONYL CYANIDE CHLOROPHENYLHYDRAZONE; CARBONYL DERIVATIVE; CHLORMETHINE; CYANIDE; DNA; DOUBLE STRANDED DNA; ETHIDIUM; HYDRAZONE DERIVATIVE; LIGAND; PROTEIN; SALICYLIC ACID;

ANTIBIOTIC RESISTANCE; ARCHAEAL GENOME; ARCHEAN; ARTICLE; BACTERIAL GENE; BACTERIUM; BINDING AFFINITY; BINDING SITE; CONFORMATIONAL TRANSITION; DISSOCIATION CONSTANT; DNA BINDING; FLUORESCENCE POLARIZATION; GENE CONTROL; LIGAND BINDING; METHODOLOGY; NONHUMAN; POLARIZATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DNA INTERACTION; REPRESSOR GENE; SULFOLOBUS; TEMPERATURE; TEMPERATURE SENSITIVITY;

ARCHAEAL PROTEINS; CARBONYL CYANIDE M-CHLOROPHENYL HYDRAZONE; CIRCULAR DICHROISM; DNA; ETHIDIUM; FLUORESCENCE POLARIZATION; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; RECOMBINANT PROTEINS; REPRESSOR PROTEINS; SODIUM SALICYLATE; SPECTROMETRY, FLUORESCENCE; SULFOLOBUS; TEMPERATURE;

ARCHAEA; BACTERIA (MICROORGANISMS); SULFOLOBUS TOKODAII;

EID: 64349108340     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi801662s     Document Type: Article

References (45)

1. Bell, S. D., Magill, C. P., and Jackson, S. P. (2001) Basal and regulated transcription in archaea. Biochem. Soc. Trans. 29, 392-395.
2. Hausner, W., Wettach, J., Hethke, C., and Thomm, M. (1996) Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase. J. Biol. Chem. 271, 30144-30148.
3. Langer, D., Hain, J., Thuriaux, P., and Zillig, W. (1995) Transcription in archaea: Similarity to that in eucarya. Proc. Natl. Acad. Sci. U.S.A. 92, 5768-5772.
4. Soppa, J. (1999) Transcription initiation in archaea: Facts, factors and future aspects. Mol. Microbiol. 31, 1295-1305.
5. Best, A. A., and Olsen, G. J. (2001) Similar subunit architecture of archaeal and eukaryal RNA polymerases. FEMS Microbiol. Lett. 195, 85-90.
6. Bell, S. D., Kosa, P. L., Sigler, P. B., and Jackson, S. P. (1999) Orientation of the transcription preinitiation complex in archaea. Proc. Natl. Acad. Sci. U.S.A. 96, 13662-13667.
7. Kyrpides, N. C., and Ouzounis, C. A. (1999) Transcription in archaea. Proc. Natl. Acad. Sci. U.S.A. 96, 8545-8550.
8. Reeve, J. N. (2003) Archaeal chromatin and transcription. Mol. Microbiol. 48, 587-598.
9. Bell, S. D. (2005) Archaeal transcriptional regulation: Variation on a bacterial theme? Trends Microbiol. 13, 262-265.
10. Bell, S. D., and Jackson, S. P. (2001) Mechanism and regulation of transcription in archaea. Curr. Opin. Microbiol. 4, 208-213.
11. Geiduschek, E. P., and Ouhammouch, M. (2005) Archaeal transcription and its regulators. Mol. Microbiol. 56, 1397-1407.
12. George, A. M., and Levy, S. B. (1983) Amplifiable resistance to the tetracycline, chloramphenicol, and other antibiotics in Escherichia coli: Involvement of a nonplasmid-determined efflux of tetracycline. J. Bacteriol. 155, 531-540.
13. George, A. M., and Levy, S. B. (1983) Gene in the major co-transduction gap of the Escherichia coli K-12 linkage map required for the expression of chromosomal resistance to tetracycline and other antibiotics. J. Bacteriol. 155, 541-548.
14. Perez-Rueda, E., and Collado-Vides, J. (2001) Common history at the origin of the position-function correlation in transcriptional regulators in archaea and bacteria. J. Mol. Evol. 53, 172-179.
15. Perez-Rueda, E., Collado-Vides, J., and Segovia, L. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput. Biol. Chem. 28, 341-350.
16. Wilkinson, S. P., and Grove, A. (2006) Ligand-responsive transcriptional regulation by members of the MarR family of winged helix proteins. Curr. Issues Mol. Biol. 8, 51-62.
17. Lim, D., Poole, K., and Strynadka, N. C. J. (2002) Crystal structure of the MexR repressor of the mexRAB-oprM multidrug efflux operon of Pseudomonas aeruginosa. J. Biol. Chem. 277, 29253-29259.
18. Wu, R. Y., Zhang, R. G., Zagnitko, O., Dementieva, I., Maltzev, N., Watson, J. D., Laskowski, R., Gornicki, P., and Joachimiak, A. (2003) Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor. J. Biol. Chem. 278, 20240-20244.
19. Saridakis, V., Shahinas, D., Xu, X. H., and Christendat, D. (2008) Structural insight on the mechanism of regulation of the MarR family of proteins: High-resolution crystal structure of a transcriptional repressor from Methanobacterium thermoautotrophicum. J. Mol. Biol. 377, 655-667.
20. Hong, M., Fuangthong, M., Helmann, J. D., and Brennan, R. G. (2005) Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol. Cell 20, 131-141.
21. Alekshun, M. N., Levy, S. B., Mealy, T. R., Seaton, B. A., and Head, J. F. (2001) The crystal structure of MarR., a regulator of multiple antibiotic resistance, at 2.3 angstrom resolution. Nat. Struct. Biol. 8, 710-714.
22. Kumarevel, T., Tanaka, T., Nishio, M., Gopinath, S. C. B., Takio, K., Shinkai, A., Kumar, P. K. R., and Yokoyama, S. (2008) Crystal structure of the MarR family regulatory protein, ST 1710, from Sulfolobus tokodaii strain. J. Struct. Biol. 161, 9-17.
23. Miyazono, K. I., Tsujimura, M., Kawarabayasi, Y., and Tanokura, M. (2007) Crystal structure of an archaeal homologue of multidrug resistance repressor protein, EmrR., from hyperthermophilic archaea Sulfolobus tokodaii strain 7. Proteins: Struct., Funct., Bioinf. 67, 1138-1146.
24. Lundblad, J. R., Laurance, M., and Goodman, R. H. (1996) Fluorescence polarization analysis of protein-DNA and protein-protein interactions. Mol. Endocrinol. 10, 607-612.
25. Hugli, T. E., and Stein, W. H. (1971) Involvement of a tyrosine residue in activity of bovine pancreatic deoxyribonuclease A. J. Biol. Chem. 246, 7191-7200.
26. Riordan, J. F., Sokolovs, M., and Vallee, B. L. (1967) Functional tyrosyl residues of carboxypepridase A. Nitration with tetrani-tromethane. Biochemistry 6, 3609-3617.
27. Riordan, J. F., Sokolovs, M., and Vallee, B. L. (1967) Environmentally sensitive tyrosyl residues. Nitration with tetranitromethane. Biochemistry 6, 358-361.
28. Kahn, P. C. (1979) The interpretation of near-ultraviolet circular dichroism. Methods Enzymol. 61, 339-378.
29. Strickland, E. H., and Mercola, D. (1976) Near-ultraviolet tyrosyl circular-dichroism of pig insulin monomers, dimmrs, and hexamers: Dipole-dipole coupling calculations in monopole approximation. Biochemistry 15, 3875-3884.
30. Kelly, S. M., and Price, N. C. (2000) The application of circular dichroism to studies of protein folding and unfolding. Biochim. Biophys. Acta 1338, 161-185.
31. Noble, M. A., Munro, A. W., Rivers, S. L., Robledo, L., Daff, S. N., Yellowlees, L. J., Shimizu, T., Sagami, I., Guillemette, J. G., and Chapman, S. K. (1999) Potentiometric analysis of the flavin cofactors of neuronal nitric oxide synthase. Biochemistry 38, 16413-16418.
32. Andersson, L. A., and Peterson, J. A. (1995) Active-site analysis of ferric P450 enzymes: Hydrogen-bonding effects on the circular dichroism spectra. Biochem. Biophys. Res. Commun. 211, 389-395.
33. Cogdell, R. J., Isaacs, N. W., Freer, A. A., Arrelano, J., Howard, T. D., Papiz, M. Z., Hawthornthwaite-Lawless, A. M., and Prince, S. (1997) The structure and function of the LH2 (B800 - 850) complex from the purple photosynthetic bacterium Rhodopseudomo-nas acidophila strain 10050. Prog. Biophys. Mol. Biol. 68, 1-27.
34. Cogdell, R. J., and Scheer, H. (1985) Circular-dichroism of light-harvesting complexes from purple photosynthetic bacteria. Pho-tochem. Photobiol. 42, 669-678.
35. West, S. M., and Price, N. C. (1990) The unfolding and attemped refolding of mitochondrial aspartate-aminotransferase from pig-heart. Biochem. J. 265, 45-50.
36. Berezovski, M., and Krylov, S. N. (2005) Thermochemistry of protein-DNA interaction studied with temperature-controlled non-equilibrium capillary electrophoresis of equilibrium mixtures. Anal. Chem. 77, 1526-1529.
37. Liu, C. C., Richard, A. J., Datta, K., and LiCata, V. J. (2008) Prevalence of temperature-dependent heat capacity changes in protein-DNA interactions. Biophys. J. 94, 3258-3265.
38. Peters, W. B., Edmondson, S. P., and Shriver, J. W. (2004) Thermodynamics of DNA binding and distortion by the hyper-thermophile chromatin protein Sac7d. J. Mol. Biol. 343, 339-360.
39. Suzuki, T., Iwasaki, T., Uzawa, T., Hara, K., Nemoto, N., Kon, T., Ueki, T., Yamagishi, A., and Oshima, T. (2002) Sulfolobus tokodaii sp nov (f. Sulfolobus sp strain 7), a new member of the genus Sulfolobus isolated from Beppu Hot Springs, Japan. Extre-mophiles 6, 39-44.
40. Oh, S. Y., Shin, J. H., and Roe, J. H. (2007) Dual role of OhrR as a repressor and an activator in response to organic hydroperoxides in Streptomyces coelicolor. J. Bacteriol. 189, 6284-6292.
41. Fiorentino, G., Ronca, R., Cannio, R., Rossi, M., and Bartolucci, S. (2007) MarR-like transcriptional regulator involved in detoxification of aromatic compounds in Sulfolobus solfataricus. J. Bacteriol. 189, 7351-7360.
42. Alekshun, M. N., and Levy, S. B. (1999) Alteration of the repressor activity of MarR., the negative regulator of the Escherichia coli marRAB locus, by multiple chemicals in vitro. J. Bacteriol. 181, 4669-4672.
43. Xiong, A., Gottman, A., Park, C., Baetens, M., Pandza, S., and Matin, A. (2000) The EmrR protein represses the Escherichia coli emrRAB multidrug resistance operon by directly binding to its promoter region. Antimicrob. Agents Chemother. 44, 2905-2907.
44. Brooun, A., Tomashek, J. J., and Lewis, K. (1999) Purification and ligand binding of EmrR., a regulator of a multidrug transporter. J. Bacteriol. 181, 5131-5133.
45. Poirot, O., O'Toole, E., and Notredame, C. (2003) Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31, 3503-3506.