Phenylacetyl coenzyme a is an effector molecule of the tetr family transcriptional repressor PaaR from Thermus thermophilus HB8

Journal of Bacteriology

Volumn 193, Issue 17, 2011, Pages 4388-4395

  Sakamoto, Keiko ^a   Agari, Yoshihiro ^a   Kuramitsu, Seiki ^a,b   Shinkai, Akeo ^a  

^a RIKEN Harima Institute Research   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COENZYME A; PHENYLACETIC ACID; PHENYLACETYL COENZYME A; TRANSCRIPTION FACTOR; TRANSCRIPTIONAL FACTOR FADR; TRANSCRIPTIONAL REPRESSOR PAAR; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; BINDING SITE; BIODEGRADATION; ESCHERICHIA COLI; GENE CLUSTER; GENE TARGETING; IN VITRO STUDY; LIGAND BINDING; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN TERTIARY STRUCTURE; PSEUDOMONAS; STOICHIOMETRY; STRUCTURAL HOMOLOGY; THERMUS THERMOPHILUS;

ACETYL COENZYME A; ACYL COENZYME A; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BIOSENSING TECHNIQUES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; OPERON; PHENYLACETATES; RECOMBINANT PROTEINS; REPRESSOR PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; THERMUS THERMOPHILUS; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PSEUDOMONAS; THERMUS THERMOPHILUS;

EID: 80052322974     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05203-11     Document Type: Article

References (28)

1. Agari, Y., K. Agari, K. Sakamoto, S. Kuramitsu, and A. Shinkai. 2011. TetR family transcriptional repressor Thermus thermophilus FadR controls fatty acid degradation. Microbiology 157:1589-1601.
2. Baker, N. A., D. Sept, S. Joseph, M. J. Holst, and J. A. McCammon. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U. S. A. 98:10037-10041.
3. del Peso-Santos, T., et al. 2006. Coregulation by phenylacetyl-coenzyme A-responsive PaaX integrates control of the upper and lower pathways for catabolism of styrene by Pseudomonas sp. strain Y2. J. Bacteriol. 188:4812-4821.
4. DiRusso, C. C., T. L. Heimert, and A. K. Metzger. 1992. Characterization of FadR, a global transcriptional regulator of fatty acid metabolism in Escherichia coli. Interaction with the fadB promoter is prevented by long chain fatty acyl coenzyme A. J. Biol. Chem. 267:8685-8691.
5. Eswar, N., et al. 2006. Comparative protein structure modeling using Modeller. Curr. Protoc. Bioinformatics 15:5.5.1-5.6.30.
6. Ferrandez, A., J. L. Garcia, and E. Diaz. 2000. Transcriptional regulation of the divergent paa catabolic operons for phenylacetic acid degradation in Escherichia coli. J. Biol. Chem. 275:12214-12222.
7. Ferrandez, A., et al. 1998. Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway. J. Biol. Chem. 273:25974-25986.
8. Garcia, B., et al. 2000. Phenylacetyl-coenzyme A is the true inducer of the phenylacetic acid catabolism pathway in Pseudomonas putida U. Appl. Environ. Microbiol. 66:4575-4578.
9. Gouet, P., X. Robert, and E. Courcelle. 2003. ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 31:3320-3323.
10. Hamlin, J. N., R. A. Bloodworth, and S. T. Cardona. 2009. Regulation of phenylacetic acid degradation genes of Burkholderia cenocepacia K56-2. BMC Microbiol. 9:222.
11. Haydon, D. J., and J. R. Guest. 1991. A new family of bacterial regulatory proteins. FEMS Microbiol. Lett. 63:291-295.
12. Hinrichs, W., et al. 1994. Structure of the Tet repressor-tetracycline complex and regulation of antibiotic resistance. Science 264:418-420.
13. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637.
14. Kunishima, N., et al. 2005. A novel induced-fit reaction mechanism of asymmetric hot dog thioesterase PAAI. J. Mol. Biol. 352:212-228.
15. Kuramitsu, S., K. Hiromi, H. Hayashi, Y. Morino, and H. Kagamiyama. 1990. Pre-steady-state kinetics of Escherichia coli aspartate aminotransferase catalyzed reactions and thermodynamic aspects of its substrate specificity. Biochemistry 29:5469-5476.
16. Larkin, M. A., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
17. Luengo, J. M., J. L. Garcia, and E. R. Olivera. 2001. The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Mol. Microbiol. 39:1434-1442.
18. Marchler-Bauer, A., et al. 2002. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res. 30:281-283.
19. Maseda, H., and T. Hoshino. 1995. Screening and analysis of DNA fragments that show promoter activities in Thermus thermophilus. FEMS Microbiol. Lett. 128:127-134.
20. Mohamed Mel, S., W. Ismail, J. Heider, and G. Fuchs. 2002. Aerobic metabolism of phenylacetic acids in Azoarcus evansii. Arch. Microbiol. 178:180-192.
21. Navarro-Llorens, J. M., et al. 2005. Phenylacetate catabolism in Rhodococcus sp. strain RHA1: a central pathway for degradation of aromatic compounds. J. Bacteriol. 187:4497-4504.
22. Oshima, T., and K. Imahori. 1974. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa. Int. J. Syst. Bacteriol. 24:102-112.
23. Ramos, J. L., et al. 2005. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69:326-356.
24. Schumacher, M. A., et al. 2001. Structural mechanisms of QacR induction and multidrug recognition. Science 294:2158-2163.
25. Shimada, T., N. Fujita, M. Maeda, and A. Ishihama. 2005. Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells 10:907-918.
26. Shinkai, A., et al. 2007. Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J. Bacteriol. 189:3891-3901.
27. Teufel, R., et al. 2010. Bacterial phenylalanine and phenylacetate catabolic pathway revealed. Proc. Natl. Acad. Sci. U. S. A. 107:14390-14395.
28. Willems, A. R., et al. 2008. Crystal structures of the Streptomyces coelicolor TetR-like protein ActR alone and in complex with actinorhodin or the actinorhodin biosynthetic precursor (S)-DNPA. J. Mol. Biol. 376: 1377-1387