Identification of an effector specificity subregion within the aromatic- responsive regulators DmpR and XylR by DNA shuffling

Journal of Bacteriology

Volumn 182, Issue 11, 2000, Pages 3008-3016

  Skärfstad, Eleonore ^a   O'Neill, Eric ^a   Garmendia, Junkal ^b   Shingler, Victoria ^a  

^a UMEÅ UNIVERSITY   (Sweden)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; AROMATIC COMPOUND; DNA;

AMINO TERMINAL SEQUENCE; ARTICLE; ENZYME ACTIVITY; GENE EXPRESSION REGULATION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PSEUDOMONAS; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BENZENE DERIVATIVES; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC TECHNIQUES; GROEL PROTEIN; MUTAGENESIS; PROTEIN BINDING; PSEUDOMONAS; RECOMBINANT FUSION PROTEINS; SEQUENCE DELETION; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; TRANS-ACTIVATORS; TRANSCRIPTION FACTORS;

NEGIBACTERIA; PSEUDOMONAS; UNIDENTIFIED BACTERIOPHAGE;

EID: 0034087222     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.11.3008-3016.2000     Document Type: Article

References (33)

1. Abril, M.-A., C. Michán, K. N. Timmis, and J. L. Ramos. 1989. Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for the degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J. Bacteriol. 171:6782-6790.
2. Applegate, B. M., S. R. Kehrmeyer, and G. S. Sayler. 1998. A chromosomally based tod-luxCDABE whole-cell reporter for benzene, toluene, ethylbenzene, and xylene (BTEX) sensing. Appl. Environ. Microbiol. 64:2730-2735.
3. Crameri, A., G. Dawes, E. Rodríguez, Jr., S. Silver, and W. P. C. Stemmer. 1997. Molecular evolution of an arsenate detoxification pathway by DNA shuffling. Nat. Biotechnol. 15:436-438.
4. Delgado, A., and J.-L. Ramos. 1994. Genetic evidence for activation of the positive transcriptional regulator XyIR, a member of the NtrC family of regulators, by effector binding. J. Biol. Chem. 269:8059-8062.
5. de Lorenzo, V., M. Herrero, M. Metzke, and K. N. Timmis. 1991. An upstream XyIR- and IHF-induced nucleoprotein complex regulates the sigma54-dependent Pu promoter of TOL plasmid. EMBO J. 10:1159-1167.
6. Fernández, S., J. Pérez-Martín, and V. de Lorenzo. 1995. Activation of the transcriptional regulator XyIR of Pseudomonas putida by release of intramolecular repression between functional domains. Mol. Microbiol. 16:205-213.
7. Fernández, S., V. Shingler, and V. de Lorenzo. 1994. Cross-regulation by XyIR and DmpR activators of Pseudomonas putida suggest that transcriptional control of biodegradative operons evolves independently of catabolic genes. J. Bacteriol. 176:5052-5058.
8. Harayama, S. 1998. Artificial evolution by DNA shuffling. Trends Biotechnol. 16:76-82.
9. Heitzer, A., O. Webb, J. Thonnard, and G. Sayler. 1992. Specific and quantitative assessment of naphthalene and salicylate bioavailability by using a bioluminescent catabolic reporter bacterium. Appl. Environ. Microbiol. 58: 1839-1845.
10. Hopp, T. P., K. S. Prickett, V. L. Price, R. T. Libby, C. J. March, D. P. Cerretti, D. L. Urdal, and P. J. Conlon. 1988. A short polypeptide marker sequence useful for recombinant protein identification and purification. Bio/ Technology 6:1204-1210.
11. Ikariyama, Y., S. Nishiguchi, T. Koyama, E. Kobatake, and M. Azawa. 1997. Fiber-optic based biomonitoring of benzene derivatives by recombinant E. coli bearing luciferase gene-fused TOL-plasmid immobilized on the fiberoptic end. Anal. Chem. 69:2600-2605.
12. Inouye, S., A. Nakazawa, and T. Nakazawa. 1988. Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene 66:301-306.
13. Layton, A. C., M. Muccini, M. M. Ghosh, and G. S. Sayler. 1998. Construction of a bioluminescent reporter strain to detect polychlorinated biphenyls. Appl. Environ. Microbiol. 64:5023-5026.
14. N). Mol. Microbiol. 10:903-909.
15. 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 178:6067-6074.
16. 54-dependent activator DmpR. J. Biol. Chem. 271:17281-17286.
17. 54-dependent regulator DmpR. Mol. Microbiol. 28:131-141.
18. 54-dependent regulator DmpR. J. Biol. Chem. 274:32425-32432.
19. Palmer, G., R. McFadzean, K. Kilham, A. Sinclair, and G. Paton. 1998. Use of lux-based biosensors for rapid diagnosis of pollution in arable soils. Chemosphere 36:2683-2696.
20. Pavel, H., M. Forsman, and V. Shingler. 1994. An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols. J. Bacteriol. 176:7550-7557.
21. Pérez-Martín, J., and V. de Lorenzo. 1995. The amino-terminal domain of the prokaryotic enhancer-binding protein XyIR is a specific intramolecular repressor. Proc. Natl. Acad. Sci. USA 92:9392-9396.
22. Pérez-Martín, J., and V. de Lorenzo. 1996. Identification of the repressor subdomain within the signal reception module of the prokaryotic enhancer-binding protein XyIR of Pseudomonas putida. J. Biol. Chem. 271:7899-7902.
23. Ramos, J. L., S. Marqués, and K. N. Timmis. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operands is achieved through an interplay of host factors and plasmid-encoded regulators. Annu. Rev. Microbiol. 51:341-373.
24. Rosenberg, A. H., B. N. Lade, D.-S. Chui, S.-W. Lin, J. J. Dunn, and F. W. Studier. 1987. Vectors for selective expression of cloned DNAs by T7 RNA polymerase. Gene 56:125-135.
25. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
26. Shingler, V. 1996. Metabolic and regulatory check points in phenol degradation by Pseudomonas CF600, p. 153-164. In T. Nakazawa (ed.), Pseudomonas: molecular biology and biotechnology. ASM Press, Washington, D.C.
27. 54-dependent regulators: derepression as a control mechanism. Mol. Microbiol. 19:409-416.
28. Shingler, V., M. Bartilson, and T. Moore. 1993. Cloning and nucleotide sequence of the positive regulator. DmpR, of the phenol catabolic pathway of pV1150: a member of the NtrC family of transcriptional activators. J. Bacteriol. 175:1596-1604.
29. Shingler, V., and T. Moore. 1994. Sensing of aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J. Bacteriol. 176:1555-1560.
30. Shingler, V., and H. Pavel. 1995. Direct activation of the ATPase activity of the transcriptional activator DmpR by aromatic compounds. Mol. Microbiol. 17:505-513.
31. Stemmer, W. P. C. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389-391.
32. Walker, J. E., M. Saraste, M. J. Runswick, and N. J. Gay. 1982. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1:945-951.
33. Willardson, B., J. Wilkins, T. Rand, J. Schupp, K. Hill, P. Keim, and P. Jackson. 1998. Development and testing of a bacterial biosensor for toluene-based environmental contaminants. Appl. Environ. Microbiol. 64:1006-1012.