Critical nucleotides in the interaction of CatR with the pheBA promoter: Conservation of the CatR-mediated regulation mechanisms between the pheBA and catBCA operons

Microbiology

Volumn 146, Issue 1, 2000, Pages 173-183

  Tover, Andres ^a   Zernant, Jana ^a   Chugani, Sudha A ^b,c   Chakrabarty, Ananda M ^b   Kivisaar, Maia ^a  

^a UNIVERSITY OF TARTU   (Estonia)

^b UNIVERSITY OF ILLINOIS   (United States)

^c UNIVERSITY OF IOWA   (United States)

Author keywords

CatR; Evolution of catabolic pathways; Operons; pheBA and catBCA; Pseudomonas putida; Transcription activation

Indexed keywords

BACTERIAL ENZYME; NUCLEOTIDE; PHENOL; SPACER DNA;

ARTICLE; BACTERIAL GENE; BINDING SITE; CONTROLLED STUDY; DNA SEQUENCE; GENETIC REGULATION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; OPERON; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PSEUDOMONAS PUTIDA; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PSEUDOMONAS; PSEUDOMONAS PUTIDA;

EID: 0033984644     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-146-1-173     Document Type: Article

References (42)

1. Adams, M. H. (1959). Bacteriophages, pp. 445-447. New York: Interscience Publishers.
2. Aldrich, T. L. & Chakrabarty, A. M. (1988). Transcriptional regulation, nucleotide sequence, and localization of the promoter of the catBC operon in Pseudomonas putida. J Bacteriol 170, 1297-1304.
3. Ansari, A. Z., Chael, M. L. & O'Halloran, T. V. (1992). Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR. Nature 355, 87-89.
4. Basak, S. & Nagaraja, V. (1998). Transcriptional activator C protein-mediated unwinding of DNA as a possible mechanism for mom gene activation. J Mol Biol 284, 893-902.
5. Bayley, S. A., Duggleby, C. J., Worsey, M. J., Williams, P. A., Hardy, K. G. & Broda, P. (1977). Two modes of loss of the TOL function from Pseudomonas putida mt-2. Mol Gen Genet 154, 203-204.
6. Bolker, M., Wulczyn, F. G. & Kahmann, R. (1989). Role of bacteriophage Mu C protein in activation of the mom gene promoter. J Bacteriol 171, 2019-2027.
7. Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72, 248-254.
8. Carter, P., Bedoulle, H. & Winter, G. (1985). Improved oligonucleotide site-directed mutagenesis using M13 vectors. Nucleic Acids Res 13, 4431-4443.
9. Chugani, S. A., Parsek, M. R., Hershberger, C. D., Murakami, K., Ishihama, A. & Chakrabarty, A. M. (1997). Activation of the catBCA promoter: probing the interaction of CatR and RNA polymerase through in vitro transcription. J Bacteriol 179, 2221-2227.
10. Chugani, S. A., Parsek, M. R. & Chakrabarty, A. M. (1998). Transcriptional repression mediated by LysR-type regulator CatR bound at multiple binding sites. J Bacteriol 180, 2367-2372.
11. Coco, W. M., Rothmel, R. K., Henikoff, S. & Chakrabarty, A. M. (1993). Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD operon in Pseudomonas putida. J Bacteriol 175, 417-427.
12. Franz, B. & Chakrabarty, A. M. (1987). Organization and nucleotide sequence determination of a gene cluster involved in 3-chlorocatechol degradation. Proc Natl Acad Sci USA 84, 4460-4464.
13. Goethals, K., Van Montagu, M. & Holsters, M. (1992). Conserved motifs in a divergent nod box of Azorhizabium caulinodans ORS571 reveal a common structure in promoters regulated by LysR-type proteins. Proc Natl Acad Sci USA 89, 1646-1650.
14. Hanahan, D. (1983). Studies on the transformation of E. coli with plasmids. J Mol Biol 166, 577-580.
15. Harayama, S. & Timmis, K. N. (1989). Catabolism of aromatic hydrocarbons by Pseudomonas. In Genetics of Bacterial Diversity, pp. 151-174. Edited by D. A. Hopwood & K. E. Chater. London: Academic Press.
16. + (meta-pathway) phenotype. Mol Gen Genet 214, 173-176.
17. Hõrak, R. & Kivisaar, M. (1998). Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J Bacteriol 180, 2822-2829.
18. Kallastu, A., Hõrak, R. & Kivisaar, M. (1998). Identification and characterization of IS1411, a new insertion sequence which causes transcriptional activation of the phenol degradation genes in Pseudomonas putida. J Bacteriol 180, 5306-5312.
19. Kasak, L., Hõrak, R., Nurk, A., Talvik, K. & Kivisaar, M. (1993). Regulation of the catechol 1,2-dioxygenase-and phenol monooxygenase-encoding pheBA operon in Pseudomonas putida PaW85. J Bacteriol 175, 8038-8042.
20. Kivisaar, M., Hõrak, R., Kasak, L., Heinaru, A. & Habicht, J. (1990). Selection of independent plasmids determining phenol degradation in Pseudomonas putida and the cloning and expression of genes encoding phenol monooxygenase and catechol 1,2-dioxygenase. Plasmid 24, 25-36.
21. Kukor, J. J. & Olsen, R. H. (1990). Molecular cloning, characterization, and regulation of a Pseudomonas pickettii PKO1 gene encoding phenol hydroxylase and expression of the gene in Pseudomonas aeruginosa PAO1. J Bacteriol 172, 4624-4630.
22. McFall, S. M., Klem, T. J., Fujita, N., Ishihama, A. & Chakrabarty, A. M. (1997). DNase I footprinting, DNA bending and in vitro transcription analyses of ClcR and CatR on the clcABD promoter: evidence of a conserved transcriptional activation mechanism. Mol Microbiol 24, 965-976.
23. McFall, S. M., Chugani, S. A. & Chakrabarty, A. M. (1998). Transcriptional activation of the catechol and chlorocatechol operons: variations on a theme. Gene 223, 257-267.
24. van der Meer, J. R., Frijters, A. C. J., Leveau, J. H. J., Eggen, R. I. L.,. Zehnder, A. J. B. & de Vos, W. M. (1991). Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tcbCDEF chlorocatechol oxidative operon, and analysis of the regulatory region. J Bacteriol 173, 3700-3708.
25. Miller, J. H. (1992). A Short Course in Bacterial Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
26. Murakami, K., Fujita, N. & Ishihama, A. (1996). Transcription factor recognition surface on the RNA polymerase a subunit is involved in contact with the DNA enhancer element. EMBO J 15, 4358-4367.
27. O'Halloran, T. V., Frantz, B., Shin, M. K., Ralston, D. M. & Wright, J. G. (1989). The MerR heavy metal receptor mediates positive activation in a topologically novel transcription complex. Cell 56, 119-129.
28. Ornston, L. N. (1966). The conversion of catechol and protocatechuate to β-ketoadipate by Pseudomonas putida. IV. Regulation. J Biol Chem 241, 3800-3810.
29. Parkhill, J. & Brown, N. L. (1990). Site-specific insertion and deletion mutants in the mer promoter-operator region of Tn501; the nineteen base-pair spacer is essential for normal induction of the promoter by MerR. Nucleic Acids Res 18, 5157-5162.
30. Parsek, M. R., Shinabarger, D. L., Rothmel, R. K. & Chakrabarty, A. M. (1992). Role of CatR and cis,cis-muconate in the activation of the catBC operon involved on benzoate degradation in Pseudomonas putida. J Bacteriol 174, 7798-7806.
31. Parsek, M. R., Ye, R. W., Pun, P. & Chakrabarty, A. M. (1994). Critical nucleotides in the interaction of a LysR-type regulator with its target promoter region. J Biol Chem 269, 11279-11284.
32. Parsek, M. R., Kivisaar, M. & Chakrabarty, A. M. (1995). Differental DNA bending introduced by the Pseudomonas putida LysR-type regulator, CatR, at the plasmid-borne pheBA and chromosomal catBC promoters. Mol Microbiol 15, 819-828.
33. Parsek, M. R., McFall, S. M. & Chakrabarty, A. M. (1996). Evolution of regulatory systems of biodegradative pathways. In Molecular Biology of Pseudomonads, pp. 135-152. Edited by T. Nakazawa, K. Furukawa, D. Haas & S. Silver, Washington, DC: American Society for Microbiology.
34. Peters, M., Heinaru, E., Talpsep, E., Wand, H., Stottmeister, U., Heinaru, A. & Nurk, A. (1997). Acquisition of a deliberately introduced phenol degradation operon, pheBA, by different indigenous Pseudomonas species. Appl Environ Microbiol 63, 4899-4906.
35. Rothmel, R. K., Aldrich, T. L., Houghton, J. E., Coco, W. M., Ornston, L. N. & Chakrabarty, A. M. (1990). Nucleotide sequencing of Pseudomonas putida catR : positive regulator of the catBC operon is a member of LysR family. J Bacteriol 172, 921-931.
36. Rothmel, R. K., Shinabarger, D. L., Parsek, M. R., Aldrich, T. L. & Chakrabarty, A. M. (1991). Functional analysis of the Pseudomonas putida regulatory protein CatR: transcriptional studies and determination of the CatR DNA-binding site by hydroxylradical footprinting. J Bacteriol 173, 4717-4724.
37. Sharma, R. C. & Schimke, R. T. (1996). Preparation of electrocompetent E. coli using salt-free growth medium. BioTechniques 20, 42-44.
38. Shingler, V., Powlowski, J. & Marklund, U. (1992). Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. Strain CF600. J Bacteriol 174, 711-724.
39. Stefano, J. E. & Gralla, J. D. (1982). Spacer mutations in the lac ps promoter. Proc Natl Acad Sci USA 79, 1069-1072.
40. Studier, F. W. & Moffatt, B. A. (1986). Use of bacteriophage T7 polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189, 113-130.
41. Tsuda, M., Minegishi, K.-I. & Iino, T. (1989). Toluene transposons Tn4651 and Tn4653 are class II transposons. J Bacteriol 171, 1386-1363.
42. Wigmore, G. J., DiBerardino, D. & Bayly, R. C. (1977). Regulation of the enzymes of the meta-cleavage pathway of Pseudomonas putida: a regulatory model. J Gen Microbiol 100, 81-87.