Transcriptional activation of quinoline degradation operons of Pseudomonas putida 86 by the AraC/XylS-type regulator OxoS and cross-regulation of the PqorM promoter by XylS

Applied and Environmental Microbiology

Volumn 71, Issue 12, 2005, Pages 8618-8626

  Carl, Birgit ^a   Fetzner, Susanne ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ESTERS; GENETIC ENGINEERING; PROTEINS;

BINDING SITE; GENE CLUSTER; QUINOLINE; TRANSCRIPTIONAL ACTIVATION;

GENES;

AROMATIC COMPOUND; BENZOIC ACID; CYTARABINE; GENE PRODUCT; MOLYBDENUM; MOLYBDENUN HYDROXYLASE; OXIDOREDUCTASE; OXOS PROTEIN; OXYGENASE; QUINOLINE; QUINOLINE DERIVATIVE; UNCLASSIFIED DRUG; XYLS PROTEIN;

ENZYME ACTIVITY;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; CARBON SOURCE; CONTROLLED STUDY; GENE CLUSTER; GENE CONTROL; GENE FUNCTION; MICROBIAL DEGRADATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; ORF3 GENE; ORF7 GENE; ORF8 GENE; ORF9 GENE; OXOO GENE; OXOR GENE; OXOS GENE; PLASMID; PQORM GENE; PROMOTER REGION; PSEUDOMONAS PUTIDA; QORM GENE; QORMSL GENE; QUINOLINE DEGRADATION; TRANSCRIPTION INITIATION; XYLS GENE;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA, BACTERIAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; KINETICS; MIXED FUNCTION OXYGENASES; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES ACTING ON CH-CH GROUP DONORS; PROMOTER REGIONS (GENETICS); PSEUDOMONAS PUTIDA; QUINOLINES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 29144453529     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.12.8618-8626.2005     Document Type: Article

References (52)

1. Blatny, J. M., T. Brautaset, H. C. Winther-Larsen, K. Haugan, and S. Valla. 1997. Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl. Environ. Microbiol. 63:370-379.
2. Bonin, I., B. M. Martins, V. Purvanov, S. Fetzner, R. Huber, and H. Dobbek. 2004. Active site geometry and substrate recognition of the molybdenum hydroxylase quinoline 2-oxidoreductase. Structure 12:1425-1435.
3. Carl, B., A. Arnold, B. Hauer, and S. Fetzner. 2004. Sequence and transcriptional analysis of a gene cluster of Pseudomonas putida 86 involved in quinoline degradation. Gene 331:177-188.
4. Cases, I., and V. de Lorenzo. 2005. Promoters in the environment: transcriptional regulation in its natural context. Nat. Rev. Microbiol. 3:105-118.
5. Chang, H.-K., P. Mohseni, and G. J. Zylstra. 2003. Characterization and regulation of the genes for a novel anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1. J. Bacteriol. 185:5871-5881.
6. Chauvaux, S., F. Chevalier, C. le Dantec, F. Fayolle, I. Miras, F. Kunst, and P. Beguin. 2001. Cloning of a genetically unstable cytochrome P-450 gene cluster involved in degradation of the pollutant ethyl tert-butyl ether by Rhodococcus ruber. J. Bacteriol. 183:6551-6557.
7. Cowles, C. E., N. N. Nichols, and C. S. Harwood. 2000. BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 182:6339-6346.
8. Davis, R. W., D. Botstein, and J. R. Roth. 1980. A manual for genetic engineering. Advanced bacterial genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
9. DeHaseth, P. L., M. L. Zupancic, and M. T. Record, Jr. 1998. RNA polymerase-promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180:3019-3025.
10. De Lorenzo, V., and J. Pérez-Martín. 1996. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:1177-1184.
11. Fernández, S., V. Shingler, and V. de Lorenzo. 1994. Cross-regulation by XylR and DmpR activators of Pseudomonas putida suggests that transcriptional control of biodegradative operons evolves independently of catabolic genes. J. Bacteriol. 176:5052-5058.
12. Fetzner, S. 1998. Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions. Appl. Microbiol. Biotechnol. 49:237-250.
13. Frerichs-Deeken, U., B. Goldenstedt, R. Gahl-Janßen, R. Kappl, J. Hüttermann, and S. Fetzner. 2003. Functional expression of the quinoline 2-oxidoreductase genes qorMSL in Pseudomonas putida KT2440 pUF1 and in Pseudomonas putida 86-1 Δqor pUF1 and analysis of the Qor proteins. Eur. J. Biochem. 270:1567-1577.
14. Gallegos, M. T., R. Schleif, A. Bairoch, K. Hofmann, and J. L. Ramos. 1997. AraC/XylS family of transcriptional regulators. Microbiol. Mol. Biol. Rev. 61:393-410.
15. 54-dependent tandem promoter according to the compound used for growth. J. Bacteriol. 178:2356-2361.
16. García-González, V., F. Govantes, O. Porrúa, and E. Cantero. 2005. Regulation of the Pseudomonas sp. strain ADP cyanuric acid degradation operon. J. Bacteriol. 187:155-167.
17. González-Pérez, M. M., J. L. Ramos, M.-T. Gallegos, and S. Marqués. 1999. Critical nucleotides in the upstream region of the XylS-dependent TOL meta-cleavage pathway operon promoter as deduced from analysis of mutants. J. Biol. Chem. 274:2286-2290.
18. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
19. Igloi, G. L., and R. Brandsch. 2003. Sequence of the 165-kilobase catabolic plasmid pAO1 from Arthrobacter nicotinovorans and identification of a pAO1-dependent nicotine uptake system. J. Bacteriol. 185:1976-1986.
20. Kaebernick, M., E. Dittmann, T. Börner, and B. A. Neilan. 2002. Multiple alternate transcripts direct the biosynthesis of microcystin, a cyanobacterial nonribosomal peptide. Appl. Environ. Microbiol. 68:449-455.
21. Kaldalu, N., U. Toots, V. de Lorenzo, and M. Ustav. 2000. Functional domains of the TOL plasmid transcription factor XylS. J. Bacteriol. 182:1118-1126.
22. Keilty, S., and M. Rosenberg. 1987. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262:6389-6395.
23. Kessler, B., V. de Lorenzo, and K. N. Timmis. 1993. Identification of a cis-acting sequence within the Pm promoter of the TOL plasmid which confers XylS-mediated responsiveness to substituted benzoates. J. Mol. Biol. 230:699-703.
24. Kovach, M. E., P. H. Elzer, D. S. Hill, G. T. Robertson, M. A. Farris, R. M. Roop II, and K. M. Peterson. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176.
25. Leahy, J. G., G. R. Johnson, and R. H. Olsen. 1997. Cross-regulation of toluene monooxygenases by the transcriptional activators TbmR and TbuT. Appl. Environ. Microbiol. 63:3736-3739.
26. Lee, S. J., and J. D. Gralla. 2004. Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol. Cell. 14:153-162.
27. Leimkühler, S., R. Hodson, G. N. George, and K. V. Rajagopalan. 2003. Recombinant Rhodobacter capsulatus xanthine dehydrogenase, a useful model system for the characterization of protein variants leading to xanthinuria I in humans. J. Biol. Chem. 278:20802-20811.
28. Leimkühler, S., and W. Klipp. 1999. Role of XdhC in molybdenum cofactor insertion into xanthine dehydrogenase of Rhodobacter capsulatus. J. Bacteriol. 181:2745-2751.
29. Martinez, B., J. Tomkins, L. P. Wackett, R. Wing, and M. J. Sadowsky. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183:5684-5697.
30. 3) for Rhizobium leguminosarum hydrogenase accessory genes hupGHIJ. Microbiology 150:665-675.
31. Martins, B. M., T. Svetlitchnaia, and H. Dobbek. 2005. 2-Oxoquinoline 8-monooxygenase oxygenase component: active site modulation by Rieske-[2Fe-2S] center oxidation/reduction. Structure 13:817-824.
32. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
33. Mitchell, J. E., D. Zheng, S. J. W. Busby, and S. D. Minchin. 2003. Identification and analysis of 'extended - 10' promoters in Escherichia coli. Nucleic Acids Res. 31:4689-4695.
34. Nagy, I., G. Schoofs, F. Compernolle, P. Proost, J. Vanderleyden, and R. de Mot. 1995. Degradation of the thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J. Bacteriol. 177:676-687.
35. Parschat, K., C. Canne, R. Kappl, J. Hüttermann, and S. Fetzner. 2001. Xanthine dehydrogenase from Pseudomonas putida 86: specificity, oxidation-reduction potentials of its redox-active centers, and first EPR studies. Biochim. Biophys. Acta 1544:151-165.
36. Parschat, K., B. Hauer, R. Kappl, R. Kraft, J. Hüttermann, and S. Fetzner. 2003. Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate. Characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J. Biol. Chem. 278:27483-27494.
37. Purvanov, V., and S. Fetzner. 2005. Replacement of active-site residues of quinoline 2-oxidoreductase involved in substrate recognition and specificity. Curr. Microbiol. 50:217-222.
38. Ramos, J. L., S. Marques, and K. N. Tinimis. 1997. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu. Rev. Microbiol. 51:341-373.
39. Ramos-González, M.-l., M. Olson, A. A. Gatenby, G. Mosqueda, M. Manzanera, M. J. Campos, S. Víchez, and J. L. Ramos. 2002. Cross-regulation between a novel two-component signal transduction system for catabolism of toluene in Pseudomonas mendocina and the TodST system from Pseudomonas putida. J. Bacteriol. 184:7062-7067.
40. Rosche, B., B. Tshisuaka, B. Hauer, F. Lingens, and S. Fetzner. 1997. 2-Oxo-1,2-dihydroquinoline 8-monooxygenase: phylogenetic relationship to other multicomponent nonheme iron oxygenases. J. Bacteriol. 179:3549-3554.
41. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
42. Santos, P. M., I. Di Bartolo, J. M. Blatny, E. Zennaro, and S. Valla. 2001. New broad-host-range promoter probe vectors based on the plasmid RK2 replicon. FEMS Microbiol. Lett. 195:91-96.
43. Schultz, A. C., P. Nygaard, and H. H. Saxild. 2001. Functional analysis of 14 genes that constitute the purine catabolic pathway in Bacillus subtilis and evidence for a novel regulon controlled by the PucR transcription factor. J. Bacteriol. 183:3293-3302.
44. Schwarz, G., E. Senghas, A. Erben, B. Schäfer, F. Lingens, and H. Höke. 1988. Microbial metabolism of quinoline and related compounds. I. Isolation and characterization of quinoline-degrading bacteria. Syst. Appl. Microbiol. 10:185-190.
45. Simon, R., U. Priefer, and A. Pühler. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Bio/Technology 1:784-791.
46. Temple, C. A., and K. V. Rajagopalan. 2000. Mechanism of assembly of the bis(molybdopterin guanine dinucleotide)molybdenum cofactor in Rhodobacter sphaeroides dimethyl sulfoxide reductase. J. Biol. Chem. 275:40202-40210.
47. Tropel, D., A. Bähler, K. Globig, and J. R. van der Meer. 2004. Design of new promoters and of a dual-bioreporter based on cross-activation by the two regulatory proteins XylR and HbpR. Env. Microbiol. 6:1186-1196.
48. Tshisuaka, B., R. Kappl, J. Hüttermann, and F. Lingens. 1993. Quinoline oxidoreductase from Pseudomonas putida 86: an improved purification procedure and electron paramagnetic resonance spectroscopy. Biochemistry 32:12928-12934.
49. Urata, M., M. Miyakoshi, S. Kai, K. Maeda, H. Habe, T. Omori, H. Yamane, and H. Nojiri. 2004. Transcriptional regulation of the ant operon, encoding two-component anthranilate 1,2-dioxygenase, on the carbazole-degradative plasmid pCAR1 of Pseudomonas resinovorans strain CA10. J. Bacteriol. 186:6815-6823.
50. Woodcock, D. M., P. J. Crowther, J. Doherty, S. Jefferson, E. DeCruz, M. Noyer-Weidner, S. S. Smith, M. Z. Michael, and M. W. Graham. 1989. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 17:3469-3478.
51. Yang, B., and T. J. Larson. 1998. Multiple promoters are responsible for transcription of the glpEGR operon of Escherichia coli K-12. Biochim. Biophys. Acta 1396:114-126.
52. Zor, T., and Z. Selinger. 1996. Linearization of Bradford protein assay increases its sensitivity: theoretical and experimental studies. Anal. Biochem. 236:302-308.