PcaU, a transcriptional activator of genes for protocatechuate utilization in Acinetobacter

Journal of Bacteriology

Volumn 180, Issue 6, 1998, Pages 1512-1524

  Gerischer, Ulrike ^a,b   Segura, Ana ^a,c   Ornston, L Nicholas ^a  

^a YALE UNIVERSITY   (United States)

^b UNIVERSITY OF ULM   (Germany)

^c CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PROTOCATECHUIC ACID;

ACINETOBACTER; AMINO ACID SEQUENCE; ARTICLE; DNA BINDING; GENE ACTIVATION; GENE LOCATION; GENE MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OPERON; PRIORITY JOURNAL; REGULATOR GENE; TRANSCRIPTION REGULATION; TUMOR GROWTH;

ACINETOBACTER; ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS PUTIDA;

EID: 0031938056     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.180.6.1512-1524.1998     Document Type: Article

References (64)

1. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1994. Current protocols in molecular biology. Wiley Interscience, New York, N.Y.
2. Averhoff, B., L. Gregg-Jolly, D. Elsemore, and L. N. Ornston. 1992. Genetic analysis of supraoperonic clustering by use of natural transformation in Acinetobacter calcoaceticus. J. Bacteriol. 174:200-204.
3. Baumann, P. 1968. Isolation of Acinetobacter from soil and water. J. Bacteriol. 96:39-42.
4. Birnboim, H. C., and J. Doly. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 7:1513-1523.
5. Canovas, J. L., and R. Y. Stanier. 1967. Regulation of the enzymes of the β-ketoadipate pathway in Moraxella calcoacetica. I. General aspects. Eur. J. Biochem. 1:289-300.
6. Canovas, J. L., M. L. Wheelis, and R. Y. Stanier. 1968. Regulation of the enzymes of the β-ketoadipate pathway in Moraxella calcoacetica. II. The role of protocatechuate as inducer. Eur. J. Biochem. 3:293-304.
7. Choi, Y. L., S. Kawase, T. Nishida, H. Sakai, T. Komano, M. Kawamukai, R. Utsumi, Y. Kohara, and K. Akiyama. 1988. Nucleotide sequence of the glpR gene encoding the repressor for the glycerol-3-phosphate regulon of Escherichia coli K12. Nucleic Acids Res. 16:7732.
8. de Lorenzo, V., and J. Perez-Martin. 1996. Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals. Mol. Microbiol. 19:1177-1184.
9. DiMarco, A. A., B. Averhoff, and L. N. Ornston. 1993. Identification of the transcriptional activator pobR and characterization of its role in the expression of pobA, the structural gene for p-hydroxybenzoate hydroxylase in Acinetobacter calcoaceticus. J. Bacteriol. 175:4499-4506.
10. DiMarco, A. A., B. A. Averhoff, E. E. Kim, and L. N. Ornston. 1993. Evolutionary divergence of pobA, the structural gene encoding p-hydroxybenzoate hydroxylase in an Acinetobacter calcoaceticus strain well-suited for genetic analysis. Gene 125:25-33.
11. DiMarco, A. A., and L. N. Ornston. 1994. Regulation of p-hydroxybenzoate hydroxylase synthesis by PobR bound to an operator in Acinetobacter calcoaceticus. J. Bacteriol. 176:4277-4284.
12. Dodd, I. B., and J. B. Egan. 1990. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18:5019-5026.
13. Doten, R. C., K. L. Ngai, D. J. Mitchell, and L. N. Ornston. 1987. Cloning and genetic organization of the pea gene cluster from Acinetobacter calcoaceticus. J. Bacteriol. 169:3168-3174.
14. Doten, R. C., and L. N. Ornston. 1987. Protocatechuate is not metabolized via catechol in Enterobacter aerogenes. J. Bacteriol. 169:5827-5830.
15. Durham, D. R., L. A. Stirling, L. N. Ornston, and J. J. Perry. 1980. Intergeneric evolutionary homology revealed by the study of protocatechuate 3,4-dioxygenase from Azotobacter vinelandii. Biochemistry 19:149-155.
16. Earhart, C. A., R. Radhakrishnan, A. M. Orville, J. D. Lipscomb, and D. H. Ohlendorf. 1994. Preliminary crystallographic study of protocatechuate 3,4-dioxygenase from Brevibacterium fuscum. J. Mol. Biol. 236:374-376.
17. Elsemore, D. A., and L. N. Ornston. 1994. The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinateshikimate dehydrogenase. J. Bacteriol. 176:7659-7666.
18. Elsemore, D. A., and L. N. Ornston. 1995. Unusual ancestry of dehydratases associated with quinate catabolism in Acinetobacter calcoaceticus. J. Bacteriol. 177:5971-5978.
19. Fewson, C. A. 1988. Microbial metabolism of mandelate: a microcosm of diversity. FEMS Microbiol. Rev. 4:85-110.
20. Gerischer, U., D. A. D'Argenio, and L. N. Ornston. 1996. IS1236, a newly discovered member of the IS3 family, exhibits varied patterns of insertion into the Acinetobacter calcoaceticus chromosome. Microbiology 142:1825-1831.
21. Gerischer, U., and L. N. Ornston. 1995. Spontaneous mutations in pcaH and -G, structural genes for protocatechuate 3,4-dioxygenase in Acinetobacter calcoaceticus. J. Bacteriol. 177:1336-1347.
22. Gerischer, U., and P. Dürre. 1990. Cloning, sequencing, and molecular analysis of the acetoacetate decarboxylase gene from Clostridium acetobutylicum. J. Bacteriol. 172:6907-6918.
23. Gerischer, U., and P. Dürre. 1992. mRNA analysis of the adc gene region of Clostridium acetobutylicum during shift to solventogenesis. J. Bacteriol. 174: 426-433.
24. Gregg-Jolly, L. A., and L. N. Ornston. 1994. Properties of Acinetobacter calcoaceticus recA and its contribution to intracellular gene conversion. Mol. Microbiol. 12:985-992.
25. Gregg-Jolly, L. A., and L. N. Ornston. 1990. Recovery of DNA from the Acinetobacter calcoaceticus chromosome by gap repair. J. Bacteriol. 172: 6169-6172.
26. Grund, E., C. Knorr, and R. Eichenlaub. 1990. Catabolism of benzoate and monohydroxylated benzoates by Amycolatopsis and Streptomyces spp. Appl. Environ. Microbiol. 56:1459-1464.
27. Hammer, A., A. Stolz, and H. Knackmuss. 1996. Purification and characterization of a novel type of protocatechuate 3,4-dioxygenase with the ability to oxidize 4-sulfocatechol. Arch. Microbiol. 166:92-100.
28. Harwood, C. S., N. N. Nichols, M. K. Kim, J. L. Ditty, and R. E. Parales. 1994. Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. J. Bacteriol. 176:6479-6488.
29. Harwood, C. S., and R. E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
30. Hunger, M., R. Schmucker, V. Kishan, and W. Hillen. 1990. Analysis and nucleotide sequence of an origin of DNA replication in Acinetobacter calcoaceticus and its use for Escherichia coli shuttle plasmids. Gene 87:45-51.
31. Juni, E. 1972. Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus. J. Bacteriol. 112:917-931.
32. Juni, E., and A. Janik. 1969. Transformation of Acinetobacter calcoaceticus (Bacterium anitratum). J. Bacteriol. 98:281-288.
33. Keen, N. T., S. Tamaki, D. Kobayashi, and D. Trollinger. 1988. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene 70:191-197.
34. Kloos, D. U., A. A. DiMarco, D. A. Elsemore, K. N. Timmis, and L. N. Ornston. 1995. Distance between alleles as a determinant of linkage in natural transformation of Acinetobacter calcoaceticus. J. Bacteriol. 177:6015-6017.
35. Kokotek, W., and W. Lotz. 1989. Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene 84:467-471.
36. Krooneman, J., E. B. Wieringa, E. R. Moore, J. Gerritse, R. A. Prins, and J. C. Gottschal. 1996. Isolation of Alcaligenes sp. strain L6 at low oxygen concentrations and degradation of 3-chlorobenzoate via a pathway not involving (chloro)catechols. Appl. Environ. Microbiol. 62:2427-2434.
37. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
38. Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall. 1951. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 176:265-275.
39. Mashetty, S. B., S. Manohar, and T. B. Karegoudar. 1996. Degradation of 3-hydroxybenzoic acid by a Bacillus species. Indian J. Biochem. Biophys. 33:145-148.
40. Middelhoven, W. J. 1993. Catabolism of benzene compounds by ascomycetous and basidiomycetous yeasts and yeastlike fungi. A literature review and an experimental approach. Antonie Leeuwenhoek 63:125-144.
41. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
42. Milstein, O., J. Trojanowski, A. Huttermann, and J. Gressel. 1988. Catabolism of single ring aromatic acids by four Aspergillus species. Microbios 55:7-16.
43. Morawski, B., R. W. Eaton, J. T. Rossiter, S. Guoping, H. Griengl, and D. W. Ribbons. 1997. 2-Naphthoate catabolic pathway in Burkholderia strain JT 1500. J. Bacteriol. 179:115-121.
44. Nasser, W., S. Reverchon, G. Condemine, and J. Robert-Baudouy. 1994. Specific interactions of Erwinia chrysanthemi KdgR repressor with different operators of genes involved in pectinolysis. J. Mol. Biol. 236:427-440.
45. Nasser, W., S. Reverchon, and J. Robert-Baudouy. 1992. Purification and functional characterization of the KdgR protein, a major repressor of pectinolysis genes of Erwinia chrysanthemi. Mol. Microbiol. 6:257-265.
46. Parales, R. E., and C. S. Harwood. 1993. Regulation of the pcalJ genes for aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 175:5829-5838.
47. Parke, D. 1997. Acquisition, reorganization, and merger of genes - novel management of the β-ketoadipate pathway in Agrobacterium tumefaciens. FEMS Microbiol. Lett. 146:3-12.
48. Parke, D. 1993. Positive regulation of phenolic catabolism in Agrobacterium tumefaciens by the pcaQ gene in response to β-carboxy-cis,cis-muconate. J. Bacteriol. 175:3529-3535.
49. Parke, D., and L. N. Ornston. 1986. Enzymes of the β-ketoadipate pathway are inducible in Rhizobium and Agrobacterium spp. and constitutive in Bradyrhizobium spp. J. Bacteriol. 165:288-292.
50. Patel, R. N., S. Mazumdar, and L. N. Ornston. 1975. β-Ketoadipate enollactone hydrolases I and II from Acinetobacter calcoaceticus. J. Biol. Chem. 250:6567-6577.
51. Prentki, P., and H. M. Krisch. 1984. In vitro insertional mutagenesis with a selectable DNA fragment. Gene 29:303-313.
52. Romero-Steiner, S., R. E. Parales, C. S. Harwood, and J. E. Houghton. 1994. Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate. J. Bacteriol. 176:5771-5779.
53. 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.
54. Simon, R., M. O'Connell, M. Labes, and A. Puhler. 1986. Plasmid vectors for the genetic analysis and manipulation of rhizobia and other gram-negative bacteria. Methods Enzymol. 118:640-659.
55. Smith, C. P., and K. F. Chater. 1988. Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. J. Mol. Biol. 204: 569-580.
56. Soisson, S. M., B. MacDougall-Shackleton, R. Schleif, and C. Wolberger. 1997. Structural basis for ligand-regulated oligomerization of AraC. Science 276:421-425.
57. Suemori, A., K. Nakajima, R. Kurane, and Y. Nakamura. 1995. o-, m-and p-hydroxybenzoate degradative pathways in Rhodococcus erythropolis. FEMS Microbiol. Lett. 125:31-35.
58. Turner, J. E., N. Allison, and C. A. Fewson. 1996. Metabolic characterisation of a novel vanillylmandelate-degrading bacterium. Arch. Microbiol. 166:252-259.
59. Valentin-Hansen, P., P. Hojrup, and S, Short. 1985. The primary structure of the DeoR repressor from Escherichia coli K-12. Nucleic Acids Res. 13:5927-5936.
60. Vasudevan, N., and A. Mahadevan. 1992. Degradation of indulin by Candida albicans. Biochem. Int. 26:317-325.
61. Wheeler, K. A., H. K. Lamb, and A. R. Hawkins. 1996. Control of metabolic flux through the quinate pathway in Aspergillus nidulans. Biochem. J. 315: 195-205.
62. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119.
63. Zhao, N., W. Oh, D. Trybul, K. S. Thrasher, T. J. Kingsbury, and T. J. Larson. 1994. Characterization of the interaction of the glp repressor of Escherichia coli K-12 with single and tandem glp operator variants. J. Bacteriol. 176:2393-2397.
64. Zylstra, G. J., R. H. Olsen, and D. P. Ballou. 1989. Genetic organization and sequence of the Pseudomonas cepacia genes for the α and β subunits of protocatechuate 3,4-dioxygenase. J. Bacteriol. 171:5915-5921.