Combining localized PCR mutagenesis and natural transformation in direct genetic analysis of a transcriptional regulator gene, pobR

Journal of Bacteriology

Volumn 179, Issue 13, 1997, Pages 4270-4276

  Kok, Ruben G ^a   D'Argenio, David A ^a   Ornston, L Nicholas ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ACINETOBACTER; ARTICLE; BACTERIUM MUTANT; BACTERIUM TRANSFORMATION; CHROMOSOME; CODON; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC ANALYSIS; MOLECULAR CLONING; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RECOMBINANT DNA TECHNOLOGY; TRANSCRIPTION REGULATION;

ACINETOBACTER; BACTERIA (MICROORGANISMS);

EID: 0030816017     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.179.13.4270-4276.1997     Document Type: Article

References (41)

1. 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.
2. Cadwell, R. C., and G. F. Joyce. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:28-33.
3. 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 Acinetobactr calcoaceticus. J. Bacteriol. 175:4499-4506.
4. 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.
5. DiMarco, A. A., and L. N. Ornston. 1994. Regulation of p-hydroxybenzoate hydroxylase synthesis hy PobR hound to an operator in Acinetobacter calcoaceticus. J. Bacteriol. 176:4277-4284.
6. Eckert, K. A., and T. A. Kunkel. 1990. High fidelity DNA synthesis by the Thermus aquaticus DNA polymerase. Nucleic Acids Res. 18:3739-3744.
7. Eckert, K. A., and T. A. Kunkel. 1991. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1:17-24.
8. 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.
9. Gerischer, U., S. Tran, and L. N. Ornston. 1993. Physiological effects exerted by pcaU, a newly discovered gene governing synthesis of enzymes for catabolism of protocatechuate in Acinetobacter calcoaceticus, abstr. H-267, p. 238. In Abstracts of the 93rd General Meeting of the American Society for Microbiology 1993. American Society for Microbiology, Washington, D.C.
10. Gerischer, U. C., 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.
11. Gold, L., D. Pribnow, T. Schneider, S. Shinedling, B. S. Singer, and G. Stormo. 1981. Translation initiation in prokaryotes. Annu. Rev. Microbiol. 94:461-478.
12. Hartnett, C., E. L. Neidle, K.-L. Ngai, and L. N. Ornston. 1990. DNA sequence of genes encoding Acinetobacter calcoaceticus protocatechuate 3,4-dioxygenase: evidence indicating shuffling of genes and of DNA sequences within genes during their evolutionary divergence. J. Bacteriol. 172:956-966.
13. Hartnett, G. B., B. Averhoff, and L. N. Ornston. 1990. Selection of Acinetobacter calcoaceticus mutants deficient in the p-hydroxybenzoate hydroxylase gene (pobA), a member of a suprooperonic cluster. J. Bacteriol. 172:6160-6161.
14. Hughes, E. J., M. K. Shapiro, J. E. Houghton, and L. N. Ornston. 1988. Cloning and expression of the pca genes from Pseudomonas putida in Escherichia coli. J. Gen. Microbiol. 134:2877-2887.
15. Hugouvieux-Cotte-Pattat, N., G. Condemine, W. Nasser, and S. Reverchon. 1996. Regulation of pectinolysis in Erwinia chrysanthemi. Annu. Rev. Microbiol. 50:213-257.
16. Juni, E. 1972. Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus. J. Bacteriol. 112:917-931.
17. Juni, E. 1974. Simple genetic transformation assay for rapid diagnosis of Moraxella osloensis. Appl. Microbiol. 27:16-24.
18. Juni, E., and A. Janik. 1969. Transformation of Acinetobacter calco-aceticus (Bacterium anitratum). J. Bacteriol. 98:281-288.
19. Kleina, L. G., and J. H. Miller. 1990. Genetic studies of the lac repressor. XIII. Extensive amino acid replacements generated by the use of natural and synthetic nonsense suppressors. J. Mol. Biol. 212:295-318.
20. Kohler, S. W., G. S. Provost, A. Fieck, P. L. Kretz, W. O. Bullock, J. A. Sorge, D. L. Putman, and J. M. Short. 1991. Spectra of spontaneous and mutagen-induced mutations in the lacI gene in transgenic mice. Proc. Natl. Acad. Sci. USA 88:7958-7962.
21. Kok, R. G., J. J. van Thor, I. M. Nugteren-Roodzant, M. B. W. Brouwer, M. R. Egmond, C. B. Nudel, B. Vosman, and K. J. Hellingwerf. 1995. Characterization of the extracellular lipase, LipA, of Acinetobacter calcoaceticus BD413 and sequence analysis of the cloned structural gene. Mol. Microbiol. 15:803-818.
22. Kok, R. C., J. J. van Thor, I. M. Nugteren-Roodzant, B. Vosman, and K. J. Hellingwerf. 1995. Characterization of lipase-deficient mutants of Acinetobacter calcoaceticus BD413: identification of a periplasmic lipase chaperone essential for the production of extracellular lipase. J. Bacteriol. 177:3295-3307.
23. Leung, D. W., E. Chen, and D. V. Goeddel. 1989. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Technique 1:11-15.
24. Lundberg, K. S., D. D. Shoemaker, M. W. W. Adams, J. M. Short, J. A. Sorge, and E. J. Mathur. 1991. High-fidelity amplification using a thermostable DNA polymerasc isolated from Pyrococcus furiosus. Gene 108:1-6.
25. Negre, D., J.-C. Cortay, I. G. Old, A. Galinier, C. Richaud, I. Saint Girons, and A. J. Cozzone. 1991. Overproduction and characterization of the iclR gene product of Escherichia coli and comparison with that of Salmonella typhimurium LT2. Gene 97:29-37.
26. Ohlendorf, D. H., A. M. Orville, and J. D. Lipscomb. 1994. Structure of protocatechuate 3,4-dioxygenase from Pseudomonas aeruginosa at 2.14 Å resolution. J. Mol. Biol. 244:568-608.
27. Ornston, L. N., and E. L. Neidle. 1991. Evolution of genes for the β-ketoadipate pathway in Acinetobacter calcoaceticus, p. 201-237. In K. J. Towner, E. Bergogne-Bérézin, and C. A. Fewson (ed.), The biology of Acinetobacter. Plenum Press, New York, N.Y.
28. Palmen, R., B. Vosman, P. Buijsman, C. K. D. Breek, and K. J. Hellingwerf. 1993. Physiological characterization of natural transformation in Acinetobacter calcoaceticus. J. Gen. Microbiol. 139:295-305.
29. Palmen, R., B. Vosman, R. G. Kok, J. R. van der Zee, and K. J. Hellingwerf. 1992. Characterization of transformation-deficient mutants of Acinetobacter calcoaceticus. Mol. Microbiol. 6:1747-1754.
30. Parke, D. 1996. Acquisition, reorganization, and merger of genes: novel management of the β-ketoadipate pathway in Agrobacterium tumefaciens. FEMS Microbiol. Lett. 146:1-10.
31. 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.
32. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
33. 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.
34. Spee, J. H., W. M. de Vos, and O. P. Kuipers. 1993. Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITP. Nucleic Acids Res. 21:777-778.
35. Sunnarborg, A., D. Klumpp, T. Chung, and D. C. LaPorte. 1990. Regulation of the glyoxylate bypass operon: cloning and characterization of iclR. J. Bacteriol. 172:2642-2649.
36. Tindall, K. R., and T. A. Kunkel. 1988. Fidelity of DNA synthesis by the Thermus aquaticus DNA polymerase. Biochemistry 27:6008-6013.
37. Vetting, M. W. Personal communication.
38. Vetting, M. W., C. A. Earhart, and D. H. Ohlendorf. 1994. Crystallization and preliminary X-ray analysis of protocatechuate 3,4-dioxygenase from Acinetobacter calcoaceticus. J. Mol. Biol. 236:372-373.
39. White, P. J., I. S. Hunter, and C. A. Fewson. 1991. Codon usage in Acinetobacter structural genes. FEMS Symp. 57:251-257.
40. Woese, C. R. EMBL Data Library, accession no. M34139.
41. Zhou, Y., X. Zhang, and R. H. Ebright. 1991. Random mutagenesis of gene-sized DNA molecules by use of PCR with Taq DNA polymerase. Nucleic Acids Res. 19:6052.