Acquisition, reorganization, and merger of genes: Novel management of the β-ketoadipate pathway in Agrobacterium tumefaciens

FEMS Microbiology Letters

Volumn 146, Issue 1, 1997, Pages 3-12

  Parke, Donna ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

4 hydroxybenzoate; Agrobacterium tumefaciens; protocatechuate; rhizobia; supraoperonic organization; ketoadipate pathway

Indexed keywords

BACTERIAL METABOLISM; GENE EXPRESSION REGULATION; MOLECULAR GENETICS; NONHUMAN; OPERON; PRIORITY JOURNAL; REVIEW; RHIZOBIUM RADIOBACTER;

EID: 0031017926     PISSN: 03781097     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1097(96)00382-5     Document Type: Article

References (51)

1. Whitehead, D.C., Dibb, H. and Hartley, R.D. (1983) Bound phenolic compounds in water extracts of soils, plant roots and leaf litter. Soil Biol. Biochem. 15, 133-136.
2. Ornston, L.N. and Stanier, R.Y. (1966) The conversion of catechol and protocatechuate to β-ketoadipate by Pseudomonas putida. I. Biochemistry. J. Biol. Chem. 241, 3776-3786.
3. Hussien, Y.A., Tewfik, M.S. and Hamdi, Y.A. (1974) Degradation of certain aromatic compounds by rhizobia. Soil Biol. Biochem. 6, 377-381.
4. Muthukumar, G., Arunakumari, A. and Mahadevan, A. (1982) Degradation of aromatic compounds by Rhizobium spp. Plant Soil 69, 163-169.
5. Parke, D. and Ornston, L.N. (1984) Nutritional diversity of Rhizobiaceae revealed by auxanography. J. Gen. Microbiol. 130, 1743-1750.
6. van Rossum, D., Schuurmans, F.P., Gilles, M., Muyotcha, A., van Verseveld, H.W., Stouthamer, A.H. and Boogerd, F.C. (1995) Genetic and phenetic analyses of Bradyrhizobium strains nodulating peanut (Arachis hypogaea L.) roots. Appl. Environ. Microbiol. 61, 1599-1609.
7. Chen, Y.P., Glenn, A.R. and Dilworth, M.J. (1984) Uptake and oxidation of aromatic substrates by Rhizobium leguminosarum MNF 3841 and Rhizobium trifolii TA1. FEMS Microbiol. Lett. 21, 201-205.
8. Chen, Y.P., Dilworth, M.J. and Glenn, A.R. (1984) Aromatic metabolism in Rhizobium trifolii-protocatechuate 3,4-dioxygenase. Arch. Microbiol. 138, 187-190.
9. Parke, D. and Ornston, L.N. (1986) Enzymes of the β-ketoadipate pathway are inducible in Rhizobium and Agrobacterium spp. and constitutive in Bradyrhizobium spp. J. Bacteriol. 165, 288-292.
10. Parke, D., Rynne, F. and Glenn, A. (1991) Regulation of phenolic catabolism in Rhizobium leguminosarum biovar trifolii. J. Bacteriol. 173, 5546-5550.
11. Ornston, L.N. and Parke, D. (1977) The evolution of induction mechanisms in bacteria: insights derived from the study of the β-ketoadipate pathway. In : Current Topics in Regulation (Horecker, B.L. and Stadtman, E.R., Eds.), Vol. 12, pp. 209-262, Academic Press, New York, NY.
12. Harwood, C.S. and Parales, R.E. (1996) The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50, in press.
13. Ornston, L.N., Houghton, J.E., Neidle, E.L. and Gregg, L.A. (1990) Subtle selection and novel mutation during evolutionary divergence of the β-ketoadipate pathway. In: Pseudomonas: Biotransformation, Pathogenesis and Evolving Biotechnology (Silver, S., Chakrabarty, A.M., Iglewski, B. and Kaplan, S., Eds.), pp. 207-225, American Society for Microbiology, Washington, DC.
14. Parales, R.E. and Harwood, C.S. (1992) Characterization of the genes encoding β-ketoadipate:succinyl-coenzyme A transferase in Pseudomonas putida. J. Bacteriol. 174, 4657-4666.
15. Kowalchuk, G.A., Hartnett, G.B., Benson, A., Houghton, J.E. and Ngai, K.-L. (1994) Contrasting patterns of evolutionary divergence within the Acinetobacter calcoaceticus pca operon. Gene 146, 23-30.
16. Frazee, R.W., Livingston, D.M., LaPorte, D.C. and Lipscomb, J. D. (1993) Cloning, sequencing, and expression of the Pseudomonas putida protocatechuate 3,4-dioxygenase genes. J. Bacteriol. 175, 6194-6202.
17. Hartnett, C., Neidle, E.L., Ngai, K.-L. and Ornston, L.N. (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.
18. Hughes, J., Shapiro, M., Houghton, J. and Ornston, L.N. (1988) Cloning and expression of pca genes from Pseudomonas putida in Escherichia coli. J. Gen. Microbiol. 134, 2877-2887.
19. Doten, R.C., Ngai, K.-L., Mitchell, D.J. and Ornston, L.N. (1987) Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus. J. Bacteriol. 169, 3168-3174.
20. Gerischer, U., Tran, S. and Ornston, L.N. (1993) Physiological effects exerted by PcaU, a newly discovered gene governing synthesis of enzymes for catabolism of protocatechuate in Acinetobacter calcoaceticus. Abstr. 93rd Annu. Meet. Am. Soc. Microbiol., p.238.
21. Elsemore, D.A. and Ornston, L.N. (1994) The pca-pob supraoperonic cluster of Acinetobacter calcoaceticus contains quiA, the structural gene for quinate-shikimate dehydrogenase. J. Bacteriol. 176, 7659-7666.
22. Romero-Steiner, S., Parales, R.E., Harwood, C.S. and Houghton, J.E. (1994) Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation p-hydroxybenzoate. J. Bacteriol. 176, 5771-5779.
23. Ditty, J.L. and Nichols, N.N. (1996) PcaK, a novel 4-hydroxybenzoate transport and chemotaxis protein in Pseudomonas putida. Abstr. 96th Annu. Meet. Am. Soc. Microbiol., p. 540.
24. Buck, G.W. and Houghton, J.E. (1996) Cloning and sequencing of a dicarboxylic acid transport protein from Pseudomonas putida. Abstr. 96th Annu. Meet. Am. Soc. Microbiol., p.556.
25. Olsen, G.J., Woese, C.R. and Overbeek, R. (1994) The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176, 1-6.
26. Parke, D. (1995) Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate, in Agrobacterium tumefaciens. J. Bacteriol. 177, 3808-3817.
27. Wong, C.M., Dilworth, M.J. and Glenn, A.R. (1994) Cloning and sequencing show that 4-hydroxybenzoate hydroxylase (PobA) is required for uptake of 4-hydroxybenzoate in Rhizobium leguminosarum. Microbiol. 140, 2775-2786.
28. 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.
29. Parke, D. (1996) Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds, from Agrobacterium tumefaciens. J. Bacteriol. 178, 266-272.
30. Schell, M.A. (1993) Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47, 597-626.
31. Schlaman, H.R.M., Okker, R.J.H. and Lugtenberg, B.J.J. (1992) Regulation of nodulation gene expression by NodD in rhizobia. J. Bacteriol. 174, 5177-5182.
32. Coco, W.M., Rothmel, R.K., Henikoff, S. and Chakrabarty, A.M. (1993) Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J. Bacteriol. 175, 417-427.
33. Viale, A.M., Kobayashi, H., Akazawa, T. and Henikoff, S. (1991) rcbR, a gene coding for a member of the LysR family of transcriptional regulators, is located upstream of the expressed set of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in the photosynthetic bacterium Chromatium vinosum. J. Bacteriol. 173, 5224-5229.
34. Parke, D. and Ornston, L.N. (1976) Constitutive synthesis of enzymes of the protocatechuate pathway and of the β-ketoadipate uptake system in mutant strains of Pseudomonas putida. J. Bacteriol. 126, 272-281.
35. Parke, D. (1996) Characterization of the role of the pcaR gene in the expression of pcaIJ, the structural genes for β-ketoadipyl CoA transferase, in Agrobacterium tumefaciens. Abstr. 96th Annu. Meet. Am. Soc. Microbiol., p.558.
36. DiMarco, A.A., Averhoff, B. and Ornston, L.N. (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.
37. Smith, C.P. and Chater, K.F. (1988) Structure and regulation of controlling sequences for the Streptomyces coelicolor glycerol operon. J. Mol. Biol. 204, 569-580.
38. Negre, D., Cortay, J.-C., Old, I.G., Galinier, A., Richaud, C., Saint Girons, I. and Cozzone, A.J. (1991) Overproduction and characterization of the iclR gene product of Escherichia coli K-12 and comparison with that of Salmonella typhimurium LT2. Gene 97, 29-37.
39. Reverchon, S., Nasser, W. and Robert-Baudouy, J. (1991) Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation. Mol. Microbiol. 5, 2203-2216.
40. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
41. Stoner, C.M. and Schleif, R. (1982) Is the amino acid but not the nucleotide sequence of the Escherichia coli araC gene conserved? J. Mol. Biol. 154, 649-652.
42. Parke, D. (1995) Localization of pobR, a gene regulating synthesis of p-hydroxybenzoate hydroxylase, within a supraoperonic cluster of the pca genes in Agrobacterium tumefaciens. Abstr. 95th Annu. Meet. Am. Soc. Microbiol., p.27.
43. Brennan, R.G. and Matthews, B.W. (1989) The helix-turn-helix DNA binding motif. J. Biol. Chem. 264, 1903-1906.
44. Dodd, I.B. and Egan, J.B. (1990) Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18, 5019-5026.
45. Wellington, C.L., Bauer, C.E. and Beatty, J.T. (1992) Photosynthesis gene superoperons in purple nonsulfur bacteria: the tip of the iceberg? Can. J. Microbiol. 38, 20-27.
46. LeStrange, K.K., Bender, G.L., Djordjevic, M.A., Rolfe, B.G. and Redmond, J.W. (1990) The Rhizobium strain NGR234 nodD1 gene product responds to activation by the simple phenolic compounds vanillin and isovanillin present in wheat seedling extracts. Mol. Plant-Microb. Interact. 3, 214-220.
47. Rao, J.R. and Cooper, J.E. (1994) Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J. Bacteriol. 176, 5409-5413.
48. Rao, J.R. and Cooper, J.E. (1995) Soybean nodulating rhizobia modify nod gene inducers daidzein and genistein to yield aromatic products that can influence gene-inducing activity. Mol. Plant-Microbe Interact. 8, 855-862.
49. Parke, D. (1996) Conservation of PcaQ, a transriptional activator of pca genes for catabolism of phenolic compounds, in Agrobacterium tumefatiens and Rhizobium species. J. Bacteriol. 178, 3671-3675.
50. Ornston, M.K. and Ornston, L.N. (1972) The regulation of the β-ketoadipate pathway in Pseudomonas acidovorans and Pseudomonas testosteroni. J. Gen. Microbiol. 73, 455-464.
51. Rynne, F.G., Glenn, A.R. and Dilworth, M.J. (1994) Effect of mutations in aromatic catabolism on the persistence and competitiveness of Rhizobium leguminosarum bv. trifolii. Soil Biol. Biochem. 26, 703-710.