Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1996 Jan;178(1):266–272. doi: 10.1128/jb.178.1.266-272.1996

Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds, from Agrobacterium tumefaciens.

D Parke 1
PMCID: PMC177648  PMID: 8550427

Abstract

Previous work demonstrated that catabolism of the phenolic compounds p-hydroxybenzoate and protocatechuate via the beta-ketoadipate pathway in Agrobacterium tumefaciens is mediated by a regulatory gene, pcaQ, that acts in trans to elicit expression of many of the enzymes encoded by the pca genes. There was evidence that five pca structural genes are organized in a polycistronic operon transcribed in the order pcaDCHGB. The pcaQ gene is upstream of this operon. The activator encoded by pcaQ was novel in having the metabolite beta-carboxy-cis,cis-muconate as a coinducer. This communication reports the nucleotide sequence of pcaQ and identifies its deduced polypeptide product as a member of the LysR family of regulatory molecules. PcaQ has a calculated molecular weight of 33,546, which is consistent with the size of LysR relatives. Like many other LysR members, PcaQ serves as an activator at the level of transcription, it has a conserved amino-terminal domain, and its gene is transcribed divergently from the operon that it regulates and is subject to negative autoregulation. Studies of coinducer specificity identified an unstable pathway metabolite, gamma-carboxymuconolactone, as a second coinducer. Analysis of expression from a pcaD::lacZ promoter probe plasmid revealed that PcaQ and the coinducer exert their effect on a 133-nucleotide region upstream of pcaD. The nucleotide sequence of this region in a mutant strain constitutive for enzymes encoded by the pcaDCHGB operon identified nucleotides likely to be involved in the pcaDCHGB promoter and substantiated the inclusion of five pca structural genes in the operon.

Full Text

The Full Text of this article is available as a PDF (290.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Coco W. M., Rothmel R. K., Henikoff S., Chakrabarty A. M. 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. 1993 Jan;175(2):417–427. doi: 10.1128/jb.175.2.417-427.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. DiMarco A. A., Averhoff B., Ornston L. N. 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. 1993 Jul;175(14):4499–4506. doi: 10.1128/jb.175.14.4499-4506.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Goethals K., Van Montagu M., Holsters M. Conserved motifs in a divergent nod box of Azorhizobium caulinodans ORS571 reveal a common structure in promoters regulated by LysR-type proteins. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1646–1650. doi: 10.1073/pnas.89.5.1646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Henikoff S., Haughn G. W., Calvo J. M., Wallace J. C. A large family of bacterial activator proteins. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6602–6606. doi: 10.1073/pnas.85.18.6602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Keen N. T., Tamaki S., Kobayashi D., Trollinger D. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene. 1988 Oct 15;70(1):191–197. doi: 10.1016/0378-1119(88)90117-5. [DOI] [PubMed] [Google Scholar]
  6. Knauf V. C., Nester E. W. Wide host range cloning vectors: a cosmid clone bank of an Agrobacterium Ti plasmid. Plasmid. 1982 Jul;8(1):45–54. doi: 10.1016/0147-619x(82)90040-3. [DOI] [PubMed] [Google Scholar]
  7. Kokotek W., Lotz W. Construction of a lacZ-kanamycin-resistance cassette, useful for site-directed mutagenesis and as a promoter probe. Gene. 1989 Dec 14;84(2):467–471. doi: 10.1016/0378-1119(89)90522-2. [DOI] [PubMed] [Google Scholar]
  8. Neidle E. L., Hartnett C., Bonitz S., Ornston L. N. DNA sequence of the Acinetobacter calcoaceticus catechol 1,2-dioxygenase I structural gene catA: evidence for evolutionary divergence of intradiol dioxygenases by acquisition of DNA sequence repetitions. J Bacteriol. 1988 Oct;170(10):4874–4880. doi: 10.1128/jb.170.10.4874-4880.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Neidle E. L., Ornston L. N. Benzoate and muconate, structurally dissimilar metabolites, induce expression of catA in Acinetobacter calcoaceticus. J Bacteriol. 1987 Jan;169(1):414–415. doi: 10.1128/jb.169.1.414-415.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ornston L. N., Stanier R. Y. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. J Biol Chem. 1966 Aug 25;241(16):3776–3786. [PubMed] [Google Scholar]
  11. Parke D. Application of p-Toluidine in Chromogenic Detection of Catechol and Protocatechuate, Diphenolic Intermediates in Catabolism of Aromatic Compounds. Appl Environ Microbiol. 1992 Aug;58(8):2694–2697. doi: 10.1128/aem.58.8.2694-2697.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Parke D. Positive regulation of phenolic catabolism in Agrobacterium tumefaciens by the pcaQ gene in response to beta-carboxy-cis,cis-muconate. J Bacteriol. 1993 Jun;175(11):3529–3535. doi: 10.1128/jb.175.11.3529-3535.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Parke D., Rynne F., Glenn A. Regulation of phenolic catabolism in Rhizobium leguminosarum biovar trifolii. J Bacteriol. 1991 Sep;173(17):5546–5550. doi: 10.1128/jb.173.17.5546-5550.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Parke D. Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens. J Bacteriol. 1995 Jul;177(13):3808–3817. doi: 10.1128/jb.177.13.3808-3817.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Romero-Steiner S., Parales R. E., Harwood C. S., Houghton J. E. Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate. J Bacteriol. 1994 Sep;176(18):5771–5779. doi: 10.1128/jb.176.18.5771-5779.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Rothmel R. K., Aldrich T. L., Houghton J. E., Coco W. M., Ornston L. N., Chakrabarty A. M. Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family. J Bacteriol. 1990 Feb;172(2):922–931. doi: 10.1128/jb.172.2.922-931.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Schell M. A. Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol. 1993;47:597–626. doi: 10.1146/annurev.mi.47.100193.003121. [DOI] [PubMed] [Google Scholar]
  19. Schlaman H. R., Okker R. J., Lugtenberg B. J. Regulation of nodulation gene expression by NodD in rhizobia. J Bacteriol. 1992 Aug;174(16):5177–5182. doi: 10.1128/jb.174.16.5177-5182.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Stanier R. Y., Ornston L. N. The beta-ketoadipate pathway. Adv Microb Physiol. 1973;9(0):89–151. [PubMed] [Google Scholar]
  21. Viale A. M., Kobayashi H., Akazawa T., Henikoff S. rbcR [correction of 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. 1991 Aug;173(16):5224–5229. doi: 10.1128/jb.173.16.5224-5229.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  23. Zylstra G. J., Olsen R. H., Ballou D. P. Cloning, expression, and regulation of the Pseudomonas cepacia protocatechuate 3,4-dioxygenase genes. J Bacteriol. 1989 Nov;171(11):5907–5914. doi: 10.1128/jb.171.11.5907-5914.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. von Lintig J., Kreusch D., Schröder J. Opine-regulated promoters and LysR-type regulators in the nopaline (noc) and octopine (occ) catabolic regions of Ti plasmids of Agrobacterium tumefaciens. J Bacteriol. 1994 Jan;176(2):495–503. doi: 10.1128/jb.176.2.495-503.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES