Abstract
Burkholderia pickettii PKO1 metabolizes toluene and benzene via a chromosomally encoded toluene-3-monooxygenase pathway. Expression of the toluene-3-monooxygenase operon (tbuA1UBVA2C) is activated by the regulator, TbuT, in the presence of toluene. We have identified the TbuT coding region downstream of the toluene-3-monooxygenase structural genes by nucleotide sequence analysis and have shown that although TbuT is similar to XylR and DmpR, two members of the NtrC family of transcriptional activators which control toluene-xylene and (methyl)phenol catabolism, respectively, it is significantly different in the domain associated with effector specificity. Using a tbuA1-lacZ fusion reporter system, we determined that TbuT is activated not only by aromatic effectors but also the chlorinated aliphatic hydrocarbon trichloroethylene. Expression of tbuT and that of the tbuA1UBVA2C operon were found to be linked by readthrough transcription of tbuT from the toluene-3-monooxygenase promoter. As a result, transcription of tbuT is low when the toluene-3-monooxygenase operon is uninduced and high when expression of tbuA1UBVA2C is induced by toluene. Thus, the toluene-3-monooxygenase promoter drives the cascade expression of both the toluene-3-monooxygenase operon and tbuT, resulting in a positive feedback circuit. Examination of the nucleotide sequence upstream of the toluene-3-monooxygenase operon for promoter-like sequences revealed a -24 TGGC, -12 TTGC sequence, characteristic of sigma54 (rpoN)-dependent promoters. Primer extension and tbuA1-lacZ fusion analyses demonstrated that this -24, -12 promoter sequence, referred to as PtbuA1, was the toluene-3-monooxygenase promoter. Upstream of PtbuA1, a DNA region with dyad symmetry exhibited homology with the XylR-binding site present upstream of the Pu promoter. Deletions within this DNA sequence resulted in complete loss of expression from PtbuA1, suggesting that this region may serve as the TbuT-binding site.
Full Text
The Full Text of this article is available as a PDF (538.6 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Abril M. A., Buck M., Ramos J. L. Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein. J Biol Chem. 1991 Aug 25;266(24):15832–15838. [PubMed] [Google Scholar]
- Abril M. A., Michan C., Timmis K. N., Ramos J. L. Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J Bacteriol. 1989 Dec;171(12):6782–6790. doi: 10.1128/jb.171.12.6782-6790.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Altendorf K., Voelkner P., Puppe W. The sensor kinase KdpD and the response regulator KdpE control expression of the kdpFABC operon in Escherichia coli. Res Microbiol. 1994 Jun-Aug;145(5-6):374–381. doi: 10.1016/0923-2508(94)90084-1. [DOI] [PubMed] [Google Scholar]
- Brosius J., Cate R. L., Perlmutter A. P. Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. J Biol Chem. 1982 Aug 10;257(15):9205–9210. [PubMed] [Google Scholar]
- Byrne A. M., Kukor J. J., Olsen R. H. Sequence analysis of the gene cluster encoding toluene-3-monooxygenase from Pseudomonas pickettii PKO1. Gene. 1995 Feb 27;154(1):65–70. doi: 10.1016/0378-1119(94)00844-i. [DOI] [PubMed] [Google Scholar]
- Craig N. L., Nash H. A. E. coli integration host factor binds to specific sites in DNA. Cell. 1984 Dec;39(3 Pt 2):707–716. doi: 10.1016/0092-8674(84)90478-1. [DOI] [PubMed] [Google Scholar]
- Delgado A., Ramos J. L. Genetic evidence for activation of the positive transcriptional regulator Xy1R, a member of the NtrC family of regulators, by effector binding. J Biol Chem. 1994 Mar 18;269(11):8059–8062. [PubMed] [Google Scholar]
- Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Drummond M., Whitty P., Wootton J. Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. EMBO J. 1986 Feb;5(2):441–447. doi: 10.1002/j.1460-2075.1986.tb04230.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fernández S., Shingler V., De Lorenzo V. Cross-regulation by XylR and DmpR activators of Pseudomonas putida suggests that transcriptional control of biodegradative operons evolves independently of catabolic genes. J Bacteriol. 1994 Aug;176(16):5052–5058. doi: 10.1128/jb.176.16.5052-5058.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Figurski D. H., Helinski D. R. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1648–1652. doi: 10.1073/pnas.76.4.1648. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gomada M., Inouye S., Imaishi H., Nakazawa A., Nakazawa T. Analysis of an upstream regulatory sequence required for activation of the regulatory gene xylS in xylene metabolism directed by the TOL plasmid of Pseudomonas putida. Mol Gen Genet. 1992 Jun;233(3):419–426. doi: 10.1007/BF00265439. [DOI] [PubMed] [Google Scholar]
- Inouye S., Gomada M., Sangodkar U. M., Nakazawa A., Nakazawa T. Upstream regulatory sequence for transcriptional activator XylR in the first operon of xylene metabolism on the TOL plasmid. J Mol Biol. 1990 Nov 20;216(2):251–260. doi: 10.1016/S0022-2836(05)80317-1. [DOI] [PubMed] [Google Scholar]
- Inouye S., Nakazawa A., Nakazawa T. Expression of the regulatory gene xylS on the TOL plasmid is positively controlled by the xylR gene product. Proc Natl Acad Sci U S A. 1987 Aug;84(15):5182–5186. doi: 10.1073/pnas.84.15.5182. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Inouye S., Nakazawa A., Nakazawa T. Nucleotide sequence of the regulatory gene xylR of the TOL plasmid from Pseudomonas putida. Gene. 1988 Jun 30;66(2):301–306. doi: 10.1016/0378-1119(88)90366-6. [DOI] [PubMed] [Google Scholar]
- Johnson G. R., Olsen R. H. Nucleotide sequence analysis of genes encoding a toluene/benzene-2-monooxygenase from Pseudomonas sp. strain JS150. Appl Environ Microbiol. 1995 Sep;61(9):3336–3346. doi: 10.1128/aem.61.9.3336-3346.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kukor J. J., Olsen R. H. Catechol 2,3-dioxygenases functional in oxygen-limited (hypoxic) environments. Appl Environ Microbiol. 1996 May;62(5):1728–1740. doi: 10.1128/aem.62.5.1728-1740.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kukor J. J., Olsen R. H. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J Bacteriol. 1991 Aug;173(15):4587–4594. doi: 10.1128/jb.173.15.4587-4594.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kustu S., North A. K., Weiss D. S. Prokaryotic transcriptional enhancers and enhancer-binding proteins. Trends Biochem Sci. 1991 Nov;16(11):397–402. doi: 10.1016/0968-0004(91)90163-p. [DOI] [PubMed] [Google Scholar]
- Leahy J. G., Byrne A. M., Olsen R. H. Comparison of factors influencing trichloroethylene degradation by toluene-oxidizing bacteria. Appl Environ Microbiol. 1996 Mar;62(3):825–833. doi: 10.1128/aem.62.3.825-833.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Marqués S., Ramos J. L. Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways. Mol Microbiol. 1993 Sep;9(5):923–929. doi: 10.1111/j.1365-2958.1993.tb01222.x. [DOI] [PubMed] [Google Scholar]
- Morett E., Segovia L. The sigma 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J Bacteriol. 1993 Oct;175(19):6067–6074. doi: 10.1128/jb.175.19.6067-6074.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Newman L. M., Wackett L. P. Purification and characterization of toluene 2-monooxygenase from Burkholderia cepacia G4. Biochemistry. 1995 Oct 31;34(43):14066–14076. doi: 10.1021/bi00043a012. [DOI] [PubMed] [Google Scholar]
- Ng L. C., Poh C. L., Shingler V. Aromatic effector activation of the NtrC-like transcriptional regulator PhhR limits the catabolic potential of the (methyl)phenol degradative pathway it controls. J Bacteriol. 1995 Mar;177(6):1485–1490. doi: 10.1128/jb.177.6.1485-1490.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Olsen R. H., DeBusscher G., McCombie W. R. Development of broad-host-range vectors and gene banks: self-cloning of the Pseudomonas aeruginosa PAO chromosome. J Bacteriol. 1982 Apr;150(1):60–69. doi: 10.1128/jb.150.1.60-69.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Olsen R. H., Kukor J. J., Kaphammer B. A novel toluene-3-monooxygenase pathway cloned from Pseudomonas pickettii PKO1. J Bacteriol. 1994 Jun;176(12):3749–3756. doi: 10.1128/jb.176.12.3749-3756.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pavel H., Forsman M., Shingler V. An aromatic effector specificity mutant of the transcriptional regulator DmpR overcomes the growth constraints of Pseudomonas sp. strain CF600 on para-substituted methylphenols. J Bacteriol. 1994 Dec;176(24):7550–7557. doi: 10.1128/jb.176.24.7550-7557.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Polarek J. W., Williams G., Epstein W. The products of the kdpDE operon are required for expression of the Kdp ATPase of Escherichia coli. J Bacteriol. 1992 Apr;174(7):2145–2151. doi: 10.1128/jb.174.7.2145-2151.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pontiggia A., Negri A., Beltrame M., Bianchi M. E. Protein HU binds specifically to kinked DNA. Mol Microbiol. 1993 Feb;7(3):343–350. doi: 10.1111/j.1365-2958.1993.tb01126.x. [DOI] [PubMed] [Google Scholar]
- Pérez-Martín J., Timmis K. N., de Lorenzo V. Co-regulation by bent DNA. Functional substitutions of the integration host factor site at sigma 54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences. J Biol Chem. 1994 Sep 9;269(36):22657–22662. [PubMed] [Google Scholar]
- Pérez-Martín J., de Lorenzo V. The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR. J Bacteriol. 1995 Jul;177(13):3758–3763. doi: 10.1128/jb.177.13.3758-3763.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rothmel R. K., Shinabarger D. L., Parsek M. R., Aldrich T. L., Chakrabarty A. M. Functional analysis of the Pseudomonas putida regulatory protein CatR: transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J Bacteriol. 1991 Aug;173(15):4717–4724. doi: 10.1128/jb.173.15.4717-4724.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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]
- Shingler V., Bartilson M., Moore T. Cloning and nucleotide sequence of the gene encoding the positive regulator (DmpR) of the phenol catabolic pathway encoded by pVI150 and identification of DmpR as a member of the NtrC family of transcriptional activators. J Bacteriol. 1993 Mar;175(6):1596–1604. doi: 10.1128/jb.175.6.1596-1604.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shingler V., Moore T. Sensing of aromatic compounds by the DmpR transcriptional activator of phenol-catabolizing Pseudomonas sp. strain CF600. J Bacteriol. 1994 Mar;176(6):1555–1560. doi: 10.1128/jb.176.6.1555-1560.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shingler V. Signal sensing by sigma 54-dependent regulators: derepression as a control mechanism. Mol Microbiol. 1996 Feb;19(3):409–416. doi: 10.1046/j.1365-2958.1996.388920.x. [DOI] [PubMed] [Google Scholar]
- Smith A. W., Iglewski B. H. Transformation of Pseudomonas aeruginosa by electroporation. Nucleic Acids Res. 1989 Dec 25;17(24):10509–10509. doi: 10.1093/nar/17.24.10509. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stock J. B., Ninfa A. J., Stock A. M. Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev. 1989 Dec;53(4):450–490. doi: 10.1128/mr.53.4.450-490.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sze C. C., Moore T., Shingler V. Growth phase-dependent transcription of the sigma(54)-dependent Po promoter controlling the Pseudomonas-derived (methyl)phenol dmp operon of pVI150. J Bacteriol. 1996 Jul;178(13):3727–3735. doi: 10.1128/jb.178.13.3727-3735.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tanaka I., Appelt K., Dijk J., White S. W., Wilson K. S. 3-A resolution structure of a protein with histone-like properties in prokaryotes. Nature. 1984 Aug 2;310(5976):376–381. doi: 10.1038/310376a0. [DOI] [PubMed] [Google Scholar]
- Ueno-Nishio S., Mango S., Reitzer L. J., Magasanik B. Identification and regulation of the glnL operator-promoter of the complex glnALG operon of Escherichia coli. J Bacteriol. 1984 Oct;160(1):379–384. doi: 10.1128/jb.160.1.379-384.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- VOGEL H. J., BONNER D. M. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem. 1956 Jan;218(1):97–106. [PubMed] [Google Scholar]
- Walderhaug M. O., Polarek J. W., Voelkner P., Daniel J. M., Hesse J. E., Altendorf K., Epstein W. KdpD and KdpE, proteins that control expression of the kdpABC operon, are members of the two-component sensor-effector class of regulators. J Bacteriol. 1992 Apr;174(7):2152–2159. doi: 10.1128/jb.174.7.2152-2159.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Worsey M. J., Williams P. A. Metabolism of toluene and xylenes by Pseudomonas (putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J Bacteriol. 1975 Oct;124(1):7–13. doi: 10.1128/jb.124.1.7-13.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yen K. M., Karl M. R., Blatt L. M., Simon M. J., Winter R. B., Fausset P. R., Lu H. S., Harcourt A. A., Chen K. K. Cloning and characterization of a Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol. 1991 Sep;173(17):5315–5327. doi: 10.1128/jb.173.17.5315-5327.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Yen K. M., Karl M. R. Identification of a new gene, tmoF, in the Pseudomonas mendocina KR1 gene cluster encoding toluene-4-monooxygenase. J Bacteriol. 1992 Nov;174(22):7253–7261. doi: 10.1128/jb.174.22.7253-7261.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- de Lorenzo V., Herrero M., Metzke M., Timmis K. N. An upstream XylR- and IHF-induced nucleoprotein complex regulates the sigma 54-dependent Pu promoter of TOL plasmid. EMBO J. 1991 May;10(5):1159–1167. doi: 10.1002/j.1460-2075.1991.tb08056.x. [DOI] [PMC free article] [PubMed] [Google Scholar]