Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

Harayama, Shigeaki; Rekik, Monique; Bairoch, Amos Marc; Neidle, Ellen L.; Ornston, L N

doi:10.1128/jb.173.23.7540-7548.1991

Cited by 135 publications

(70 citation statements)

References 40 publications

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“…BenABC of Acinetobacter sp. ADP1, on the other hand, exhibits narrow substrate specificity, showing little or no oxidation of most substituted benzoates (Neidle et al, 1991). The 3CB degrader Pseudomonas sp.…”

Section: Discussionmentioning

confidence: 99%

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

et al. 2001

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Burkholderia sp. NK8 grows abundantly on 3-chlorobenzoate (3CB), 4-chlorobenzoate (4CB) and benzoate. The genes encoding the oxidation of (chloro)benzoates (cbeABCD) and catechol (catA, catBC), the LysR-type regulatory gene cbeR and the gene cbeE with unknown function, all of which form a single cluster in NK8, were cloned and analysed. The protein sequence of chlorobenzoate 1,2-dioxygenase (CbeABC) is 50-65 % identical to the benzoate dioxygenase (BenABC) of Acinetobacter sp. ADP1, toluate dioxygenase (XylXYZ) of the TOL plasmid pWW0 and 2-halobenzoate dioxygenase (CbdABC) of Burkholderia cepacia 2CBS. Disruption of the cbeA gene resulted in the simultaneous loss of the ability to grow on benzoate and monochlorobenzoates, indicating the involvement of the cbeABCD genes in the degradation of these aromatics. The cbeABCD genes are preceded by catA, the gene for catechol dioxygenase. lacZ transcriptional fusion studies in Pseudomonas putida showed that catA and cbeA are co-expressed under the positive control of cbeR, a LysR-type transcriptional regulatory gene. The cbeA ::lacZ transcriptional fusion studies showed that the inducers of the genes are 3CB, 4CB, benzoate and probably cis,cis-muconate. On the other hand, 2-chlorobenzoate (2CB) did not activate the expression of the genes. The chlorobenzoate dioxygenase was able to transform 2CB, 3CB, 4CB and benzoate at considerable rates. 2CB yielded both catechol and 3-chlorocatechol (3CC), and 3CB gave rise to 4-chlorocatechol and 3CC as the major and minor intermediate products, respectively, indicating that the NK8 dioxygenase lacks absolute regiospecificity. The absence of growth of NK8 on 2CB, despite its considerable degradation activity against 2CB, is apparently due to the inability of CbeR to recognize 2CB as an inducer of the expression of the cbe genes.

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Section: Discussionmentioning

confidence: 99%

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

et al. 2001

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“….... (Taylor, 1988 (Gowri & Campbell, 1989) DMPP-PSEPU = Hydroxylase P5 protein (EC 1.14.13.7) phenol 2-monooxygenase P5 component-Pseudomonas (Nordlund et al, 1990) S15303 = Hypothetical protein 7.6-Salmonella typhimurium (Jiang et al, 1991) MEMC-METCA = Methane monooxygenase component C (EC 1.14.13.25) methane hydroxylase -Methylococcus capsula (Stainthorpe et al, 1990) XYLZ-PSEPU = E 1.2-dioxygenase electron transfer component contains ferredoxin and ferredoxin-NAD(+) (Harayama et al, 1991 (Karplus et al, 1991) amino-terminus was revealed, comprising G[QK] [HFYS] (close to strand S1-5 in Fig. 3).…”

Section: Sequence Alignmentmentioning

confidence: 99%

A structural model for the nucleotide binding domains of the flavocytochrome b_–245 β‐chain

Taylor¹,

1993

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NADPH is a system in phagocytic cells that generates 02-and hydrogen peroxide in the endocytic vacuole, both of which are important for killing of the engulfed microbe. Dysfunction of this oxidase results in the syndrome of chronic granulomatous disease, characterized by a profound predisposition to bacterial and fungal infections. A flavocytochrome b is the site of most of the mutations causing this syndrome. The FAD and NADPH binding sites have been located on the / 3 subunit of this molecule, the C-terminal half of which showed weak sequence similarity to other reductases, including the ferredoxin-NADP reductase (FNR) of known structure. This enabled us to build a model of the nucleotide binding domains of the flavocytochrome using this structure as a template. The model was built initially using a novel automatic modeling method based on distance-matrix projection and then refined using energy minimization with appropriate side-chain torsional constraints. The resulting model rationalized much of the observed sequence conservation and identified a large insertion as a potential regulatory domain. It confirms the inclusion of the neutrophil flavocytochrome b"245 (Cb-245) as a member of the FNR family of reductases and strongly supports its function as the proximal electron transporting component of the NADPH oxidase.

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“…The purified protein had a molecular mass of 42 kDA by the gel filtration analysis, indicating that the reductase is monomeric. The NADH :acceptor reductase component of xylene monooxygenase is a member of the protein family comprising the electron-transfer components of benzoate 1,2-dioxygenase from Pseudomonas arvilla [26,271, and from Acinetobacter calcoaceticus [28], toluate 1,2-dioxygenase from P. putida (pWW0) [29], phenol hydroxylase from Pseudomonas sp. CF600 [30,311, and soluble methane monooxygenase from Methylcoccus capsufutus (Bath) [15, 32, 331.…”

Section: General Characteristics Of the Nadh: Acceptor Reductasementioning

confidence: 99%

Purification and characterisation of the NADH: acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWWO of Pseudomonas putida mt‐2

Shaw¹,

Harayama²

1992

European Journal of Biochemistry

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The xylene monooxygenase system encoded by the TOL plasmid pWWO of Pseudomonas putida catalyses the hydroxylation of a methyl side-chain of toluene and xylenes. Genetic studies have suggested that this monooxygenase consists of two different proteins, products of the xylA and xylM genes, which function as an electron-transfer protein and a terminal hydroxylase, respectively. In this study, the electron-transfer component of xylene monooxygenase, the product of xylA, was purified to homogeneity. Fractions containing the xylA gene product were identified by its NADH : cytochrome c reductase activity. The molecular mass of the eniyme was determined to be 40 kDa by SDS/PAGE, and 42 kDa by gel filtration. The enzyme was found to contain 1 mol/mol of tightly but not covalently bound FAD, as well as 2 mol/mol of non-haem iron and 2 mol/mol of acid-labile sulfide, suggesting the presence of two redox centers, one FAD and one [2Fe-2S] cluster/protein molecule. The oxidised form of the protein had absorbance maxima at 457 nm and 390 nm, with shoulders at 350 nm and 550 nm. These absorbance maxima disappeared upon reduction of the protein by NADH or dithionite. The NADH :acceptor reductase was capable of reducing either one-or two-electron acceptors, such as horse heart cytochrome c or 2,6-dichloroindophenol, at an optimal pH of 8.5. The reductase was found to have a K , value for NADH of 22 pM. The oxidation of NADH was determined to be stereospecific; the enzyme is pro-R (class A enzyme). The titration of the reductase with NADH or dithionite yielded three distinct reduced forms of the enzyme: the reduction of the [2Fe-2S] center occurred with a midpoint redox potential of -171 mV; and the reduction of FAD to FAD' (semiquinone fbrm), with a calculated midpoint redox potential of -244 mV. The reduction of FAD' to FAD" (dihydroquinone form), the last stage of the titration, occurred with a midpoint redox potential of -297 mV. The [2Fe-2S] center could be removed from the protein by treatment with an excess of mersalyl acid. 'The [2Fe-2S]-depleted protein was still reduced by NADH, giving rise to the formation of the anionic flavin semiquinone observed in the native enzyme, thus suggesting that the electron flow was NADH+FAD+[2Fe-2S] in this reductase. The resulting protein could no longer reduce cytochrome c, but could reduce 2.6-dichloroindophenol at a reduced rate.Pseudomonas putida containing the TOL plasmid pWWO is capable of utilising aromatic hydrocarbons such as xylenes and toluenc as sole sources of carbon and energy. The TOL plasmid encodes an inducible metabolic pathway permitting the degradation of the hydrocarbons to Krebs cycle intermediates [l]. The genes for this pathway are organised into two operons, the first one encoding three enzymes catalysing the successive oxidation of the methyl side-chain of the aromatic substrates to the carboxylate group [2]. Two of these enzymes, benzyl alcohol dehydrogenasc and benzaldehyde dehydrogenCorrespondence to S . Harayama,

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Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

Cited by 135 publications

References 40 publications

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

A structural model for the nucleotide binding domains of the flavocytochrome b_–245 β‐chain

Purification and characterisation of the NADH: acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWWO of Pseudomonas putida mt‐2

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Potential DNA slippage structures acquired during evolutionary divergence of Acinetobacter calcoaceticus chromosomal benABC and Pseudomonas putida TOL pWW0 plasmid xylXYZ, genes encoding benzoate dioxygenases

Cited by 135 publications

References 40 publications

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

The chlorobenzoate dioxygenase genes of Burkholderia sp. strain NK8 involved in the catabolism of chlorobenzoates

A structural model for the nucleotide binding domains of the flavocytochrome b–245 β‐chain

Purification and characterisation of the NADH: acceptor reductase component of xylene monooxygenase encoded by the TOL plasmid pWWO of Pseudomonas putida mt‐2

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A structural model for the nucleotide binding domains of the flavocytochrome b_–245 β‐chain