Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63

Habe, Hiroshi; Miyakoshi, Masatoshi; Chung, Jane; Kasuga, Kano; Yoshida, Takako; Nojiri, Hideaki; Omori, Toshio

doi:10.1007/s00253-002-1166-6

Cited by 60 publications

(52 citation statements)

References 34 publications

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“…Genes involved in the metabolism of phthalate isomers are present either on plasmids, chromosome, insertion elements, or both on plasmid and chromosome [11,15,26,39,84,87,91,112]. Compared to terephthalate and isophthalate, phthalate degrading genes are well characterized with respect to their organization and regulation.…”

Section: Genetics Of Phthalate Degradationmentioning

confidence: 99%

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Bacterial degradation of phthalate isomers and their esters

Vamsee-Krishna

Phale

2008

Indian J Microbiol

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Phthalate isomers and their esters are used heavily in various industries. Excess use and leaching from the product pose them as major pollutants. These chemicals are toxic, teratogenic, mutagenic and carcinogenic in nature. Various aspects like toxicity, diversity in the aerobic bacterial degradation, enzymes and genetic organization of the metabolic pathways from various bacterial strains are reviewed here. Degradation of these esters proceeds by the action of esterases to form phthalate isomers, which are converted to dihydroxylated intermediates by specifi c and inducible phthalate isomer dioxygenases. Metabolic pathways of phthalate isomers converge at 3,4-dihydroxybenzoic acid, which undergoes either ortho-or meta-ring cleavage and subsequently metabolized to the central carbon pathway intermediates. The genes involved in the degradation are arranged in operons present either on plasmid or chromosome or both, and induced by specifi c phthalate isomer. Understanding metabolic pathways, diversity and their genetic regulation may help in constructing bacterial strains through genetic engineering approach for effective bioremediation and environmental clean up.

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Section: Genetics Of Phthalate Degradationmentioning

confidence: 99%

“…5). The genes are part of insertional sequence ISTesp2, which was also identifi ed in another Terrabacter strain DPO360 [39].…”

Section: Genetics Of Phthalate Degradationmentioning

confidence: 99%

Bacterial degradation of phthalate isomers and their esters

Vamsee-Krishna

Phale

2008

Indian J Microbiol

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“…Phthalate is an intermediate in the biodegradation pathways of some polycyclic aromatic hydrocarbons (PAHs), including pyrene (Heitkamp et al, 1988b), phenanthrene (Barnsley, 1983;Kiyohara & Nagao, 1978;Moody et al, 2001), fluorene (Grifoll et al, 1994) and fluoranthene (Kelley et al, 1993;Sepic et al, 1998). The phthalate degradation pathway of Gram-positive bacteria involves oxygenation to form 3,4-dihydro-3,4-dihydroxyphthalate, dehydrogenation to 3,4-dihydroxyphthalate and finally decarboxylation to form protocatechuate (Eaton, 2001;Habe et al, 2003) (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1

et al. 2004

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Mycobacterium vanbaalenii PYR-1 is capable of degrading polycyclic aromatic hydrocarbons (PAHs) to ring cleavage metabolites. This study identified and characterized a putative phthalate degradation operon in the M. vanbaalenii PYR-1 genome. A putative regulatory protein ( phtR) was encoded divergently with five tandem genes: phthalate dioxygenase large subunit ( phtAa), small subunit ( phtAb), phthalate dihydrodiol dehydrogenase ( phtB), phthalate dioxygenase ferredoxin subunit ( phtAc) and phthalate dioxygenase ferredoxin reductase ( phtAd ). A 6?7 kb EcoRI fragment containing these genes was cloned into Escherichia coli and converted phthalate to 3,4-dihydroxyphthalate. Homologues to the operon region were detected in a number of PAH-degrading Mycobacterium spp. isolated from various geographical locations. The operon differs from those of other Gram-positive bacteria in both the placement and orientation of the regulatory gene. In addition, the M. vanbaalenii PYR-1 pht operon contains no decarboxylase gene and none was identified within a 37 kb region containing the operon. This study is the first report of a phthalate degradation operon in Mycobacterium spp.

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“…The aldolases and epimerase belong to the superfamily of AraD-like proteins and class II aldolases. L-Fuculose 1-phosphate aldolase from E. coli showed the highest structural similarity with a Z score of 24 The structures of the L-fuculose 1-phosphate aldolases, L-ribulose 5-phosphate epimerase, and the rhamnulose 1-phosphate aldolase superimpose well on the structure of HMPDdc, as seen in Figure 6. The topology of the long β-sheet is conserved for each of the aldolases and HMPDdc; however, HMPDdc has a C-terminal α-helix not observed in the other structures.…”

Section: Comparison Of Hmpddc To Other Proteinsmentioning

confidence: 89%

Gene Identification and Structural Characterization of the Pyridoxal 5‘-Phosphate Degradative Protein 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate Decarboxylase from Mesorhizobium loti MAFF303099^,

et al. 2007

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The function of the mlr6791 gene from Mesorhizobium loti MAFF303099 has been identified. This gene encodes 3-hydroxy-2-methylpyridine-4,5-dicarboxylate decarboxylase (HMPDdc), an enzyme involved in the catabolism of pyridoxal 5-phosphate (Vitamin B 6 ). This enzyme was overexpressed in Escherichia coli and characterized. HMPDdc is a 26 kDa protein that catalyzes the decarboxylation of 3-hydroxy-2-methylpyridine-4,5-dicarboxylate to 3-hydroxy-2-methylpyridine-5-carboxylate. The K M and k cat were found to be 366 μM and 0.6 s -1 respectively. The structure of this enzyme was determined at 1.9 Å resolution using SAD phasing and belongs to the class II aldolase/adducin superfamily. While the decarboxylation of hydroxy-substituted benzene rings is a common motif in biosynthesis, the mechanism of this reaction is still poorly characterized. The structural studies described here suggest that catalysis of such decarboxylations proceeds by an aldolase-like mechanism.In contrast to our understanding of cofactor biosynthetic pathways, very little is known about cofactor catabolism. Cofactor catabolism is likely to be rare because cofactors are trace metabolites and therefore not good food sources for bacteria. Pyridoxine, 1 (vitamin B 6 ) catabolism is the best understood cofactor catabolic pathway and a small number of bacteria that can grow on vitamin B 6 as the sole source of carbon and nitrogen have been identified (1). Two catabolic pathways have been proposed (2). In the first pathway Figure 1, (pathway A), found in Pseudomonas sp. vitamin B 6 is degraded in eight steps to form succinic semialdehyde, 9, while in the second pathway (pathway B) observed in Pseudomonas IA and in Arthrobacter Cr-7, vitamin B 6 is catabolized in seven steps to 2-(hydroxymethyl)-4-oxobutanoate, 14. A related catabolic pathway in Mesorhizobium loti MAFF303099 which is very similar to the degradative pathway A has recently been discovered. 3-hydroxy-2-methylpyridine-5-carboxylate, 7 is an intermediate in this catabolic pathway. The gene coding for the enzyme producing this metabolite has not previously been discovered and is the subject of this paper.Previously, the genes encoding pyridoxine-4-oxidase (mlr6785), 4-pyridoxolactonase (mlr6805), pyridoxal-4-dehydrogenase (mlr6807) and the 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (mlr6788) were identified in Mesorhizobium loti MAFF303099 (3-6). Recently we have reported the identification of a fifth gene (mlr6793), encoding 4-* To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-4137. E-mail: tpb2@cornell.edu or see3@cornell.edu # These authors contributed equally to the research reported in this paper. ‡ The Brookhaven Protein Data Bank code is 2Z7B. pyridoxic acid dehydrogenase (7). These genes are not part of an operon, but are all close to each other on the M. loti chromosome, Figure 1. This suggested that other PLP catabolic genes might also be found in this r...

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Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63

Cited by 60 publications

References 34 publications

Bacterial degradation of phthalate isomers and their esters

Bacterial degradation of phthalate isomers and their esters

Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1

Gene Identification and Structural Characterization of the Pyridoxal 5‘-Phosphate Degradative Protein 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate Decarboxylase from Mesorhizobium loti MAFF303099^,

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Phthalate catabolic gene cluster is linked to the angular dioxygenase gene in Terrabacter sp. strain DBF63

Cited by 60 publications

References 34 publications

Bacterial degradation of phthalate isomers and their esters

Bacterial degradation of phthalate isomers and their esters

Novel organization of genes in a phthalate degradation operon of Mycobacterium vanbaalenii PYR-1

Gene Identification and Structural Characterization of the Pyridoxal 5‘-Phosphate Degradative Protein 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate Decarboxylase from Mesorhizobium loti MAFF303099,

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Gene Identification and Structural Characterization of the Pyridoxal 5‘-Phosphate Degradative Protein 3-Hydroxy-2-methylpyridine-4,5-dicarboxylate Decarboxylase from Mesorhizobium loti MAFF303099^,