Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying the<i>dbfA1A2</i>gene homologues isolated from activated sludge

Noumura, Takashi; Habe, Hiroshi; Widada, Jaka; Chung, Jane; Yoshida, Takako; Nojiri, Hideaki; Omori, Toshio

doi:10.1016/j.femsle.2004.08.032

Cited by 14 publications

(10 citation statements)

References 34 publications

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“…Other examples include Pseudomonas veronii PH-03 [Hong et al, 2004], Rhodococcus sp. strain DFA3 [Noumura et al, 2004], Janthinobacterium [Inoue et al, 2004], several strains of Janibacter sp. [Iwai et al, 2005;Jin et al, 2006;Yamozoe et al, 2004a, b], Nocardioides aromaticivorans IC177 [Inoue et al, 2005;, and Paenibacillus sp strain YK5 [Idia et al, 2006].…”

Section: Dioxin Degradation By Angular Dioxygenationmentioning

confidence: 99%

Recent Developments in Microbial Biotransformation and Biodegradation of Dioxins

Chang

2008

Microb Physiol

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Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs), commonly known as dioxins (PCDD/Fs), are toxic environmental pollutants formed from various sources. Elimination of these pollutants from the environment is a difficult task due to their persistent and ubiquitous nature. Removal of dioxins by biological degradation (biodegradation) is considered a feasible method as an alternative to other expensive physicochemical approaches. Biodegradation of dioxins has been extensively studied in several microorganisms, and details concerning biodiversity, biodegradation, biochemistry and molecular biology of this process have accumulated during the last three decades. There are several microbial mechanisms responsible for biodegradation of dioxins, including oxidative degradation by dioxygenase-containing aerobic bacteria, bacterial and fungal cytochrome P-450, fungal lignolytic enzymes, reductive dechlorination by anaerobic bacteria, and direct ether ring cleavage by fungi containing etherase-like enzymes. Many attempts have been made to bioremediate PCDD/Fs using this basic knowledge of microbial dioxin degradation. This review emphasizes the present knowledge and recent advancements in the microbial biotransformation, biodegradation and bioremediation of dioxins.

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Section: Dioxin Degradation By Angular Dioxygenationmentioning

confidence: 99%

Recent Developments in Microbial Biotransformation and Biodegradation of Dioxins

Chang

2008

Microb Physiol

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“…strain DFA10, both of which possess dbfA1A2 gene homologues, were isolated, and the gene organizations of the regions flanking the dbfA1A2 gene homologues were analysed. Sequence comparisons of these DNA regions among strains DBF63, DFA1 and DFA10 showed that the organizations of both pht and dbf-fln gene clusters were completely conserved (Noumura et al, 2004). These results strongly suggest that pDBF1 of strain DBF63 is a transmissible plasmid, and may play an important role in the distribution of FN-degradation genes.…”

Section: Discussionmentioning

confidence: 77%

The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

et al. 2005

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The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the b-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria Terrabacter sp. strain DBF63 is capable of degrading fluorene (FN) to tricarboxylic acid cycle intermediates via phthalate and protocatechuate. Genes were identified for the protocatechuate branch of the b-ketoadipate pathway (pcaR, pcaHGBDCFIJ) by sequence analysis of a 70 kb DNA region of the FN-catabolic linear plasmid pDBF1. RT-PCR analysis of RNA from DBF63 cells grown with FN, dibenzofuran, and protocatechuate indicated that the pcaHGBDCFIJ operon was expressed during both FN and protocatechuate degradation in strain DBF63. The gene encoding b-ketoadipate enol-lactone hydrolase (pcaD) was not fused to the next gene, which encodes c-carboxymuconolactone decarboxylase (pcaC), in strain DBF63, even though the presence of the pcaL gene (the fusion of pcaD and pcaC) within a pca gene cluster has been thought to be a Gram-positive trait. Quantitative RT-PCR analysis revealed that pcaD mRNA levels increased sharply in response to protocatechuate, and a biotransformation experiment with cis,cis-muconate using Escherichia coli carrying both catBC and pcaD indicated that PcaD exhibited b-ketoadipate enol-lactone hydrolase activity. The location of the pca gene cluster on the linear plasmid, and the insertion sequences around the pca gene cluster suggest that the ecologically important b-ketoadipate pathway genes, usually located chromosomally, may be spread widely among bacterial species via horizontal transfer or transposition events.

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“…It has been previously suggested that enzymes similar to DfdA YK3 are distributed among DBF-degrading actinobacteria (22), while enzymes similar to DbfA DBF63 have been recently reported in Rhodococcus strains, such as Rhodococcus sp. strain YK2 or DFA3 (44).…”

Section: Discussionmentioning

confidence: 99%

Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading Rhodococcus sp. Strain HA01

Aly¹,

Huu²,

Wray

et al. 2008

Appl Environ Microbiol

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Rhodococcus sp. strain HA01, isolated through its ability to utilize dibenzofuran (DBF) as the sole carbon and energy source, was also capable, albeit with low activity, of transforming dibenzo-p-dioxin (DD). This strain could also transform 3-chlorodibenzofuran (3CDBF), mainly by angular oxygenation at the ether bond-carrying carbon (the angular position) and an adjacent carbon atom, to 4-chlorosalicylate as the end product. Similarly, 2-chlorodibenzofuran (2CDBF) was transformed to 5-chlorosalicylate. However, lateral oxygenation at the 3,4-positions was also observed and yielded the novel product 2-chloro-3,4-dihydro-3,4-dihydroxydibenzofuran. Two gene clusters encoding enzymes for angular oxygenation (dfdA1A2A3A4 and dbfA1A2) were isolated, and expression of both was observed during growth on DBF. Heterologous expression revealed that both oxygenase systems catalyze angular oxygenation of DBF and DD but exhibited complementary substrate specificity with respect to CDBF transformation. While DfdA1A2A3A4 oxygenase, with high similarity to DfdA1A2A3A4 oxygenase from Terrabacter sp. strain YK3, transforms 3CDBF by angular dioxygenation at a rate of 29% ؎ 4% that of DBF, 2CDBF was not transformed. In contrast, DbfA1A2 oxygenase, with high similarity to the DbfA1A2 oxygenase from Terrabacter sp. strain DBF63, exhibited complementary activity with angular oxygenase activity against 2CDBF but negligible activity against 3CDBF. Thus, Rhodococcus sp. strain HA01 constitutes the first described example of a bacterial strain where coexpression of two angular dioxygenases was observed. Such complementary activity allows for the efficient transformation of chlorinated DBFs.Biarylethers, comprising dibenzo-p-dioxin (DD), dibenzofuran (DBF), diphenyl ether, and their halogenated derivatives, are widespread environmental pollutants. Polychlorinated DDs and DBFs, the contaminating by-products formed during the manufacture of pesticides or the incineration of industrial and domestic wastes, can cause a wide range of serious health effects (1,4,13).Microorganisms play important roles in the degradation and mineralization of xenobiotic and aromatic compounds in natural environments. Their aerobic degradation is frequently initiated by Rieske nonheme iron oxygenases which catalyze the incorporation of two oxygen atoms into the aromatic ring to form arene cis-diols (15). This is then followed by a dehydrogenation reaction catalyzed by a cis-dihydrodiol dehydrogenase to give catechol or substituted catechols, which serve as substrates for oxygenolytic aromatic ring cleavage. Rieske nonheme iron oxygenases are typically composed of a terminal oxygenase (iron-sulfur protein) and different electron transport proteins (8). The catalytic iron-sulfur proteins are homoor heteromultimers with the ␣-subunit containing a Riesketype [2Fe-2S] cluster, a mononuclear nonheme iron oxygen activation center, and a substrate-binding site (8) that is responsible for substrate specificity (15). Comparison of the amino acid sequences of the ␣-subunits ...

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Genetic characterization of the dibenzofuran-degrading Actinobacteria carrying thedbfA1A2gene homologues isolated from activated sludge

Cited by 14 publications

References 34 publications

Recent Developments in Microbial Biotransformation and Biodegradation of Dioxins

Recent Developments in Microbial Biotransformation and Biodegradation of Dioxins

The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the β-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria

Two Angular Dioxygenases Contribute to the Metabolic Versatility of Dibenzofuran-Degrading Rhodococcus sp. Strain HA01

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