Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches

Suenaga, Hikaru; Mizuta, Shiori; Miyazaki, Kentaro; Yaoi, Katsuro

doi:10.1111/1574-6941.12390

Cited by 12 publications

(13 citation statements)

References 41 publications

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“…In group II, six relative proteins were from sequenced microbial genomes, and thus none of them was characterized; while the C23O in Pseudomona s sp. G67 was just verified its expression activity on the gene level 39 . The two C23Os in our study were characterized and thus could be the representative of this new group.…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium

Guo

Fang

Wang

et al. 2015

Sci Rep

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Study of enzymes in halophiles will help to understand the mechanism of aromatic hydrocarbons degradation in saline environment. In this study, two novel catechol 2,3-dioxygenases (C23O1 and C23O2) were cloned and overexpressed from a halophilic bacterial consortium enriched from an oil-contaminated saline soil. Phylogenetic analysis indicated that the novel C23Os and their relatives formed a new branch in subfamily I.2.A of extradiol dioxygenases and the sequence differences were further analyzed by amino acid sequence alignment. Two enzymes with the halotolerant feature were active over a range of 0–30% salinity and they performed more stable at high salinity than in the absence of salt. Surface electrostatic potential and amino acids composition calculation suggested high acidic residues content, accounting for their tolerance to high salinity. Moreover, two enzymes were further characterized. The enzymes activity both increased in the presence of Fe3+, Fe2+, Cu2+ and Al3+ and showed no significant inhibition by other tested metal ions. The optimal temperatures for the C23Os were 40 °C and 60 °C and their best substrates were catechol and 4-methylcatechol respectively. As the firstly isolated and characterized catechol dioxygenases from halophiles, the two halotolerant C23Os presented novel characteristics suggesting their potential application in aromatic hydrocarbons biodegradation.

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Section: Discussionmentioning

confidence: 99%

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium

Guo

Fang

Wang

et al. 2015

Sci Rep

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“…Compared to type I Edos, type II Edos have been less well characterized, have fewer available sequences, and have not been previously identified in metagenomic functional analysis. This has been attributed to their presumed scarcity in the environment (41). However, the present analysis revealed that most of the clones encoding type II Edos (UPO51, UPO64, and UPO67) were detected using 2,3-DHB and had very low relative activities with catechol.…”

Section: Discussionmentioning

confidence: 53%

“…The screening using 2,3-DHBP as an indicator resulted in 2.5-foldmore positive clones than the screening on the same number of colonies using catechol (44 versus 17). This resulted in the iden- tification of only 16 edo genes using catechol, compared to the 27 genes that were identified using 2,3-DHBP (6 genes were identified with both substrates [ Table 1]), which suggests that many of the enzymes in the current sample are not sufficiently active toward catechol to enable detection; therefore, although catechol has been the most common substrate used to detect Edo activity (15,16,40,41), it should not be the indicator of choice for its functional detection.…”

Section: Discussionmentioning

confidence: 99%

“…In the case of the coke plant sample, 20 of the 38 identified sequences were actually repetitions of a few highly similar variant sequences of an Mn 2ϩ -dependent Edo (42) encoded by a plasmid that was designated pSKYE1 (43). Although the coke plant wastewater had a mixture of several aromatic compounds that could be used as carbon sources (15), it was highly enriched in phenol, and the high prevalence of Edo enzymes may be explained by their proposed roles in phenol detoxification (41). In the case of the contaminated soil, the edo sequences were initially amplified from positive clones with selected primers, which may impose a bias toward selecting highly similar sequences.…”

Section: Discussionmentioning

confidence: 99%

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Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases

Terrón-González

Martín-Cabello

Ferrer

et al. 2016

Appl Environ Microbiol

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A metagenomic library of a petroleum-contaminated soil was constructed in a fosmid vector that allowed heterologous expression of metagenomic DNA. The library, consisting of 6.5 Gb of metagenomic DNA, was screened for extradiol dioxygenase (Edo) activity using catechol and 2,3-dihydroxybiphenyl as the substrates. Fifty-eight independent clones encoding extradiol dioxygenase activity were identified. Forty-one different Edo-encoding genes were identified. The population of Edo genes was not dominated by a particular gene or by highly similar genes; rather, the genes had an even distribution and high diversity. Phylogenetic analyses revealed that most of the genes could not be ascribed to previously defined subfamilies of Edos. Rather, the Edo genes led to the definition of 10 new subfamilies of type I Edos. Phylogenetic analysis of type II enzymes defined 7 families, 2 of which harbored the type II Edos that were found in this work. Particularly striking was the diversity found in family I.3 Edos; 15 out of the 17 sequences assigned to this family belonged to 7 newly defined subfamilies. A strong bias was found that depended on the substrate used for the screening: catechol mainly led to the detection of Edos belonging to the I.2 family, while 2,3-dihydroxybiphenyl led to the detection of most other Edos. Members of the I.2 family showed a clear substrate preference for monocyclic substrates, while those from the I.3 family showed a broader substrate range and high activity toward 2,3-dihydroxybiphenyl. This metagenomic analysis has substantially increased our knowledge of the existing biodiversity of Edos. Large amounts of several types of contaminants are released into the environment due to industrial activities and accidental spills. Many of these contaminants, such as aromatic hydrocarbons, have complex and stable chemical structures, which make them prevail in the environment for a long time, thus resulting in the contamination of ecosystems. Biological treatment of industrial wastewater and bioremediation of contaminated soils and water are therefore critical to prevent or combat this contamination.Standardized culturing techniques have been successfully applied for many years to isolate many different types of bacteria that are capable of utilizing a variety of aromatic hydrocarbons and to characterize their biodegradation pathways and the coding genes responsible for these capabilities, which have shown that bacteria can adapt to utilize a plethora of organic contaminants, including xenobiotics. The aerobic biodegradation of aromatics has been well documented and has been shown to follow two pathways, involving either intradiol or extradiol cleavage of the aromatic rings of di-or trihydroxylated intermediates. The intradiol dioxygenases that have been described to date appear to belong to the same superfamily, but extradiol dioxygenases (Edos) of three different phylogenetic origins have been reported (1, 2). Type I extradiol dioxygenases are more numerous and belong to the vicinal oxygen chelate superfa...

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“…Orthocleavage , also known as the β-ketoadipate pathway, is between two hydroxyl groups and catalyzed by intradiol-type dioxygenases using Fe(II) as cofactor (Guzik et al 2013 ). Meta-cleavage is on the carbon-carbon bond adjacent to the hydroxyl groups through the formation of an α-keto-lactone intermediate, catalyzed by extradiol-type dioxygenases, using Fe(III) as cofactor (Suenaga et al 2014 ). Ortho cleavage of the catechol ring is catalyzed by catechol 1,2-dioxygenase to cis,cis-muconate; catechol meta-cleavage is catalyzed by catechol 2,3-dioxygenase to 2-hydroxy-muconic semialdehyde.…”

Section: Aromatic Hydrocarbon Biodegradation Under Aerobic Conditionsmentioning

confidence: 99%

Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria

Ladino-Orjuela

Gomes

Silva

et al. 2016

Reviews of Environmental Contamination and Toxicology

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The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.

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Diversity of extradiol dioxygenases in aromatic-degrading microbial community explored using both culture-dependent and culture-independent approaches

Cited by 12 publications

References 41 publications

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium

Isolation and characterization of two novel halotolerant Catechol 2, 3-dioxygenases from a halophilic bacterial consortium

Functional Metagenomics of a Biostimulated Petroleum-Contaminated Soil Reveals an Extraordinary Diversity of Extradiol Dioxygenases

Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria

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