A New Classification System for Bacterial Rieske Non-Heme Iron Aromatic Ring-Hydroxylating Oxygenases

Kweon, Ohgew; Kim, Seong-Jae; Baek, Songjoon; Chae, Jong‐Chan; Adjei, Michael D.; Baek, Dong-Heon; Kim, Young-Chang; Cerniglia, Carl E.

doi:10.1201/b13131-10

Cited by 17 publications

(45 citation statements)

References 64 publications

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“…This type includes enzymes typically found in Gram-positive microorganisms (mostly Actinobacteria): phenanthrene ⁄naphthalene/anthracene dioxygenase from the marine bacterium Nocardioides sp. KP7, phenanthrene and pyrene dioxygenases from Mycobacterium, as well as phthalate dioxygenases from Rhodococcus, Mycobacterium, Terrabacter and Arthrobacter (Kweon et al, 2008).…”

Section: Resultsmentioning

confidence: 99%

“…One group (IV) included the majority of amino acid sequences obtained in this work, gathering most of the dominant OPC in all samples. This enzyme type includes mainly biphenyl and polychlorinated biphenyl dioxygenases from diverse genera, it is characterized by the presence of [2Fe-2S]-type ferredoxins in the electron transport chain (Kweon et al, 2008), and is related to the toluene/biphenyl dioxygenase gene, represented by Pseudomonas, Burkholderia, Rhodococcus and Sphingomonas reference sequences. Another major group held a higher number of OPC clustering with the PAH (polycyclic aromatic hydrocarbon) dioxygenase gene (IIIαβ) represented by bacterial naphthalene/phenanthrene degraders.…”

Section: Resultsmentioning

confidence: 99%

“…In an effort to classify these highly divergent sequences, it was used a new classification system, recently proposed by Kweon et al (2008). (Kweon et al, 2008). Bootstrap percentages higher than 50% are shown in the nodes (51-75%, white circles; 76-100%, black circles).…”

Section: Resultsmentioning

confidence: 99%

“…Regarding the phylogenetic relationships among dioxygenase sequences, most sequences formed deeply rooted branches with previously described dioxygenases (Figure 4). In an effort to classify these highly divergent sequences, it was used a new classification system, recently proposed by Kweon et al (2008). (Kweon et al, 2008).…”

Section: Resultsmentioning

confidence: 99%

“…Rieske non-heme iron aromatic ring-hydroxylating dioxygenases (ARHD) comprise a reductase which obtains electrons from NAD(P)H, often a ferredoxin which shuttles the electrons and a catalytic oxygenase component. The oxygenase frequently incorporates both atoms of oxygen into the substrate and can have either a homo-(αn) or a hetero-oligomeric (αnβn) structure (Kweon et al, 2008). The alpha subunit contains the catalytic domain, and genes encoding for this subunit are often used as markers to study the biodegradation of aromatic compounds in the environment (Gibson & Parales, 2000).…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Germano

Cannavan

Mendes

et al. 2012

Pesq. agropec. bras.

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The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE) and their biochar (BC). Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene) were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF) and agriculture (AG) -, and the biochar (SF_BC and AG_BC, respectively). Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC) in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD) gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Germano

Cannavan

Mendes

et al. 2012

Pesq. agropec. bras.

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Aromatic Hydrocarbon Degradation Genes from Chronically Polluted Subantarctic Marine Sediments

Dionisi

Lozada

Marcos

et al. 2011

Handbook of Molecular Microbial Ecology II

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Aim:The goal of this study was to identify functional targets to detect polycyclic aromatic hydrocarbon (PAH)-degrading bacterial populations in cold marine ecosystems. Methods and Results: We designed a degenerate primer set targeting genes encoding the a subunit of PAH-dioxygenases from Gram-positive bacteria. This primer set was used to amplify gene fragments from metagenomic DNA isolated from Subantarctic marine sediments (Ushuaia Bay, Argentina). These gene fragments were cloned and sequenced. We identified 14 distinct groups of genes, most of them showing significant relatedness with dioxygenases from Gram-positive bacteria of the genera Rhodococcus, Mycobacterium, Nocardioides, Terrabacter and Bacillus. The level of identity with these genes, however, was low to moderate (33-62% at the amino acid level). Conclusion: These results indicate the presence of a high diversity of hitherto unidentified dioxygenase genes in this cold polluted environment. Significance and Impact of the Study: Subantarctic marine ecosystems are particularly vulnerable to hydrocarbon pollution, and the development of environmental restoration strategies for these environments is pressing. The information obtained in this work will be the starting point for the design of quantitative molecular tools to analyse the abundance and dynamics of these aromatic hydrocarbon-degrading bacterial populations in the marine environment.

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Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

Zhang¹,

Liu

Dai

et al. 2022

mLife

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Polycyclic aromatic hydrocarbons (PAHs) are a class of persistent pollutants with adverse biological effects and pose a serious threat to ecological environments and human health. The previously isolated phenanthrene‐degrading bacterial consortium (PDMC) consists of the genera Sphingobium and Pseudomonas and can degrade a wide range of PAHs. To identify the degradation mechanism of PAHs in the consortium PDMC, metagenomic binning was conducted and a Sphingomonadales assembly genome with 100% completeness was obtained. Additionally, Sphingobium sp. SHPJ‐2, an efficient degrader of PAHs, was successfully isolated from the consortium PDMC. Strain SHPJ‐2 has powerful degrading abilities and various degradation pathways of high‐molecular‐weight PAHs, including fluoranthene, pyrene, benzo[a]anthracene, and chrysene. Two ring‐hydroxylating dioxygenases, five cytochrome P450s, and a pair of electron transfer chains associated with PAH degradation in strain SHPJ‐2, which share 83.0%–99.0% similarity with their corresponding homologous proteins, were identified by a combination of Sphingomonadales assembly genome annotation, reverse‐transcription quantitative polymerase chain reaction and heterologous expression. Furthermore, when coexpressed in Escherichia coli BL21(DE3) with the appropriate electron transfer chain, PhnA1B1 could effectively degrade chrysene and benzo[a]anthracene, while PhnA2B2 degrade fluoranthene. Altogether, these results provide a comprehensive assessment of strain SHPJ‐2 and contribute to a better understanding of the molecular mechanism responsible for the PAH degradation.

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A New Classification System for Bacterial Rieske Non-Heme Iron Aromatic Ring-Hydroxylating Oxygenases

Cited by 17 publications

References 64 publications

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

Aromatic Hydrocarbon Degradation Genes from Chronically Polluted Subantarctic Marine Sediments

Unveiling degradation mechanism of PAHs by a Sphingobium strain from a microbial consortium

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