Dockyu Kim

Monocyclic aromatic hydrocarbon degradation by Rhodococcus sp. strain DK17.

ABSTRACT Rhodococcus sp. strain DK17 was isolated from soil and analyzed for the ability to grow on o-xylene as the sole carbon and energy source. Although DK17 cannot grow on m- and p-xylene, it is capable of growth on benzene, phenol, toluene, ethylbenzene, isopropylbenzene, and other alkylbenzene isomers. One UV-generated mutant strain, DK176, simultaneously lost the ability to grow on o-xylene, ethylbenzene, isopropylbenzene, toluene, and benzene, although it could still grow on phenol. The mutant strain was also unable to oxidize indole to indigo following growth in the presence of o-xylene. This observation suggests the loss of an oxygenase that is involved in the initial oxidation of the (alkyl)benzenes tested. Another mutant strain, DK180, isolated for the inability to grow on o-xylene, retained the ability to grow on benzene but was unable to grow on alkylbenzenes due to loss of a meta-cleavage dioxygenase needed for metabolism of methyl-substituted catechols. Further experiments showed that DK180 as well as the wild-type strain DK17 have an ortho-cleavage pathway which is specifically induced by benzene but not by o-xylene. These results indicate that DK17 possesses two different ring-cleavage pathways for the degradation of aromatic compounds, although the initial oxidation reactions may be catalyzed by a common oxygenase. Gas chromatography-mass spectrometry and 300-MHz proton nuclear magnetic resonance spectrometry clearly show that DK180 accumulates 3,4-dimethylcatechol from o-xylene and both 3- and 4-methylcatechol from toluene. This means that there are two initial routes of oxidation of toluene by the strain. Pulsed-field gel electrophoresis analysis demonstrated the presence of two large megaplasmids in the wild-type strain DK17, one of which (pDK2) was lost in the mutant strain DK176. Since several other independently derived mutant strains unable to grow on alkylbenzenes are also missing pDK2, the genes encoding the initial steps in alkylbenzene metabolism (but not phenol metabolism) appear to be present on this approximately 330-kb plasmid.

Identification of a Novel Dioxygenase Involved in Metabolism of o-Xylene, Toluene, and Ethylbenzene by Rhodococcus sp. Strain DK17

ABSTRACT Rhodococcus sp. strain DK17 is able to grow on o-xylene, benzene, toluene, and ethylbenzene. DK17 harbors at least two megaplasmids, and the genes encoding the initial steps in alkylbenzene metabolism are present on the 330-kb pDK2. The genes encoding alkylbenzene degradation were cloned in a cosmid clone and sequenced completely to reveal 35 open reading frames (ORFs). Among the ORFs, we identified two nearly exact copies (one base difference) of genes encoding large and small subunits of an iron sulfur protein terminal oxygenase that are 6 kb apart from each other. Immediately downstream of one copy of the dioxygenase genes (akbA1a and akbA2a) is a gene encoding a dioxygenase ferredoxin component (akbA3), and downstream of the other copy (akbA1b and akbA2b) are genes putatively encoding a meta-cleavage pathway. RT-PCR experiments show that the two copies of the dioxygenase genes are operonic with the downstream putative catabolic genes and that both operons are induced by o-xylene. When expressed in Escherichia coli, AkbA1a-AkbA2a-AkbA3 transformed o-xylene into 2,3- and 3,4-dimethylphenol. These were apparently derived from an unstable o-xylene cis-3,4-dihydrodiol, which readily dehydrates. This indicates a single point of attack of the dioxygenase on the aromatic ring. In contrast, attack of AkbA1a-AkbA2a-AkbA3 on ethylbenzene resulted in the formation of two different cis-dihydrodiols resulting from an oxidation at the 2,3 and the 3,4 positions on the aromatic ring, respectively.

Trisindoline synthesis and anticancer activity

Expression of a Rhodococcus-derived oxygenase gene in Escherichia coli yielded indigo metabolites with cytotoxic activity against cancer cells. Bioactivity-guided fractionation of these indigo metabolites led to the isolation of trisindoline as the agent responsible for the observed in vitro cytotoxic activity against cancer cells. While the cytotoxicity of etoposide, a common anticancer drug, was dramatically decreased in multidrug-resistant (MDR) cancer cells compared with treatment of parental cells, trisindoline was found to have similar cytotoxicity effects on both parental and MDR cell lines. In addition, the cytotoxic effects of trisindoline were resistant to P-glycoprotein overexpression, one of the most common mechanisms of drug resistance in cancer cells, supporting its use to kill MDR cancer cells.

Substrate Binding Mechanism of a Type I Extradiol Dioxygenase

A meta-cleavage pathway for the aerobic degradation of aromatic hydrocarbons is catalyzed by extradiol dioxygenases via a two-step mechanism: catechol substrate binding and dioxygen incorporation. The binding of substrate triggers the release of water, thereby opening a coordination site for molecular oxygen. The crystal structures of AkbC, a type I extradiol dioxygenase, and the enzyme substrate (3-methylcatechol) complex revealed the substrate binding process of extradiol dioxygenase. AkbC is composed of an N-domain and an active C-domain, which contains iron coordinated by a 2-His-1-carboxylate facial triad motif. The C-domain includes a β-hairpin structure and a C-terminal tail. In substrate-bound AkbC, 3-methylcatechol interacts with the iron via a single hydroxyl group, which represents an intermediate stage in the substrate binding process. Structure-based mutagenesis revealed that the C-terminal tail and β-hairpin form part of the substrate binding pocket that is responsible for substrate specificity by blocking substrate entry. Once a substrate enters the active site, these structural elements also play a role in the correct positioning of the substrate. Based on the results presented here, a putative substrate binding mechanism is proposed.

Regioselective oxidation of xylene isomers by Rhodococcus sp. strain DK17

Rhodococcus sp. strain DK17 is able to utilize a variety of monocyclic aromatic hydrocarbons, including benzene, phenol, toluene, and o-xylene, as growth substrates. Although DK17 is unable to grow on m- and p-xylene, this strain could transform these two xylene isomers to some extent after induction by o-xylene. The major accumulating compounds formed during the degradation of m- and p-xylene by DK17 were isolated by high-pressure liquid chromatography and identified by gas chromatography-mass spectrometric and (1)H nuclear magnetic resonance spectral techniques. Both xylene isomers were transformed to dihydroxylated compounds by what must be two successive hydroxylation events: m-xylene was converted to 2,4-dimethylresorcinol and p-xylene was converted to 2,5-dimethylhydroquinone. The rigorous structural identification of 2,4-dimethylresorcinol and 2,5-dimethylhydroquinone demonstrates that DK17 can perform distinct regioselective hydroxylations depending on the position of the substituent groups on the aromatic ring.

Draft genome sequence and comparative analysis of the superb aromatic-hydrocarbon degrader Rhodococcus sp. strain DK17.

Rhodococcus sp. strain DK17 is capable of utilizing various derivatives of benzene and bicyclics containing both aromatic and alicyclic moieties as sole carbon and energy sources. Here, we present the 9,107,362-bp draft genome sequence of DK17 and its genomic analysis in comparison with other members of the genus Rhodococcus.

Isolation and characterization of humic substances-degrading bacteria from the subarctic Alaska grasslands

Humic substances (HS), an important fraction of soil organic carbon, are distributed widely throughout cold environments. A total of cold‐adapted 122 bacterial strains were isolated from 66 Alaska grassland soil samples based on their ability to grow on humic acids (HA), a main fraction of HS, as a carbon and energy source. These isolates were identified based on 16S rRNA gene sequencing, with class Bacilli (79.5%) and γ‐Proteobacteria (17.1%) comprising the largest groups. Among them, 45 strains, mainly Paenibacillus (27 strains) and Pseudomonas (15 strains), were selected for further screening. Two strains (Pseudomonas sp. PAMC 26793 and Paenibacillus sp. PAMC 26794) most efficiently degraded HA, but showed significant differences in their ability to grow on various monocyclic aromatics, which are putative degradative metabolites of HS. Fourier transform infrared spectra also showed substantial but different changes in HA chemical structure after incubation with each strain. Gel permeation chromatography demonstrated that depolymerization and polymerization of HA occurred during HS degradation by these newly isolated microbes.

Differential degradation of bicyclics with aromatic and alicyclic rings by Rhodococcus sp. strain DK17

ABSTRACT The metabolically versatile Rhodococcus sp. strain DK17 is able to grow on tetralin and indan but cannot use their respective desaturated counterparts, 1,2-dihydronaphthalene and indene, as sole carbon and energy sources. Metabolite analyses by gas chromatography-mass spectrometry and nuclear magnetic resonance spectrometry clearly show that (i) the meta-cleavage dioxygenase mutant strain DK180 accumulates 5,6,7,8-tetrahydro-1,2-naphthalene diol, 1,2-indene diol, and 3,4-dihydro-naphthalene-1,2-diol from tetralin, indene, and 1,2-dihydronaphthalene, respectively, and (ii) when expressed in Escherichia coli, the DK17 o-xylene dioxygenase transforms tetralin, indene, and 1,2-dihydronaphthalene into tetralin cis-dihydrodiol, indan-1,2-diol, and cis-1,2-dihydroxy-1,2,3,4-tetrahydronaphthalene, respectively. Tetralin, which is activated by aromatic hydroxylation, is degraded successfully via the ring cleavage pathway to support growth of DK17. Indene and 1,2-dihydronaphthalene do not serve as growth substrates because DK17 hydroxylates them on the alicyclic ring and further metabolism results in a dead-end metabolite. This study reveals that aromatic hydroxylation is a prerequisite for proper degradation of bicyclics with aromatic and alicyclic rings by DK17 and confirms the unique ability of the DK17 o-xylene dioxygenase to perform distinct regioselective hydroxylations.

Root canal length measurement in teeth with electrolyte compensation

Electronic root canal length measurement devices have made it easier and faster to measure the root canal length of a tooth compared with the conventional radiographic method. Of these electronic apex locators, the frequency-dependent type features greater accuracy and convenience in operation. However, its accuracy is still influenced by the presence of blood and/or the various electrolytes used in root canal therapy. This study describes the development of a new frequency-dependent electronic apex locator featuring electrolyte compensation, utilising an impedance ratio and voltage difference technique to minimise the influence of electrolytes on the accuracy of root canal length measurement. The errors for distances from file tips to apical constrictions were determined in vivo with the device operating with electrolyte compensation. The measured lengths were compared with the true lengths of the extracted teeth determined using a microscope. The mean error was +0.14±0.27 mm, and 95.2% of the measurements were within the clinical tolerance of ±0.5 mm. It was also found that the degree of accuracy was not dependent on the size of the apical foramen (p=0.74).

Aromatic hydroxylation of indan by o-xylene-degrading Rhodococcus sp. strain DK17.

ABSTRACT The metabolically versatile Rhodococcus sp. strain DK17 utilizes indan as a growth substrate via the o-xylene pathway. Metabolite and reverse transcription-PCR analyses indicate that o-xylene dioxygenase hydroxylates indan at the 4,5 position of the aromatic moiety to form cis-indan-4,5-dihydrodiol, which is dehydrogenated to 4,5-indandiol by a dehydrogenase. 4,5-Indandiol undergoes ring cleavage by a meta-cleavage dioxygenase.