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Kim, Dockyu,Yoo, Miyoun,Choi, Ki Young,Kang, Beom Sik,Kim, Tai Kyoung,Hong, Soon Gyu,Zylstra, Gerben J,Kim, Eungbin American Society for Microbiology 2011 Applied and environmental microbiology Vol.77 No.23
<P>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.</P>
Kim, Dockyu,Kim, Si Wouk,Choi, Ki Young,Lee, Jong Suk,Kim, Eungbin Oxford University Press 2008 FEMS microbiology letters Vol.280 No.2
<P>Chromohalobacter sp. strain HS-2 was isolated from salted fermented clams and analyzed for the ability to grow on benzoate and p-hydroxybenzoate as the sole carbon and energy source. HS-2 was characterized as moderately halophilic, with an optimal NaCl concentration of 10%. The genes encoding the benzoate metabolism were cloned into a cosmid vector, sequenced, and then analyzed to reveal the benzoate (benABCD) and catechol (catBCA) catabolic genes, both of which are flanked on either side by LysR-type transcriptional regulator (catR) and membrane transport protein for benzoate (benE) in the gene order catRBCAbenABCDE. Near the large cat-ben cluster, a p-hydroxybenzoate hydroxylase gene (pobA) and two putative regulatory genes (pcaQ and pobR) were additionally detected. The HS-2 genes involved in benzoate and p-hydroxybenzoate degradation are tightly clustered within a c. 19 kb region, and show quite a different genetic organization from those of other benzoate catabolic genes. Reverse transcriptase-PCR experiments show that benzoate induces the expression of benzoate 1,2-dioxygenase, catechol 1,2-dioxygenase, and protocatechuate 3,4-dioxygenase while p-hydroxybenzoate only induced the expression of p-hydroxybenzoate hydroxylase. When expressed in Escherichia coli, benzoate 1,2-dioxygenase (BenABC) and p-hydroxybenzoate hydroxylase (PobA) transformed benzoate and p-hydroxybenzoate into cis-benzoate dihydrodiol and protocatechuate, respectively.</P>
Kim, Dockyu,Lee, Jong Suk,Choi, Ki Young,Kim, Young-Soo,Choi, Jung Nam,Kim, Seong-Ki,Chae, Jong-Chan,Zylstra, Gerben J.,Lee, Choong Hwan,Kim, Eungbin IPC Science and Technology Press 2007 Enzyme and microbial technology Vol.41 No.3
<P><B>Abstract</B></P><P>The <I>o</I>-xylene dioxygenase from <I>Rhodococcus</I> sp. strain DK17 possesses the ability to perform distinct regioselective hydroxylations depending on the position of the substituent groups on the aromatic ring. Bioconversion experiments were performed against the non-growth substrates <I>p</I>-xylene, biphenyl, and naphthalene, using induced cells of <I>Escherichia coli</I> BL21(DE3) harboring a recombinant expression plasmid of the DK17 <I>o</I>-xylene dioxygenase. Oxidation metabolites transformed from each substrate during the incubation were identified by a gas chromatography–mass spectrometry. <I>p</I>-Xylene was oxidized to <I>cis</I>-<I>p</I>-xylene dihydrodiol. Biphenyl and naphthalene were transformed into <I>cis</I>-2,3-biphenyl dihydrodiol and <I>cis</I>-1,2-naphthalene dihydrodiol, respectively. Considering that the DK17 <I>o</I>-xylene dioxygenase hydroxylates toluene and ethylbenzene at the 2,3 and the 3,4 positions on the aromatic ring in the ratios of 8:2 and 9:1, it is apparent that the size as well as the position of the substituent groups on the aromatic ring affect the regioselectivity of aromatic oxidation by this enzyme.</P>
Dockyu Kim,Namyi Chae,Mincheol Kim,Sungjin Nam,Eungbin Kim,Hyoungseok Lee 한국미생물학회 2020 The journal of microbiology Vol.58 No.12
Recent increases in air temperature across the Antarctic Peninsula may prolong the thawing period and directly affect the soil temperature (Ts) and volumetric soil water content (SWC) in maritime tundra. Under an 8°C soil warming scenario, two customized microcosm systems with maritime Antarctic soils were incubated to investigate the differential influence of SWC on the bacterial community and degradation activity of humic substances (HS), the largest constituent of soil organic carbon and a key component of the terrestrial ecosystem. When the microcosm soil (KS1-4Feb) was incubated for 90 days (T = 90) at a constant SWC of ~32%, the initial HS content (167.0 mg/g of dried soil) decreased to 156.0 mg (approximately 6.6% loss, p < 0.05). However, when another microcosm soil (KS1-4Apr) was incubated with SWCs that gradually decreased from 37% to 9% for T = 90, HS degradation was undetected. The low HS degradative activity persisted, even after the SWC was restored to 30% with water supply for an additional T = 30. Overall bacterial community structure remained relatively stable at a constant SWC setting (KS1-4Feb). In contrast, we saw marked shifts in the bacterial community structure with the changing SWC regimen (KS1-4Apr), suggesting that the soil bacterial communities are vulnerable to drying and re-wetting conditions. These microcosm experiments provide new information regarding the effects of constant SWC and higher Ts on bacterial communities for HS degradation in maritime Antarctic tundra soil.
Kim Dockyu,Chae Namyi,Kim Mincheol,Nam Sungjin,Kim Tai Kyoung,Park Ki-Tea,Lee Bang Yong,Kim Eungbin,Lee Hyoungseok 한국미생물학회 2022 The journal of microbiology Vol.60 No.12
Recent rapid air temperature increases across the northernlatitude tundra have prolonged permafrost thawing and snow melting periods, resulting in increased soil temperature (Ts) and volumetric soil water content (SWC). Under prolonged soil warming at 8°C, Alaskan tundra soils were incubated in a microcosm system and examined for the SWC differential influence on the microbial decomposition activity of large molecular weight (MW) humic substances (HS). When one microcosm soil (AKC1-1) was incubated at a constant SWC of 41% for 90 days (T = 90) and then SWC was gradually decreased from 41% to 29% for another T = 90, the initial HS was partly depolymerized. In contrast, in AKC1-2 incubated at a gradually decreasing SWC from the initial 32% to 10% for T = 90 and then increasing to 27% for another T = 90, HS depolymerization was undetected. Overall, the microbial communities in AKC1-1 could maintain metabolic activity at sufficient and constant SWC during the initial T = 90 incubation. In contrast, AKC1-2 microbes may have been damaged by drought stress during the drying SWC regimen, possibly resulting in the loss of HS decomposition activity, which did not recover even after re-wetting to an optimal SWC range (20–40%). After T = 90, the CO2 production in both treatments was attributed to the increased decomposition of small-MW organic compounds (including aerobic HS-degradative products) within an optimal SWC range. We expect this study to provide new insights into the early effects of warming- and topography-induced SWC variations on the microbial contribution to CO2 emissions via HS decomposition in northern-latitude tundra soil.
Kim, Dockyu,Choi, Ki Young,Yoo, Miyoun,Choi, Jung Nam,Lee, Choong Hwan,Zylstra, Gerben J,Kang, Beom Sik,Kim, Eungbin Springer International 2010 Applied microbiology and biotechnology Vol.86 No.6
<P>Escherichia coli cells expressing Rhodococcus DK17 o-xylene dioxygenase genes were used for bioconversion of m-xylene. Gas chromatography-mass spectrometry analysis of the oxidation products detected 3-methylbenzylalcohol and 2,4-dimethylphenol in the ratio 9:1. Molecular modeling suggests that o-xylene dioxygenase can hold xylene isomers at a kink region between alpha6 and alpha7 helices of the active site and alpha9 helix covers the substrates. m-Xylene is unlikely to locate at the active site with a methyl group facing the kink region because this configuration would not fit within the substrate-binding pocket. The m-xylene molecule can flip horizontally to expose the meta-position methyl group to the catalytic motif. In this configuration, 3-methylbenzylalcohol could be formed, presumably due to the meta effect. Alternatively, the m-xylene molecule can rotate counterclockwise, allowing the catalytic motif to hydroxylate at C-4 yielding 2,4-dimethylphenol. Site-directed mutagenesis combined with structural and functional analyses suggests that the alanine-218 and the aspartic acid-262 in the alpha7 and the alpha9 helices play an important role in positioning m-xylene, respectively.</P>
Aromatic Hydroxylation of Indan by o-Xylene-Degrading Rhodococcus sp. Strain DK17
Kim, Dockyu,Lee, Choong Hwan,Choi, Jung Nam,Choi, Ki Young,Zylstra, Gerben J.,Kim, Eungbin American Society for Microbiology 2010 Applied and environmental microbiology Vol.76 No.1
<B>ABSTRACT</B><P>The metabolically versatile <I>Rhodococcus</I> sp. strain DK17 utilizes indan as a growth substrate via the <I>o</I>-xylene pathway. Metabolite and reverse transcription-PCR analyses indicate that <I>o</I>-xylene dioxygenase hydroxylates indan at the 4,5 position of the aromatic moiety to form <I>cis</I>-indan-4,5-dihydrodiol, which is dehydrogenated to 4,5-indandiol by a dehydrogenase. 4,5-Indandiol undergoes ring cleavage by a <I>meta</I>-cleavage dioxygenase.</P>