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Ivanovski Igor,Zylstra Gerben J. 한국미생물학회 2023 The journal of microbiology Vol.61 No.12
Pseudomonas stutzeri strain AJR13 was isolated for growth on the related compounds biphenyl (BPH) and diphenylmethane (DPM). The BPH and DPM degradative pathway genes are present on an integrative and conjugative element (ICE) in the chromosome. Examination of the genome sequence of AJR13 revealed a gene encoding a salicylate 1-monooxygenase (salA) associated with the ICE even though AJR13 did not grow on salicylate. Transfer of the ICE to the well-studied Pseudomonas putida KT2440 resulted in a KT2440 strain that could grow on salicylate. Knockout mutagenesis of the salA gene on the ICE in KT2440 eliminated the ability to grow on salicylate. Complementation of the knockout with the cloned salA gene restored growth on salicylate. Transfer of the cloned salA gene under control of the lac promoter to KT2440 resulted in a strain that could grow on salicylate. Heterologous expression of the salA gene in E. coli BL21 DE3 resulted in the production of catechol from salicylate, confirming that it is indeed a salicylate 1-monooxygenase. Interestingly, transfer of the cloned salA gene under control of the lac promoter to AJR13 resulted in a strain that could now grow on salicylate, suggesting that gene expression for the downstream catechol pathway is intact.
Chang, Hung-Kuang,Zylstra, Gerben J.,Chae, Jong-Chan American Society for Microbiology 2012 Journal of Bacteriology Vol.194 No.18
<B>ABSTRACT</B><P>Hydrocarboniphaga effusastrain AP103<SUP>T</SUP>(ATCC BAA-332<SUP>T</SUP>) is a member of theGammaproteobacteriautilizing<I>n</I>-alkanes as the sole source of carbon and energy. Here we report the draft genome sequence of AP103<SUP>T</SUP>, which consists of 5,193,926 bp with a G + C content of 65.18%.</P>
Benzoate Catabolite Repression of the Phthalate Degradation Pathway in Rhodococcus sp. Strain DK17
Choi, Ki Young,Zylstra, Gerben J.,Kim, Eungbin American Society for Microbiology 2007 Applied and environmental microbiology Vol.73 No.4
<B>ABSTRACT</B><P><I>Rhodococcus</I> sp. strain DK17 exhibits a catabolite repression-like response when provided simultaneously with benzoate and phthalate as carbon and energy sources. Benzoate in the medium is depleted to detection limits before the utilization of phthalate begins. The transcription of the genes encoding benzoate and phthalate dioxygenase paralleled the substrate utilization profile. Two mutant strains with defective benzoate dioxygenases were unable to utilize phthalate in the presence of benzoate, although they grew normally on phthalate in the absence of benzoate.</P>
Kim, Doc-Kyu,Chae Jong-Chan,Zylstra Gerben J.,Sohn Ho-Yong,Kwon, Gi-Seok,Kim, Eung-Bin The Microbiological Society of Korea 2005 The journal of microbiology Vol.43 No.1
Putative genes for a two-component signal transduction system (akbS and akbT) were detected near the alkylbenzene-degrading operon of Rhodococcus sp. DK17. Sequence analysis indicates that AkbS possesses potential ATP-binding and histidine autophosphorylation sites in the N- and C-terminal regions, respectively, and that AkbT has a typical response regulator domain. Mutant analysis combined with RT-PCR experiments further shows that AkbS is required to induce the expression of o-xylene dioxygenase in DK17.
Biotechnological Potential of Rhodococcus Biodegradative Pathways
( Dockyu Kim ),( Ki Young Choi ),( Miyoun Yoo ),( Gerben J. Zylstra ),( Eungbin Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2018 Journal of microbiology and biotechnology Vol.28 No.7
The genus Rhodococcus is a phylogenetically and catabolically diverse group that has been isolated from diverse environments, including polar and alpine regions, for its versatile ability to degrade a wide variety of natural and synthetic organic compounds. Their metabolic capacity and diversity result from their diverse catabolic genes, which are believed to be obtained through frequent recombination events mediated by large catabolic plasmids. Many rhodococci have been used commercially for the biodegradation of environmental pollutants and for the biocatalytic production of high-value chemicals from low-value materials. Recent studies of their physiology, metabolism, and genome have broadened our knowledge regarding the diverse biotechnological applications that exploit their catabolic enzymes and pathways.
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>
Choi, Ki Young,Kim, Dockyu,Sul, Woo Jun,Chae, Jong-Chan,Zylstra, Gerben J.,Kim, Young Min,Kim, Eungbin Elsevier 2005 FEMS microbiology letters Vol.252 No.2
<P><B>Abstract</B></P><P>Alkylbenzene-degrading <I>Rhodococcus</I> sp. strain DK17 is able to utilize phthalate and terephthalate as growth substrates. The genes encoding the transformation of phthalate and terephthalate to protocatechuate are organized as two separate operons, located 6.7kb away from each other. Interestingly, both the phthalate and terephthalate operons are induced in response to terephthalate while expression of the terephthalate genes is undetectable in phthalate-grown cells. In addition to two known plasmids (380-kb pDK1 and 330-kb pDK2), a third megaplasmid (750-kb pDK3) was newly identified in DK17. The phthalate and terephthalate operons are duplicated and are present on both pDK2 and pDK3. RT-PCR experiments, coupled with sequence analysis, suggest that phthalate and terephthalate degradation in DK17 proceeds through oxygenation at carbons 3 and 4 and at carbons 1 and 2 to form 3,4-dihydro-3,4-dihydroxyphthalate and 1,2-dihydro-1,2-dihydroxyterephthalate, respectively. The 3,4-dihydroxyphthalate pathway was further corroborated through colorometric tests. Apparently, the two dihydrodiol metabolites are subsequently dehydrogenated and decarboxylated to form protocatechuate, which is further degraded by a protocatechuate 3,4-dioxygenase as confirmed by a ring-cleavage enzyme assay.</P>
Sul, Woo Jun,Park, Joonhong,Quensen III, John F.,Rodrigues, Jorge L. M.,Seliger, Laurie,Tsoi, Tamara V.,Zylstra, Gerben J.,Tiedje, James M. American Society for Microbiology 2009 Applied and environmental microbiology Vol.75 No.17
<B>ABSTRACT</B><P>Stable isotope probing with [<SUP>13</SUP>C]biphenyl was used to explore the genetic properties of indigenous bacteria able to grow on biphenyl in PCB-contaminated River Raisin sediment. A bacterial 16S rRNA gene clone library generated from [<SUP>13</SUP>C]DNA after a 14-day incubation with [<SUP>13</SUP>C]biphenyl revealed the dominant organisms to be members of the genera <I>Achromobacter</I> and <I>Pseudomonas</I>. A library built from PCR amplification of genes for aromatic-ring-hydroxylating dioxygenases from the [<SUP>13</SUP>C]DNA fraction revealed two sequence groups similar to <I>bphA</I> (encoding biphenyl dioxygenase) of <I>Comamonas testosteroni</I> strain B-356 and of <I>Rhodococcus</I> sp. RHA1. A library of 1,568 cosmid clones was produced from the [<SUP>13</SUP>C]DNA fraction. A 31.8-kb cosmid clone, detected by aromatic dioxygenase primers, contained genes of biphenyl dioxygenase subunits <I>bphAE</I>, while the rest of the clone's sequence was similar to that of an unknown member of the <I>Gammaproteobacteria</I>. A discrepancy in G+C content near the <I>bphAE</I> genes implies their recent acquisition, possibly by horizontal transfer. The biphenyl dioxygenase from the cosmid clone oxidized biphenyl and unsubstituted and <I>para</I>-only-substituted rings of polychlorinated biphenyl (PCB) congeners. A DNA-stable isotope probing-based cosmid library enabled the retrieval of functional genes from an uncultivated organism capable of PCB metabolism and suggest dispersed dioxygenase gene organization in nature.</P>
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>