Journal of Microbiology

Do Young Kim

6 Articles

Biocatalytic Properties and Substrate-binding Ability of a Modular GH10 β-1,4-Xylanase from an Insect-symbiotic Bacterium, Streptomyces mexicanus HY-14: Do Young Kim , Dong-Ha Shin , Sora Jung , Jong Suk Lee , Han-Young Cho , Kyung Sook Bae , Chang-Keun Sung , Young Ha Rhee , Kwang-Hee Son , Ho-Yong Park; J. Microbiol. 2014;52(10):863-870. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4390-8

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The gene (1350-bp) encoding a modular β-1,4-xylanase (XylU), which consists of an N-terminal catalytic GH10 domain and a C-terminal carbohydrate-binding module 2 (CBM 2), from Streptomyces mexicanus HY-14 was cloned and functionally characterized. The purified His-tagged recombinant enzyme (rXylU, 44.0 kDa) was capable of efficiently hydrolyze diverse xylosidic compounds, p-nitrophenyl-cellobioside, and pnitrophenyl- xylopyranoside when incubated at pH 5.5 and 65°C. Especially, the specific activities (649.8 U/mg and 587.0 U/mg, respectively) of rXylU toward oat spelts xylan and beechwood xylan were relatively higher than those (<500.0 U/mg) of many other GH10 homologs toward the same substrates. The results of enzymatic degradation of birchwood xylan and xylooligosaccharides (xylotriose to xylohexaose) revealed that rXylU preferentially hydrolyzed the substrates to xylobiose (>75%) as the primary degradation product. Moreover, a small amount (4%<) of xylose was detected as the degradation product of the evaluated xylosidic substrates, indicating that rXylU was a peculiar GH10 β-1,4- xylanase with substrate specificity, which was different from its retaining homologs. A significant reduction of the binding ability of rXylU caused by deletion of the C-terminal CBM 2 to various insoluble substrates strongly suggested that the additional domain might considerably contribute to the enzyme-substrate interaction.

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Gene cloning, expression, and characterization of two endo-xylanases from Bacillus velezensis and Streptomyces rochei, and their application in xylooligosaccharide production
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Extremophilic Prokaryotic Endoxylanases: Diversity, Applicability, and Molecular Insights
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Novel Bi-Modular GH19 Chitinase with Broad pH Stability from a Fibrolytic Intestinal Symbiont of Eisenia fetida, Cellulosimicrobium funkei HY-13
Lu Bai, Jonghoon Kim, Kwang-Hee Son, Chung-Wook Chung, Dong-Ha Shin, Bon-Hwan Ku, Do Kim, Ho-Yong Park
Biomolecules.2021; 11(11): 1735. CrossRef
Identification and Characterization of a Novel, Cold-Adapted d-Xylobiose- and d-Xylose-Releasing Endo-β-1,4-Xylanase from an Antarctic Soil Bacterium, Duganella sp. PAMC 27433
Do Young Kim, Jonghoon Kim, Yung Mi Lee, Jong Suk Lee, Dong-Ha Shin, Bon-Hwan Ku, Kwang-Hee Son, Ho-Yong Park
Biomolecules.2021; 11(5): 680. CrossRef
Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes
Matias Romero Victorica, Marcelo A. Soria, Ramón Alberto Batista-García, Javier A. Ceja-Navarro, Surendra Vikram, Maximiliano Ortiz, Ornella Ontañon, Silvina Ghio, Liliana Martínez-Ávila, Omar Jasiel Quintero García, Clara Etcheverry, Eleonora Campos, Don
Scientific Reports.2020;[Epub] CrossRef
Biochemical Characterization of Xylanases from Streptomyces sp. B6 and Their Application in the Xylooligosaccharide Production from Viscose Fiber Production Waste
Lin Liu, Mingyuan Xu, Yanli Cao, Hai Wang, Jing Shao, Meiqing Xu, Yuancheng Zhang, Yunhe Wang, Weixin Zhang, Xiangfeng Meng, Weifeng Liu
Journal of Agricultural and Food Chemistry.2020; 68(10): 3184. CrossRef
A novel neutral and thermophilic endoxylanase from Streptomyces ipomoeae efficiently produced xylobiose from agricultural and forestry residues
Liang Xian, Zhong Li, Ai-Xing Tang, Yi-Min Qin, Qing-Yun Li, Hai-Bo Liu, You-Yan Liu
Bioresource Technology.2019; 285: 121293. CrossRef
Draft genome of Streptomyces sp. strain 130 and functional analysis of extracellular enzyme producing genes
Munendra Kumar, Prateek Kumar, Payal Das, Monisha Khanna Kapur
Molecular Biology Reports.2019; 46(5): 5063. CrossRef
In silico Screening and Heterologous Expression of a Polyethylene Terephthalate Hydrolase (PETase)-Like Enzyme (SM14est) With Polycaprolactone (PCL)-Degrading Activity, From the Marine Sponge-Derived Strain Streptomyces sp. SM14
Eduardo L. Almeida, Andrés Felipe Carrillo Rincón, Stephen A. Jackson, Alan D. W. Dobson
Frontiers in Microbiology.2019;[Epub] CrossRef
Genetic and functional characterization of a novel GH10 endo-β- 1,4-xylanase with a ricin-type β-trefoil domain-like domain from Luteimicrobium xylanilyticum HY-24
Do Young Kim, Sun Hwa Lee, Min Ji Lee, Han-Young Cho, Jong Suk Lee, Young Ha Rhee, Dong-Ha Shin, Kwang-Hee Son, Ho-Yong Park
International Journal of Biological Macromolecules.2018; 106: 620. CrossRef
Streptomyces spp. in the biocatalysis toolbox
Jelena Spasic, Mina Mandic, Lidija Djokic, Jasmina Nikodinovic-Runic
Applied Microbiology and Biotechnology.2018; 102(8): 3513. CrossRef
Genetic and functional characterization of an extracellular modular GH6 endo-β-1,4-glucanase from an earthworm symbiont, Cellulosimicrobium funkei HY-13
Do Young Kim, Min Ji Lee, Han-Young Cho, Jong Suk Lee, Mi-Hwa Lee, Chung Wook Chung, Dong-Ha Shin, Young Ha Rhee, Kwang-Hee Son, Ho-Yong Park
Antonie van Leeuwenhoek.2016; 109(1): 1. CrossRef
Molecular Characterization of Xylobiose- and Xylopentaose-Producing β-1,4-Endoxylanase SCO5931 from Streptomyces coelicolor A3(2)
Bolormaa Enkhbaatar, Chang-Ro Lee, Young-Soo Hong, Soon-Kwang Hong
Applied Biochemistry and Biotechnology.2016; 180(2): 349. CrossRef
High Genetic Diversity of Microbial Cellulase and Hemicellulase Genes in the Hindgut of Holotrichia parallela Larvae
Ping Sheng, Yushan Li, Sean Marshall, Hongyu Zhang
International Journal of Molecular Sciences.2015; 16(7): 16545. CrossRef
Characterization of a Novel Xylanase Gene from Rumen Content of Hu Sheep
Qian Wang, Yang Luo, Bo He, Lin-Shu Jiang, Jian-Xin Liu, Jia-Kun Wang
Applied Biochemistry and Biotechnology.2015; 177(7): 1424. CrossRef

Biosynthesis of Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Copolyesters with a High Molar Fraction of 3-Hydroxyvalerate by an Insect-Symbiotic Burkholderia sp. IS-01: Do Young Kim , Doo-Sang Park , Soon Bum Kwon , Moon Gyu Chung , Kyung Sook Bae , Ho-Yong Park , Young Ha Rhee; J. Microbiol. 2009;47(5):651-656. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0109-7

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Burkholderia sp. IS-01 capable of biosynthesizing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [poly(3HB- co-3HV)] copolyesters with a high molar fraction of 3HV was isolated from the gut of the adult longicorn beetle, Moechotypa diphysis. The strain IS-01 was relatively tolerant to high concentrations of levulinic acid and accumulated a poly(13.5 mol% 3HB-co-86.5 mol% 3HV) copolyester when cultivated on a mixture of gluconate (20 g/L) and levulinic acid (12.5 g/L). In this case, the content of the copolyester in the cells was approximately 60.0%. The compositions of the copolyesters were easily regulated by altering the molar ratio of gluconate and levulinic acid in the medium. The organism was found to possess a class I PHA synthase (PhaC) gene (1,881 bp) that encodes a protein with a deduced molecular mass of 68,538 Da that consists of 626 amino acids. The PhaC of this organism was most similar to that of B. cenocepacia PC184 (92% similarity).

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D. Li, J.K. March, T.M. Bills, B.C. Holt, C.E. Wilson, W. Lowe, H.D. Tolley, M.L. Lee, R.A. Robison
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Biosynthesis and Thermal Properties of PHBV Produced from Levulinic Acid by Ralstonia eutropha
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Biosynthesis of Copolyesters Consisting of 3-Hydroxyvalerate and Medium-chain-length 3-hydroxyalkanoates by the Pseudomonas aeruginosa P-5 Strain
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The Korean Journal of Microbiology.2012; 48(3): 200. CrossRef

Paenibacillus camelliae sp. nov., Isolated from Fermented Leaves of Camellia sinensis: Hyun-Woo Oh , Byung-Chun Kim , Kang Hyun Lee , Do Young Kim , Doo-Sang Park , Hee-Moon Park , Kyung Sook Bae; J. Microbiol. 2008;46(5):530-534. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0233-9

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A novel bacterium, strain b11s-2T was isolated from Pu’er tea. The isolate was Gram-positive, endosporeforming motile rod that grew at 15~42°C and pH 6.0~10.2. The DNA G+C content was 48.3 mol%, the predominant isoprenoid quinone was MK-7, and the predominant cellular fatty acid was anteiso-C15:0 (54.2%) followed by C16:0 (15.5%) and iso-C16:0 (8.2%). The polar lipid pattern of b11s-2T was characterized by the presence of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequence showed that the strain was affiliated within the Paenibacillaceae. The strain was most closely related to Paenibacillus granivorans A30T, with a similarity of 97.1%. Based on the phylogenetic and phenotypic characteristics of strain b11s-2T, the isolate is thought to represent a novel taxon in the genus Paenibacillus. The name Paenibacillus camelliae sp. nov. is proposed for the fermented tea isolate; the type strain is b11s-2T (= KCTC 13220T= CECT 7361T).

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Biosynthesis, Modification, and Biodegradation of Bacterial Medium-Chain-Length Polyhydroxyalkanoates: Do Young Kim , Hyung Woo Kim , Moon Gyu Chung , Young Ha Rhee; J. Microbiol. 2007;45(2):87-97.; DOI: https://doi.org/2528 [pii]

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Abstract PDF: Medium-chain-length polyhydroxyalkanoates (MCL-PHAs), which have constituents with a typical chain length of C6-C14, are polyesters that are synthesized and accumulated in a wide variety of Gram-negative bacteria, mainly pseudomonads. These biopolyesters are promising materials for various applications because they have useful mechanical properties and are biodegradable and biocompatible. The versatile metabolic capacity of some Pseudomonas spp. enables them to synthesize MCL-PHAs that contain various functional substituents; these MCL-PHAs are of great interest because these functional groups can improve the physical properties of the polymers, allowing the creation of tailor-made products. Moreover, some functional substituents can be modified by chemical reactions to obtain more useful groups that can extend the potential applications of MCL-PHAs as environmentally friendly polymers and functional biomaterials for use in biomedical fields. Although MCL-PHAs are water-insoluble, hydrophobic polymers, they can be degraded by microorganisms that produce extracellular MCL-PHA depolymerase. MCL-PHA-degraders are relatively uncommon in natural environments and, to date, only a limited number of MCL-PHA depolymerases have been investigated at the molecular level. All known MCL-PHA depolymerases share a highly significant similarity in amino acid sequences, as well as several enzymatic characteristics. This paper reviews recent advances in our knowledge of MCL-PHAs, with particular emphasis on the findings by our research group.

Molecular Characterization of Extracellular Medium-chain-length Poly(3-hydroxyalkanoate) Depolymerase Genes from Pseudomonas alcaligenes Strains: Do Young Kim , Hyun Chul Kim , Sun Young Kim , Young Ha Rhee; J. Microbiol. 2005;43(3):285-294.; DOI: https://doi.org/2211 [pii]

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Abstract PDF: A bacterial strain M4-7 capable of degrading various polyesters, such as poly(e-caprolactone), poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(3-hydroxyoctanoate), and poly(3-hydroxy-5-phenylvalerate), was isolated from a marine environment and identified as Pseudomonas alcaligenes. The relative molecular mass of a purified extracellular medium-chain-length poly(3-hydroxyalkanoate) (MCL-PHA) depolymerase (PhaZ_PalM4-7) from P. alcaligenes M4-7 was 28.0 kDa, as determined by SDS-PAGE. The PhaZ_PalM4-7 was most active in 50 mM glycine-NaOH buffer (pH 9.0) at 35^oC. It was insensitive to dithiothreitol, sodium azide, and iodoacetamide, but susceptible to p-hydroxymercuribenzoic acid, N-bromosuccinimide, acetic anhydride, EDTA, diisopropyl fluorophosphate, phenylmethylsulfonyl fluoride, Tween 80, and Triton X-100. In this study, the genes encoding MCL-PHA depolymerase were cloned, sequenced, and characterized from a soil bacterium, P. alcaligenes LB19 (Kim et al., 2002, Biomacromolecules 3, 291-296) as well as P. alcaligenes M4-7. The structural gene (phaZ_PalLB19) of MCL-PHA depolymerase of P. alcaligenes LB19 consisted of an 837 bp open reading frame (ORF) encoding a protein of 278 amino acids with a deduced M_r of 30,188 Da. However, the MCL-PHA depolymerase gene (phaZ_PalM4-7) of P. alcaligenes M4-7 was composed of an 834 bp ORF encoding a protein of 277 amino acids with a deduced M_r of 30,323 Da. Amino acid sequence analyses showed that, in the two different polypeptides, a substrate-binding domain and a catalytic domain are located in the N-terminus and in the C-terminus, respectively. The PhaZ_PalLB19 and the PhaZ_PalM4-7 commonly share the lipase box, GISSG, in their catalytic domains, and utilize ^111Asn and ^110Ser residues, respectively, as oxyanions that play an important role in transition-state stabilization of hydrolytic reactions.

Purification and Characterization of Poly(3-hydroxybutyrate) Depolymerase from a Fungal Isolate, Emericellopsis minima W2: Do Young Kim , Ji Hye Yun , Hyung Woo Kim , Kyung Sook Bae , Young Ha Rhee; J. Microbiol. 2002;40(2):129-133.

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Abstract PDF: The fungus, Emericellopsis minima W2, capable of degrading poly(3-hydroxybutyrate) (PHB) was isolated from a waste water sample. Production of the PHB depolymerase from E. minima W2 (PhaZ_Emi ) was significantly repressed in the presence of glucose. PhaZ_Emi was purified by column chromatography on Octyl-Sepharose CL-4B and Sephadex G-100. The molecular mass of the PhaZ_Emi , which consisted of a single polypeptide chain, was estimated to be 48.0 kDa by SDS-PAGE and its pI value was 4.4. The maximum activity of the PhaZ_Emi was observed at pH 9.0 and 55 C. It was significantly inactivated by 1 mM dithiothreitol, 2 mM diisopropyl fluorophosphate, 0.1 mM Tween 80, and 0.1 mM Triton X-100, but insensitive to phenylmethylsulfonyl fluoride and N-ethylmaleimide. The PhaZ_Emi efficiently hydrolyzed PHB and its copolyester with 30 mol% 3-hydroxyvalerate, but did not act on poly(3-hydroxyoctanoate). It also hydrolyzed p-nitrophenylacetate and p-nitrophenylbutyrate but hardly affected the longer-chain forms. The main hydrolysis product of PHB was identified as a dimer of 3-hydroxybutyrate.

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