Journal of Microbiology

Hyun Park

7 Articles

Structural and sequence comparisons of bacterial enoyl-CoA isomerase and enoyl-CoA hydratase: Jisub Hwang , Chang-Sook Jeong , Chang Woo Lee , Seung Chul Shin , Han-Woo Kim , Sung Gu Lee , Ui Joung Youn , Chang Sup Lee , Tae-Jin Oh , Hak Jun Kim , Hyun Park , Hyun Ho Park , Jun Hyuck Lee; J. Microbiol. 2020;58(7):606-613. Published online April 22, 2020; DOI: https://doi.org/10.1007/s12275-020-0089-1

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Crystal structures of enoyl-coenzyme A (CoA) isomerase from Bosea sp. PAMC 26642 (BoECI) and enoyl-CoA hydratase from Hymenobacter sp. PAMC 26628 (HyECH) were determined at 2.35 and 2.70 Å resolution, respectively. BoECI and HyECH are members of the crotonase superfamily and are enzymes known to be involved in fatty acid degradation. Structurally, these enzymes are highly similar except for the orientation of their C-terminal helix domain. Analytical ultracentrifugation was performed to determine the oligomerization states of BoECI and HyECH revealing they exist as trimers in solution. However, their putative ligand-binding sites and active site residue compositions are dissimilar. Comparative sequence and structural analysis revealed that the active site of BoECI had one glutamate residue (Glu135), this site is occupied by an aspartate in some ECIs, and the active sites of HyECH had two highly conserved glutamate residues (Glu118 and Glu138). Moreover, HyECH possesses a salt bridge interaction between Glu98 and Arg152 near the active site. This interaction may allow the catalytic Glu118 residue to have a specific conformation for the ECH enzyme reaction. This salt bridge interaction is highly conserved in known bacterial ECH structures and ECI enzymes do not have this type of interaction. Collectively, our comparative sequential and structural studies have provided useful information to distinguish and classify two similar bacterial crotonase superfamily enzymes.

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Genome-based characterization of a halotolerant strain, Planococcus antioxidans PAB314, with potential for PAH degradation
Mobina Bayatian, Ahmad Ali Pourbabaee, Mohammad Ali Amoozegar
World Journal of Microbiology and Biotechnology.2026;[Epub] CrossRef
Exploring the Antimicrobial Perspective of Citronella (Cymbopogon nardus) Oil Through GC/MS-based Compound Identification, Molecular Docking, and MD Simulation Insights
Pooja Sankaranarayanan, Aarya Sreedevi, J. Parvathy, Denoj Sebastian, Suchithra Tharamel Vasu
Journal of Computational Biophysics and Chemistry.2026; 25(11): 2711. CrossRef
Breaking aromaticity in the anaerobic degradation pathway of phenanthrene comprises only ATP-independent type III aryl-CoA reductases
Nadia A. Samak, Marvin Häßler, Oliver J. Schmitz, Khadija Adjir, Rainer U. Meckenstock
Communications Biology.2026;[Epub] CrossRef
ECHDC2 inhibits the proliferation of gastric cancer cells by binding with NEDD4 to degrade MCCC2 and reduce aerobic glycolysis
Jiancheng He, Jianfeng Yi, Li Ji, Lingchen Dai, Yu Chen, Wanjiang Xue
Molecular Medicine.2024;[Epub] CrossRef
Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite
Zhenhong Chen, Bo Song, Hongyu Guo, Dapin Xia, Yidong Cai, Yongjun Wang, Weizhong Zhao
Environmental Research.2023; 227: 115777. CrossRef
Crystal structure of multi-functional enzyme FadB from Cupriavidus necator: Non-formation of FadAB complex
Hyeoncheol Francis Son, Jae-Woo Ahn, Jiyeon Hong, Jihye Seok, Kyeong Sik Jin, Kyung-Jin Kim
Archives of Biochemistry and Biophysics.2022; 730: 109391. CrossRef
Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8
Sivaraman Padavattan, Sneha Jos, Hemanga Gogoi, Bagautdin Bagautdinov
Acta Crystallographica Section F Structural Biology Communications.2021; 77(5): 148. CrossRef

Crystal structure of the inactive state of the receiver domain of Spo0A from Paenisporosarcina sp. TG-14, a psychrophilic bacterium isolated from an Antarctic glacier: Chang Woo Lee , Sun-Ha Park , Sung Gu Lee , Seung Chul Shin , Se Jong Han , Han-Woo Kim , Hyun Ho Park , Sunghwan Kim , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2017;55(6):464-474. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6599-9

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The two-component phosphorelay system is the most pre-valent mechanism for sensing and transducing environ-mental signals in bacteria. Spore formation, which relies on the two-component phosphorelay system, enables the long- term survival of the glacial bacterium Paenisporosarcina sp. TG-14 in the extreme cold environment. Spo0A is a key re-sponse regulator of the phosphorelay system in the early stage of spore formation. The protein is composed of a regu-latory N-terminal phospho-receiver domain and a DNA- binding C-terminal activator domain. We solved the three- dimensional structure of the unphosphorylated (inactive) form of the receiver domain of Spo0A (PaSpo0A-R) from Paenisporosarcina sp. TG-14. A structural comparison with phosphorylated (active form) Spo0A from Bacillus stearo-thermophilus (BsSpo0A) showed minor notable differences. A molecular dynamics study of a model of the active form and the crystal structures revealed significant differences in the α4 helix and the preceding loop region where phosphorylation occurs. Although an oligomerization study of PaSpo0A-R by analytical ultracentrifugation (AUC) has shown that the protein is in a monomeric state in solution, both crosslinking and crystal-packing analyses indicate the possibility of weak dimer formation by a previously undocumented mechanism. Collectively, these observations provide insight into the me-chanism of phosphorylation-dependent activation unique to Spo0A.

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Identification of Functional Spo0A Residues Critical for Sporulation in Clostridioides difficile
Michael A. DiCandia, Adrianne N. Edwards, Joshua B. Jones, Grace L. Swaim, Brooke D. Mills, Shonna M. McBride
Journal of Molecular Biology.2022; 434(13): 167641. CrossRef

Crystal structure and modeling of the tetrahedral intermediate state of methylmalonate-semialdehyde dehydrogenase (MMSDH) from Oceanimonas doudoroffii: Hackwon Do , Chang Woo Lee , Sung Gu Lee , Hara Kang , Chul Min Park , Hak Jun Kim , Hyun Park , HaJeung Park , Jun Hyuck Lee; J. Microbiol. 2016;54(2):114-121. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-016-5549-2

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The gene product of dddC (Uniprot code G5CZI2), from the Gram-negative marine bacterium Oceanimonas doudoroffii, is a methylmalonate-semialdehyde dehydrogenase (OdoMMSDH) enzyme. MMSDH is a member of the aldehyde dehydrogenase superfamily, and it catalyzes the NADdependent decarboxylation of methylmalonate semialdehyde to propionyl-CoA. We determined the crystal structure of OdoMMSDH at 2.9 Å resolution. Among the twelve molecules in the asymmetric unit, six subunits complexed with NAD, which was carried along the protein purification steps. OdoMMSDH exists as a stable homodimer in solution; each subunit consists of three distinct domains: an NAD-binding domain, a catalytic domain, and an oligomerization domain. Computational modeling studies of the OdoMMSDH structure revealed key residues important for substrate recognition and tetrahedral intermediate stabilization. Two basic residues (Arg103 and Arg279) and six hydrophobic residues (Phe150, Met153, Val154, Trp157, Met281, and Phe449) were found to be important for tetrahedral intermediate binding. Modeling data also suggested that the backbone amide of Cys280 and the side chain amine of Asn149 function as the oxyanion hole during the enzymatic reaction. Our results provide useful insights into the substrate recognition site residues and catalytic mechanism of OdoMMSDH.

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Where do the electrons go? How numerous redox processes drive phytochemical diversity
Patrick J. Horn
Phytochemistry Reviews.2021; 20(2): 367. CrossRef
Crystal Structure of Aldehyde Dehydrogenase 16 Reveals Trans-Hierarchical Structural Similarity and a New Dimer
Li-Kai Liu, John J. Tanner
Journal of Molecular Biology.2019; 431(3): 524. CrossRef
Reconstructing the Electron Density of Intermediates of the Hydrolysis of N-Acetylaspartate by Aspartoacylase
M. G. Khrenova, E. D. Kots, A. M. Kulakova, A. V. Nemukhin
Russian Journal of Physical Chemistry A.2019; 93(10): 1873. CrossRef
NAD+ promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1
David A. Korasick, Tommi A. White, Srinivas Chakravarthy, John J. Tanner
FEBS Letters.2018; 592(19): 3229. CrossRef
Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde
Lourdes Gómez-Gómez, Luis F. Pacios, Araceli Diaz-Perales, María Garrido-Arandia, Javier Argandoña, Ángela Rubio-Moraga, Oussama Ahrazem
International Journal of Molecular Sciences.2018; 19(5): 1409. CrossRef
X-ray crystal structure of a malonate-semialdehyde dehydrogenase fromPseudomonassp. strain AAC
Matthew Wilding, Colin Scott, Thomas S. Peat, Janet Newman
Acta Crystallographica Section F Structural Biology Communications.2017; 73(1): 24. CrossRef

Morphological and Genetic Characteristics of Newly Crossbred Cauliflower Mushroom (Sparassis latifolia): Hong-Duck Sou , Rhim Ryoo , Sung-Ryul Ryu , Kang-Hyeon Ka , Hyun Park , Sung-Hyun Joo; J. Microbiol. 2013;51(5):552-557. Published online June 25, 2013; DOI: https://doi.org/10.1007/s12275-013-2666-z

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Cauliflower mushroom (Sparassis latifolia or S. crispa) is popular for food and medicine. Importance of new varieties of Sparassis was raised and studied widely by protection system of UPOV. In this study, 10 crossbred strains of Sparassis latifolia that specifically expressed distinctive features during basidiocarp formation and mycelium growth were applied to sawdust medium inoculated with S. latifolia mycelia. The 10 crossbred strains were divided into 3 groups on the basis of morphological (size of marginal wave and basidiocarp color) and genetic characteristics. Each phenotype of the parent and crossbred strains represented 3 marginal wave-sizes (large, medium, and small) and 3 color notations (NN155D, 163C, and 8D). Our result suggests that morphological characteristics of cauliflower mushroom can be affected by various environmental and genetic stimuli under artificial conditions such as crossbreed. Also this research showed genetic differences among breeding isolates and their morphological characteristics were correlated with the molecular data within parent and crossed strain.

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Agrobacterium-Mediated Genetic Transformation of the Edible and Medicinal Cauliflower Mushroom Sparassis latifolia
Wen Cao, Xinyu Zhou, Ruiheng Yang, Yingying Wu, Yan Li, Chenli Zhou, Jianing Wan, Rongping Li, Xiangying Luo, Zhenhui Shen, Dapeng Bao, Lihua Tang, Junjun Shang
Journal of Fungi.2026; 12(4): 255. CrossRef
First successful cultivation of wild strains of Irpex rosettiformis from the Brazilian Atlantic Rainforest
Mariana de Paula Drewinski, Diego Cunha Zied, Nelson Menolli
Mycological Progress.2025;[Epub] CrossRef
Neuroprotective Effects of Sparassis crispa Ethanol Extract through the AKT/NRF2 and ERK/CREB Pathway in Mouse Hippocampal Cells
Malk Eun Pak, Wei Li
Journal of Fungi.2023; 9(9): 910. CrossRef
Breeding of a high-yield strain for commercial cultivation by crossing Pholiota adiposa
Chengbo Rong, Shuang Song, Li Yang, Xuejiao Pan, Yu Liu, Shouxian Wang
Ciência e Agrotecnologia.2021;[Epub] CrossRef
Elicitor-induced β-glucan contents in fruit body of cauliflower mushroom (Sparassis latifolia)
Rhim Ryoo, Hong-Duck Sou, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2018; 14(3): 119. CrossRef
Development of a highly productive strain of Pleurotus tuoliensis for commercial cultivation by crossbreeding
Shouxian Wang, Shuang Zhao, Zhenxing Huang, Limin Yin, Jie Hu, Jianghong Li, Yu Liu, Chengbo Rong
Scientia Horticulturae.2018; 234: 110. CrossRef
Effects of Sparassis crispa in Medical Therapeutics: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Le Thi Nhu Ngoc, You-Kwan Oh, Young-Jong Lee, Young-Chul Lee
International Journal of Molecular Sciences.2018; 19(5): 1487. CrossRef
The mycelial growth and ligninolytic enzyme activity of cauliflower mushroom ( Sparassis latifolia )
Hong-Duck Sou, Rhim Ryoo, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2017; 13(4): 158. CrossRef

Phylogenetic Relationships of Korean Sparassis latifolia Based on Morphological and ITS rDNA Characteristics: Rhim Ryoo , Hong-Duck Sou , Kang-Hyeon Ka , Hyun Park; J. Microbiol. 2013;51(1):43-48. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2503-4

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Recent studies based on morphological characteristics and molecular analyses have revealed that the characteristics of Sparassis crispa from Asia are not concordant with those of collections from Europe and North America. Consequently, the Asian isolate was redefined as Sparassis latifolia. This study is the first report of Sparassis latifolia collected in Korea. The taxonomic relationships and replacement of Sparassis species were inferred from a comparison of the morphological characteristics and by molecular sequence analysis of the internal transcribed spacer (ITS) rDNA regions. In particular, this study focused on the phylogenetic relationships inferred from the biogeographical distribution of isolates within the genus Sparassis.

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Cauliflower mushroom ( Sparassis ): a promising functional food with nutritional and medicinal properties
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Critical Reviews in Food Science and Nutrition.2026; 66(2): 352. CrossRef
Agrobacterium-Mediated Genetic Transformation of the Edible and Medicinal Cauliflower Mushroom Sparassis latifolia
Wen Cao, Xinyu Zhou, Ruiheng Yang, Yingying Wu, Yan Li, Chenli Zhou, Jianing Wan, Rongping Li, Xiangying Luo, Zhenhui Shen, Dapeng Bao, Lihua Tang, Junjun Shang
Journal of Fungi.2026; 12(4): 255. CrossRef
Extracts from the Edible Mushroom Sparassis crispa: Nematicidal, Antimicrobial, and Antiviral Properties Supporting Its Functional Food Potential
Marta Ziaja-Sołtys, Barbara Rajtar, Łukasz Świątek, Anna Biernasiuk, Katarzyna Dos Santos Szewczyk, Sebastian Granica, Andrzej Parzonko, Daniel Zalewski, Łucja Smolarska, Sebastian Skowron, Anna Bogucka-Kocka
Foods.2026; 15(9): 1559. CrossRef
A Comprehensive Review of Bioactive Constituents, Health-Promoting Effects, Processing Technologies, and Industrial Applications of Sparassis crispa Sensu Lato
Xin Chen, Yunzhe Guo, Xiaotong Dong, Yujin Cao, Min Xie, Yibin Li, Li Wu
Foods.2026; 15(12): 2152. CrossRef
ПОШИРЕННЯ ТА ОХОРОНА В УКРАЇНІ РІДКІСНОГО ВИДУ ГРИБА SPARASSIS BREVIPES KROMBH.
А. С. Усіченко
Вісті Біосферного заповідника «Асканія-Нова».2026; (28): 5. CrossRef
Molecular insights into two wild edible mushrooms from Jammu and Kashmir, India
Ayushi Mahajan, Sandhya Rajput, Komal Verma, Yash Pal Sharma
Indian Phytopathology.2025; 78(3): 689. CrossRef
Medicinal, nutritional, and nutraceutical potential of Sparassis crispa s. lat.: a review
Neha Sharma, Ashwani Tapwal, Rachna Verma, Dinesh Kumar, Eugenie Nepovimova, Kamil Kuca
IMA Fungus.2022;[Epub] CrossRef
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia
Lili Shu, Miaoyue Wang, Hui Xu, Zhiheng Qiu, Tianlai Li
Scientific Reports.2022;[Epub] CrossRef
Promising Potential of Crude Polysaccharides from Sparassis crispa against Colon Cancer: An In Vitro Study
Natalia Nowacka-Jechalke, Renata Nowak, Marta Kinga Lemieszek, Wojciech Rzeski, Urszula Gawlik-Dziki, Nikola Szpakowska, Zbigniew Kaczyński
Nutrients.2021; 13(1): 161. CrossRef
Alginate-Derived Elicitors Enhance β-Glucan Content and Antioxidant Activities in Culinary and Medicinal Mushroom, Sparassis latifolia
Yong-Woon Kim, Yuanzheng Wu, Moon-Hee Choi, Hyun-Jae Shin, Jishun Li
Journal of Fungi.2020; 6(2): 92. CrossRef
The complete mitochondrial genome of an edible mushroom, Sparassis crispa
Khawaja Muhammad Imran Bashir, Kyoung Min Rheu, Moo-Sang Kim, Man-Gi Cho
Mitochondrial DNA Part B.2020; 5(1): 862. CrossRef
Sparassis crispa exerts anti-inflammatory activity via suppression of TLR-mediated NF-κB and MAPK signaling pathways in LPS-induced RAW264.7 macrophage cells
Jang Mi Han, Eun Kyeong Lee, So Youn Gong, Jae Kyung Sohng, Yue Jai Kang, Hye Jin Jung
Journal of Ethnopharmacology.2019; 231: 10. CrossRef
Notes, outline and divergence times of Basidiomycota
Mao-Qiang He, Rui-Lin Zhao, Kevin D. Hyde, Dominik Begerow, Martin Kemler, Andrey Yurkov, Eric H. C. McKenzie, Olivier Raspé, Makoto Kakishima, Santiago Sánchez-Ramírez, Else C. Vellinga, Roy Halling, Viktor Papp, Ivan V. Zmitrovich, Bart Buyck, Damien Er
Fungal Diversity.2019; 99(1): 105. CrossRef
Elicitor-induced β-glucan contents in fruit body of cauliflower mushroom (Sparassis latifolia)
Rhim Ryoo, Hong-Duck Sou, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2018; 14(3): 119. CrossRef
Sequence Analysis and Expression of a Blue-light Photoreceptor Gene, Slwc-1 from the Cauliflower Mushroom Sparassis latifolia
Chi Yang, Lu Ma, Zhenghe Ying, Xiaoling Jiang, Yanquan Lin
Current Microbiology.2017; 74(4): 469. CrossRef
The mycelial growth and ligninolytic enzyme activity of cauliflower mushroom ( Sparassis latifolia )
Hong-Duck Sou, Rhim Ryoo, Kang-Hyeon Ka, Hyun Park
Forest Science and Technology.2017; 13(4): 158. CrossRef
First Report of Sparassis latifolia Causing Basal Rot of Pinus koraiensis in China
L. L. Shu, Y. Li
Plant Disease.2017; 101(5): 833. CrossRef
Nematicidal effect of Sparassis latifolia-derived sparassol and disodium sparassol against Bursaphelenchus xylophilus
Sun Keun Lee, Kyoung-Tae Lee, Yong Bae Park, Ga-Heon Jin, Kang-Hyeon Ka, Sang-Tae Seo
Journal of Asia-Pacific Entomology.2016; 19(1): 81. CrossRef
Transatlantic disjunction in fleshy fungi. II. The Sparassis spathulata – S. brevipes complex
Ronald H. Petersen, Jan Borovička, Ana Reboredo Segovia, Karen W. Hughes
Mycological Progress.2015;[Epub] CrossRef
The Quantities of Methyl Orsellinate and Sparassol of Sparassis latifolia by Host Plants
Min-Soo Kim, Kyoung-Tae Lee, Sung-Min Jeon, Kang-Hyeon Ka
The Korean Journal of Mycology.2013; 41(4): 236. CrossRef
Morphological and genetic characteristics of newly crossbred cauliflower mushroom (Sparassis latifolia)
Hong-Duck Sou, Rhim Ryoo, Sung-Ryul Ryu, Kang-Hyeon Ka, Hyun Park, Sung-Hyun Joo
Journal of Microbiology.2013; 51(5): 552. CrossRef

Effects of Nutritional Input and Diesel Contamination on Soil Enzyme Activities and Microbial Communities in Antarctic Soils: Jiwon Han , Jaejoon Jung , Seunghun Hyun , Hyun Park , Woojun Park; J. Microbiol. 2012;50(6):916-924. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2636-x

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Pollution of Antarctic soils may be attributable to increased nutritional input and diesel contamination via anthropogenic activities. To investigate the effect of these environmental changes on the Antarctic terrestrial ecosystem, soil enzyme activities and microbial communities in 3 types of Antarctic soils were evaluated. The activities of alkaline phosphomonoesterase and dehydrogenase were dramatically increased, whereas the activities of β-glucosidase, urease, arylsulfatase, and fluorescein diacetate hydrolysis were negligible. Alkaline phosphomonoesterase and dehydrogenase activities in the 3 types of soils increased 3- to 10-fold in response to nutritional input, but did not increase in the presence of diesel contamination. Consistent with the enzymatic activity data, increased copy numbers of the phoA gene, encoding an alkaline phosphomonoesterase, and the 16S rRNA gene were verified using quantitative real-time polymerase chain reaction. Interestingly, dehydrogenase activity and 16S rRNA gene copy number increased slightly after 30 days, even under diesel contamination, probably because of adaptation of the bacterial population. Intact Antarctic soils showed a predominance of Actinobacteria phylum (mostly Pseudonorcarida species) and other phyla such as Proteobacteria, Chloroflexi, Planctomycetes, Firmicutes, and Verrucomicrobia were present in successively lower proportions. Nutrient addition might act as a selective pressure on the bacterial community, resulting in the prevalence of Actinobacteria phylum (mostly Arthrobacter species). Soils contaminated by diesel showed a predominance of Proteobacteria phylum (mostly Phyllobacterium species), and other phyla such as Actinobacteria, Bacteroidetes, Planctomycetes, and Gemmatimonadetes were present in successively lower proportions. Our data reveal that nutritional input has a dramatic impact on bacterial communities in Antarctic soils and that diesel contamination is likely toxic to enzymes in this population.

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Pseudarthrobacter psychrotolerans sp. nov., a cold-adapted bacterium isolated from Antarctic soil
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Synergistic Effects of the Combination of Galangin with Gentamicin against Methicillin-Resistant Staphylococcus aureus: Young-Seob Lee , Ok-Hwa Kang , Jang-Gi Choi , You-Chang Oh , Hee-Sung Chae , Jong Hak Kim , Hyun Park , Dong Hwan Sohn , Zheng-Tao Wang , Dong-Yeul Kwon; J. Microbiol. 2008;46(3):283-288. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-008-0012-7

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The antimicrobial killing activity toward methicillin-resistant Staphylococcus aureus (MRSA) has been a serious emerging global issue. New effective antimicrobials and/or new approaches to settle this issue are urgently needed. The oriental herb, Alpinia officinarum, has been used in Korea for several hundreds of years to treat various infectious diseases. As it is well known, one of the active constituents of Alpinia officinarum is galangin. Against the 17 strains, the minimum inhibitory concentrations (MICs) of galangin (GAL) were in the range of 62.5~125 μg/ml, and the MICs of gentamicin (GEN) ranged from 1.9 μg/ml to 2,000 μg/ml. The fractional inhibitory concentrations (FICs) of GAL, in combination with GEN, against 3 test strains were 0.4, 3.9, and 250 μg/ml, and were all 15.62 μg/ml in GEN. The FIC index showed marked synergism in the value range of 0.19 to 0.25. By determining time-kill curves, also confirmed the low synergism of the GAL and GEN combination against 4 h, 8 h, 12 h, and 24 h cultured MRSA. The time-kill study results indicated a low synergistic effect against 3 test strains. Thus, the mixture of GAL and GEN could lead to the development of new combination antibiotics against MRSA infection.

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