Journal of Microbiology

Jungho Kim

3 Articles

Structural analysis of N-/O-glycans assembled on proteins in yeasts: Eun Jung Thak , Jungho Kim , Dong-Jik Lee , Jeong Yoon Kim , Hyun Ah Kang; J. Microbiol. 2018;56(1):11-23. Published online January 4, 2018; DOI: https://doi.org/10.1007/s12275-018-7468-x

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Protein glycosylation, the most universal and diverse posttranslational modification, can affect protein secretion, stability, and immunogenicity. The structures of glycans attached to proteins are quite diverse among different organisms and even within yeast species. In yeast, protein glycosylation plays key roles in the quality control of secretory proteins, and particularly in maintaining cell wall integrity. Moreover, in pathogenic yeasts, glycans assembled on cell-surface glycoproteins can mediate their interactions with host cells. Thus, a comprehensive understanding of protein glycosylation in various yeast species and defining glycan structure characteristics can provide useful information for their biotechnological and clinical implications. Yeast-specific glycans are a target for glyco-engineering; implementing human-type glycosylation pathways in yeast can aid the production of recombinant glycoproteins with therapeutic potential. The virulenceassociated glycans of pathogenic yeasts could be exploited as novel targets for antifungal agents. Nowadays, several glycomics techniques facilitate the generation of species- and strain-specific glycome profiles and the delineation of modified glycan structures in mutant and engineered yeast cells. Here, we present the protocols employed in our laboratory to investigate the N- and O-glycan chains released from purified glycoproteins or cell wall mannoproteins in several yeast species.

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Phytopathology Research.2026;[Epub] CrossRef
Evolutionary unique N-glycan-dependent protein quality control system plays pivotal roles in cellular fitness and extracellular vesicle transport in Cryptococcus neoformans
Catia Mota, Kiseung Kim, Ye Ji Son, Eun Jung Thak, Su-Bin Lee, Ju-El Kim, Jeong-Kee Yoon, Min-Ho Kang, Heeyoun Hwang, Yong-Sun Bahn, J Andrew Alspaugh, Hyun Ah Kang
eLife.2025;[Epub] CrossRef
Integrative glycomic analysis reveals the crucial role of protein glycosylation in fungal pathogenesis
Heeji Moon, Eun Jung Thak, Yejin Choi, Sieun Kim, Jiyeun Park, Nahyun Lee, Soobin Shin, Hosung Jeon, Jessica Winarto, Soyoung Choi, Ji Young Shin, Jung-Eun Kim, Dae-Geun Song, Hun Kim, Gyung Ja Choi, Hyun Ah Kang, Hokyoung Son, Jin-Rong Xu
PLOS Pathogens.2025; 21(7): e1013325. CrossRef
Evolutionary unique N-glycan-dependent protein quality control system plays pivotal roles in cellular fitness and extracellular vesicle transport in Cryptococcus neoformans
Catia Mota, Kiseung Kim, Ye Ji Son, Eun Jung Thak, Su-Bin Lee, Ju-El Kim, Jeong-Kee Yoon, Min-Ho Kang, Heeyoun Hwang, Yong-Sun Bahn, J Andrew Alspaugh, Hyun Ah Kang
eLife.2025;[Epub] CrossRef
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Extension of O -Linked Mannosylation in the Golgi Apparatus Is Critical for Cell Wall Integrity Signaling and Interaction with Host Cells in Cryptococcus neoformans Pathogenesis
Eun Jung Thak, Ye Ji Son, Dong-Jik Lee, Hyunah Kim, Jung Ho Kim, Su-Bin Lee, Yu-Byeong Jang, Yong-Sun Bahn, Connie B. Nichols, J. Andrew Alspaugh, Hyun Ah Kang, Michael Lorenz
mBio.2022;[Epub] CrossRef
Metabolic labeling of glycans with isotopic glucose for quantitative glycomics in yeast
Ji-Yeon Kim, Woo Hong Joo, Dong-Soo Shin, Yong-Ill Lee, Chin Fen Teo, Jae-Min Lim
Analytical Biochemistry.2021; 621: 114152. CrossRef
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Jinkai Zang, Yuanfei Zhu, Yu Zhou, Chenjian Gu, Yufang Yi, Shuxia Wang, Shiqi Xu, Gaowei Hu, Shujuan Du, Yannan Yin, Yalei Wang, Yong Yang, Xueyang Zhang, Haikun Wang, Feifei Yin, Chao Zhang, Qiang Deng, Youhua Xie, Zhong Huang
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Özge Ata, Burcu Gündüz Ergün, Patrick Fickers, Lina Heistinger, Diethard Mattanovich, Corinna Rebnegger, Brigitte Gasser
FEMS Yeast Research.2021;[Epub] CrossRef
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Marta Calatayud, Rosa Aragao Börner, Jonas Ghyselinck, Lynn Verstrepen, Jelle De Medts, Pieter Van den Abbeele, Claire L. Boulangé, Sarah Priour, Massimo Marzorati, Sami Damak
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David J. Harvey
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Yeast synthetic biology for designed cell factories producing secretory recombinant proteins
Eun Jung Thak, Su Jin Yoo, Hye Yun Moon, Hyun Ah Kang
FEMS Yeast Research.2020;[Epub] CrossRef
Core N -Glycan Structures Are Critical for the Pathogenicity of Cryptococcus neoformans by Modulating Host Cell Death
Eun Jung Thak, Su-Bin Lee, Shengjie Xu-Vanpala, Dong-Jik Lee, Seung-Yeon Chung, Yong-Sun Bahn, Doo-Byoung Oh, Mari L. Shinohara, Hyun Ah Kang, J. Andrew Alspaugh
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Tohru Ikegami
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Impact of ∼omics in the detection and validation of potential anti-infective drugs
Nidia Maldonado-Carmona, Melissa Vázquez-Hernández, Osiris Jair Patiño Chávez, Stefany Daniela Rodríguez-Luna, Omar Jiménez Rodríguez, Sergio Sanchez, Corina Diana Ceapă
Current Opinion in Pharmacology.2019; 48: 1. CrossRef

Chitinibacter suncheonensis sp. nov., a Chitinolytic Bacterium from a Mud Flat in Suncheon Bay: Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Han Beur Na , Jungho Kim , Keun Sik Baik , Han Dae Yun , Jung-Kul Lee , Hoon Kim; J. Microbiol. 2012;50(6):1058-1062. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2333-9

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Abstract PDF

A chitinolytic bacterium, designated strain SK16T, was isolated from a mud flat in Suncheon Bay, Republic of Korea. Strain SK16T is Gram-negative, strictly aerobic, motile by a polar flagellum, and short rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter and was most closely related to Chitinibacter tainanensis S1T (98.2% similarity). DNA-DNA hybridization analyses showed a low association value of 20.45±4.08% between them. The major cellular fatty acids, the G+C content of the genomic DNA, and the predominant quinone of the strain were summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c; 50.5%) and C12:0 (12.5%), 52.26 mol%, and Q-8, respectively. Based on the phylogenetic, chemotaxonomic, and phenotypic properties, strain SK16T represents a novel species of the genus Chitinibacter, for which the name Chitinibacter suncheonensis sp. nov. is proposed. The type strain is SK16T (=KCTC 23839T =DSM 25421T).

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International Journal of Molecular Sciences.2021; 22(23): 12822. CrossRef
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The Role of Carbohydrate-Binding Module (CBM) Repeat of a Multimodular Xylanase (XynX) from Clostridium thermocellum in Cellulose and Xylan Binding: Thangaswamy Selvaraj , Sung Kyum Kim , Yong Ho Kim , Yu Seok Jeong , Yu-Jeong Kim , Nguyen Dinh Phuong , Kyung Hwa Jung , Jungho Kim , Han Dae Yun , Hoon Kim; J. Microbiol. 2010;48(6):856-861. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0285-5

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Abstract PDF

A non-cellulosomal xylanase from Clostridium thermocellum, XynX, consists of a family-22 carbohydratebinding module (CBM22), a family-10 glycoside hydrolase (GH10) catalytic module, two family-9 carbohydrate-binding modules (CBM9-I and CBM9-II), and an S-layer homology (SLH) module. E. coli BL21(DE3) (pKM29), a transformant carrying xynX', produced several truncated forms of the enzyme. Among them, three major active species were purified by SDS-PAGE, activity staining, gel-slicing, and diffusion from the gel. The truncated xylanases were different from each other only in their C-terminal regions. In addition to the CBM22 and GH10 catalytic modules, XynX1 had the CBM9-I and most of the CBM9-II, XynX2 had the CBM9-I and about 40% of the CBM9-II, and XynX3 had about 75% of the CBM9-I. The truncated xylanases showed higher binding capacities toward Avicel than those toward insoluble xylan. XynX1 showed a higher affinity toward Avicel (70.5%) than XynX2 (46.0%) and XynX3 (42.1%); however, there were no significant differences in the affinities toward insoluble xylan. It is suggested that the CBM9 repeat, especially CBM9-II, of XynX plays a role in xylan degradation in nature by strengthening cellulose binding rather than by enhancing xylan binding.

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Environmental Technology & Innovation.2026; 43: 105058. CrossRef
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Wenjing Lu, Biqing Zha, Jie Lyu, Chenxi LingHu, Jing Chen, Sisi Deng, Xiangling Zhang, Liang Li, Guoqing Wang
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Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes
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Biotechnology Advances.2024; 73: 108365. CrossRef
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Pedro R. V. Hamann, Eliane F. Noronha
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Journal of Environmental Sciences.2016; 43: 199. CrossRef
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Journal of Molecular Catalysis B: Enzymatic.2014; 107: 8. CrossRef
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FEMS Microbiology Reviews.2014; 38(3): 393. CrossRef
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Journal of Basic Microbiology.2013; 53(3): 231. CrossRef
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Molecular Biotechnology.2013; 54(1): 37. CrossRef
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Rui Cheng, Jinping Chen, Xiaohong Yu, Yang Wang, Shiming Wang, Jianfa Zhang
BMC Biotechnology.2013;[Epub] CrossRef
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Applied Biochemistry and Biotechnology.2012; 168(2): 375. CrossRef
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Journal of Biological Chemistry.2012; 287(42): 34946. CrossRef
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