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Han DM, Baek JH, Choi DG, Jeon MS, Eyun SI, Jeon CO. Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity. Food Microbiol 2024; 119:104435. [PMID: 38225047 DOI: 10.1016/j.fm.2023.104435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 01/17/2024]
Abstract
Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.
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Affiliation(s)
- Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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Lee H, Nam J, Jang H, Park YS, Son MH, Lee IH, Eyun SI, Yang JH, Jeon J, Yang S. BRD2-specific inhibitor, BBC0403, inhibits the progression of osteoarthritis pathogenesis in osteoarthritis-induced C57BL/6 male mice. Br J Pharmacol 2024. [PMID: 38600628 DOI: 10.1111/bph.16359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND AND PURPOSE The discovery of new bromo- and extra-terminal inhibitors presents new drugs to treat osteoarthritis (OA). EXPERIMENTAL APPROACH The new drug, BBC0403, was identified in the DNA-encoded library screening system by searching for compounds that target BRD (bromodomain-containing) proteins. The binding force with BRD proteins was evaluated using time-resolved fluorescence energy transfer (TR-FRET) and binding kinetics assays. Subsequently, in vitro and ex vivo analyses demonstrated the effects of the BRD2 inhibitor, BBC0403, on OA. For animal experiments, medial meniscus destabilization was performed to create a 12-week-old male C57BL/6 mouse model, and intra-articular (i.a.) injections were administered. Histological and immunohistochemical analyses were then performed. The underlying mechanism was confirmed by gene set enrichment analysis (GSEA) using RNA-seq. KEY RESULTS TR-FRET and binding kinetics assays revealed that BBC0403 exhibited higher binding specificity for BRD2 compared to BRD3 and BRD4. The anti-OA effects of BBC0403 were tested at concentrations of 5, 10 and 20 μM (no cell toxicity in the range tested). The expression of catabolic factors, prostaglandin E2 (PGE2) production and extracellular matrix (ECM) degradation was reduced. Additionally, the i.a. injection of BBC0403 prevented OA cartilage degradation in mice. Finally, BBC0403 was demonstrated to suppress NF-κB and MAPK signalling pathways. CONCLUSION AND IMPLICATIONS This study demonstrated that BBC0403 is a novel BRD2-specific inhibitor and a potential i.a.-injectable therapeutic agent to treat OA.
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Affiliation(s)
- Hyemi Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Jiho Nam
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Hahyeong Jang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | | | | | | | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute Harvard Medical School (HMS), Boston, Massachusetts, USA
| | - Jimin Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Siyoung Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
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Yun HJ, Li M, Guo D, Jeon SM, Park SH, Lim JS, Lee SB, Liu R, Du L, Kim SH, Shin TH, Eyun SI, Park YY, Lu Z, Lee JH. AMPK-HIF-1α signaling enhances glucose-derived de novo serine biosynthesis to promote glioblastoma growth. J Exp Clin Cancer Res 2023; 42:340. [PMID: 38098117 PMCID: PMC10722853 DOI: 10.1186/s13046-023-02927-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Cancer cells undergo cellular adaptation through metabolic reprogramming to sustain survival and rapid growth under various stress conditions. However, how brain tumors modulate their metabolic flexibility in the naturally serine/glycine (S/G)-deficient brain microenvironment remain unknown. METHODS We used a range of primary/stem-like and established glioblastoma (GBM) cell models in vitro and in vivo. To identify the regulatory mechanisms of S/G deprivation-induced metabolic flexibility, we employed high-throughput RNA-sequencing, transcriptomic analysis, metabolic flux analysis, metabolites analysis, chromatin immunoprecipitation (ChIP), luciferase reporter, nuclear fractionation, cycloheximide-chase, and glucose consumption. The clinical significances were analyzed in the genomic database (GSE4290) and in human GBM specimens. RESULTS The high-throughput RNA-sequencing and transcriptomic analysis demonstrate that the de novo serine synthesis pathway (SSP) and glycolysis are highly activated in GBM cells under S/G deprivation conditions. Mechanistically, S/G deprivation rapidly induces reactive oxygen species (ROS)-mediated AMP-activated protein kinase (AMPK) activation and AMPK-dependent hypoxia-inducible factor (HIF)-1α stabilization and transactivation. Activated HIF-1α in turn promotes the expression of SSP enzymes phosphoglycerate dehydrogenase (PHGDH), phosphoserine aminotransferase 1 (PSAT1), and phosphoserine phosphatase (PSPH). In addition, the HIF-1α-induced expression of glycolytic genes (GLUT1, GLUT3, HK2, and PFKFB2) promotes glucose uptake, glycolysis, and glycolytic flux to fuel SSP, leading to elevated de novo serine and glycine biosynthesis, NADPH/NADP+ ratio, and the proliferation and survival of GBM cells. Analyses of human GBM specimens reveal that the levels of overexpressed PHGDH, PSAT1, and PSPH are positively correlated with levels of AMPK T172 phosphorylation and HIF-1α expression and the poor prognosis of GBM patients. CONCLUSION Our findings reveal that metabolic stress-enhanced glucose-derived de novo serine biosynthesis is a critical metabolic feature of GBM cells, and highlight the potential to target SSP for treating human GBM.
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Affiliation(s)
- Hye Jin Yun
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Min Li
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Dong Guo
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - So Mi Jeon
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Su Hwan Park
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Je Sun Lim
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Su Bin Lee
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Rui Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, People's Republic of China
| | - Linyong Du
- Key Laboratory of Laboratory of Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, People's Republic of China
| | - Seok-Ho Kim
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea
| | - Tae Hwan Shin
- Department of Biomedical Sciences, Dong-A University, Busan, 49315, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Yun-Yong Park
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Zhimin Lu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.
| | - Jong-Ho Lee
- Department of Health Sciences, The Graduate School of Dong-A University, Busan, 49315, Republic of Korea.
- Department of Biomedical Sciences, Dong-A University, Busan, 49315, Republic of Korea.
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Lee H, Nam J, Jang H, Park YS, Son MH, Lee IH, Eyun SI, Jeon J, Yang S. Novel molecule BBC0901 inhibits BRD4 and acts as a catabolic regulator in the pathogenesis of osteoarthritis. Biomed Pharmacother 2023; 166:115426. [PMID: 37666177 DOI: 10.1016/j.biopha.2023.115426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023] Open
Abstract
Osteoarthritis (OA) is induced by matrix degradation and inflammation mediated by bromo-domain-containing protein 4 (BRD4)-dependent catabolic factors. BRD4 acts as both a transcriptional regulator and an epigenetic reader. BBC0901 was identified as an inhibitor of BRD4 using a DNA-encoded library screening system. We aimed to demonstrate the effects of BBC0901 on OA pathogenesis by in vitro, ex vivo, and in vivo analyses. BBC0901 inhibited the expression of catabolic factors that degrade cartilage without significantly affecting the viability of mouse articular chondrocytes. Additionally, ex vivo experiments under conditions mimicking OA showed that BBC0901 suppressed extracellular matrix degradation. RNA sequencing analysis of gene expression patterns showed that BBC0901 inhibited the expression of catabolic factors, such as matrix metalloproteinases (MMPs) and cyclooxygenase (COX)2, along with reactive oxygen species (ROS) production. Furthermore, intra-articular (IA) injection of BBC0901 into the knee joint blocked osteoarthritic cartilage destruction by inhibition of MMP3, MMP13, COX2, interleukin (IL)6, and ROS production, thereby obstructing the nuclear factor kappa-light-chain-enhancer of activated B cell and mitogen activated protein kinase signaling. In conclusion, BBC0901-mediated BRD4 inhibition prevented OA development by attenuating catabolic signaling and hence, can be considered a promising IA therapeutic for OA.
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Affiliation(s)
- Hyemi Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Jiho Nam
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Hahyeong Jang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Young-Sik Park
- Benobio Co., Ltd., Gyeonggi-do 13494, Republic of Korea.
| | - Min-Hee Son
- Benobio Co., Ltd., Gyeonggi-do 13494, Republic of Korea.
| | - In-Hyun Lee
- Benobio Co., Ltd., Gyeonggi-do 13494, Republic of Korea.
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
| | - Jimin Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Siyoung Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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Jeon J, Lee H, Jeon MS, Kim SJ, Choi C, Kim KW, Yang DJ, Lee S, Bae YS, Choi WI, Jung J, Eyun SI, Yang S. Blockade of Activin Receptor IIB Protects Arthritis Pathogenesis by Non-Amplification of Activin A-ACVR2B-NOX4 Axis Pathway. Adv Sci (Weinh) 2023; 10:e2205161. [PMID: 36950748 DOI: 10.1002/advs.202205161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/10/2023] [Indexed: 05/18/2023]
Abstract
Although activin receptor IIB (ACVR2B) is emerging as a novel pathogenic receptor, its ligand and assembled components (or assembly) are totally unknown in the context of osteoarthritis (OA) pathogenesis. The present results suggest that upregulation of ACVR2B and its assembly could affect osteoarthritic cartilage destruction. It is shown that the ACVR2B ligand, activin A, regulates catabolic factor expression through ACVR2B in OA development. Activin A Tg mice (Col2a1-Inhba) exhibit enhanced cartilage destruction, whereas heterozygous activin A KO mice (Inhba+/- ) show protection from cartilage destruction. In silico analysis suggests that the Activin A-ACVR2B axis is involved in Nox4-dependent ROS production. Activin A Tg:Nox4 KO (Col2a1-Inhba:Nox4-/- ) mice show inhibition of experimental OA pathogenesis. NOX4 directly binds to the C-terminal binding site on ACVR2B-ACVR1B and amplifies the pathogenic signal for cartilage destruction through SMAD2/3 signaling. Together, the findings reveal that the ACVR2B assembly, which comprises Activin A, ACVR2B, ACVR1B, Nox4, and AP-1-induced HIF-2α, accelerates OA development. Furthermore, it is shown that shRNA-mediated ACVR2B knockdown or trapping ligands of ACVR2B abrogate OA development by competitively disrupting the ACVR2B-Activin A interaction. These results suggest that the ACVR2B assembly is required to amplify osteoarthritic cartilage destruction and could be a potential therapeutic target in efforts to treat OA.
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Affiliation(s)
- Jimin Jeon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyemi Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Seok-Jung Kim
- Department of Orthopaedic Surgery, Uijeongbu St. Mary's Hospital, The Catholic University of Korea College of Medicine, Uijeongbu, 11765, Republic of Korea
| | - Cham Choi
- MicroCT Applications, 3rd floor, 11, Sumyeong-ro 1-gil, Gangseo-gu, Seoul, 07644, Republic of Korea
| | - Ki Woo Kim
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
- Department of Applied Biological Science, BK21 FOUR, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Dong Joo Yang
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
- Department of Applied Biological Science, BK21 FOUR, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong-Soo Bae
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Won Il Choi
- Center for Bio-Healthcare Materials, Bio-Convergence Materials R&D Division, Korea Institute of Ceramic Engineering and Technology, Cheongju, Chungbuk, 28160, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Siyoung Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
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Jeon MS, Jeong DM, Doh H, Kang HA, Jung H, Eyun SI. A practical comparison of the next-generation sequencing platform and assemblers using yeast genome. Life Sci Alliance 2023; 6:e202201744. [PMID: 36746534 PMCID: PMC9902641 DOI: 10.26508/lsa.202201744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/08/2023] Open
Abstract
Assembling fragmented whole-genomic information from the sequencing data is an inevitable process for further genome-wide research. However, it is intricate to select the appropriate assembly pipeline for unknown species because of the species-specific genomic properties. Therefore, our study focused on relatively more static proclivities of sequencing platforms and assembly algorithms than the fickle genome sequences. A total of 212 draft and polished de novo assemblies were constructed under the different sequencing platforms and assembly algorithms with the repetitive yeast genome. Our comprehensive data indicated that sequencing reads from Oxford Nanopore with R7.3 flow cells generated more continuous assemblies than those derived from the PacBio Sequel, although the homopolymer-based assembly errors and chimeric contigs exist. In addition, the comparison between two second-generation sequencing platforms showed that Illumina NovaSeq 6000 provides more accurate and continuous assembly in the second-generation-sequencing-first pipeline, but MGI DNBSEQ-T7 provides a cheap and accurate read in the polishing process. Furthermore, our insight into the relationship among the computational time, read length, and coverage depth provided clues to the optimal pipelines of yeast assembly.
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Affiliation(s)
- Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Da Min Jeong
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Huijeong Doh
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Hyungtaek Jung
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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Lee IG, Joo YH, Jeon H, Jeong R, Kim EH, Chung H, Eyun SI, Kim J, Seo YJ, Hong SH. Galectin-4 increases the ability of M2 macrophages to enhance antiviral CD4+ T-cell responses. J Leukoc Biol 2023; 113:71-83. [PMID: 36822160 DOI: 10.1093/jleuko/qiac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 01/12/2023] Open
Abstract
Galectin-4 (Gal-4) is a β-galactoside-binding protein belonging to the galectin family. Although Gal-4 is known to be involved in several physiologic processes of the gastrointestinal tract, its immunomodulatory roles remain unclear. In this study, we investigated whether Gal-4 influences the function of M1 and M2 macrophages. Gal-4 treatment drove more robust changes in the gene expression of M2 macrophages compared to M1 macrophages. Antiviral immune response-related genes were significantly upregulated in Gal-4-treated M2 macrophages. Gal-4 significantly enhanced the immunostimulatory activity of M2 macrophages upon Toll-like receptor 7 stimulation or infection with lymphocytic choriomeningitis virus (LCMV). Moreover, the antibody production against LCMV infection and the antiviral CD4+ T-cell responses, but not the antiviral CD8+ T-cell responses, were greatly increased by Gal-4-treated M2 macrophages in vivo. The present results indicate that Gal-4 enhances the ability of M2 macrophages to promote antiviral CD4+ T-cell responses. Thus, Gal-4 could be used to boost antiviral immune responses.
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Affiliation(s)
- In-Gu Lee
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Yong-Hyun Joo
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Hoyeon Jeon
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Raehyuk Jeong
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Eui Ho Kim
- Viral Immunology Laboratory, Institut Pasteur Korea, 16 Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam 13488, Republic of Korea
| | - Hyunwoo Chung
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jeongkyu Kim
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - So-Hee Hong
- Department of Microbiology, College of Medicine, Ewha Womans University, 25 Magokdong-ro 2-gil, Gangseo-gu, Seoul 07804, Republic of Korea
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Jeong DM, Kim HJ, Jeon MS, Yoo SJ, Moon HY, Jeon EJ, Jeon CO, Eyun SI, Kang HA. Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products. FEMS Yeast Res 2023; 23:6958799. [PMID: 36564017 DOI: 10.1093/femsyr/foac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang. Through gene inventory analysis based on the high-quality reference genome of S. fibuligera, new genes involved in cellulose degradation and volatile aroma biosynthesis and applicable to the production of novel valuable enzymes and chemicals can be discovered. The integrated genomic and transcriptomic analysis of Hyphopichia yeasts, which exhibit strong halotolerance, provides insights into the novel mechanisms of salt and osmo-stress tolerance for survival in fermentation environments with a low-water activity and high-concentration salts. In addition, Jang yeast isolates, such as D. hansenii, show probiotic potential for the industrial application of yeast species beyond fermentation starters to diverse human health sectors.
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Affiliation(s)
- Da Min Jeong
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyeon Jin Kim
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Min-Seung Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Eun-Joo Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Che Ok Jeon
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Seong-Il Eyun
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, Seoul 06974, South Korea
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Jeong DM, Yoo SJ, Jeon MS, Chun BH, Han DM, Jeon CO, Eyun SI, Seo YJ, Kang HA. Genomic features, aroma profiles, and probiotic potential of the Debaryomyces hansenii species complex strains isolated from Korean soybean fermented food. Food Microbiol 2022; 105:104011. [PMID: 35473972 DOI: 10.1016/j.fm.2022.104011] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
Fermented soybean products are gaining attention in the food industry owing to their nutritive value and health benefits. In this study, we performed genomic analysis and physiological characterization of two Debaryomyces spp. yeast isolates obtained from a Korean traditional fermented soy sauce "ganjang". Both Debaryomyces hansenii ganjang isolates KD2 and C11 showed halotolerance to concentrations of up to 15% NaCl and improved growth in the presence of salt. Ploidy and whole-genome sequencing analyses indicated that the KD2 genome is haploid, whereas the C11 genome is heterozygous diploid with two distinctive subgenomes. Interestingly, phylogenetic analysis using intron sequences indicated that the C11 strain was generated via hybridization between D. hansenii and D. tyrocola ancestor strains. The D. hansenii KD2 and D. hansenii-hybrid C11 produced various volatile flavor compounds associated with butter, caramel, cheese, and fruits, and showed high bioconversion activity from ferulic acid to 4-vinylguaiacol, a characteristic flavor compound of soybean products. Both KD2 and C11 exhibited viability in the presence of bile salts and at low pH and showed immunomodulatory activity to induce high levels of the anti-inflammatory cytokine IL-10. The safety of the yeast isolates was confirmed by analyzing virulence and acute oral toxicity. Together, the D. hansenii ganjang isolates possess physiological properties beneficial for improving the flavor and nutritional value of fermented products.
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Affiliation(s)
- Da Min Jeong
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Su Jin Yoo
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Byung Hee Chun
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Hyun Ah Kang
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea.
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10
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Lee J, Ryu M, Bae D, Kim HM, Eyun SI, Bae J, Lee K. Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:659-667. [PMID: 35731347 DOI: 10.1007/s12275-022-2235-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/17/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides capable of binding with high affinity and specificity to target molecules. Because of their durability and ease of synthesis, aptamers are used in a wide range of biomedical fields, including the diagnosis of diseases and targeted delivery of therapeutic agents. The aptamers were selected using a process called systematic evolution of ligands by exponential enrichment (SELEX), which has been improved for various research purposes since its development in 1990. In this protocol, we describe a modified SELEX method that rapidly produces high aptamer screening yields using two types of magnetic beads. Using this method, we isolated an aptamer that specifically binds to an antimicrobial peptide. We suggest that by conjugating a small therapeutic-specific aptamer to a gold nanoparticle-based delivery system, which enhances the stability and intracellular delivery of peptides, aptamers selected by our method can be used for the development of therapeutic agents utilizing small therapeutic peptides.
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Affiliation(s)
- Jaemin Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Minkyung Ryu
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Dayeong Bae
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Hong-Man Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.,NES biotechnology, Seoul, 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jeehyeon Bae
- NES biotechnology, Seoul, 06974, Republic of Korea. .,Department of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea. .,NES biotechnology, Seoul, 06974, Republic of Korea.
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11
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Kim SL, Choi H, Eyun SI, Kim D, Yu OH. A New Branchipolynoe (Aphroditiformia: Polynoidae) Scale Worm from the Onnuri Deep-sea Hydrothermal Vent Field, Northern Central Indian Ridge. Zool Stud 2022; 61:e21. [PMID: 36330019 PMCID: PMC9537048 DOI: 10.6620/zs.2022.61-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Abstract
Deep-sea hydrothermal vents are dynamic environments with exotic fauna, including bathymodiolin mussels and scale worm annelids that are often in close association. In this study, we found a new species of Branchipolynoe (Aphroditiformia: Polynoidae) living in the recently discovered mussel Gigantidas vrijenhoeki in deep-sea hydrothermal vents and methane seeps at 2,014-2,023 m depth. Based on the morphology and full mitochondrial genome sequences of specimens of Branchipolynoe from the Onnuri vent field (OVF) on the northern Central Indian Ridge, we describe them as a new species: Branchipolynoe onnuriensis sp. nov. This species resembles B. longqiensis and B. tjiasmantoi, but can be distinguished from these species by the shape of the notopodial acicular lobe and the tips of the subacicular neurochaetae. This identity is well-supported by genetic distance and phylogenetic analyses based on the mitochondrial c oxidase subunit I (COI) gene, with the new species being closest to the Western Pacific species B. tjiasmantoi. Phylogenetic analyses support close relationships between the Indian Ocean and Western Pacific hydrothermal polychaetes. Our data provide a foundation for exploring the evolutionary relationship between scale worms and bathymodiolin mussels.
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Affiliation(s)
- Sang Lyeol Kim
- Marine Ecosystem and Biological Research Centre, Korea Institute of Ocean Science and Technology, Busan 49111, Korea. E-mail: (Yu); (SL Kim); (Choi); (Eyun); (D Kim)
- Korea Maritime University, Busan 49111, Korea
| | - Hyeongwoo Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Dongsung Kim
- Marine Ecosystem and Biological Research Centre, Korea Institute of Ocean Science and Technology, Busan 49111, Korea. E-mail: (Yu); (SL Kim); (Choi); (Eyun); (D Kim)
- Korea Maritime University, Busan 49111, Korea
| | - Ok Hwan Yu
- Marine Ecosystem and Biological Research Centre, Korea Institute of Ocean Science and Technology, Busan 49111, Korea. E-mail: (Yu); (SL Kim); (Choi); (Eyun); (D Kim)
- Korea Maritime University, Busan 49111, Korea
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12
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Lee HM, Ren J, Yu MS, Kim H, Kim WY, Shen J, Yoo SM, Eyun SI, Na D. Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production. Biotechnol Biofuels 2021; 14:228. [PMID: 34863247 PMCID: PMC8645107 DOI: 10.1186/s13068-021-02077-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/16/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform because of its relatively fast growth. However, the lack of genetic engineering tools hampers its wide use in the bioindustry. RESULTS Through three different approaches, we constructed a tunable promoter library comprising 33 promoters that can be used for the metabolic engineering of Methylomonas sp. DH-1. The library had an expression level of 0.24-410% when compared with the strength of the lac promoter. For practical application of the promoter library, we fine-tuned the expressions of cadA and cadB genes, required for cadaverine synthesis and export, respectively. The strain with PrpmB-cadA and PDnaA-cadB produced the highest cadaverine titre (18.12 ± 1.06 mg/L) in Methylomonas sp. DH-1, which was up to 2.8-fold higher than that obtained from a non-optimized strain. In addition, cell growth and lysine (a precursor of cadaverine) production assays suggested that gene expression optimization through transcription tuning can afford a balance between the growth and precursor supply. CONCLUSIONS The tunable promoter library provides standard and tunable components for gene expression, thereby facilitating the use of methanotrophs, specifically Methylomonas sp. DH-1, as a sustainable cell factory.
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Affiliation(s)
- Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Hyunjoo Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Woo Young Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea.
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13
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Yoon JH, Jeon MS, Eyun SI, Seok YJ. Evidence for reciprocal evolution of the global repressor Mlc and its cognate phosphotransferase system sugar transporter. Environ Microbiol 2021; 24:122-136. [PMID: 34708498 DOI: 10.1111/1462-2920.15803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/28/2021] [Accepted: 10/02/2021] [Indexed: 11/27/2022]
Abstract
Because the bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) is involved in the regulation of various physiological processes in addition to carbohydrate transport, its expression is precisely regulated in response to the availability of PTS sugars. The PTS consists of enzyme I and histidine phosphocarrier protein, and several sugar-specific enzymes II. In Escherichia coli, genes for enzymes II specific for glucose and related sugars are co-regulated by the global repressor Mlc, and glucose induction of the Mlc regulon genes is achieved by its interaction with glucose-specific enzyme II (EIIGlc ). In this study, we revealed that, in Vibrio species, which are phylogenetically older than Enterobacteriaceae, the membrane sequestration of Mlc and thereby the induction of its regulon genes is mediated by N-acetylglucosamine (NAG)-specific EII. While Vibrio Mlc interacts only with the EIIB domain of EIINag , E. coli Mlc interacts with the EIIB domain of both EIIGlc and EIINag . The present data suggest that EIINag may be the primordial regulator of Mlc, and EIIGlc has evolved to interact with Mlc since an EIIA domain was fused to EIINag in Enterobacteriaceae. Our findings provide insight into the coevolutionary dynamics between a transcription factor and its cognate regulator according to long-term resource availability in the bacterial natural habitat.
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Affiliation(s)
- Ji-Hee Yoon
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul, South Korea.,School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
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14
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Tran KM, Lee HM, Thai TD, Shen J, Eyun SI, Na D. Synthetically engineered microbial scavengers for enhanced bioremediation. J Hazard Mater 2021; 419:126516. [PMID: 34218189 DOI: 10.1016/j.jhazmat.2021.126516] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.
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Affiliation(s)
- Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Thi Duc Thai
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, Republic of Korea.
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15
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Kang MH, Eyun SI, Park YY. Estrogen-related receptor-gamma influences Helicobacter pylori infection by regulating TFF1 in gastric cancer. Biochem Biophys Res Commun 2021; 563:15-22. [PMID: 34058470 DOI: 10.1016/j.bbrc.2021.05.076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 05/19/2021] [Indexed: 12/23/2022]
Abstract
Helicobacter pylori infection is a crucial factor in the development of gastric cancer (GC). Molecular therapeutic targets and mechanisms contributing to H. pylori infection-associated GC induction are poorly understood and this study aimed to fill that research gap. We found that the nuclear receptor estrogen-related receptor gamma (ESRRG) is a candidate factor influencing H. pylori infection-driven GC. ESRRG suppressed H. pylori infection and cell growth induced by H. pylori infection in GC cells and organoid models In addition, H. pylori infection downregulates ESRRG expression. Gene expression profiling revealed that trefoil factor 1 (TFF1), a well-known tumor suppressor in GC, is a downstream target of ESRRG. Mechanistically, ESRRG directly binds to the TFF1 promoter and induces TFF1 gene expression. Furthermore, TFF1 activation by ESRRG was inhibited by nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB)/p65, which is induced by inflammation, such as by H. pylori infection. Our current study provides new molecular insights into how ESRRG regulates H. pylori infection, contributing to GC development. We suggest that modulation of ESRRG-suppressing H. pylori infection could be a therapeutic target for the treatment of GC patients.
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Affiliation(s)
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Yun-Yong Park
- Department of Life Science, Chung-Ang University, Seoul, South Korea.
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16
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Seo YL, Jung J, Song CU, Kwon YM, Jung HS, Eyun SI, Jeon CO. Nonlabens ponticola sp. nov., isolated from seawater and reclassification of Nonlabens sediminis as a later heterotypic synonym of Nonlabens tegetincola. Int J Syst Evol Microbiol 2020; 71. [PMID: 33332255 DOI: 10.1099/ijsem.0.004603] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, orange-pigmented and strictly aerobic bacterium, designated strain MJ115T, was isolated from seawater in Pohang, South Korea. Cells were non-motile rods and showed positive reactions for catalase and oxidase tests. Growth of strain MJ115T was observed at 4-35 °C (optimum, 30 °C), pH 6.0-7.0 (optimum, pH 6.5) and in the presence of 0-8.0 % (w/v) NaCl (optimum, 2.0%). Strain MJ115T contained iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 1 ω9c, C17 : 0 2-OH, iso-C16 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) as major cellular fatty acids and menaquinone-6 as the major respiratory quinone. Phosphatidylethanolamine, two unidentified aminolipids and four unidentified lipids were detected as major polar lipids. The G+C content of the genomic DNA was 40.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ115T formed a phyletic lineage with Nonlabens marinus S1-08T, Nonlabens agnitus JC2678T and Nonlabens antarcticus AKS 622T within the genus Nonlabens. Strain MJ115T was also most closely related to N. marinus S1-08T, N. agnitus JC2678T and N. antarcticus AKS 622T with 96.5, 96.4 and 96.0 % 16S rRNA sequence similarities, respectively. Here it is proposed that strain MJ115T represents a new species of the genus Nonlabens, for which the name Nonlabens ponticola sp. nov. is proposed. The type strain is MJ115T (=KCTC 72237T=NBRC 113963T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that Nonlabens tegetincola and Nonlabens sediminis belong to the same species. Therefore, it is proposed that N. sediminis is reclassified as a later heterotypic synonym of N. tegetincola.
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Affiliation(s)
- Ye Lin Seo
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Chi-Une Song
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Yong Min Kwon
- National Biodiversity Institute of Korea, Seocheon, Chungcheongnam-do 33662, Republic of Korea
| | - Hye Su Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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17
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Jeon J, Noh HJ, Lee H, Park HH, Ha YJ, Park SH, Lee H, Kim SJ, Kang HC, Eyun SI, Yang S, Kim YS. TRIM24-RIP3 axis perturbation accelerates osteoarthritis pathogenesis. Ann Rheum Dis 2020; 79:1635-1643. [PMID: 32895234 PMCID: PMC7677493 DOI: 10.1136/annrheumdis-2020-217904] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVES Recently, necroptosis has attracted increasing attention in arthritis research; however, it remains unclear whether its regulation is involved in osteoarthritis (OA) pathogenesis. Since receptor-interacting protein kinase-3 (RIP3) plays a pivotal role in necroptosis and its dysregulation is involved in various pathological processes, we investigated the role of the RIP3 axis in OA pathogenesis. METHODS Experimental OA was induced in wild-type or Rip3 knockout mice by surgery to destabilise the medial meniscus (DMM) or the intra-articular injection of adenovirus carrying a target gene (Ad-Rip3 and Ad-Trim24 shRNA). RIP3 expression was examined in OA cartilage from human patients; Trim24, a negative regulator of RIP3, was identified by microarray and in silico analysis. Connectivity map (CMap) and in silico binding approaches were used to identify RIP3 inhibitors and to examine their direct regulation of RIP3 activation in OA pathogenesis. RESULTS RIP3 expression was markedly higher in damaged cartilage from patients with OA than in undamaged cartilage. In the mouse model, adenoviral RIP3 overexpression accelerated cartilage disruption, whereas Rip3 depletion reduced DMM-induced OA pathogenesis. Additionally, TRIM24 knockdown upregulated RIP3 expression; its downregulation promoted OA pathogenesis in knee joint tissues. The CMap approach and in silico binding assay identified AZ-628 as a potent RIP3 inhibitor and demonstrated that it abolished RIP3-mediated OA pathogenesis by inhibiting RIP3 kinase activity. CONCLUSIONS TRIM24-RIP3 axis perturbation promotes OA chronicity by activating RIP3 kinase, suggesting that the therapeutic manipulation of this pathway could provide new avenues for treating OA.
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Affiliation(s)
- Jimin Jeon
- Department of Pharmacology, Ajou University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea.,Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,CIRNO, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hyun-Jin Noh
- Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyemi Lee
- Department of Pharmacology, Ajou University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea.,Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,CIRNO, Sungkyunkwan University, Suwon, Republic of Korea
| | - Han-Hee Park
- Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yu-Jin Ha
- Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seok Hee Park
- CIRNO, Sungkyunkwan University, Suwon, Republic of Korea.,Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Haeseung Lee
- Intellectual Information Team, Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Seok-Jung Kim
- Department of Orthopaedic Surgery, Uijeongbu St. Mary's Hospital, The Catholic University of Korea College of Medicine, Uijeongbu, Republic of Korea
| | - Ho Chul Kang
- Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Siyoung Yang
- Department of Pharmacology, Ajou University School of Medicine, Suwon, Gyeonggi-do, Republic of Korea .,Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea.,CIRNO, Sungkyunkwan University, Suwon, Republic of Korea
| | - You-Sun Kim
- Department of Biomedical Sciences, Graduate School, Ajou University School of Medicine, Suwon, Republic of Korea .,Department of Biochemistry & Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
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18
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Jung H, Jeon MS, Hodgett M, Waterhouse P, Eyun SI. Comparative Evaluation of Genome Assemblers from Long-Read Sequencing for Plants and Crops. J Agric Food Chem 2020; 68:7670-7677. [PMID: 32530283 DOI: 10.1021/acs.jafc.0c01647] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The availability of recent state-of-the-art long-read sequencing technologies has significantly increased the ease and speed of producing high-quality plant genome assemblies. A wide variety of genome-related software tools are now available and they are typically benchmarked using microbial or model eukaryotic genomes such as Arabidopsis and rice. However, many plant species have much larger and more complex genomes than these, and the choice of tools, parameters, and/or strategies that can be used is not always obvious. Thus, we have compared the metrics of assemblies generated by various pipelines to discuss how assembly quality can be affected by two different assembly strategies. First, we focused on optimizing read preprocessing and assembler variables using eight different de novo assemblers on five different Pacific Biosciences long-read datasets of diploid and tetraploid species. Then, we examined a single scaffolding tool (quickmerge) that has been employed for the postprocessing step. We then merged the outputs from multiple assemblies to produce a higher quality consensus assembly. Then, we benchmarked the assemblies for completeness and accuracy (assembly metrics and BUSCO), computer memory, and CPU times. Two lightweight assemblers, Miniasm/Minimap/Racon and WTDBG, were deemed good for novice users because they involved smaller required learning curves and light computational resources. However, two heavyweight tools, CANU and Flye, should be the first choice when the goal is to achieve accurate and complete assemblies. Our results will provide valuable guidance in future plant genome projects and beyond.
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Affiliation(s)
- Hyungtaek Jung
- Centre for Agriculture and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
| | - Matthew Hodgett
- Information Technology Services, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Peter Waterhouse
- Centre for Agriculture and Biocommodities, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea
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19
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Kang LJ, Oh E, Cho C, Kwon H, Lee CG, Jeon J, Lee H, Choi S, Han SJ, Nam J, Song CU, Jung H, Kim HY, Park EJ, Choi EJ, Kim J, Eyun SI, Yang S. 3'-Sialyllactose prebiotics prevents skin inflammation via regulatory T cell differentiation in atopic dermatitis mouse models. Sci Rep 2020; 10:5603. [PMID: 32221370 PMCID: PMC7101440 DOI: 10.1038/s41598-020-62527-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/12/2020] [Indexed: 02/01/2023] Open
Abstract
3'-Sialyllactose (3'-SL), a natural prebiotic, maintains immune homeostasis and exerts anti-inflammatory and anti-arthritic effects. Although regulatory T cells (Tregs) prevent excessive inflammation and maintain immune tolerance, the effect of 3'-SL on Treg regulation is unclear. This study aimed to investigate the effect of 3'-SL on Treg responses in atopic dermatitis (AD) pathogenesis. Oral administration of 3'-SL reduced AD-like symptoms such as ear, epidermal, and dermal thickness in repeated topical application of house dust mites (HDM) and 2,4-dinitrochlorobenzene (DNCB). 3'-SL inhibited IgE, IL-1β, IL-6, and TNF-α secretion and markedly downregulated AD-related cytokines including IL-4, IL-5, IL-6, IL-13, IL-17, IFN-γ, TNF-α, and Tslp through regulation of NF-κB in ear tissue. Additionally, in vitro assessment of Treg differentiation revealed that 3'-SL directly induced TGF-β-mediated Treg differentiation. Furthermore, 3'-SL administration also ameliorated sensitization and elicitation of AD pathogenesis by suppressing mast cell infiltration and production of IgE and pro-inflammatory cytokines in mouse serum by mediating the Treg response. Furthermore, Bifidobacterium population was also increased by 3'-SL administration as prebiotics. Our data collectively show that 3'-SL has therapeutic effects against AD progression by inducing Treg differentiation, downregulating AD-related cytokines, and increasing the Bifidobacterium population.
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Affiliation(s)
- Li-Jung Kang
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Eunjeong Oh
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chanmi Cho
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - HoKeun Kwon
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, 03722, Korea
| | - Choong-Gu Lee
- Korea Institute of Science & Technology (KIST) Gangneung Institute of Natural Products, Gangwon-do, 25451, Republic of Korea
| | - Jimin Jeon
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyemi Lee
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Sangil Choi
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seong Jae Han
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jiho Nam
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chi-Une Song
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyunho Jung
- Synovizen Inc, Seoul, 06621, Republic of Korea
| | - Hye Young Kim
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea
- Laboratory of mucosal immunology, Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Eun-Jung Park
- East-West Medical Research Institute, Medical Science Research Institute, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Eun-Ju Choi
- Department of Physical Education, College of Education, Daegu Catholic University, Gyeongsan, 38430, Republic of Korea
| | - Jooyoung Kim
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Siyoung Yang
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, 16499, Republic of Korea.
- Department of Pharmacology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea.
- CIRNO, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
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20
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Kim S, Jeon D, Lee JY, Cho SJ, Lim Y, Eyun SI, Park SC, Seo YJ. Upregulation of cellulase activity and mRNA levels by bacterial challenge in the earthworm Eisenia andrei, supporting the involvement of cellulases in innate immunity. Biochem Biophys Res Commun 2019; 521:15-18. [PMID: 31640857 DOI: 10.1016/j.bbrc.2019.09.134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 09/28/2019] [Indexed: 10/25/2022]
Abstract
To investigate whether earthworm cellulases contribute to the innate immune system, the responsiveness of cellulase activity and mRNA expression to bacterial challenge was examined by zymography and RNA sequencing. A zymographic analysis revealed that the activity levels of earthworm cellulases were upregulated in response to either a bacterial (Bacillus subtilis or Escherichia coli) or LPS challenge. After the challenge, significant increases in cellulase 1 and cellulase 2 activity levels were observed within 8-16 and 16-24 h, respectively. In the coelomic fluid, both activities were significantly upregulated at 8 h post-injection with B. subtilis. Based on RNA sequencing, cellulase-related mRNAs encoding beta-1,4-endoglucanases were upregulated by 3-fold within 6 h after B. subtilis injection. Our results clearly demonstrated that earthworm cellulases are upregulated by bacterial challenge at the mRNA and protein levels. These results support the view that earthworm cellulases act as inducible humoral effectors of innate immunity against bacterial infection.
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Affiliation(s)
- Seyoung Kim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Donggu Jeon
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Ju-Young Lee
- Department of Biomedical Engineering, College of Medical Convergence, Catholic Kwandong University, Gangneung, Republic of Korea
| | - Sung-Jin Cho
- School of Biological Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Younghyun Lim
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea
| | - Soon Cheol Park
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea.
| | - Young-Jin Seo
- Department of Life Science, Chung-Ang University, Seoul, Republic of Korea.
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21
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Cho C, Kang LJ, Jang D, Jeon J, Lee H, Choi S, Han SJ, Oh E, Nam J, Kim CS, Park E, Jeong SY, Park CH, Shin YS, Eyun SI, Yang S. Cirsium japonicum var. maackii and apigenin block Hif-2α-induced osteoarthritic cartilage destruction. J Cell Mol Med 2019; 23:5369-5379. [PMID: 31148341 PMCID: PMC6652892 DOI: 10.1111/jcmm.14418] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/19/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022] Open
Abstract
Although Hif-2α is a master regulator of catabolic factor expression in osteoarthritis development, Hif-2α inhibitors remain undeveloped. The aim of this study was to determine whether Cirsium japonicum var. maackii (CJM) extract and one of its constituents, apigenin, could attenuate the Hif-2α-induced cartilage destruction implicated in osteoarthritis progression. In vitro and in vivo studies demonstrated that CJM reduced the IL-1β-, IL-6, IL-17- and TNF-α-induced up-regulation of MMP3, MMP13, ADAMTS4, ADAMTS5 and COX-2 and blocked osteoarthritis development in a destabilization of the medial meniscus mouse model. Activation of Hif-2α, which directly up-regulates MMP3, MMP13, ADAMTS4, IL-6 and COX-2 expression, is inhibited by CJM extract. Although cirsimarin, cirsimaritin and apigenin are components of CJM and can reduce inflammation, only apigenin effectively reduced Hif-2α expression and inhibited Hif-2α-induced MMP3, MMP13, ADAMTS4, IL-6 and COX-2 expression in articular chondrocytes. IL-1β induction of JNK phosphorylation and IκB degradation, representing a critical pathway for Hif-2α expression, was completely blocked by apigenin in a concentration-dependent manner. Collectively, these effects indicate that CJM and one of its most potent constituents, apigenin, can lead to the development of therapeutic agents for blocking osteoarthritis development as novel Hif-2α inhibitors.
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Affiliation(s)
- Chanmi Cho
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Li-Jung Kang
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Dain Jang
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Jimin Jeon
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Hyemi Lee
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Sangil Choi
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Seong Jae Han
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Eunjeong Oh
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Jiho Nam
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
| | - Chun Sung Kim
- Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Korea
| | - Eunkuk Park
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Seon-Yong Jeong
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Medical Genetics, Ajou University School of Medicine, Suwon, Korea
| | - Chan Hum Park
- Department of Medicinal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Yu Su Shin
- Department of Medicinal Crop Research, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Siyoung Yang
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Korea.,Department of Pharmacology, Ajou University School of Medicine, Suwon, Korea.,CIRNO, Sungkyunkwan University, Suwon, Korea
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22
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Eyun SI. Accelerated pseudogenization of trace amine-associated receptor genes in primates. Genes Brain Behav 2019; 18:e12543. [PMID: 30536583 PMCID: PMC6849804 DOI: 10.1111/gbb.12543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/03/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023]
Abstract
Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine‐associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species‐specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity.
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Affiliation(s)
- Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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23
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Wang H, Eyun SI, Arora K, Tan SY, Gandra P, Moriyama E, Khajuria C, Jurzenski J, Li H, Donahue M, Narva K, Siegfried B. Patterns of Gene Expression in Western Corn Rootworm (Diabrotica virgifera virgifera) Neonates, Challenged with Cry34Ab1, Cry35Ab1 and Cry34/35Ab1, Based on Next-Generation Sequencing. Toxins (Basel) 2017; 9:toxins9040124. [PMID: 28358336 PMCID: PMC5408198 DOI: 10.3390/toxins9040124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 03/22/2017] [Accepted: 03/27/2017] [Indexed: 11/16/2022] Open
Abstract
With Next Generation Sequencing technologies, high-throughput RNA sequencing (RNAseq) was conducted to examine gene expression in neonates of Diabrotica virgifera virgifera (LeConte) (Western Corn Rootworm, WCR) challenged with individual proteins of the binary Bacillus thuringiensis insecticidal proteins, Cry34Ab1 and Cry35Ab1, and the combination of Cry34/Cry35Ab1, which together are active against rootworm larvae. Integrated results of three different statistical comparisons identified 114 and 1300 differentially expressed transcripts (DETs) in the Cry34Ab1 and Cry34/35Ab1 treatment, respectively, as compared to the control. No DETs were identified in the Cry35Ab1 treatment. Putative Bt binding receptors previously identified in other insect species were not identified in DETs in this study. The majority of DETs (75% with Cry34Ab1 and 68.3% with Cry34/35Ab1 treatments) had no significant hits in the NCBI nr database. In addition, 92 DETs were shared between Cry34Ab1 and Cry34/35Ab1 treatments. Further analysis revealed that the most abundant DETs in both Cry34Ab1 and Cry34/35Ab1 treatments were associated with binding and catalytic activity. Results from this study confirmed the nature of these binary toxins against WCR larvae and provide a fundamental profile of expression pattern of genes in response to challenge of the Cry34/35Ab1 toxin, which may provide insight into potential resistance mechanisms.
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Affiliation(s)
- Haichuan Wang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583-0915, USA.
| | - Seong-Il Eyun
- Center for Biotechnology, School of Biological Sciences, UNL, Lincoln, NE 68583, USA.
| | | | - Sek Yee Tan
- Dow AgroSciences, Indianapolis, IN 46268, USA.
| | | | - Etsuko Moriyama
- Center for Biotechnology, School of Biological Sciences, UNL, Lincoln, NE 68583, USA.
| | | | - Jessica Jurzenski
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583-0915, USA.
| | - Huarong Li
- Dow AgroSciences, Indianapolis, IN 46268, USA.
| | | | - Ken Narva
- Dow AgroSciences, Indianapolis, IN 46268, USA.
| | - Blair Siegfried
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611-0620, USA.
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24
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Eyun SI. Phylogenomic analysis of Copepoda (Arthropoda, Crustacea) reveals unexpected similarities with earlier proposed morphological phylogenies. BMC Evol Biol 2017; 17:23. [PMID: 28103796 PMCID: PMC5244711 DOI: 10.1186/s12862-017-0883-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 01/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level. RESULTS This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of Copepoda among five other crustacean groups (Anostraca, Cladocera, Sessilia, Amphipoda, and Decapoda) using 24 nuclear protein-coding genes. Phylogenomics has confirmed the monophyly of Copepoda and Podoplea. However, this study reveals surprising differences with the majority of the copepod phylogenies and unexpected similarities with postembryonic characters and earlier proposed morphological phylogenies; More precisely, Cyclopoida is more closely related to Siphonostomatoida than to Harpacticoida which is likely the most basally-branching group of Podoplea. Divergence time estimation suggests that the origin of Harpacticoida can be traced back to the Devonian, corresponding well with recently discovered fossil evidence. Copepoda has a close affinity to the clade of Malacostraca and Thecostraca but not to Branchiopoda. This result supports the hypothesis of the newly proposed clades, Communostraca, Multicrustacea, and Allotriocarida but further challenges the validity of Hexanauplia and Vericrustacea. CONCLUSIONS The first phylogenomic study of Copepoda provides new insights into taxonomic relationships and represents a valuable resource that improves our understanding of copepod evolution and their wide range of ecological adaptations.
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Affiliation(s)
- Seong-Il Eyun
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
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25
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Nanoth Vellichirammal N, Wang H, Eyun SI, Moriyama EN, Coates BS, Miller NJ, Siegfried BD. Transcriptional analysis of susceptible and resistant European corn borer strains and their response to Cry1F protoxin. BMC Genomics 2015. [PMID: 26220297 PMCID: PMC4518661 DOI: 10.1186/s12864-015-1751-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Despite a number of recent reports of insect resistance to transgenic crops expressing insecticidal toxins from Bacillus thuringiensis (Bt), little is known about the mechanism of resistance to these toxins. The purpose of this study is to identify genes associated with the mechanism of Cry1F toxin resistance in European corn borer (Ostrinia nubilalis Hübner). For this, we compared the global transcriptomic response of laboratory selected resistant and susceptible O. nubilalis strain to Cry1F toxin. We further identified constitutive transcriptional differences between the two strains. Results An O. nubilalis midgut transcriptome of 36,125 transcripts was assembled de novo from 106 million Illumina HiSeq and Roche 454 reads and used as a reference for estimation of differential gene expression analysis. Evaluation of gene expression profiles of midgut tissues from the Cry1F susceptible and resistant strains after toxin exposure identified a suite of genes that responded to the toxin in the susceptible strain (n = 1,654), but almost 20-fold fewer in the resistant strain (n = 84). A total of 5,455 midgut transcripts showed significant constitutive expression differences between Cry1F susceptible and resistant strains. Transcripts coding for previously identified Cry toxin receptors, cadherin and alkaline phosphatase and proteases were also differentially expressed in the midgut of the susceptible and resistant strains. Conclusions Our current study provides a valuable resource for further molecular characterization of Bt resistance and insect response to Cry1F toxin in O. nubilalis and other pest species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1751-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Haichuan Wang
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Seong-Il Eyun
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Etsuko N Moriyama
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Brad S Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, USA.
| | - Nicholas J Miller
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Blair D Siegfried
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE, USA.
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26
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Eyun SI, Lee YH, Suh HL, Kim S, Soh HY. Genetic identification and molecular phylogeny of Pseudodiaptomus species (Calanoida, Pseudodiaptomidae) in Korean waters. Zoolog Sci 2008; 24:265-71. [PMID: 17551247 DOI: 10.2108/zsj.24.265] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Five species of the genus Pseudodiaptomus, P. inopinus, P. poplesia, P. marinus, P. nihonkaiensis, and P. sp. occur in Korea nearshore waters. Although the four species except for P. sp. have been classified into Lobus and Ramosus groups, two for each group, based on morphological characters, this classification had yet to be confirmed by molecular characters. Here, we determined molecular characters and phylogenetic relationships of the five species in order to evaluate the morphology-based groupings and the species identifications. For this, a 625-bp DNA region of the mitochondrial gene cytochrome oxidase subunit I (mtCOI) was sequenced and compared among the species. Intraspecific variation of the sequences is less than 0.6%, while interspecific variation ranges from 17.6-26.7%, indicating every species, including P. sp., is a genetically distinct, valid species. Phylogenetic trees of the mtCOI DNA reveal that the Lobus-group species including P. inopinus and P. poplesia form a well-supported clade and that P. sp. belongs to this group. On the other hand, the Ramosus group clade consisting of P. marinus and P. nihonkaiensis is not well supported by bootstrap analyses, suggesting that further evaluation of the validity of this group assignment is needed.
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Affiliation(s)
- Seong-Il Eyun
- School of Biological Sciences, University of Nebraska-Lincoln, NE, USA
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