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Unveiling microbial complexity within Astragalus propinquus and Glycyrrhiza uralensis roots

Annals of Microbiology 2025年第1期75卷 1-15页

作者： Kim, Zerrin Kozma Park, Young Sang Yang, Tae-Jin Kim, Hyun Lee, Yong-Hwan Department of Agricultural Biotechnology Seoul National University Seoul South Korea Department of Agriculture Forestry and Bioresources Seoul National University Seoul South Korea Plant Genomics & Breeding Institute Seoul National University Seoul South Korea Research Institute of Agriculture and Life Sciences Seoul National University Seoul South Korea Center for Plant Microbiome Research Seoul National University Seoul South Korea Plant Immunity Research Center Seoul National University Seoul South Korea Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul South Korea

Background: Astragalus propinquus (AP) and Glycyrrhiza uralensis (GU), members of the Fabaceae family, are widely used for their therapeutic properties. However, the endophytic microbial communities in their roots remain largely unknown. Herein, we compared the structure and properties of root-associated bacterial and fungal communities of AP and GU, specifically excluding the microbial communities thriving in the rhizosphere, using both culture-dependent and -independent methods. Results: A metabarcoding-based approach revealed a higher abundance of Proteobacteria in the root microbiome of GU than in that of AP. Fungal communities showed similar distinctions, with AP and GU predominantly harboring Ascomycota and Basidiomycota, respectively. The bacterial community in AP exhibited significantly higher diversity than in GU and included unique taxa, e.g., Steroidobacterales and Micromonosporales. However, the bacterial community in GU was relatively less diverse and dominated by Xanthomonadales. Differential abundance analysis revealed that the plant species significantly impacted 301 bacterial and 228 fungal amplicon sequence variants (ASVs) in AP and GU. Among these, B5_f_Comamonadaceae was markedly more enriched in AP than in GU. A random forest model analyzing bacterial ASVs with significant differences in abundance indicated that most bacterial ASVs were enriched in AP. A pan-microbial community of 1,243 ASVs was identified, including 96 co-detected ASVs between AP and GU, with 3 core ASVs (B2_f_Pseudomonas, B5_Comamonadaceae, and B70_Cutibacterium). The fungal community comprised 435 ASVs, with 98 shared ASVs and 8 core ASVs (F5_Paraphoma, F6_f_Lysurus, F22_Alternaria, F30_Phaeosphaeria, F53_Cladosporium, F36_Moesziomyces, F55_f_Neocucurbitaria, and F56_Malassezia). Hub nodes were identified to elucidate the roles of microorganisms within microbial networks. In AP, B152_o_Burkholderiales, F14_Exophiala, and F33_Fusarium were the key hub nodes, whereas, in GU, B3

关键词： Astragalus propinquus Endophytic bacteria Endophytic fungi Glycyrrhiza uralensis Root microbiome

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Mutation of Oryza sativa CORONATINE INSENSITIVE 1b(OsCOI1b) delays leaf senescence

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Journal of Integrative Plant Biology 2015年第6期57卷 562-576页

作者： Sang-Hwa Lee Yasuhito Sakuraba Taeyoung Lee Kyu-Won Kim Gynheung An Han Yong Lee Nam-Chon Paek Department of Plant Science Plant Genomics and Breeding InstituteResearch Institute of Agriculture and Life SciencesSeoul National University Interdisciplinary Program in Bioinformatics Seoul National University Department of Plant Molecular Systems Biotechnology Crop Biotech InstituteKyung Hee University Department of Agricultural Biotechnology Seoul National University

Jasmonic acid （JA） functions in plant development, including senescence and immunity. Arabidopsis thaliana CORONATINE INSENSITIVE 1 encodes a JA receptor and functions in the JA‐responsive signaling pathway. The Arabidopsis genome harbors a single COI gene, but the rice （Oryza sativa） genome harbors three COI homologs, OsCOI1a, OsCOI1b, and OsCOI2. Thus, it remains unclear whether each OsCOI has distinct, additive, synergistic, or redundant func-tions in development. Here, we use the oscoi1b‐1 knockout mutants to show that OsCOI1b mainly affects leaf senescence under senescence‐promoting conditions. oscoi1b‐1 mutants stayed green during dark‐induced and natural senescence, with substantial retention of chlorophylls and photosyn-thetic capacity. Furthermore, several senescence‐associated genes were downregulated in oscoi1b‐1 mutants, including homologs of Arabidopsis thaliana ETHYLENE INSENSITIVE 3 and ORESARA 1, important regulators of leaf senescence. These results suggest that crosstalk between JA signaling and ethylene signaling affects leaf senescence. The Arabidopsis coi1‐1 plants containing 35S：OsCOI1a or 35S：OsCOI1b rescued the delayed leaf senescence during dark incubation, sug-gesting that both OsCOI1a and OsCOI1b are required for promoting leaf senescence in rice. oscoi1b‐1 mutants showed significant decreases in spikelet fertility and grain weight, leading to severe reduction of grain yield, indicating that OsCOI1‐mediated JA signaling affects spikelet fertility and grain filling.

关键词： Jasmonic acid leaf senescence OsCOI1b rice stay-green

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Development of virus-induced genome editing methods in Solanaceous crops

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园艺研究（英文） 2024年第1期11卷 13-26页

作者： Seo-Young Lee Bomi Kang Jelli Venkatesh Joung-Ho Lee Seyoung Lee Jung-Min Kim Seungki Back Jin-Kyung Kwon Byoung-Cheorl Kang Department of Agriculture Forestry and BioresourcesResearch Institute of Agriculture and Life SciencesPlant Genomics Breeding InstituteCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Program in Agricultural Biotechnology College of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Department of Agriculture Forestry and BioresourcesResearch Institute of Agriculture and Life SciencesPlant Genomics Breeding InstituteCollege of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Program in Agricultural Biotechnology College of Agriculture and Life SciencesSeoul National UniversitySeoul 08826Republic of Korea

Genome editing(GE)using CRISPR/Cas systems has revolutionized plant ***,conventional transgene-mediated GE methods have limitations due to the time-consuming generation of stable transgenic lines expressing the Cas9/single guide RNA(sgRNA)module through tissue ***-induced genome editing(VIGE)systems have been successfully employed in model plants,such as Arabidopsis thaliana and Nicotiana *** this study,we developed two VIGE methods for Solanaceous ***,we used the tobacco rattle virus(TRV)vector to deliver sgRNAs into a transgenic tomato(Solanum lycopersicum)line of cultivar Micro-Tom expressing ***,we devised a transgene-free GE method based on a potato virus X(PVX)vector to deliver Cas9 and *** designed and cloned sgRNAs targeting Phytoene desaturase in the VIGE vectors and determined optimal conditions for *** evaluated VIGE efficiency through deep sequencing of the target gene after viral vector inoculation,detecting 40.3％and 36.5％mutation rates for TRV-and PVX-mediated GE,*** improve editing efficiency,we applied a 37℃ heat treatment,which increased the editing efficiency by 33％to 46％and 56％to 76％for TRV-and PVX-mediated VIGE,*** obtain edited plants,we subjected inoculated cotyledons to tissue culture,yielding successful editing *** also demonstrated that PVX-mediated GE can be applied to other Solanaceous crops,such as potato(Solanum tuberosum)and eggplant(Solanum melongena).These simple and highly efficient VIGE methods have great potential for generating genome-edited plants in Solanaceous crops.

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Guardian of the rice:Unveiling OsSSP1 for broad-spectrum disease resistance

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Molecular Plant 2024年第7期17卷 996-998页

作者： You-Jin Lim Yong-Hwan Lee Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Republic of Korea interdisciplinary Program in Agricultural Genomics Center for Fungal Genetic ResourcesPlant Immunity Research Centerand Center for Plant Microbiome ResearchSeoul National UniversitySeoul 08826Republic of Korea

Plants are continuously exposed to numerous biotic stresses throughout their *** arms race-driven coevolution with pathogens,plants have developed sophisticated immune systems,including pathogen-associated molecular pattern(PAMP)-triggered immunity(PTI)and effector-triggered immunity(ETI).PTI is initiated by the binding of danger signals to extracellular membrane-localized receptors calledpattern recognition receptors(PRRs).PTI triggers responses,including reactive oxygen species(ROS)bursts and the expression of defenseassociated ***,pathogens adapted to PTl secrete virulence proteins,effectors,to aid colonization,and ETl is then triggered by the recognition of these effectors by resistance proteins with a nucleotide-binding domain leucinerich repeat receptor(NLR).To circumvent this immune response,pathogens secrete various effectors into the host intracellular region and induce effector-triggered susceptibility(Zhou and Zhang.,2020).Currently,research on plant immunity has been primarily focused on plasma membrane and cytoplasmlocalized proteins,including oligomeric NLRs,resistosomes,and the secretion mechanisms of cytoplasmic effectors.

关键词： immunity resistance Guard

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ESR2–HDA6 complex negatively regulates auxin biosynthesis to delay callus initiation in Arabidopsis leaf explants during tissue culture

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Plant Communications 2024年第7期5卷 200-214页

作者： Kyounghee Lee Hobin Yoon Ok-Sun Park Jongbu Lim Sang-Gyu Kim Pil Joon Seo Department of Chemistry Seoul National UniversitySeoul 08826Korea Research Institute of Basic Sciences Seoul National UniversitySeoul 08826Korea Interdisciplinary Program in Agricultural Biotechnology Seoul National UniversitySeoul 08826Korea Plant Genomics and Breeding Institute Seoul National UniversitySeoul 08826Korea Department of Biological Sciences KAISTDaejeon 34141Korea

Plants exhibit an astonishing ability to regulate organ regeneration upon *** of leaf explants promotes the biosynthesis of indole-3-acetic acid(IAA),which is polar-transported to excised regions,where cell fate transition leads to root founder cell specification to induce de novo root *** regeneration capacity of plants has been utilized to develop in vitro tissue culture ***,we report that IAA accumulation near the wounded site of leaf explants is essential for callus formation on 2,4-dichlorophenoxyacetic acid(2,4-D)-rich callus-inducing medium(CIM).Notably,a high concentration of 2,4-D does not compensate for the action of IAA because of its limited efflux;rather,it lowers IAA biosynthesis via a negative feedback mechanism at an early stage of in vitro tissue culture,delaying callus *** auxin negative feedback loop in CIM-cultured leaf explants is mediated by an auxin-inducible APETALA2 transcription factor,ENHANCER OF SHOOT REGENERATION 2(ESR2),along with its interacting partner HISTONE DEACETYLASE 6(HDA6).The ESR2–HDA6 complex binds directly to,and removes the H3ac mark from,the YUCCA1(YUC1),YUC7,and YUC9 loci,consequently repressing auxin biosynthesis and inhibiting cell fate transition on 2,4-D-rich *** findings indicate that negative feedback regulation of auxin biosynthesis by ESR2 and HDA6 interferes with proper cell fate transition and callus initiation.

关键词： auxin biosynthesis negative feedback loop ESR2 HDA6 YUCCA chromatin modification

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Ambivalent response in pathogen defense: A double-edged sword?

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Plant Communications 2022年第6期3卷 190-207页

作者： Chi-Yeol Kim Hyeunjeong Song Yong-Hwan Lee Department of Agricultural Biotechnology Seoul National UniversitySeoul 08826Korea Plant Immunity Research Center Seoul National UniversitySeoul 08826Korea Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul 08826Korea Interdisciplinary Program in Agricultural Genomics Seoul National UniversitySeoul 08826Korea Center for Fungal Genetic Resources Seoul National UniversitySeoul 08826Korea

Plants possess effective immune systems that defend against most microbial *** plant immunity research has focused on the classic binary defense model involving the pivotal role of small-molecule hormones in regulating the plant defense signaling *** most of our current understanding comes from studies that relied on information derived from a limited number of pathosystems,newer studies concerning the incredibly diverse interactions between plants and microbes are providing additional insights into other novel ***,we review the roles of both classical and more recently identified components of defense signaling pathways and stress hormones in regulating the ambivalence effect during responses to diverse *** of their different lifestyles,effective defense against biotrophic pathogens normally leads to increased susceptibility to necrotrophs,and vice *** these opposing forces,the plant potentially faces a trade-off when it mounts resistance to a specific pathogen,a phenomenon referred to here as the ambivalence *** also highlight a novel mechanism by which translational control of the proteins involved in the ambivalence effect can be used to engineer durable and broad-spectrum disease resistance,regardless of the lifestyle of the invading pathogen.

关键词： ambivalence effect crop protection hormone crosstalk pathogen plant defense susceptibility(S)gene

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Hair growth-promoting effects of Stellera chamaejasme L. extract on C57BL/6 mice via induction of anagen phase genes

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Journal of Traditional Chinese Medical Sciences 2025年

作者： Jin-Woo Kim Banzragch Dorjsembe Chu Won Nho Pahn-Shick Chang Jin-Chul Kim Interdisciplinary Program in Agricultural Genomics Seoul National University Seoul 08826 Republic of Korea Center for Natural Product Efficacy Optimization Korea Institute of Science and Technology Gangneung 25451 Republic of Korea Smart Farm Research Center Korea Institute of Science and Technology (KIST) Gangneung 25451 Republic of Korea Division of Bio-Medical Science and Technology University of Science and Technology (UST) Daejeon 34113 Republic of Korea Department of Agricultural Biotechnology Seoul National University Seoul 08826 Republic of Korea Research Institute of Agriculture and Life Sciences Seoul National University Seoul 08826 Republic of Korea Center for Food and Bioconvergence Seoul National University Seoul 08826 Republic of Korea Center for Agricultural Microorganism and Enzyme Seoul National University Seoul 08826 Republic of Korea

Objective To evaluate the effects of Stellera chamaejasme L. ( S. chamaejasme , Rui Xiang Lang Du) extract on hair growth in a mouse model. Methods The extract was prepared using 95% ethanol and topically applied as a 1% or 3% solution to the dorsal skin of shaved mice for 16 consecutive days. A control mouse group received an equal volume of vehicle for the same period. After 16 days, the dorsal skin was histologically examined through hematoxylin-eosin staining. Further, quantitative real time - polymerase chain reaction was performed on skin tissue lysates to evaluate the expression levels of mRNAs encoding proteins involved in hair growth, including WNT10A, noggin (NOG), transforming growth factor-β receptor 1 (TBR1), epidermal growth factor (EGF), versican, fibroblast growth factor 10 (FGF10), lymphoid enhancer-binding factor 1 (LEF1), and transforming growth factor-β (TGF-β). Results Compared with vehicle, S. chamaejasme extract dose-dependently enhanced hair growth. Histological analysis revealed that S. chamaejasme extract increased the number and diameter of hair follicles in subcutaneous tissue, as well as dermal layer thickness, which are indicative of anagen phase induction. Additionally, S. chamaejasme extract upregulated the mRNA expression levels of WNT10A, NOG, TBR1, EFG, FGF10, LEF1, and TGF-β. Conclusion The results suggest that S. chamaejasme extract could be a potential treatment for promoting hair growth.

关键词： Stellera chamaejasme L. Traditional medicinal herb Hair growth Anagen phase

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Discovering the underground ecology of Tricholoma matsutake habitat using whole-metagenome shotgun sequencing

Discovering the underground ecology of Tricholoma matsutake ...

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2024年亚洲植物病理学大会

作者： In-Hyup Bae Hyun Kim Yong-Hwan Lee Department of Agricultural Biotechnology Seoul National University Research Institute of Agriculture and Life Sciences Seoul National University Interdisciplinary Program in Agricultural Genomics Seoul National University Center for Plant Microbiome Research Seoul National University Plant Immunity Research Center Seoul National University

Forest soil often lacks nutrients,and essential elements like nitrogen and phosphorus are in insoluble forms that plants cannot directly *** overcome this,land plants have developed symbioticrelationships with microorganisms that can make these nutrients *** different mutualistic functions have been accumulated over the long evolutionary time,but the specific functions and mechanisms underlying these symbiotic relationships remain poorly understood.

关键词： Discovering the underground ecology of Tricholoma matsutake habitat using whole-metagenome shotgun sequencing shotgun

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Unveiling genome diversity associated with host specialization of Magnaporthe oryzae using the pan-genome analysis

Unveiling genome diversity associated with host specializati...

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2024年亚洲植物病理学大会

作者： Jaeno Ko Kyeongchae Cheong Jaehyun Bae Seung-Gyun Ko Jaeyoung Choi Yong-Hwan Lee Department of Agricultural Biotechnology Seoul National University Research Institute of Agriculture and Life Sciences Seoul National University Department of Oriental Medicine Biotechnology College of Life SciencesKyung Hee University Interdisciplinary Program in Agricultural Genomics Seoul National University Center for Plant Microbiome Research Seoul National University Plant Immunity Research Center Seoul National University

Magnaporthe oryzae is a destructive fungal plant pathogen that infects many host species within the Poaceae family,including rice and *** to the significant agricultural and economic damage it causes to cereal crops,M... 详细信息

关键词： Unveiling genome diversity associated with host specialization of Magnaporthe oryzae using the pan-genome analysis

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Differentially expressed genes in adipose tissues reveals that ECM-receptor interaction affects on the depot-specific adipogenesis in Hanwoo

Differentially expressed genes in adipose tissues reveals th...

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第11届世界畜产大会(WCAP2013)

作者： Mi Jang Hyun-Jeong Lee Hyeongmin Kim Woori Kwak WonCheoul Park Jae-Yeon Hwang Chang-Kyu Lee Gul Won Jang Mi Na Park Hyeong-Cheol Kim Jin Young Jeong Kang Seok Seo Heebal Kim Seoae Cho Bo-Young Lee C&K Genomics Seoul National University NakSeoungDaeGwanakguSeoulKorea Department of Agricultural Biotechnology and Research Institute for Agriculture and Life ScienceSeoul National UniversitySeoulKorea Department of Animal Science and TechnologyCollege of Life Science and Natural ResourcesSunchon National UniversitySeoulRepublic of Korea C&K GenomicsSeoul National University NakSeoungDaeGwanakguSeoulKorea C&K Genomics Seoul National University NakSeoungDaeGwanakguSeoulKorea Department of Agricultural Biotechnology and Research Institute of Population GenomicsSeoul National UniversitySeoulRepublic of Korea Department of Animal Science and Technology College of Life Science and Natural ResourcesSunchon National UniversitySeoulRepublic of Korea Division of Animal Genomics and BioinformaticsNational Institute of Animal scienceRural Development AdministrationSuwonRepublic of Korea Department of Agricultural Biotechnology and Research Institute of Population GenomicsSeoul National UniversitySeoulRepublic of Korea Interdisciplinary Program in BioinformaticsSeoul National UniversityKorea Division of Animal Genomics and Bioinformatics National Institute of Animal scienceRural Development AdministrationSuwonRepublic of Korea

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