Scholars@Duke
Eunyu Kim

Eunyu Kim

Assistant Professor of Biology at Duke Kunshan University
DKU Faculty
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Selected Publications

Draft genome for Pseudomonas alkylphenolica IMGN1, isolated from soil.

Journal Article Microbiology resource announcements · September 2024 Biocontrol using organisms like Pseudomonas alkylphenolica offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of Pseudomonas alkylphenolica IMGN1, a stra ... Full text Cite

Complete genome sequence of Bacillus paramobilis sp. strain IMGN7 from soil.

Journal Article Microbiology resource announcements · September 2024 Here, we report the complete genome sequence of Bacillus paramobilis sp. strain IMGN7, which was isolated from soil in South Korea. Its complete genome size is 5.28 Mbp. This genome will provide various insights for further studies about their funct ... Full text Cite

Draft genome sequence of Priestia megaterium strain IMGN3 derived from soil.

Journal Article Microbiology resource announcements · September 2024 Priestia megaterium sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic ... Full text Cite

Complete genome sequence of bacterium Peribacillus simplex strain IMGN11 from soil.

Journal Article Microbiology resource announcements · September 2024 We report the complete genome sequence of Peribacillus simplex, a spore-forming bacterium originally classified within the Bacillus genus. Peribacillus simplex exhibits antibiotic, plant growth-promoting, and xenobiotic-degrading activ ... Full text Cite

Draft genome sequence of bacterium Bacillus proteolyticus strain IMGN4 from soil.

Journal Article Microbiology resource announcements · August 2024 Here, we present the draft genome of Bacillus proteolyticus IMGN4, the gram-positive, soil-dwelling bacterium discovered in mountain Maemi, Republic of Korea in May 2019. The assembly resulted in 7 contigs, comprising a total of 6,063,502 base pairs ... Full text Cite

Complete genome sequence of Pseudomonas fluorescens IMGN2 isolated from undisturbed soil.

Journal Article Microbiology resource announcements · August 2024 Here, we report the complete genome sequence of Pseudomonas fluorescens IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotech ... Full text Cite

The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis.

Journal Article The Plant cell · February 2024 N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thalian ... Full text Cite

Cosuppression of AtGELP22 and AtGELP23, two ubiquitinated target proteins of RING E3 ligase AtAIRP5, increases tolerance to drought stress in Arabidopsis.

Journal Article Plant molecular biology · August 2023 AtAIRP5 RING E3 ubiquitin ligase was recently identified as a positive regulator of the abscisic acid (ABA)-mediated drought stress response by stimulating the degradation of serine carboxypeptidase-like 1. Here, we identified GDSL-type esterase/lipase 22 ... Full text Cite

Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids.

Journal Article The Plant journal : for cell and molecular biology · April 2023 Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts ... Full text Cite

Harnessing epigenetic variability for crop improvement: current status and future prospects.

Journal Article Genes & genomics · March 2022 BackgroundThe epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supp ... Full text Cite

Tracing Mobile DNAs: From Molecular to Population Scales.

Journal Article Frontiers in plant science · January 2022 Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile na ... Full text Cite

Phase separation of chromatin and small RNA pathways in plants.

Journal Article The Plant journal : for cell and molecular biology · December 2021 Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the funda ... Full text Cite

Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings.

Journal Article Bio-protocol · November 2021 RNA granules (RGs) are membraneless intracellular compartments that play important roles in the post-transcriptional control of gene expression. Stress granules (SGs) are a type of RGs that form under environmental challenges and/or internal cellular stres ... Full text Cite

Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons.

Journal Article Nature plants · March 2021 Transposable elements (TEs, transposons) are mobile DNAs that can cause fatal mutations1. To suppress their activity, host genomes deploy small interfering RNAs (siRNAs) that trigger and maintain their epigenetic silencing2,3. Whereas ... Full text Cite

Determination of TE Insertion Positions Using Transposon Display.

Chapter · January 2021 Mapping the genomic location to which transposons jumped is of greatest interest to transposon biologists. Transposon display (TD) is the technique of choice that is easy and fast in determining the neo-insertion positions of a target transposon. Essential ... Full text Cite

High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.

Chapter · January 2021 Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs) (Cho et al., Nat Plants 5:26-33, 2018). Given that the eclDNAs are the final intermediate of LTR-TE life c ... Full text Cite

PLANT NATRIURETIC PEPTIDE A and Its Putative Receptor PNP-R2 Antagonize Salicylic Acid-Mediated Signaling and Cell Death.

Journal Article The Plant cell · July 2020 The plant stress hormone salicylic acid (SA) participates in local and systemic acquired resistance, which eventually leads to whole-plant resistance to bacterial pathogens. However, if SA-mediated signaling is not appropriately controlled, plants incur de ... Full text Cite

Draft genome for Pseudomonas alkylphenolica IMGN1, isolated from soil.

Journal Article Microbiology resource announcements · September 2024 Biocontrol using organisms like Pseudomonas alkylphenolica offers a viable alternative to chemical pesticides, enhancing plant growth and reducing environmental impact. This study details the genome of Pseudomonas alkylphenolica IMGN1, a stra ... Full text Cite

Complete genome sequence of Bacillus paramobilis sp. strain IMGN7 from soil.

Journal Article Microbiology resource announcements · September 2024 Here, we report the complete genome sequence of Bacillus paramobilis sp. strain IMGN7, which was isolated from soil in South Korea. Its complete genome size is 5.28 Mbp. This genome will provide various insights for further studies about their funct ... Full text Cite

Draft genome sequence of Priestia megaterium strain IMGN3 derived from soil.

Journal Article Microbiology resource announcements · September 2024 Priestia megaterium sp. strain IMGN3 was isolated from the soil in South Korea. Here, we report its draft genome sequence, comprising 12 contigs with a total sequence length of 5.64 Mbp. This genome will provide valuable resources for future genomic ... Full text Cite

Complete genome sequence of bacterium Peribacillus simplex strain IMGN11 from soil.

Journal Article Microbiology resource announcements · September 2024 We report the complete genome sequence of Peribacillus simplex, a spore-forming bacterium originally classified within the Bacillus genus. Peribacillus simplex exhibits antibiotic, plant growth-promoting, and xenobiotic-degrading activ ... Full text Cite

Draft genome sequence of bacterium Bacillus proteolyticus strain IMGN4 from soil.

Journal Article Microbiology resource announcements · August 2024 Here, we present the draft genome of Bacillus proteolyticus IMGN4, the gram-positive, soil-dwelling bacterium discovered in mountain Maemi, Republic of Korea in May 2019. The assembly resulted in 7 contigs, comprising a total of 6,063,502 base pairs ... Full text Cite

Complete genome sequence of Pseudomonas fluorescens IMGN2 isolated from undisturbed soil.

Journal Article Microbiology resource announcements · August 2024 Here, we report the complete genome sequence of Pseudomonas fluorescens IMGN2, highlighting its biocontrol and plant growth-promoting capabilities. The genome analysis reveals genetic features that contribute to its potential in agricultural biotech ... Full text Cite

The m6A reader ECT1 drives mRNA sequestration to dampen salicylic acid-dependent stress responses in Arabidopsis.

Journal Article The Plant cell · February 2024 N 6-methyladenosine (m6A) is a common epitranscriptional mRNA modification in eukaryotes. Thirteen putative m6A readers, mostly annotated as EVOLUTIONARILY CONSERVED C-TERMINAL REGION (ECT) proteins, have been identified in Arabidopsis (Arabidopsis thalian ... Full text Cite

Cosuppression of AtGELP22 and AtGELP23, two ubiquitinated target proteins of RING E3 ligase AtAIRP5, increases tolerance to drought stress in Arabidopsis.

Journal Article Plant molecular biology · August 2023 AtAIRP5 RING E3 ubiquitin ligase was recently identified as a positive regulator of the abscisic acid (ABA)-mediated drought stress response by stimulating the degradation of serine carboxypeptidase-like 1. Here, we identified GDSL-type esterase/lipase 22 ... Full text Cite

Cooperative role of AtRsmD and AtRimM proteins in modification and maturation of 16S rRNA in plastids.

Journal Article The Plant journal : for cell and molecular biology · April 2023 Chloroplast pre-ribosomal RNA (rRNA) undergoes maturation, which is critical for ribosome assembly. While the central and auxiliary factors in rRNA maturation have been elucidated in bacteria, their mode of action remains largely unexplored in chloroplasts ... Full text Cite

Harnessing epigenetic variability for crop improvement: current status and future prospects.

Journal Article Genes & genomics · March 2022 BackgroundThe epigenetic mechanisms play critical roles in a vast diversity of biological processes of plants, including development and response to environmental challenges. Particularly, DNA methylation is a stable epigenetic signature that supp ... Full text Cite

Tracing Mobile DNAs: From Molecular to Population Scales.

Journal Article Frontiers in plant science · January 2022 Transposable elements (TEs, transposons) are mobile DNAs that are prevalent in most eukaryotic genomes. In plants, their mobility has vastly contributed to genetic diversity which is essential for adaptive changes and evolution of a species. Such mobile na ... Full text Cite

Phase separation of chromatin and small RNA pathways in plants.

Journal Article The Plant journal : for cell and molecular biology · December 2021 Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the funda ... Full text Cite

Enrichment of Cytoplasmic RNA Granules from Arabidopsis Seedlings.

Journal Article Bio-protocol · November 2021 RNA granules (RGs) are membraneless intracellular compartments that play important roles in the post-transcriptional control of gene expression. Stress granules (SGs) are a type of RGs that form under environmental challenges and/or internal cellular stres ... Full text Cite

Ribosome stalling and SGS3 phase separation prime the epigenetic silencing of transposons.

Journal Article Nature plants · March 2021 Transposable elements (TEs, transposons) are mobile DNAs that can cause fatal mutations1. To suppress their activity, host genomes deploy small interfering RNAs (siRNAs) that trigger and maintain their epigenetic silencing2,3. Whereas ... Full text Cite

Determination of TE Insertion Positions Using Transposon Display.

Chapter · January 2021 Mapping the genomic location to which transposons jumped is of greatest interest to transposon biologists. Transposon display (TD) is the technique of choice that is easy and fast in determining the neo-insertion positions of a target transposon. Essential ... Full text Cite

High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq.

Chapter · January 2021 Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs) (Cho et al., Nat Plants 5:26-33, 2018). Given that the eclDNAs are the final intermediate of LTR-TE life c ... Full text Cite

PLANT NATRIURETIC PEPTIDE A and Its Putative Receptor PNP-R2 Antagonize Salicylic Acid-Mediated Signaling and Cell Death.

Journal Article The Plant cell · July 2020 The plant stress hormone salicylic acid (SA) participates in local and systemic acquired resistance, which eventually leads to whole-plant resistance to bacterial pathogens. However, if SA-mediated signaling is not appropriately controlled, plants incur de ... Full text Cite

The B cell death function of obinutuzumab-HDEL produced in plant (Nicotiana benthamiana L.) is equivalent to obinutuzumab produced in CHO cells.

Journal Article PloS one · January 2018 Plants have attracted attention as bio-drug production platforms because of their economical and safety benefits. The preliminary efficacy of ZMapp, a cocktail of antibodies produced in N. benthamiana (Nicotiana benthamiana L.), suggested plants may serve ... Full text Cite

The proper localization of RESPONSIVE TO DESICCATION 20 in lipid droplets depends on their biogenesis induced by STRESS-RELATED PROTEINS in vegetative tissues.

Journal Article Biochemical and biophysical research communications · January 2018 Arabidopsis LD surface proteins, SRPs are found only in higher plants and are important for LD biogenesis and abiotic stress signaling. However, the cellular mechanism of SRPs is still unclear. To investigate molecular functions of SRPs, we used tobacco tr ... Full text Cite

The N-Terminal UND Motif of the Arabidopsis U-Box E3 Ligase PUB18 Is Critical for the Negative Regulation of ABA-Mediated Stomatal Movement and Determines Its Ubiquitination Specificity for Exocyst Subunit Exo70B1.

Journal Article The Plant cell · December 2016 The Arabidopsis thaliana U-box E3 ligases PUB18/PUB19 and PUB22/PUB23 are negative regulators of drought stress responses. PUB18/PUB19 regulate the drought stress response in an abscisic acid (ABA)-dependent manner, whereas PUB22/PUB23 regulate this respon ... Full text Cite

Arabidopsis Small Rubber Particle Protein Homolog SRPs Play Dual Roles as Positive Factors for Tissue Growth and Development and in Drought Stress Responses.

Journal Article Plant physiology · April 2016 Lipid droplets (LDs) act as repositories for fatty acids and sterols, which are used for various cellular processes such as energy production and membrane and hormone synthesis. LD-associated proteins play important roles in seed development and germinatio ... Full text Cite

Constitutive expression of CaPLA1 conferred enhanced growth and grain yield in transgenic rice plants.

Journal Article Plant molecular biology · March 2016 Phospholipids are not only important components of cell membranes, but participate in diverse processes in higher plants. In this study, we generated Capsicum annuum phospholipiase A1 (CaPLA1) overexpressing transgenic rice (Oryza sativa L.) plants under t ... Full text Cite

Expression, subcellular localization, and enzyme activity of a recombinant human extra-cellular superoxide dismutase in tobacco (Nicotiana benthamiana L.).

Journal Article Protein expression and purification · March 2016 Human extracellular superoxide dismutase (hEC-SOD) is an enzyme that scavenges reactive oxygen species (ROS). Because of its antioxidant activity, hEC-SOD has been used as a therapeutic protein to treat skin disease and arthritis in mammalian systems. In t ... Full text Cite

Overexpression of CaDSR6 increases tolerance to drought and salt stresses in transgenic Arabidopsis plants.

Journal Article Gene · November 2014 The partial CaDSR6 (Capsicum annuum Drought Stress Responsive 6) cDNA was previously identified as a drought-induced gene in hot pepper root tissues. However, the cellular role of CaDSR6 with regard to drought stress tolerance was unknown. In this report, ... Full text Cite

The Arabidopsis sn-1-specific mitochondrial acylhydrolase AtDLAH is positively correlated with seed viability.

Journal Article Journal of experimental botany · November 2011 Lipid-derived molecules produced by acylhydrolases play important roles in the regulation of diverse cellular functions in plants. In Arabidopsis, the DAD1-like phospholipase A1 family consists of 12 members, all of which possess a lipase 3 domain. In this ... Full text Cite

AtDSEL, an Arabidopsis cytosolic DAD1-like acylhydrolase, is involved in negative regulation of storage oil mobilization during seedling establishment.

Journal Article Journal of plant physiology · September 2011 Mobilization of seed storage reserves is essential for seed germination and seedling establishment. Here, we report that AtDSEL, an Arabidopsis thalianaDAD1-like Seedling Establishment-related Lipase, is involved in the mobilization of storage oils for ear ... Full text Cite

Constitutive expression of CaSRP1, a hot pepper small rubber particle protein homolog, resulted in fast growth and improved drought tolerance in transgenic Arabidopsis plants.

Journal Article Planta · June 2010 Transient and long-term shortages of fresh water are major adverse environmental factors that cause dramatic reductions in crop production and distribution globally. In this study, we isolated a full-length CaSRP1 (Capsicum annuum stress-related protein 1) ... Full text Cite

Overexpression of a Brassica rapa NGATHA gene in Arabidopsis thaliana negatively affects cell proliferation during lateral organ and root growth.

Journal Article Plant & cell physiology · December 2009 In an effort to elucidate biological functions of transcription factors of Brassica rapa L. (ssp. pekinensis), an NGATHA homolog, BrNGA1, that belongs to the B3-type transcription factor superfamily was identified and expressed in Arabidopsis thaliana unde ... Full text Cite

Enzymatic characterization of class I DAD1-like acylhydrolase members targeted to chloroplast in Arabidopsis.

Journal Article FEBS letters · July 2009 In Arabidopsis, there are at least seven class I acylhydrolase members, which have a putative N-terminal chloroplast-targeting signal. Here, we show that all seven class I proteins are localized to the chloroplasts and hydrolyze phosphatidylcholine at the ... Full text Cite

Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase.

Journal Article Plant cell reports · April 2009 Ubiquitination affects diverse physiological processes in eukaryotic cells. AtRMA1 was previously identified as an Arabidopsis homolog of human RING membrane-anchor E3 ubiquitin (Ub) ligase. Here, we identified two additional AtRMA homologs, AtRMA2 and AtR ... Full text Cite

Heterologous expression, and biochemical and cellular characterization of CaPLA1 encoding a hot pepper phospholipase A1 homolog.

Journal Article The Plant journal : for cell and molecular biology · March 2008 Phospholipid signaling has been recently implicated in diverse cellular processes in higher plants. We identified a cDNA encoding the phospholipase A1 homolog (CaPLA1) from 5-day-old early roots of hot pepper. The deduced amino acid sequence showed that th ... Full text Cite

Cooperation and functional diversification of two closely related galactolipase genes for jasmonate biosynthesis.

Journal Article Developmental cell · February 2008 Jasmonic acid (JA) plays pivotal roles in diverse plant biological processes, including wound response. Chloroplast lipid hydrolysis is a critical step for JA biosynthesis, but the mechanism of this process remains elusive. We report here that DONGLE (DGL) ... Full text Cite

Brassinosteroid induction of AtACS4 encoding an auxin‐responsive 1‐aminocyclopropane‐1‐carboxylate synthase 4 in Arabidopsis seedlings

Journal Article Physiologia Plantarum · April 2006 Brassinosteroid (BR), an endogenous steroid growth regulator of higher plants, enhances expansion and division of the cell in a number of plant species. It has been recently reported that a shared auxin–BR signalling pathway is involved in the seed ... Full text Cite

Structure and expression ofOsMRE11 in rice

Journal Article Journal of Plant Biology · June 2005 Full text Cite