73 results on '"Seok Keun Cho"'
Search Results
2. Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses
- Author
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Moon Young Ryu, Seok Keun Cho, Yourae Hong, Jinho Kim, Jong Hum Kim, Gu Min Kim, Yan-Jun Chen, Eva Knoch, Birger Lindberg Møller, Woo Taek Kim, Michael Foged Lyngkjær, and Seong Wook Yang
- Subjects
Barley ,Hordeum vulgare ,Ubiquitin proteasome system (UPS) ,Biotic stress ,Abiotic stress ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.
- Published
- 2019
- Full Text
- View/download PDF
3. MicroRNA Biomarkers in Neurodegenerative Diseases and Emerging Nano-Sensors Technology
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Pratik Shah, Seok Keun Cho, Peter Waaben Thulstrup, Morten Jannik Bjerrum, Phil Hyu Lee, Ju-Hee Kang, Yong-Joo Bhang, and Seong Wook Yang
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miRNAs ,neurodegenerative diseases ,silver nanoclusters ,DNA sensor ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
MicroRNAs (miRNAs) are essential small RNA molecules (20–24 nt) that negatively regulate the expression of target genes at the post-transcriptional level. Due to their roles in a variety of biological processes, the aberrant expression profiles of miRNAs have been identified as biomarkers for many diseases, such as cancer, diabetes, cardiovascular disease and neurodegenerative diseases. In order to precisely, rapidly and economically monitor the expression of miRNAs, many cutting-edge nanotechnologies have been developed. One of the nanotechnologies, based on DNA encapsulated silver nanoclusters (DNA/AgNCs), has increasingly been adopted to create nanoscale bio-sensing systems due to its attractive optical properties, such as brightness, tuneable emission wavelengths and photostability. Using the DNA/AgNCs sensor methods, the presence of miRNAs can be detected simply by monitoring the fluorescence alteration of DNA/AgNCs sensors. We introduce these DNA/ AgNCs sensor methods and discuss their possible applications for detecting miRNA biomarkers in neurodegenerative diseases.
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- 2017
- Full Text
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4. Cesium Toxicity Alters MicroRNA Processing and AGO1 Expressions in Arabidopsis thaliana.
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Il Lae Jung, Moonyoung Ryu, Seok Keun Cho, Pratik Shah, Ju Hye Lee, Hansol Bae, In Gyu Kim, and Seong Wook Yang
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Medicine ,Science - Abstract
MicroRNAs (miRNAs) are short RNA fragments that play important roles in controlled gene silencing, thus regulating many biological processes in plants. Recent studies have indicated that plants modulate miRNAs to sustain their survival in response to a variety of environmental stimuli, such as biotic stresses, cold, drought, nutritional starvation, and toxic heavy metals. Cesium and radio-cesium contaminations have arisen as serious problems that both impede plant growth and enter the food chain through contaminated plants. Many studies have been performed to define plant responses against cesium intoxication. However, the complete profile of miRNAs in plants during cesium intoxication has not been established. Here we show the differential expression of the miRNAs that are mostly down-regulated during cesium intoxication. Furthermore, we found that cesium toxicity disrupts both the processing of pri-miRNAs and AGONOUTE 1 (AGO1)-mediated gene silencing. AGO 1 seems to be especially destabilized by cesium toxicity, possibly through a proteolytic regulatory pathway. Our study presents a comprehensive profile of cesium-responsive miRNAs, which is distinct from that of potassium, and suggests two possible mechanisms underlying the cesium toxicity on miRNA metabolism.
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- 2015
- Full Text
- View/download PDF
5. HYL1-CLEAVAGE SUBTILASE 1 (HCS1) suppresses miRNA biogenesis in response to light-to-dark transition
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Hyun Ju Jung, Suk Won Choi, Kyung-Hwan Boo, Jee-Eun Kim, Young Kyoung Oh, Min Kyun Han, Moon Young Ryu, Chang Woo Lee, Christian Møller, Pratik Shah, Gu Min Kim, Woorim Yang, Seok Keun Cho, and Seong Wook Yang
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Cell Nucleus ,Plant Leaves ,MicroRNAs ,Multidisciplinary ,Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Ubiquitin-Protein Ligases ,Arabidopsis ,RNA-Binding Proteins ,Cell Cycle Proteins ,RNA Processing, Post-Transcriptional - Abstract
Significance HYPONASTIC LEAVES 1 (HYL1)-CLEAVAGE SUBTILASE 1 (HCS1) is a novel negative regulator of microRNA (miRNA) biogenesis that degrades HYL1 in the cytoplasm. Furthermore, cytoplasm CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) E3 ligase inhibit HCS1-mediated HYL1 degradation. The COP1-HYL1-HCS1 network may integrate two essential cellular pathways: the miRNA-biogenetic pathway and light signaling pathway. Our finding suggests a regulatory pathway in the miRNA-biogenetic system.
- Published
- 2021
6. Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses
- Author
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Woo Taek Kim, Seong Wook Yang, Michael F. Lyngkjær, Moon Young Ryu, Jinho Kim, Seok Keun Cho, Yan-Jun Chen, Gu Min Kim, Yourae Hong, Birger Lindberg Møller, Eva Knoch, and Jong Hum Kim
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0106 biological sciences ,lcsh:QH426-470 ,Ubiquitin-Protein Ligases ,lcsh:Biotechnology ,Arabidopsis ,01 natural sciences ,Host-Parasite Interactions ,03 medical and health sciences ,Ascomycota ,Biotic stress ,Gene Expression Regulation, Plant ,Barley ,lcsh:TP248.13-248.65 ,Genetics ,Plant defense against herbivory ,Amino Acid Sequence ,Ubiquitin proteasome system (UPS) ,Phylogeny ,Plant Proteins ,030304 developmental biology ,Hordeum vulgare ,0303 health sciences ,Expressed sequence tag ,biology ,Abiotic stress ,food and beverages ,Hordeum ,Oryza ,biology.organism_classification ,Droughts ,Ubiquitin ligase ,lcsh:Genetics ,Proteasome ,Seedlings ,biology.protein ,Sequence Alignment ,Genome, Plant ,Research Article ,010606 plant biology & botany ,Biotechnology - Abstract
Background Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley. Electronic supplementary material The online version of this article (10.1186/s12864-019-5696-z) contains supplementary material, which is available to authorized users.
- Published
- 2019
7. Inverse Correlation Between MPSR1 E3 Ubiquitin Ligase and HSP90.1 Balances Cytoplasmic Protein Quality Control
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Seong Wook Yang, Jong Hum Kim, Tae Rin Oh, Seok Keun Cho, and Woo Taek Kim
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0106 biological sciences ,Cytoplasm ,Protein Folding ,Physiology ,Ubiquitin-Protein Ligases ,Arabidopsis ,Plant Science ,01 natural sciences ,Downregulation and upregulation ,Gene Expression Regulation, Plant ,Stress, Physiological ,Transcription (biology) ,Genetics ,Gene silencing ,Gene Silencing ,HSP90 Heat-Shock Proteins ,Regulation of gene expression ,biology ,Arabidopsis Proteins ,Chemistry ,Articles ,biology.organism_classification ,Hsp90 ,Ubiquitin ligase ,Cell biology ,MicroRNAs ,biology.protein ,Protein folding ,Transcriptome ,010606 plant biology & botany - Abstract
MISFOLDED PROTEIN SENSING RING1 (MPSR1) is a chaperone-independent E3 ubiquitin ligase that participates in protein quality control by eliminating misfolded proteins in Arabidopsis (Arabidopsis thaliana). Here, we report that in the early stages of proteotoxic stress, cellular levels of MPSR1 increased immediately, whereas levels of HEAT SHOCK PROTEIN90.1 (AtHSP90.1) were unaltered despite massively upregulated transcription. At this stage, the gene-silencing pathway mediated by microRNA 414 (miR414) suppressed AtHSP90.1 translation. By contrast, under prolonged stress, AtHSP90.1 was not suppressed, and instead competed with MPSR1 to act on misfolded proteins, promoting the destruction of MPSR1. Deficiency or excess of MPSR1 significantly abolished or intensified the suppression of AtHSP90.1, respectively. Similar to the MPSR1-overexpressing transgenic plants, the miR414-overexpressing plants showed an increased tolerance to proteotoxic stress as compared to the wild-type plants. Although the functional relationship between MPSR1 and miR414 remains unclear, both MPSR1 and miR414 demonstrated negative modulation of the expression of AtHSP90.1. The inverse correlation between MPSR1 and AtHSP90.1 via miR414 may adjust the set-point of the HSP90-mediated protein quality control process in response to increasing stress intensity in Arabidopsis.
- Published
- 2019
8. Light triggers the miRNA-biogenetic inconsistency for de-etiolated seedling survivability in Arabidopsis thaliana
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Agustín Lucas Arce, Stephan Wenkel, Attila Molnar, András Viczián, Seong Wook Yang, Seok Keun Cho, Moon Young Ryu, Hyun Ju Jung, Sukwon Choi, Pablo Andrés Manavella, Ulla Dolde, Ferenc Nagy, Natalia Patricia Achkar, and Gu Min Kim
- Subjects
0106 biological sciences ,0301 basic medicine ,Small RNA ,Light ,Arabidopsis ,Plant Science ,HYL1 ,Biology ,Skotomorphogenesis ,01 natural sciences ,law.invention ,Ciencias Biológicas ,Transcriptome ,03 medical and health sciences ,law ,microRNA ,Arabidopsis thaliana ,Molecular Biology ,miRNA biogenesis ,light signaling ,Bioquímica y Biología Molecular ,biology.organism_classification ,Up-Regulation ,Cell biology ,MicroRNAs ,030104 developmental biology ,Seedlings ,Etiolation ,Suppressor ,CIENCIAS NATURALES Y EXACTAS ,Biogenesis ,010606 plant biology & botany - Abstract
The shift of dark-grown seedlings into light causes enormous transcriptome changes followed by a dramatic developmental transition. Here, we show that miRNA biogenesis also undergoes regulatory changes during de-etiolation. Etiolated seedlings maintain low levels of primary-miRNAs (pri-miRNAs) and miRNA processing core proteins, such as Dicer-like 1 (DCL1), SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1), whereas during de-etiolation, both pri-miRNAs and the processing components accumulated to high levels. However, most miRNA levels did not notably increase in response to light. To reconcile this inconsistency, we demonstrate that an unknown suppressor decreases miRNA-processing activity and light-induced SMALL RNA DEGRADING NUCLEASE 1 (SDN1) shortens the half-life of several miRNAs in de-etiolated seedlings. Taken together, we suggest a novel mechanism, miRNA-biogenetic inconsistency, which accounts for the intricacy of miRNA biogenesis during de-etiolation. This mechanism is essential for the survival of de-etiolated seedlings after long-term skotomorphogenesis and their optimal adaptation to ever-changing light conditions. Fil: Choi, Suk Won. Yonsei University; Corea del Sur Fil: Ryu, Moon Young. Yonsei University; Corea del Sur Fil: Viczián, András. Hungarian Academy Of Sciences; Hungría Fil: Jung, Hyun Ju. Yonsei University; Corea del Sur Fil: Kim, Gu Min. Yonsei University; Corea del Sur Fil: Arce, Agustín Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Achkar, Natalia Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Manavella, Pablo Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Dolde, Ulla. Laboratoire de Recherche En Sciences Végétales; Francia Fil: Wenkel, Stephan. University Of Copenhagen; Dinamarca Fil: Molnár, Attila. University of Edinburgh; Reino Unido Fil: Nagy, Ferenc. Hungarian Academy Of Sciences; Hungría Fil: Cho, Seok Keun. Yonsei University; Corea del Sur Fil: Yang, Seong Wook. Yonsei University; Corea del Sur
- Published
- 2020
9. The ubiquitin ligase COP1 regulates cell cycle and apoptosis by affecting p53 function in human breast cancer cell lines
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Seok Keun Cho, Byung Nyun Chun, Sang Yo Byun, Won Hye Ka, and Jong Cheol Ahn
- Subjects
Cyclin-Dependent Kinase Inhibitor p21 ,0301 basic medicine ,Cell cycle checkpoint ,Ubiquitin-Protein Ligases ,Apoptosis ,Breast Neoplasms ,Small hairpin RNA ,03 medical and health sciences ,0302 clinical medicine ,Cell Line, Tumor ,Proto-Oncogene Proteins ,Humans ,Medicine ,Pharmacology (medical) ,Radiology, Nuclear Medicine and imaging ,Cell Proliferation ,biology ,Protein Stability ,business.industry ,Cell growth ,Cell Cycle ,fungi ,Cyclin-dependent kinase 2 ,Cancer ,General Medicine ,Cell cycle ,medicine.disease ,Ubiquitin ligase ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,Oncology ,Gene Knockdown Techniques ,030220 oncology & carcinogenesis ,Cancer cell ,biology.protein ,Cancer research ,Female ,Tumor Suppressor Protein p53 ,Apoptosis Regulatory Proteins ,business - Abstract
The E3 ubiquitin ligase constitutive photomorphogenic 1 (COP1) mediates cell survival, growth, and development, and interacts with the tumor suppressor protein p53 to induce its ubiquitination and degradation. Recent studies reported that COP1 overexpression is associated with increased cell proliferation, transformation, and disease progression in a variety of cancer types. In this study, we investigated whether COP1 regulates p53-mediated cell cycle arrest and apoptosis in human breast cancer cell lines. We downregulated COP1 expression using lentiviral particles expressing short hairpin RNA (shRNA) targeting COP1 and measured the effects of the knockdown in three different breast cancer cell lines. COP1 silencing resulted in p53 activation, which induced the expression of p21 and p53-upregulated modulator of apoptosis (PUMA) expression, and reduced the levels of cyclin-dependent kinase 2 (CDK2). Notably, knockdown of COP1 was associated with cell cycle arrest during the G0/G1 phase. The COP1-mediated degradation of p53 regulates cancer cell growth and apoptosis. Our results indicate that COP1 regulates human breast cancer cell proliferation and apoptosis in a p53-dependent manner. These findings suggest that COP1 might be a promising potential target for breast cancer-related gene therapy.
- Published
- 2018
10. The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs
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Pratik Shah, Seong Wook Yang, Phil Hyu Lee, Tae-Hwan Kim, Riddhi Nagda, Il Lae Jung, Seok Keun Cho, Yong Joo Bhang, Peter W. Thulstrup, Tae Yang Song, Reka Geczy, Ju-Hee Kang, Sukwon Choi, and Morten J. Bjerrum
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Silver ,Dimer ,Metal Nanoparticles ,Sequence (biology) ,Biosensing Techniques ,02 engineering and technology ,010402 general chemistry ,01 natural sciences ,DNA sequencing ,Nanoclusters ,chemistry.chemical_compound ,Molecule ,General Materials Science ,A-DNA ,Base Sequence ,DNA ,021001 nanoscience & nanotechnology ,Fluorescence ,0104 chemical sciences ,MicroRNAs ,Spectrometry, Fluorescence ,chemistry ,Biophysics ,Nucleic Acid Conformation ,0210 nano-technology ,Dimerization - Abstract
The scaffolding DNA sequence and the size of silver nanoclusters (AgNCs), confined in a DNA template are the key parameters in determining the fluorescent properties of DNA-stabilized silver nanoclusters (DNA/AgNCs). In addition, we suggest here that the structural shift of a DNA hairpin-dimer is as important as the DNA sequence in determining the emission wavelength of DNA/AgNCs. Furthermore, we show that the structural shift post AgNC formation can be triggered by incubation time and pre-AgNC formation under salt conditions. As an important factor in predicting the emission properties of DNA/AgNCs, the modulation of DNA secondary structures with either sequence changes or ionic conditions can be applied for the dual-color detection system of a target molecule. Particularly, the dual-color detection method may increase the reliability of DNA/AgNC sensors for miRNAs.
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- 2018
11. Optimization of Agrobacterium-mediated transient expression of heterologous genes in spinach
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Jiwon Kim, Seok Keun Cho, Kyung Hwan Boo, Seong Wook Yang, Jongcheol Ahn, Key Zung Riu, Reniel S. Pamplona, Young Kyoung Oh, and Dang Viet Cao
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0106 biological sciences ,0301 basic medicine ,Agroinfiltration ,Reporter gene ,Agrobacterium ,food and beverages ,Plant Science ,Beta-glucuronidase ,Biology ,biology.organism_classification ,01 natural sciences ,Molecular biology ,03 medical and health sciences ,RNA silencing ,030104 developmental biology ,Gene expression ,Functional genomics ,Gene ,010606 plant biology & botany ,Biotechnology - Abstract
The Agrobacterium-mediated transient assay is a relatively rapid technique and a promising approach for assessing the expression of a gene of interest. Despite the successful application of this transient expression system in several plant species, it is not well understood in spinach. In this study, we analyzed various factors, including infiltration method, Agrobacterium strain and density, and co-infiltration of an RNA silencing suppressor (p19), that affect transient expression following agroinfiltration in spinach. To evaluate the effects of these factors on the transient expression system, we used the β-glucuronidase (GUS) reporter gene construct pB7WG2D as a positive control. The vacuum-based infiltration method was much more effective at GUS gene expression than was the syringe-based infiltration method. Among the three Agrobacterium strains examined (EHA105, LBA4404, and GV2260), infiltration with the GV2260 strain suspension at a final optical cell density (OD600) of 1.0 resulted in the highest gene expression. Furthermore, co-expression of suppressor p19 also increased the efficiency and duration of gene expression and protein accumulation. The results indicate that the use of optimized conditions for transient gene expression could be a simple, rapid, and effective tool for functional genomics in spinach.
- Published
- 2017
12. HYL1-CLEAVAGE SUBTILASE 1 (HCS1) suppresses miRNA biogenesis in response to light-to-dark transition.
- Author
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Hyun Ju Jung, Suk Won Choi, Kyung-Hwan Boo, Jee-Eun Kim, Young Kyoung Oh, Min Kyun Han, Moon Young Ryu, Chang Woo Lee, Møller, Christian, Shah, Pratik, Gu Min Kim, Woorim Yang, Seok Keun Cho, and Seong Wook Yang
- Subjects
MICRORNA ,UBIQUITIN ligases ,CELLULAR signal transduction ,MICROPROCESSORS - Abstract
The core plant microprocessor consists of DICER-LIKE 1 (DCL1), SERRATE (SE), and HYPONASTIC LEAVES 1 (HYL1) and plays a pivotal role in microRNA (miRNA) biogenesis. However, the proteolytic regulation of each component remains elusive. Here, we show that HYL1-CLEAVAGE SUBTILASE 1 (HCS1) is a cytoplasmic protease for HYL1-destabilization. HCS1-excessiveness reduces HYL1 that disrupts miRNA biogenesis, while HCS1-deficiency accumulates HYL1. Consistently, we identified the HYL1
K154A mutant that is insensitive to the proteolytic activity of HCS1, confirming the importance of HCS1 in HYL1 proteostasis. Moreover, HCS1-activity is regulated by light/dark transition. Under light, cytoplasmic CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) E3 ligase suppresses HCS1-activity. COP1 sterically inhibits HCS1 by obstructing HYL1 access into the catalytic sites of HCS1. In contrast, darkness unshackles HCS1-activity for HYL1-destabilization due to nuclear COP1 relocation. Overall, the COP1-HYL1-HCS1 network may integrate two essential cellular pathways: the miRNA-biogenetic pathway and light signaling pathway. [ABSTRACT FROM AUTHOR]- Published
- 2022
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13. RING E3 ligases: key regulatory elements are involved in abiotic stress responses in plants
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Woo Taek Kim, Jong Hum Kim, Seong Wook Yang, Jeong Soo Hong, Tae Rin Oh, Seok Keun Cho, and Moon Young Ryu
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0106 biological sciences ,0301 basic medicine ,Ubiquitin-Protein Ligases ,News ,01 natural sciences ,Biochemistry ,Fight-or-flight response ,03 medical and health sciences ,Ubiquitin ,Stress, Physiological ,RING E3 ligase ,Amino Acid Sequence ,Ubiquitin proteasome system (UPS) ,Molecular Biology ,Plant Proteins ,Abiotic component ,biology ,Mechanism (biology) ,Abiotic stress ,fungi ,Ubiquitination ,food and beverages ,General Medicine ,Plants ,Invited Mini Review ,Ubiquitin ligase ,Cell biology ,26s proteasome ,030104 developmental biology ,Proteasome ,biology.protein ,010606 plant biology & botany - Abstract
Plants are constantly exposed to a variety of abiotic stresses, such as drought, heat, cold, flood, and salinity. To survive under such unfavorable conditions, plants have evolutionarily developed their own resistant-mechanisms. For several decades, many studies have clarified specific stress response pathways of plants through various molecular and genetic studies. In particular, it was recently discovered that ubiquitin proteasome system (UPS), a regulatory mechanism for protein turn over, is greatly involved in the stress responsive pathways. In the UPS, many E3 ligases play key roles in recognizing and tethering poly-ubiquitins on target proteins for subsequent degradation by the 26S proteasome. Here we discuss the roles of RING ligases that have been defined in related to abiotic stress responses in plants. [BMB Reports 2017; 50(8): 393-400].
- Published
- 2017
14. AtAIRP2 E3 Ligase Affects ABA and High-Salinity Responses by Stimulating Its ATP1/SDIRIP1 Substrate Turnover
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Jong Hum Kim, Tae Rin Oh, Woo Taek Kim, Moon Young Ryu, Seong Wook Yang, and Seok Keun Cho
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0106 biological sciences ,0301 basic medicine ,Proteasome Endopeptidase Complex ,Salinity ,Physiology ,Arabidopsis ,Down-Regulation ,Germination ,Plant Science ,Models, Biological ,01 natural sciences ,Plant Epidermis ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,Bimolecular fluorescence complementation ,Cytosol ,Ubiquitin ,Tobacco ,MG132 ,Genetics ,Arabidopsis thaliana ,Abscisic acid ,biology ,Arabidopsis Proteins ,Genetic Complementation Test ,fungi ,food and beverages ,Epistasis, Genetic ,Articles ,biology.organism_classification ,Cell Compartmentation ,Ubiquitin ligase ,Protein Subunits ,Proton-Translocating ATPases ,030104 developmental biology ,Biochemistry ,Proteasome ,chemistry ,Seeds ,biology.protein ,Abscisic Acid ,Molecular Chaperones ,Protein Binding ,Subcellular Fractions ,010606 plant biology & botany - Abstract
AtAIRP2 is a cytosolic RING-type E3 ubiquitin ligase that positively regulates an abscisic acid (ABA) response in Arabidopsis (Arabidopsis thaliana). Yeast two-hybrid screening using AtAIRP2 as bait identified ATP1 (AtAIRP2 Target Protein1) as a substrate of AtAIRP2. ATP1 was found to be identical to SDIRIP1, which was reported recently to be a negative factor in ABA signaling and a target protein of the RING E3 ligase SDIR1. Accordingly, ATP1 was renamed ATP1/SDIRIP1. A specific interaction between AtAIRP2 and ATP1/SDIRIP1 and ubiquitination of ATP1/SDIRIP1 by AtAIRP2 were demonstrated in vitro and in planta. The turnover of ATP1/SDIRIP1 was regulated by AtAIRP2 in cell-free degradation and protoplast cotransfection assays. The ABA-mediated germination assay of 35S:ATP1/SDIRIP1-RNAi/atairp2 double mutant progeny revealed that ATP1/SDIRIP1 acts downstream of AtAIRP2. AtAIRP2 and SDIR1 reciprocally complemented the ABA- and salt-insensitive germination phenotypes of sdir1 and atairp2 mutants, respectively, indicating their combinatory roles in seed germination. Subcellular localization and bimolecular fluorescence complementation experiments in the presence of MG132, a 26S proteasome inhibitor, showed that AtAIRP2 and ATP1/SDIRIP1 were colocalized to the cytosolic spherical body, which lies in close proximity to the nucleus, in tobacco (Nicotiana benthamiana) leaf cells. The 26S proteasome subunits RPN12a and RPT1 and the molecular chaperones HSP70 and HSP101 were colocalized to these discrete punctae-like structures. These results raised the possibility that AtAIRP2 and ATP1/SDIRIP1 interact in the cytosolic spherical compartment. Collectively, our data suggest that the down-regulation of ATP1/SDIRIP1 by AtAIRP2 and SDIR1 RING E3 ubiquitin ligases is critical for ABA and high-salinity responses during germination in Arabidopsis.
- Published
- 2017
15. HIGLE is a bifunctional homing endonuclease that directly interacts with HYL1 and SERRATE inArabidopsis thaliana
- Author
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Mi Jung Kim, Tae Rin Oh, Kyung Hwan Boo, Jong Hum Kim, Jun-Yi Yang, Christian Peter Poulsen, Seok Keun Cho, Seong Wook Yang, Naomi Geshi, Sukwon Choi, Moon Young Ryu, and Woo Taek Kim
- Subjects
0301 basic medicine ,RNase P ,Protein domain ,Arabidopsis ,Biophysics ,RNA-binding protein ,Biochemistry ,Homing endonuclease ,03 medical and health sciences ,Endonuclease ,Protein Domains ,Structural Biology ,Catalytic Domain ,Two-Hybrid System Techniques ,Endoribonucleases ,Genetics ,Arabidopsis thaliana ,Endodeoxyribonucleases ,Molecular Biology ,Phylogeny ,biology ,Arabidopsis Proteins ,Chemistry ,RNA-Binding Proteins ,Cell Biology ,Endonucleases ,biology.organism_classification ,Molecular biology ,Cell biology ,MicroRNAs ,030104 developmental biology ,biology.protein - Abstract
A highly coordinated complex known as the microprocessor precisely processes primary transcripts of MIRNA genes into mature miRNAs. In plants, the microprocessor minimally consists of three components: Dicer-like protein 1 (DCL1), HYPONASTIC LEAF 1 (HYL1), and SERRATE (SE). To precisely modulate miRNA maturation, the microprocessor cooperates with at least 12 proteins in plants. In addition, we here show the involvement of a novel gene, HYL1-interacting GIY-YIG-like endonuclease (HIGLE). The encoded protein has a GIY-YIG domain that is generally found within a class of homing endonucleases. HIGLE directly interacts with the microprocessor components HYL1 and SE. Unlike the functions of other GIY-YIG endonucleases, the catalytic core of HIGLE has both DNase and RNase activities that sufficiently processes miRNA precursors into short fragments in vitro.
- Published
- 2017
16. Development of a virus-induced gene silencing (VIGS) system for Spinacia oleracea L
- Author
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Jongcheol Ahn, Reniel S. Pamplona, Jiwon Kim, Jungmin Lee, Dang Viet Cao, Key Zung Riu, Seok Keun Cho, Seong Wook Yang, and Kyung Hwan Boo
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Phytoene desaturase ,biology ,Agrobacterium ,food and beverages ,Plant Science ,biology.organism_classification ,01 natural sciences ,Marker gene ,Reverse genetics ,03 medical and health sciences ,030104 developmental biology ,Tobacco rattle virus ,Gene silencing ,Spinach ,Gene ,010606 plant biology & botany ,Biotechnology - Abstract
Virus-induced gene silencing (VIGS) is known as a rapid and efficient system for studying functions of interesting genes in plants. Tobacco rattle virus (TRV) is widely applied for the gene silencing of many plants. Although spinach is a TRV-susceptible plant, a TRV-based VIGS system has not yet been developed for spinach. In this study, we established a TRV-based VIGS system for spinach. To evaluate the functionality of the TRV-based VIGS system, the phytoene desaturase gene (SoPDS) was first isolated from spinach as a marker gene. Then, the VIGS vector pTRV2 was combined with the partial fragment of SoPDS gene in sense or antisense orientation. Using the Agrobacterium infiltration method, we introduced the pTRV2-SoPDS clone to silence the SoPDS gene in spinach. SoPDS was efficiently silenced, and consequently, greater than 90% of newly emerging leaves exhibited severe chlorosis symptoms in the treated plants. Levels of chlorosis symptoms were similar in both plants infected with pTRV2 vectors harboring sense (SoPDS_S) or antisense (SoPDS_A) gene fragments. Quantitative analysis of SoPDS gene expression by qRT-PCR revealed that gene expression was reduced by greater than 90% in both SoPDS_S and SoPDS_A VIGS plants. Chlorosis on leaves was prolonged up to 4~5 wk after Agrobacterium infiltration. The TRV-based VIGS system was effective in silencing the SoPDS gene in spinach, suggesting that it can be a useful reverse genetics tool for the functional study of spinach genes.
- Published
- 2017
17. Arabidopsis Tóxicos en Levadura 78 ( AtATL78 ) mediates ABA-dependent ROS signaling in response to drought stress
- Author
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Tae Rin Oh, Woo Taek Kim, Soo Jin Kim, Seong Wook Yang, Ji Yeon Suh, and Seok Keun Cho
- Subjects
0106 biological sciences ,0301 basic medicine ,Ubiquitin-Protein Ligases ,Mutant ,Arabidopsis ,Biophysics ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Stress, Physiological ,Molecular Biology ,Abscisic acid ,chemistry.chemical_classification ,Reactive oxygen species ,biology ,fungi ,food and beverages ,Cell Biology ,biology.organism_classification ,Adaptation, Physiological ,Droughts ,Ubiquitin ligase ,030104 developmental biology ,chemistry ,Catalase ,biology.protein ,Signal transduction ,Function (biology) ,Abscisic Acid ,Signal Transduction ,010606 plant biology & botany - Abstract
Plants have developed a variety of complicated responses to cope with drought, one of the most challenging environmental stresses. As a quick response, plants rapidly inhibit stomatal opening under the control of abscisic acid (ABA) signaling pathway, in order to preserve water. Here, we report that Arabidopsis Tóxicos en Levadura (ATL), a RING-type E3 ubiquitin ligase, mediates the ABA-dependent stomatal closure. In contrast to wild-type plants, the stomatal closure was fully impaired in atatl78 mutant plants even in the presence of exogenous ABA and reactive oxygen species (ROS). Besides, under high concentrations of Ca(2+), a down-stream signaling molecule of ABA signaling pathway, atatl78 mutant plants successfully closed the pores. Furthermore, AtATL78 protein indirectly associated with catalases and the deficiency of AtATL78 led the reduction of catalase activity and H2O2, implying the function of AtATL78 in the modulation of ROS activity. Based on these results, we suggest that AtATL78 possibly plays a role in promoting ROS-mediated ABA signaling pathway during drought stress.
- Published
- 2016
18. A Quick HYL1-Dependent Reactivation of MicroRNA Production Is Required for a Proper Developmental Response after Extended Periods of Light Deprivation
- Author
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Sukwon Choi, Elizabeth Karayekov, Pablo Andrés Manavella, Delfina Adela Ré, Seok Keun Cho, Axel J. Giudicatti, Natalia Patricia Achkar, Seong Wook Yang, Moon Young Ryu, Christian Peter Poulsen, Jorge J. Casal, Agustín Lucas Arce, and Jesper Harholt
- Subjects
0301 basic medicine ,Light ,MICRORNAS ,SHADE ,Arabidopsis ,Biology ,HYL1 ,General Biochemistry, Genetics and Molecular Biology ,Ciencias Biológicas ,purl.org/becyt/ford/1 [https] ,03 medical and health sciences ,Gene Expression Regulation, Plant ,LIGHT RESPONSE ,microRNA ,Gene silencing ,Gene Silencing ,Phosphorylation ,RNA Processing, Post-Transcriptional ,PHOSPHORYLATION ,purl.org/becyt/ford/1.6 [https] ,Molecular Biology ,Cell Nucleus ,Light response ,Arabidopsis Proteins ,RNA-Binding Proteins ,Cell Biology ,Bioquímica y Biología Molecular ,biology.organism_classification ,ARABIDOPSIS ,Cell biology ,Plant Leaves ,MicroRNAs ,030104 developmental biology ,Light deprivation ,Mutation ,GENE SILENCING ,CIENCIAS NATURALES Y EXACTAS ,Developmental Biology - Abstract
Achkar et al. show that a nuclear reserve pool of inactive phosphorylated HYL1, an essential cofactor for microRNA biogenesis, is resistant to dark- or shade-induced degradation. Upon light restoration, this HYL1 pool is quickly dephosphorylated to rapidly restore miRNA production and switch the developmental program to light-dependent growth. Fil: Achkar, Natalia Patricia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Cho, Seok Keun. Yonsei University; Corea del Sur Fil: Poulsen, Christian. Carlsberg Research Laboratory; Dinamarca Fil: Arce, Agustín Lucas. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Ré, Delfina Adela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Giudicatti, Axel Joel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina Fil: Karayekov, Elizabeth Irene. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina Fil: Ryu, Moon Young. Yonsei University; Corea del Sur Fil: Choi, Suk Won. Yonsei University; Corea del Sur Fil: Harholt, Jesper. Carlsberg Research Laboratory; Dinamarca Fil: Casal, Jorge José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina Fil: Yang, Seong Wook. Yonsei University; Corea del Sur. Universidad de Copenhagen; Dinamarca Fil: Manavella, Pablo Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Agrobiotecnología del Litoral. Universidad Nacional del Litoral. Instituto de Agrobiotecnología del Litoral; Argentina
- Published
- 2018
19. MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in
- Author
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Jong Hum, Kim, Seok Keun, Cho, Tae Rin, Oh, Moon Young, Ryu, Seong Wook, Yang, and Woo Taek, Kim
- Subjects
Cytoplasm ,Proteasome Endopeptidase Complex ,Protein Folding ,proteostasis ,DNA, Plant ,Arabidopsis Proteins ,Sequence Analysis, RNA ,Ubiquitin-Protein Ligases ,Arabidopsis ,Plant Biology ,Biological Sciences ,Genes, Plant ,Recombinant Proteins ,Phenotype ,PNAS Plus ,Gene Expression Regulation, Plant ,Two-Hybrid System Techniques ,Yeasts ,Proteolysis ,Protein Interaction Domains and Motifs ,Sequence Analysis ,Ubiquitins ,PQC ,Stress, Psychological ,E3 ligase - Abstract
Significance The essential roles of cytoplasmic E3 ligases in the protein quality control (PQC) pathways have been increasingly highlighted in yeast and animal studies. However, in plants, only CHIP E3 ligase has been characterized, while the knowledge of cytoplasmic PQC E3 ligases remains rudimentary. Misfolded Protein Sensing RING E3 ligase 1 (MPSR1), a self-regulatory sensor system that functions only in the occurrence of misfolded proteins, is an identified cytoplasmic PQC E3 ligase in plants that directly recognizes emergent misfolded proteins independently of chaperones. In addition, MPSR1 sustains the integrity and activity of the 26S proteasome under proteotoxic stress. Given that MPSR1 RING E3 ligase is well conserved in eukaryotes, this study sheds light on a PQC pathway that is present particularly in plants and beyond., Ubiquitin E3 ligases are crucial for eliminating misfolded proteins before they form cytotoxic aggregates that threaten cell fitness and survival. However, it remains unclear how emerging misfolded proteins in the cytoplasm can be selectively recognized and eliminated by E3 ligases in plants. We found that Misfolded Protein Sensing RING E3 ligase 1 (MPSR1) is an indispensable E3 ligase required for plant survival after protein-damaging stress. Under no stress, MPSR1 is prone to rapid degradation by the 26S proteasome, concealing its protein quality control (PQC) E3 ligase activity. Upon proteotoxic stress, MPSR1 directly senses incipient misfolded proteins and tethers ubiquitins for subsequent degradation. Furthermore, MPSR1 sustains the structural integrity of the proteasome complex at the initial stage of proteotoxic stress. Here, we suggest that the MPSR1 pathway is a constitutive mechanism for proteostasis under protein-damaging stress, as a front-line surveillance system in the cytoplasm.
- Published
- 2017
20. MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in Arabidopsis thaliana
- Author
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Woo Taek Kim, Tae Rin Oh, Moon Young Ryu, Seok Keun Cho, Jong Hum Kim, and Seong Wook Yang
- Subjects
0106 biological sciences ,0301 basic medicine ,proteostasis ,Multidisciplinary ,biology ,Ubiquitin-Protein Ligases ,Proteasome complex ,01 natural sciences ,Cell biology ,Ubiquitin ligase ,03 medical and health sciences ,Ubiquitins ,030104 developmental biology ,Proteostasis ,Aggresome ,JUNQ and IPOD ,Proteasome ,biology.protein ,PQC ,E3 ligase ,010606 plant biology & botany - Abstract
Ubiquitin E3 ligases are crucial for eliminating misfolded proteins before they form cytotoxic aggregates that threaten cell fitness and survival. However, it remains unclear how emerging misfolded proteins in the cytoplasm can be selectively recognized and eliminated by E3 ligases in plants. We found that Misfolded Protein Sensing RING E3 ligase 1 (MPSR1) is an indispensable E3 ligase required for plant survival after protein-damaging stress. Under no stress, MPSR1 is prone to rapid degradation by the 26S proteasome, concealing its protein quality control (PQC) E3 ligase activity. Upon proteotoxic stress, MPSR1 directly senses incipient misfolded proteins and tethers ubiquitins for subsequent degradation. Furthermore, MPSR1 sustains the structural integrity of the proteasome complex at the initial stage of proteotoxic stress. Here, we suggest that the MPSR1 pathway is a constitutive mechanism for proteostasis under protein-damaging stress, as a front-line surveillance system in the cytoplasm.
- Published
- 2017
21. BPH1, a novel substrate receptor of CRL3, plays a repressive role in ABA signal transduction
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Han Nim Lee, Seong Wook Yang, Sang Hoon Kim, Taijoon Chung, Jae-Hoon Lee, Seok Keun Cho, Soon Hee Kim, and Og Geum Woo
- Subjects
0106 biological sciences ,0301 basic medicine ,Scaffold protein ,Ubiquitin-Protein Ligases ,Mutant ,Arabidopsis ,Germination ,Plant Science ,Biology ,Sodium Chloride ,medicine.disease_cause ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Genetics ,medicine ,Amino Acid Sequence ,Receptor ,Gene ,Abscisic acid ,Phylogeny ,Mutation ,Arabidopsis Proteins ,organic chemicals ,Gene Expression Profiling ,fungi ,food and beverages ,General Medicine ,biology.organism_classification ,Ubiquitin ligase ,Cell biology ,030104 developmental biology ,chemistry ,Plant Stomata ,Seeds ,biology.protein ,Agronomy and Crop Science ,010606 plant biology & botany ,Abscisic Acid ,Protein Binding ,Signal Transduction - Abstract
BPH1 acts as a substrate receptor of CRL3 complex and negatively regulates ABA-mediated cellular responses. The study on its function provides information that helps further understand the relationship between ABA signaling and UPS. Abscisic acid (ABA) plays a crucial role in a variety of cellular processes, including seed dormancy, inhibition of seedling growth, and drought resistance in plants. Cullin3-RING E3 ligase (CRL3) complex is a type of multi-subunit E3 ligase, and BTB/POZ protein, a component of CRL3 complex, functions as a receptor to determine a specific substrate. To elucidate the CRL3 complex that participates in ABA-mediated cellular processes, we first investigated ABA-inducible BTB/POZ genes based on data from the AtGenExpress Visualization Tool (AVT). We then isolated an ABA-inducible gene encoding a potential CRL3 substrate receptor in Arabidopsis, BPH1 (BTB/POZ protein hypersensitive to ABA 1). The isolate gene has a BTB/POZ domain and a NPH3 domain within its N-terminal and C-terminal region, respectively. Yeast two-hybrid and co-immunoprecipitation assays showed that BPH1 physically interacted with cullin3a, a scaffold protein of CRL3, suggesting that it functions as an Arabidopsis CRL3 substrate receptor. The functional mutation of BPH1 caused delayed seed germination in response to ABA and enhanced sensitivity by NaCl and mannitol treatments as ABA-related stresses. Moreover, bph1 mutants exhibited enhanced stomatal closure under ABA application and reduced water loss when compared with wild-type, implying their enhanced tolerance to drought stress. Based on the information from microarray/AVT data and expression analysis of various ABA-inducible genes between wild-type and bph1 plants following ABA treatments, we concluded loss of BPH1 resulted in hyper-induction of a large portion of ABA-inducible genes in response to ABA. Taken together, these results show that BPH1 is negatively involved in ABA-mediated cellular events.
- Published
- 2017
22. MicroRNA Biomarkers in Neurodegenerative Diseases and Emerging Nano-Sensors Technology
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Peter W. Thulstrup, Phil Hyu Lee, Morten J. Bjerrum, Seong Wook Yang, Seok Keun Cho, Yong-Joo Bhang, Ju-Hee Kang, and Pratik Shah
- Subjects
0301 basic medicine ,Small RNA ,Dna sensor ,DNA sensor ,Computational biology ,Review Article ,lcsh:RC346-429 ,silver nanoclusters ,lcsh:RC321-571 ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,microRNA ,Medicine ,neurodegenerative diseases ,Gene ,lcsh:Neurosciences. Biological psychiatry. Neuropsychiatry ,lcsh:Neurology. Diseases of the nervous system ,business.industry ,030104 developmental biology ,Neurology ,chemistry ,miRNAs ,Neurology (clinical) ,business ,030217 neurology & neurosurgery ,DNA - Abstract
MicroRNAs (miRNAs) are essential small RNA molecules (20-24 nt) that negatively regulate the expression of target genes at the post-transcriptional level. Due to their roles in a variety of biological processes, the aberrant expression profiles of miRNAs have been identified as biomarkers for many diseases, such as cancer, diabetes, cardiovascular disease and neurodegenerative diseases. In order to precisely, rapidly and economically monitor the expression of miRNAs, many cutting-edge nanotechnologies have been developed. One of the nanotechnologies, based on DNA encapsulated silver nanoclusters (DNA/AgNCs), has increasingly been adopted to create nanoscale bio-sensing systems due to its attractive optical properties, such as brightness, tuneable emission wavelengths and photostability. Using the DNA/AgNCs sensor methods, the presence of miRNAs can be detected simply by monitoring the fluorescence alteration of DNA/AgNCs sensors. We introduce these DNA/ AgNCs sensor methods and discuss their possible applications for detecting miRNA biomarkers in neurodegenerative diseases.
- Published
- 2017
23. Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity
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Seong Wook Yang, Felix Ott, Carolyn Ohno, Seok Keun Cho, Monica Pia Caggiano, Hathi Ram, Stephan Wenkel, Marcus G. Heisler, Daniel Straub, Moritz Graeff, and Paz Merelo
- Subjects
0301 basic medicine ,Leucine zipper ,Arabidopsis ,Plant Development ,Biology ,Response Elements ,Models, Biological ,03 medical and health sciences ,Quantitative Trait, Heritable ,Gene Expression Regulation, Plant ,microRNA ,Gene ,Transcription factor ,Conserved Sequence ,Genetics ,Homeodomain Proteins ,Leucine Zippers ,Multidisciplinary ,Polarity (international relations) ,Arabidopsis Proteins ,fungi ,Promoter ,Biological Sciences ,Plant Leaves ,MicroRNAs ,030104 developmental biology ,Leaf morphogenesis ,Homeobox ,Biomarkers ,Protein Binding - Abstract
Significance Leaves, being the prime photosynthetic organ of plants, are critical in many ways to our current biosphere. A defining characteristic, which also optimizes their function, is their flat shape that depends on the correct patterning of their upper and lower tissues during development. Here, we show that the correct patterning of upper and lower leaf tissues depends on two types of transcription factors (class II and class III homeodomain leucine zipper (HD-ZIPs) that act together to repress a set of miRNAs ( MIR165/166 ), which in turn, represses the activity of these transcription factors (class III HD-ZIPs). This three-way interaction maintains the balance of tissue identities during growth, leading to the formation of a flat leaf.
- Published
- 2016
24. Overexpression of OsRDCP1, a rice RING domain-containing E3 ubiquitin ligase, increased tolerance to drought stress in rice (Oryza sativa L.)
- Author
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Woo Taek Kim, Bin Goo Kang, Hansol Bae, Seok Keun Cho, and Sung Keun Kim
- Subjects
Time Factors ,Ubiquitin-Protein Ligases ,Molecular Sequence Data ,Mutant ,Gene Expression ,Plant Science ,Gene Expression Regulation, Plant ,Stress, Physiological ,Botany ,Gene expression ,Genetics ,Poaceae ,Amino Acid Sequence ,Peptide sequence ,Plant Proteins ,Oryza sativa ,Models, Genetic ,biology ,fungi ,Ubiquitination ,food and beverages ,Oryza ,General Medicine ,Plants, Genetically Modified ,Genetically modified rice ,Droughts ,Ubiquitin ligase ,Complementation ,Seedlings ,Mutation ,biology.protein ,RING Finger Domains ,Sequence Alignment ,Agronomy and Crop Science - Abstract
CaRma1H1 was previously identified as a hot pepper drought-induced RING E3 Ub ligase. We have identified five putative proteins that display a significant sequence identity with CaRma1H1 in the rice genome database (http://signal.salk.edu/cgi-bin/RiceGE). These five rice paralogs possess a single RING motif in their N-terminal regions, consistent with the notion that RING proteins are encoded by a multi-gene family. Therefore, these proteins were named OsRDCPs (Oryza sativa RING domain-containing proteins). Among these paralogs, OsRDCP1 was induced by drought stress, whereas the other OsRDCP members were constitutively expressed, with OsRDCP4 transcripts expressed at the highest level in rice seedlings. osrdcp1 loss-of-function knockout mutant and OsRDCP1-overexpressing transgenic rice plants were developed. Phenotypic analysis showed that wild-type plants and the homozygous osrdcp1 G2 mutant line displayed similar phenotypes under normal growth conditions and in response to drought stress. This may be due to complementation by other OsRDCP paralogs. In contrast, 35S:OsRDCP1 T2 transgenic rice plants exhibited improved tolerance to severe water deficits. Although the physiological function of OsRDCP1 remains unclear, there are several possible mechanisms for its involvement in a subset of physiological responses to counteract dehydration stress in rice plants.
- Published
- 2011
25. OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment
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Jakyung Yi, Seok Keun Cho, Hee Joong Jeong, Lae Hyeon Cho, Jong-Jin Park, Jin Ping, Jinmi Yoon, Gynheung An, and Woo Taek Kim
- Subjects
Regulation of gene expression ,Mutant ,Wild type ,Mutagenesis (molecular biology technique) ,Cell Biology ,Plant Science ,Biology ,Ascorbic acid ,Molecular biology ,Ubiquitin ligase ,Ubiquitin ,Gene expression ,Genetics ,biology.protein - Abstract
The plant U-box (PUB) protein functions as an E3 ligase to poly-ubiquitinate a target protein for its degradation or post-translational modification. Here, we report functional roles for OsPUB15, which encodes a cytosolic U-box protein in the class-II PUB family. Self-ubiquitination assays showed that bacterially expressed MBP-OsPUB15 protein has E3 ubiquitin ligase activity. A T-DNA insertional mutation in OsPUB15 caused severe growth retardation and a seedling-lethal phenotype. Mutant seeds did not produce primary roots, and their shoot development was significantly delayed. Transgenic plants expressing the OsPUB15 antisense transcript phenocopied these mutant characters. The abnormal phenotypes were partially rescued by two antioxidants, catechin and ascorbic acid. Germinating seeds in the dark also recovered the rootless defect. Levels of H2O2 and oxidized proteins were higher in the knock-out mutant compared with the wild type. OsPUB15 transcript levels were increased upon H2O2, salt and drought stresses; plants overexpressing the gene grew better than the wild type under high salinity. These results indicate that PUB15 is a regulator that reduces reactive oxygen species (ROS) stress and cell death.
- Published
- 2010
26. The Arabidopsis C3H2C3-Type RING E3 Ubiquitin Ligase AtAIRP1 Is a Positive Regulator of an Abscisic Acid-Dependent Response to Drought Stress
- Author
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Moon Young Ryu, Woo Taek Kim, and Seok Keun Cho
- Subjects
chemistry.chemical_classification ,DNA ligase ,food.ingredient ,Physiology ,fungi ,Mutant ,food and beverages ,Plant Science ,Biology ,biology.organism_classification ,Ubiquitin ligase ,chemistry.chemical_compound ,food ,chemistry ,Ubiquitin ,Biochemistry ,Arabidopsis ,Genetics ,biology.protein ,Ligase activity ,Abscisic acid ,Cotyledon - Abstract
Ubiquitination is a eukaryotic posttranslational protein modification that is mediated by the cascade of E1, E2, and E3 ubiquitin (Ub) ligases and is involved in regulating numerous cellular functions. In this study, we obtained 100 different Arabidopsis (Arabidopsis thaliana) T-DNA insertion mutant plants in which RING E3 Ub ligase genes were suppressed and monitored their phenotypes in the presence of exogenous abscisic acid (ABA), a plant stress hormone. One of these loss-of-function mutants displayed ABA-insensitive phenotypes at the germination stage and was named atairp1 (for Arabidopsis ABA-insensitive RING protein 1). AtAIRP1 encodes a cytosolic protein containing a single C3H2C3-type RING motif with in vitro E3 Ub ligase activity. AtAIRP1 was significantly induced by ABA and drought stress. In contrast to atairp1 mutant plants, AtAIRP1-overexpressing transgenic plants (35S:AtAIRP1-sGFP) were hypersensitive to exogenous ABA in terms of radicle emergence, cotyledon development, root elongation, and stomatal closure. Ectopic expression of AtAIRP1-sGFP in atairp1 effectively rescued the loss-of-function ABA-insensitive phenotype. Both 35S:AtAIRP1-sGFP and atairp1/35S:AtAIRP1-sGFP plants accumulated higher amounts of hydrogen peroxide in response to exogenous ABA than did wild-type and atairp1 mutant plants. AtAIRP1 overexpressors were markedly tolerant to severe drought stress, as opposed to atairp1, which was highly susceptible. The levels of drought stress-related genes and basic leucine zipper transcription factor genes were up-regulated in the 35S:AtAIRP1-sGFP lines relative to wild-type and atairp1 mutant plants in response to ABA. Overall, these results suggest that AtAIRP1, a C3H2C3-type RING E3 Ub ligase, is a positive regulator in the Arabidopsis ABA-dependent drought response.
- Published
- 2010
27. In vitro and in vivo interaction of AtRma2 E3 ubiquitin ligase and auxin binding protein 1
- Author
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Woo Taek Kim, Soo Jin Kim, Ora Son, and Seok Keun Cho
- Subjects
Leupeptins ,Ubiquitin-Protein Ligases ,Arabidopsis ,Biophysics ,Nicotiana benthamiana ,Receptors, Cell Surface ,Cysteine Proteinase Inhibitors ,Biochemistry ,chemistry.chemical_compound ,Ubiquitin ,Two-Hybrid System Techniques ,Tobacco ,MG132 ,Molecular Biology ,Plant Proteins ,chemistry.chemical_classification ,DNA ligase ,biology ,Arabidopsis Proteins ,Ubiquitination ,Cell Biology ,biology.organism_classification ,Ubiquitin ligase ,Proteasome ,chemistry ,biology.protein - Abstract
E3 ubiquitin (Ub) ligases play diverse roles in cellular regulation in eukaryotes. Three homologous AtRmas (AtRma1, AtRma2, and AtRma3) were recently identified as ER-localized Arabidopsis homologs of human RING membrane-anchor E3 Ub ligase. Here, auxin binding protein 1 (ABP1), one of the auxin receptors in Arabidopsis, was identified as a potential substrate of AtRma2 through a yeast two-hybrid assay. An in vitro pull-down assay confirmed the interaction of full-length AtRma2 with ABP1. AtRma2 was transiently expressed in tobacco (Nicotiana benthamiana) plants through an Agrobacterium-mediated infiltration method and bound ABP1 in vivo. In vitro ubiquitination assays revealed that bacterially-expressed AtRma2 ubiquitinated ABP1. ABP1 was poly-ubiquitinated in tobacco cells and its stability was significantly increased in the presence of MG132, a 26S proteasome inhibitor. This suggests that ABP1 is controlled by the Ub/26S proteasome system. Therefore, AtRma2 is likely involved in the cellular regulation of ABP1 expression levels.
- Published
- 2010
28. Diurnal regulation of cyanogenic glucoside biosynthesis and endogenous turnover in cassava
- Author
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Frederik Bøgeskov Schmidt, Carl Erik Olsen, Seong Wook Yang, Kirsten Jørgensen, Seok Keun Cho, and Birger Lindberg Møller
- Subjects
0106 biological sciences ,0301 basic medicine ,Linamarase ,Manihot esculenta ,cytochrome P450 ,Period (gene) ,Endogeny ,Plant Science ,Linamarin ,01 natural sciences ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,03 medical and health sciences ,Lotaustralin ,chemistry.chemical_compound ,transcriptional regulation ,Ecology, Evolution, Behavior and Systematics ,Original Research ,enzyme turnover ,Ecology ,biology ,Abiotic stress ,linamarin ,Cytochrome P450 ,030104 developmental biology ,Biochemistry ,chemistry ,Cyanogenic Glucoside ,UDPG‐dependent glycosyltransferase ,biology.protein ,pathway regulation ,lotaustralin ,biosynthesis ,010606 plant biology & botany - Abstract
Cyanogenic glucosides are present in many plants, including eudicots, monocots, and ferns and function as defence compounds based on their ability to release hydrogen cyanide. In this study, the diurnal rhythm of cyanogenic glucoside content and of transcripts and enzymes involved in their biosynthesis was monitored in cassava plants grown in a glasshouse under natural light conditions. Transcripts of CYP79D1, CYP79D2, CYP71E7/11, and UGT85K5 were at minimal levels around 9 p.m., increased during the night and decreased following onset of early morning light. Transcripts of UGT85K4 and HNL10 showed more subtle variations with a maximum reached in the afternoon. Western blots showed that the protein levels of CYP71E7/11 and UGT85K4/5 decreased during the light period to a near absence around 4 p.m. and then recovered during the dark period. Transcript and protein levels of linamarase were stable throughout the 24‐hr cycle. The linamarin content increased during the dark period. In the light period, spikes in the incoming solar radiation were found to result in concomitantly reduced linamarin levels. In silico studies of the promoter regions of the biosynthetic genes revealed a high frequency of light, abiotic stress, and development‐related transcription factor binding motifs. The synthesis and endogenous turnover of linamarin are controlled both at the transcript and protein levels. The observed endogenous turnover of linamarin in the light period may offer a source of reduced nitrogen to balance photosynthetic carbon fixation. The rapid decrease in linamarin content following light spikes suggests an additional function of linamarin as a ROS scavenger.
- Published
- 2018
29. RNAi suppression of RPN12a decreases the expression of type-A ARRs, negative regulators of cytokinin signaling pathway, in Arabidopsis
- Author
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Moon Young Ryu, Seok Keun Cho, and Woo Taek Kim
- Subjects
Proteasome Endopeptidase Complex ,Cytokinins ,Protein subunit ,Biology ,Gene Expression Regulation, Plant ,RNA interference ,Guard cell ,Arabidopsis ,RNA, Antisense ,Molecular Biology ,Genetics ,Messenger RNA ,Arabidopsis Proteins ,fungi ,Wild type ,food and beverages ,Cell Biology ,General Medicine ,Plants, Genetically Modified ,biology.organism_classification ,Phenotype ,Cell biology ,DNA-Binding Proteins ,Proteasome ,RNA Interference ,Signal Transduction ,Transcription Factors - Abstract
The 26S proteasome is a 2-MDa complex with a central role in protein turn over. The 26S proteasome is comprised of one 20S core particle and two 19S regulatory particles (RPs). The RPN12a protein, a non-ATPase subunit of the 19S RP, was previously shown to be involved in cytokinin signaling in Arabidopsis. To further investigate cellular roles of RPN12a, RNAi transgenic plants of RPN12a were constructed. As expected, the 35S:RNAi-RPN12a plants showed cytokinin signaling defective phenotypes, including abnormal formation of leaves and inflorescences. Furthermore, RNAi knock-down transgenic plants exhibited additional unique phenotypes, including concave and heart-shape cotyledons, triple cotyledons, irregular and clustered guard cells, and defects in phyllotaxy, all of which are typical for defective cytokinin signaling. We next examined the mRNA level of cytokinin signaling components, including type-A ARRs, type-B ARRs, and CRFs. The expression of type-A ARRs, encoding negative regulators of cytokinin signaling, was markedly reduced in 35S:RNAi-RPN12a transgenic plants relative to that in wild type plants, while type-B ARRs and CRFs were unaffected. Our results also indicate that in vivo stability of the ARR5 protein, a negative regulator of cytokinin signaling, is mediated by the 26S proteasome complex. These results suggest that RPN12a participates in feedback inhibitory mechanism of cytokinin signaling through modulation of the abundance of ARR5 protein in Arabidopsis.
- Published
- 2009
30. Drought Stress-Induced Rma1H1, a RING Membrane-Anchor E3 Ubiquitin Ligase Homolog, Regulates Aquaporin Levels via Ubiquitination in TransgenicArabidopsisPlants
- Author
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Zheng-Yi Xu, Woo Taek Kim, Seok Keun Cho, Ora Son, Inhwan Hwang, and Hyun-Kyung Lee
- Subjects
Proteasome Endopeptidase Complex ,Recombinant Fusion Proteins ,Ubiquitin-Protein Ligases ,Green Fluorescent Proteins ,Molecular Sequence Data ,Arabidopsis ,Aquaporin ,Plant Science ,Aquaporins ,Endoplasmic Reticulum ,Ubiquitin ,Stress, Physiological ,Arabidopsis thaliana ,Amino Acid Sequence ,Ligase activity ,Research Articles ,Plant Proteins ,biology ,Arabidopsis Proteins ,Endoplasmic reticulum ,fungi ,Cell Membrane ,Ubiquitination ,food and beverages ,Intracellular Membranes ,Cell Biology ,Plants, Genetically Modified ,biology.organism_classification ,Droughts ,Ubiquitin ligase ,Protein Transport ,Biochemistry ,Proteasome ,biology.protein ,lipids (amino acids, peptides, and proteins) ,Capsicum ,Sequence Alignment - Abstract
Ubiquitination is involved in a variety of biological processes, but the exact role of ubiquitination in abiotic responses is not clearly understood in higher plants. Here, we investigated Rma1H1, a hot pepper (Capsicum annuum) homolog of a human RING membrane-anchor 1 E3 ubiquitin (Ub) ligase. Bacterially expressed Rma1H1 displayed E3 Ub ligase activity in vitro. Rma1H1 was rapidly induced by various abiotic stresses, including dehydration, and its overexpression in transgenic Arabidopsis thaliana plants conferred strongly enhanced tolerance to drought stress. Colocalization experiments with marker proteins revealed that Rma1H1 resides in the endoplasmic reticulum (ER) membrane. Overexpression of Rma1H1 in Arabidopsis inhibited trafficking of an aquaporin isoform PIP2;1 from the ER to the plasma membrane and reduced PIP2;1 levels in protoplasts and transgenic plants. This Rma1H1-induced reduction of PIP2;1 was inhibited by MG132, an inhibitor of the 26S proteasome. Furthermore, Rma1H1 interacted with PIP2;1 in vitro and ubiquitinated it in vivo. Similar to Rma1H1, Rma1, an Arabidopsis homolog of Rma1H1, localized to the ER, and its overexpression reduced the PIP2;1 protein level and inhibited trafficking of PIP2;1 from the ER to the plasma membrane in protoplasts. In addition, reduced expression of Rma homologs resulted in the increased level of PIP2;1 in protoplasts. We propose that Rma1H1 and Rma1 play a critical role in the downregulation of plasma membrane aquaporin levels by inhibiting aquaporin trafficking to the plasma membrane and subsequent proteasomal degradation as a response to dehydration in transgenic Arabidopsis plants.
- Published
- 2009
31. ArabidopsisPUB22 and PUB23 Are Homologous U-Box E3 Ubiquitin Ligases That Play Combinatory Roles in Response to Drought Stress
- Author
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Seok Keun Cho, June M. Kwak, Charlotte Song, Woo Taek Kim, and Moon Young Ryu
- Subjects
Ubiquitin-Protein Ligases ,Protein subunit ,Molecular Sequence Data ,Drought tolerance ,Mutant ,Arabidopsis ,Plant Science ,chemistry.chemical_compound ,Ubiquitin ,Gene Expression Regulation, Plant ,Two-Hybrid System Techniques ,Immunoprecipitation ,Arabidopsis thaliana ,Amino Acid Sequence ,Abscisic acid ,Phylogeny ,Research Articles ,Genetics ,Sequence Homology, Amino Acid ,biology ,Arabidopsis Proteins ,fungi ,Ubiquitination ,food and beverages ,Cell Biology ,biology.organism_classification ,Adaptation, Physiological ,Droughts ,Cell biology ,Proteasome ,chemistry ,Chromatography, Gel ,biology.protein ,Protein Binding - Abstract
Ubiquitination is involved in diverse cellular processes in higher plants. In this report, we describe Arabidopsis thaliana PUB22 and PUB23, two homologous U-box–containing E3 ubiquitin (Ub) ligases. The PUB22 and PUB23 genes were rapidly and coordinately induced by abiotic stresses but not by abscisic acid. PUB22- and PUB23-overexpressing transgenic plants were hypersensitive to drought stress. By contrast, loss-of-function pub22 and pub23 mutant plants were significantly more drought-tolerant, and a pub22 pub23 double mutant displayed even greater drought tolerance. These results indicate that PUB22 and PUB23 function as negative regulators in the water stress response. Yeast two-hybrid, in vitro pull-down, and in vivo coimmunoprecipitation experiments revealed that PUB22 and PUB23 physically interacted with RPN12a, a subunit of the 19S regulatory particle (RP) in the 26S proteasome. Bacterially expressed RPN12a was effectively ubiquitinated in a PUB-dependent fashion. RPN12a was highly ubiquitinated in 35S:PUB22 plants, but not in pub22 pub23 double mutant plants, consistent with RPN12a being a substrate of PUB22 and PUB23 in vivo. In water-stressed wild-type and PUB-overexpressing plants, a significant amount of RPN12a was dissociated from the 19S RP and appeared to be associated with small-molecular-mass protein complexes in cytosolic fractions, where PUB22 and PUB23 are localized. Overall, our results suggest that PUB22 and PUB23 coordinately control a drought signaling pathway by ubiquitinating cytosolic RPN12a in Arabidopsis.
- Published
- 2008
32. PUB22 and PUB23 U-BOX E3 ligases directly ubiquitinate RPN6, a 26S proteasome lid subunit, for subsequent degradation in Arabidopsis thaliana
- Author
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Seong Wook Yang, Moon Young Ryu, Hansol Bae, Woo Taek Kim, and Seok Keun Cho
- Subjects
Proteasome Endopeptidase Complex ,Protein subunit ,Ubiquitin-Protein Ligases ,Biophysics ,Arabidopsis ,Genes, Plant ,Biochemistry ,Gene Knockout Techniques ,Two-Hybrid System Techniques ,Enzyme Stability ,Arabidopsis thaliana ,Molecular Biology ,biology ,Arabidopsis Proteins ,fungi ,Ubiquitination ,food and beverages ,Cell Biology ,biology.organism_classification ,Plants, Genetically Modified ,Yeast ,In vitro ,Recombinant Proteins ,Ubiquitin ligase ,Cell biology ,Droughts ,Ubiquitins ,Protein Subunits ,Proteasome ,Proteolysis ,biology.protein ,Function (biology) - Abstract
Drought stress strongly affects plant growth and development, directly connected with crop yields, accordingly. However, related to the function of U-BOX E3 ligases, the underlying molecular mechanisms of desiccation stress response in plants are still largely unknown. Here we report that PUB22 and PUB23, two U-box E3 ligase homologs, tether ubiquitins to 19S proteasome regulatory particle (RP) subunit RPN6, leading to its degradation. RPN6 was identified as an interacting substrate of PUB22 by yeast two-hybrid screening, and in vitro pull-down assay confirmed that RPN6 interacts not only with PUB22, but also with PUB23. Both PUB22 and PUB23 were able to conjugate ubiquitins on RPN6 in vitro. Furthermore, RPN6 showed a shorter protein half-life in PUB22 overexpressing plants than in wild-type, besides RPN6 was significantly stabilized in pub22pub23 double knockout plants. Taken together, these results solidify a notion that PUB22 and PUB23 can alter the activity of 26S proteasome in response to drought stress.
- Published
- 2015
33. DNA/RNA chimera templates improve the emission intensity and target the accessibility of silver nanocluster-based sensors for human microRNA detection
- Author
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Seok Keun Cho, Jong Cheol Ahn, Sukwon Choi, Ho Jin Kim, Morten J. Bjerrum, Seong Wook Yang, Yong Joo Bhang, Pratik Shah, and Peter W. Thulstrup
- Subjects
Silver ,Metal Nanoparticles ,Biosensing Techniques ,Computational biology ,Biochemistry ,Cell Line ,Analytical Chemistry ,Chimera (genetics) ,chemistry.chemical_compound ,microRNA ,Electrochemistry ,Humans ,Environmental Chemistry ,Base sequence ,Monitoring methods ,Spectroscopy ,Base Sequence ,Chemistry ,RNA ,RNA Probes ,Human cell ,Molecular biology ,MicroRNAs ,Spectrometry, Fluorescence ,Template ,DNA Probes ,DNA - Abstract
In recent years microRNAs (miRNAs) have been established as important biomarkers in a variety of diseases including cancer, diabetes, cardiovascular disease, aging, Alzheimer's disease, asthma, autoimmune disease and liver diseases. As a consequence, a variety of monitoring methods for miRNAs have been developed, including a fast and simple method for miRNA detection by exploitation of the unique photoluminescence of DNA-templated silver nanoclusters (DNA/AgNCs). To increase the versatility of the AgNC-based method, we have adopted DNA/RNA chimera templates for AgNC-based probes, allowing response from several human miRNAs which are hardly detectable with DNA-based probes. Here, we demonstrate in detail the power of DNA/RNA chimera/AgNC probes in detecting two human miRNAs, let-7a and miR-200c. The DNA/RNA chimera-based probes are highly efficient to determine the level of miRNAs in several human cell lines.
- Published
- 2015
34. Inverse Correlation Between MPSR1 E3 Ubiquitin Ligase and HSP90.1 Balances Cytoplasmic Protein Quality Control.
- Author
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Jong Hum Kim, Tae Rin Oh, Seok Keun Cho, Seong Wook Yang, and Woo Taek Kim
- Published
- 2019
- Full Text
- View/download PDF
35. Isolation of cDNAs differentially expressed in response to drought stress and characterization of the Ca-LEAL1 gene encoding a new family of atypical LEA-like protein homologue in hot pepper (Capsicum annuum L. cv. Pukang)
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Jee Eun Kim, Jong A. Park, Jong Pil Hong, Baik Hwang, Seok Keun Cho, Hoo Sun Chung, Choo Bong Hong, and Woo Taek Kim
- Subjects
Abiotic component ,Ethylene ,fungi ,food and beverages ,Plant Science ,General Medicine ,Biology ,Protein degradation ,biology.organism_classification ,Cell biology ,chemistry.chemical_compound ,chemistry ,Botany ,Pepper ,Gene expression ,Genetics ,Agronomy and Crop Science ,Gene ,Cell wall modification ,Solanaceae - Abstract
Among various abiotic stresses, water deficit is one of the most severe environmental factors responsible for the reduction of crop yield in many parts of the world. By means of the mRNA differential display technique, seven cDNAs (pCa-DIs for Capsicum annuum drought induced) have been isolated that are rapidly induced when hot pepper plants are subjected to water stress (5–20% loss of fresh weight). For all of the isolated Ca-DIs , database search provided significant sequence similarity to previously described genes from different plant species. The predicted proteins encoded by the Ca-DI genes are putatively involved in processes as diverse as primary metabolism, protein degradation, cell wall modification and stress response, suggesting the complexity of cellular responses to drought stress in hot pepper plants. Particularly, we analyzed the detailed structural property and expression pattern of the Ca-DI4 ( Ca-LEAL1 ) gene. Sequence homology studies indicate that Ca-LEAL1 ( M r =19.3 kDa) belongs to a new family of atypical hydrophobic late embryogenesis-abundant-like (LEA-like) proteins. Expression analysis showed that Ca-LEAL1 was strongly activated by drought and salt stresses, and also in response to mechanical wounding in both local and systemic leaves. Moreover, the level of Ca-LEAL1 transcript was rapidly enhanced by exogenous application of ABA and ethylene. These results are consistent with the notion that an atypical hydrophobic Ca-LEAL1 protein is subject to control by diverse environmental factors and that ethylene, in conjunction with ABA, plays an important role in the regulation of the stress gene in hot pepper plants. The possible physiological functions of Ca-LEAL1 as well as other Ca-DI proteins in the adaptive process against drought stress are discussed
- Published
- 2003
36. DNA-RNA chimera indicates the flexibility of the backbone influences the encapsulation of fluorescent AgNC emitters
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Seong Wook Yang, Pratik Shah, Morten J. Bjerrum, Peter W. Thulstrup, and Seok Keun Cho
- Subjects
Silver ,Circular Dichroism ,Metals and Alloys ,Metal Nanoparticles ,Nanotechnology ,General Chemistry ,DNA ,Fluorescence ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Nanoclusters ,Chimera (genetics) ,chemistry.chemical_compound ,chemistry ,Materials Chemistry ,Ceramics and Composites ,Nucleic acid ,Nucleic Acid Conformation ,RNA - Abstract
Many DNA scaffolds efficiently encapsulate highly emissive silver nanoclusters (AgNCs). The secondary structures and the arrangement of sequences of DNA scaffolds are important factors by which the specific features of AgNCs emitters can be determined. By introducing DNA–RNA chimera scaffolds, we here explore another factor – the flexibility of the backbone of nucleic acid-templates – in creating highly fluorescent AgNC emitters.
- Published
- 2014
37. Multiplexed microRNA detection using lanthanide-labeled DNA probes and laser ablation inductively coupled plasma mass spectrometry
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Thomas C. de Bang, Pratik Shah, Seok Keun Cho, Seong Wook Yang, and Søren Husted
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Regulation of gene expression ,Chemistry ,Laser ablation inductively coupled plasma mass spectrometry ,Hybridization probe ,Arabidopsis ,Phosphorus Isotopes ,Membranes, Artificial ,Computational biology ,Blotting, Northern ,Molecular biology ,Lanthanoid Series Elements ,Sensitivity and Specificity ,Mass Spectrometry ,Analytical Chemistry ,MicroRNAs ,Laser therapy ,RNA, Plant ,microRNA ,Laser Therapy ,DNA Probes - Abstract
In the past decade, microRNAs (miRNAs) have drawn increasing attention due to their role in regulation of gene expression. Especially, their potential as biomarkers in disease diagnostics has motivated miRNA research, including the development of simple, accurate, and sensitive detection methods. The narrow size range of miRNAs (20–24 nucleotides) combined with the chemical properties of conventional reporter tags has hampered the development of multiplexed miRNA assays. In this study, we have used lanthanide-labeled DNA probes for the detection of miRNAs on membranes using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). Three miRNAs from Arabidopsis thaliana were analyzed simultaneously with high specificity, and the sensitivity of the method was comparable to radioactive detection (low femtomol range). The perspective of the developed method is highly multiplexed and quantitative miRNA analysis with high specificity and sensitivity.
- Published
- 2014
38. COP1 E3 ligase protects HYL1 to retain microRNA biogenesis
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Samir Ben Chaabane, Seok Keun Cho, Pratik Shah, Christian Peter Poulsen, and Seong Wook Yang
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Light ,medicine.medical_treatment ,Ubiquitin-Protein Ligases ,Mutant ,Arabidopsis ,General Physics and Astronomy ,General Biochemistry, Genetics and Molecular Biology ,Gene Expression Regulation, Plant ,medicine ,Arabidopsis thaliana ,RNA Processing, Post-Transcriptional ,Transcription factor ,Genetics ,Regulation of gene expression ,Multidisciplinary ,Protease ,biology ,Arabidopsis Proteins ,fungi ,RNA-Binding Proteins ,General Chemistry ,biology.organism_classification ,Cell biology ,Ubiquitin ligase ,Plant Leaves ,MicroRNAs ,RNA, Plant ,biology.protein ,Photomorphogenesis ,Function (biology) ,Peptide Hydrolases - Abstract
Constitutive photomorphogenic 1 (COP1) is a RING-finger E3 ligase that plays a central role in photomorphogenesis by destabilizing many light-regulated transcription factors and photoreceptors. Here, we reveal a novel function for COP1 E3 ligase in controlling global miRNA biogenesis in Arabidopsis thaliana. In cop1 mutants, the level of miRNAs is dramatically reduced because of the diminution of HYPONASTIC LEAVES 1 (HYL1), an RNA-binding protein required for precise miRNA processing. HYL1 is destabilized by an unidentified protease, which we tentatively call protease X, that specifically cleaves the N-terminal region from HYL1, thus neutralizing its function. Our results further show that the cytoplasmic partitioning of COP1 under light is essential to protect HYL1 against protease X. Taken together, we suggest a novel regulatory network involving HYL1, protease X, COP1 and light signalling that is indispensable for miRNA biogenesis in Arabidopsis thaliana.
- Published
- 2014
39. In-solution multiplex miRNA detection using DNA-templated silver nanocluster probes
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Peter W. Thulstrup, Seok Keun Cho, Seong Wook Yang, Yong Joo Bhang, Pratik Shah, Morten J. Bjerrum, Jong Cheol Ahn, and Sukwon Choi
- Subjects
Silver ,Base Sequence ,Chemistry ,Nanotechnology ,DNA ,Biochemistry ,Fluorescence ,DNA sequencing ,Analytical Chemistry ,Nanoclusters ,Nanostructures ,Native Polyacrylamide Gel Electrophoresis ,chemistry.chemical_compound ,MicroRNAs ,Molecular Probes ,Sequence Homology, Nucleic Acid ,microRNA ,Electrochemistry ,Environmental Chemistry ,A-DNA ,Multiplex ,Spectroscopy - Abstract
MicroRNAs (miRNAs) are small regulatory RNAs (size ∼21nt to ∼25nt) that can be used as biomarkers of disease diagnosis, and efforts have been directed towards the invention of a rapid, simple and sequence-selective detection method for miRNAs. We recently developed a DNA/silver nanoclusters (AgNCs)-based turn-off fluorescence method in the presence of target miRNA. To further advance our method toward multiplex miRNA detection in solution, the design of various fluorescent DNA/AgNCs probes was essential. Therefore, tethering of DNA-12nt scaffolds with 9 different AgNCs emitters to target-sensing DNA sequences was investigated. Interestingly, for the creation of spectrally different DNA/AgNCs probes, not only were the emitters encapsulated in 9 different DNA-12nt scaffolds necessary but the tethered target-sensing DNA sequences are also crucial to tune the fluorescence across the visible to infra-red region. In this study, we obtained three spectrally distinctive emitters of each DNA/AgNCs probes such as green, red, and near-infrared (NIR) fluorescence. Using these DNA/AgNCs probes, we here show a proof of concept for a rapid, one-step, in-solution multiplex miRNA detection method.
- Published
- 2014
40. Locking-to-unlocking system is an efficient strategy to design DNA/silver nanoclusters (AgNCs) probe for human miRNAs
- Author
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Seok Keun Cho, Seong Wook Yang, Moon Young Ryu, Morten J. Bjerrum, Suk Won Choi, Pratik Shah, Yong Joo Bhang, Ho Jin Kim, and Peter W. Thulstrup
- Subjects
Silver ,Base pair ,Molecular Sequence Data ,Metal Nanoparticles ,02 engineering and technology ,Computational biology ,Biology ,010402 general chemistry ,Bioinformatics ,01 natural sciences ,Nanoclusters ,Cytosine ,chemistry.chemical_compound ,Cell Line, Tumor ,microRNA ,Genetics ,Humans ,RNA, Neoplasm ,Base Pairing ,Protein secondary structure ,Chromatography, High Pressure Liquid ,Fluorescent Dyes ,Base Sequence ,Oligonucleotide ,Circular Dichroism ,RNA ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,MicroRNAs ,Spectrometry, Fluorescence ,Template ,chemistry ,Nucleic Acid Conformation ,Methods Online ,Oligonucleotide Probes ,0210 nano-technology ,DNA - Abstract
MicroRNAs (miRNAs), small non-coding RNA molecules, are important biomarkers for research and medical purposes. Here, we describe the development of a fast and simple method using highly fluorescent oligonucleotide-silver nanocluster probes (DNA/AgNCs) to efficiently detect specific miRNAs. Due to the great sequence diversity of miRNAs in humans and other organisms, a uniform strategy for miRNA detection is attractive. The concept presented is an oligonucleotide- based locking-to-unlocking system that can be endowed with miRNA complementarity while maintaining the same secondary structure. The locking-to-unlocking system is based on fold-back anchored DNA templates that consist of a cytosine-rich loop for AgNCs stabilization, an miRNA recognition site and an overlap region for hairpin stabilization. When an miRNA is recognized, fluorescence in the visible region is specifically extinguished in a concentration-dependent manner. Here, the exact composition of the fold-back anchor for the locking-to-unlocking system has been systematically optimized, balancing propensity for loop-structure formation, encapsulation of emissive AgNCs and target sensitivity. It is demonstrated that the applied strategy successfully can detect a number of cancer related miRNAs in RNA extracts from human cancer cell lines.
- Published
- 2015
41. The Arabidopsis RING E3 ubiquitin ligase AtAIRP2 plays combinatory roles with AtAIRP1 in abscisic acid-mediated drought stress responses
- Author
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Seok Keun Cho, Woo Taek Kim, Dong Hye Seo, Moon Young Ryu, and Bin Goo Kang
- Subjects
Physiology ,Transgene ,Ubiquitin-Protein Ligases ,Mutant ,Molecular Sequence Data ,Arabidopsis ,Germination ,Plant Science ,Plant Roots ,Gene Expression Regulation, Enzymologic ,chemistry.chemical_compound ,Cytosol ,Ubiquitin ,Gene Expression Regulation, Plant ,Stress, Physiological ,Genetics ,Arabidopsis thaliana ,Amino Acid Sequence ,Promoter Regions, Genetic ,Abscisic acid ,biology ,Arabidopsis Proteins ,fungi ,food and beverages ,biology.organism_classification ,Ubiquitin ligase ,Droughts ,Up-Regulation ,Systems Biology, Molecular Biology, and Gene Regulation ,Complementation ,Plant Leaves ,chemistry ,Biochemistry ,Seedlings ,Mutation ,Seeds ,biology.protein ,Sequence Alignment ,Abscisic Acid - Abstract
The ubiquitin (Ub)-26S proteasome pathway is implicated in various cellular processes in higher plants. AtAIRP1, a C3H2C3-type RING (for Really Interesting New Gene) E3 Ub ligase, is a positive regulator in the Arabidopsis (Arabidopsis thaliana) abscisic acid (ABA)-dependent drought response. Here, the AtAIRP2 (for Arabidopsis ABA-insensitive RING protein 2) gene was identified and characterized. AtAIRP2 encodes a cytosolic C3HC4-type RING E3 Ub ligase whose expression was markedly induced by ABA and dehydration stress. Thus, AtAIRP2 belongs to a different RING subclass than AtAIRP1 with a limited sequence identity. AtAIRP2-overexpressing transgenic (35S:AtAIRP2-sGFP) and atairp2 loss-of-function mutant plants exhibited hypersensitive and hyposensitive phenotypes, respectively, to ABA in terms of seed germination, root growth, and stomatal movement. 35S:AtAIRP2-sGFP plants were highly tolerant to severe drought stress, and atairp2 alleles were more susceptible to water stress than were wild-type plants. Higher levels of drought-induced hydrogen peroxide production were detected in 35S:AtAIRP2-sGFP as compared with atairp2 plants. ABA-inducible drought-related genes were up-regulated in 35S:AtAIRP2-sGFP and down-regulated in atairp2 progeny. The positive effects of AtAIRP2 on ABA-induced stress genes were dependent on SNF1-related protein kinases, key components of the ABA signaling pathway. Therefore, AtAIRP2 is involved in positive regulation of ABA-dependent drought stress responses. To address the functional relationship between AtAIRP1 and AtAIRP2, FLAG-AtAIRP1 and AtAIRP2-sGFP genes were ectopically expressed in atairp2-2 and atairp1 plants, respectively. Constitutive expression of FLAG-AtAIRP1 and AtAIRP2-sGFP in atairp2-2 and atairp1 plants, respectively, reciprocally rescued the loss-of-function ABA-insensitive phenotypes during germination. Additionally, atairp1/35S:AtAIRP2-sGFP and atairp2-2/35S:FLAG-AtAIRP1 complementation lines were more tolerant to dehydration stress relative to atairp1 and atairp2-2 single knockout plants. Overall, these results suggest that AtAIRP2 plays combinatory roles with AtAIRP1 in Arabidopsis ABA-mediated drought stress responses.
- Published
- 2011
42. OsPUB15, an E3 ubiquitin ligase, functions to reduce cellular oxidative stress during seedling establishment
- Author
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Jong-Jin, Park, Jakyung, Yi, Jinmi, Yoon, Lae-Hyeon, Cho, Jin, Ping, Hee Joong, Jeong, Seok Keun, Cho, Woo Taek, Kim, and Gynheung, An
- Subjects
Base Sequence ,Cell Death ,Ubiquitin-Protein Ligases ,Genetic Complementation Test ,Molecular Sequence Data ,Oryza ,Hydrogen Peroxide ,Salt Tolerance ,Plants, Genetically Modified ,Adaptation, Physiological ,Plant Roots ,Mutagenesis, Insertional ,Oxidative Stress ,Phenotype ,Gene Expression Regulation, Plant ,Seedlings ,Seeds ,Escherichia coli ,Plant Proteins - Abstract
The plant U-box (PUB) protein functions as an E3 ligase to poly-ubiquitinate a target protein for its degradation or post-translational modification. Here, we report functional roles for OsPUB15, which encodes a cytosolic U-box protein in the class-II PUB family. Self-ubiquitination assays showed that bacterially expressed MBP-OsPUB15 protein has E3 ubiquitin ligase activity. A T-DNA insertional mutation in OsPUB15 caused severe growth retardation and a seedling-lethal phenotype. Mutant seeds did not produce primary roots, and their shoot development was significantly delayed. Transgenic plants expressing the OsPUB15 antisense transcript phenocopied these mutant characters. The abnormal phenotypes were partially rescued by two antioxidants, catechin and ascorbic acid. Germinating seeds in the dark also recovered the rootless defect. Levels of H2O2 and oxidized proteins were higher in the knock-out mutant compared with the wild type. OsPUB15 transcript levels were increased upon H2O2, salt and drought stresses; plants overexpressing the gene grew better than the wild type under high salinity. These results indicate that PUB15 is a regulator that reduces reactive oxygen species (ROS) stress and cell death.
- Published
- 2011
43. Characterization of three Arabidopsis homologs of human RING membrane anchor E3 ubiquitin ligase
- Author
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Ora Son, Seok Keun Cho, Eun Yu Kim, and Woo Taek Kim
- Subjects
Transgene ,Ubiquitin-Protein Ligases ,Molecular Sequence Data ,Arabidopsis ,Plant Science ,Endoplasmic Reticulum ,Genes, Plant ,Ubiquitin ,Gene Expression Regulation, Plant ,Gene expression ,Amino Acid Sequence ,RNA, Messenger ,Promoter Regions, Genetic ,Gene ,chemistry.chemical_classification ,DNA ligase ,biology ,Arabidopsis Proteins ,Ubiquitination ,Membrane Proteins ,Promoter ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Ubiquitin ligase ,Biochemistry ,chemistry ,RNA, Plant ,Mutation ,biology.protein ,Agronomy and Crop Science - Abstract
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 AtRMA3. The predicted AtRMA proteins contain a RING motif and a trans-membrane domain in their N-terminal and extreme C-terminal regions, respectively. Bacterially expressed AtRMAs exhibited E3 ligase activity in vitro, which was abrogated by mutation of the conserved cysteine residue in their RING domains. In vivo targeting experiments using an Arabidopsis protoplast-transfection system showed that all three AtRMAs are localized to the ER. Although RT-PCR analysis indicated that AtRMA mRNAs were expressed constitutively in all tissues examined, their promoter activities were differentially detected in a tissue-specific fashion in AtRMA-promoter::GUS transgenic Arabidopsis plants. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot–root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. We suggest that a ubiquitnation pathway involving these AtRMA E3 Ub ligases may play a role in the growth and development of Arabidopsis.
- Published
- 2009
44. Heterologous expression and molecular and cellular characterization of CaPUB1 encoding a hot pepper U-Box E3 ubiquitin ligase homolog
- Author
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Seok Keun Cho, Hyun Sook Pai, Jungmook Kim, Hoo Sun Chung, Young Yil Bahk, Moon Young Ryu, Woo Taek Kim, Myeong Min Lee, and Mi Jin Park
- Subjects
Proteomics ,DNA, Complementary ,Saccharomyces cerevisiae Proteins ,Physiology ,Transgene ,Ubiquitin-Protein Ligases ,Amino Acid Motifs ,Molecular Sequence Data ,Arabidopsis ,Plant Science ,Saccharomyces cerevisiae ,Ubiquitin ,Endopeptidases ,Genetics ,Escherichia coli ,Electrophoresis, Gel, Two-Dimensional ,Amino Acid Sequence ,Gene ,Cell Proliferation ,Plant Proteins ,biology ,Wild type ,food and beverages ,biology.organism_classification ,Plants, Genetically Modified ,Ubiquitin ligase ,Phenotype ,Biochemistry ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,biology.protein ,Heterologous expression ,Cauliflower mosaic virus ,Capsicum ,Sequence Alignment ,Research Article - Abstract
The U-box motif is a conserved domain found in the diverse isoforms of E3 ubiquitin ligase in eukaryotes. From water-stressed hot pepper (Capsicum annuum L. cv Pukang) plants, we isolated C. annuum putative U-box protein 1 (CaPUB1), which encodes a protein containing a single U-box motif in its N-terminal region. In vitro ubiquitination and site-directed mutagenesis assays revealed that CaPUB1 possessed E3 ubiquitin ligase activity and that the U-box motif was indeed essential for its enzyme activity. RNA gel-blot analysis showed that CaPUB1 mRNA was induced rapidly by a broad spectrum of abiotic stresses, including drought, high salinity, cold temperature, and mechanical wounding, but not in response to ethylene, abscisic acid, or a bacterial pathogen, suggesting its role in the early events in the abiotic-related defense response. Because transgenic work was extremely difficult in hot pepper, in this study we overexpressed CaPUB1 in Arabidopsis (Arabidopsis thaliana) to provide cellular information on the function of this gene in the development and plant responses to abiotic stresses. Transgenic Arabidopsis plants that constitutively expressed the CaPUB1 gene under the control of the cauliflower mosaic virus 35S promoter had markedly longer hypocotyls and roots and grew more rapidly than the wild type, leading to an early bolting phenotype. Microscopic analysis showed that 35S∷CaPUB1 roots had increased numbers of small-sized cells, resulting in disordered, highly populated cell layers in the cortex, endodermis, and stele. In addition, CaPUB1-overexpressing plants displayed increased sensitivity to water stress and mild salinity. These results indicate that CaPUB1 is functional in Arabidopsis cells, thereby effectively altering cell and tissue growth and also the response to abiotic stresses. Comparative proteomic analysis showed that the level of RPN6 protein, a non-ATPase subunit of the 26S proteasome complex, was significantly reduced in 35S∷CaPUB1 seedlings as compared to the wild type. Pull-down and ubiquitination assays demonstrated that RPN6 interacted physically with CaPUB1 and was ubiquitinated in a CaPUB1-dependent manner in vitro. Although the physiological function of CaPUB1 is not yet clear, there are several possibilities for its involvement in a subset of physiological responses to counteract dehydration and high-salinity stresses in transgenic Arabidopsis seedlings.
- Published
- 2006
45. Constitutive expression of abiotic stress-inducible hot pepper CaXTH3, which encodes a xyloglucan endotransglucosylase/hydrolase homolog, improves drought and salt tolerance in transgenic Arabidopsis plants
- Author
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Tae Jin Eom, Jong A. Park, Jee Eun Kim, Seok Keun Cho, and Woo Taek Kim
- Subjects
Transcriptional Activation ,Transgene ,Molecular Sequence Data ,Biophysics ,Arabidopsis ,Drug Resistance ,Gene Expression ,Genetically modified crops ,Biology ,Sodium Chloride ,Genes, Plant ,Biochemistry ,Transgenic Arabidopsis ,Cell wall ,Disasters ,Structural Biology ,Botany ,Pepper ,Genetics ,Coordinated gene expression ,Xyloglucan endotransglucosylase/hydrolase ,Amino Acid Sequence ,Molecular Biology ,Plant Proteins ,Abiotic component ,Saline Solution, Hypertonic ,Abiotic stress ,food and beverages ,Glycosyltransferases ,Cell Biology ,Xyloglucan endotransglucosylase ,biology.organism_classification ,Plants, Genetically Modified ,Cell biology ,Plant Leaves ,Capsicum ,Hot pepper - Abstract
Xyloglucan endotransglucosylase/hydrolase (XTH) has been recognized as a cell wall-modifying enzyme, participating in the diverse physiological roles. From water-stressed hot pepper plants, we isolated three different cDNA clones (pCaXTH1, pCaXTH2, and pCaXTH3) that encode XTH homologs. RT-PCR analysis showed that three CaXTH mRNAs were concomitantly induced by a broad spectrum of abiotic stresses, including drought, high salinity and cold temperature, and in response to stress hormone ethylene, suggesting their role in the early events in the abiotic-related defense response. Transgenic Arabidopsis plants that constitutively expressed the CaXTH3 gene under the control of the CaMV 35S promoter exhibited abnormal leaf morphology; the transgenic leaves showed variable degrees of twisting and bending along the edges, resulting in a severely wrinkled leaf shape. Microscopic analysis showed that 35S-CaXTH3 leaves had increased numbers of small-sized cells, resulting in disordered, highly populated mesophyll cells in each dorsoventral layer, and appeared to contain a limited amount of starch. In addition, the 35S-CaXTH3 transgenic plants displayed markedly improved tolerance to severe water deficit, and to lesser extent to high salinity in comparison with the wild-type plants. These results indicate that CaXTH3 is functional in heterologous Arabidopsis cells, thereby effectively altering cell growth and also the response to abiotic stresses. Although the physiological function of CaXTHs is not yet clear, there are several possibilities for their involvement in a subset of physiological responses to counteract dehydration and high salinity stresses in transgenic Arabidopsis plants.
- Published
- 2006
46. AtAIRP2 E3 Ligase Affects ABA and High-Salinity Responses by Stimulating Its ATP1/SDIRIP1 Substrate Turnover.
- Author
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Tae Rin Oh, Jong Hum Kim, Seok Keun Cho, Moon Young Ryu, Seong Wook Yang, and Woo Taek Kim
- Published
- 2017
- Full Text
- View/download PDF
47. Regulation of MIR165/166 by class II and class III homeodomain leucine zipper proteins establishes leaf polarity.
- Author
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Merelo, Paz, Ram, Hathi, Caggiano, Monica Pia, Ohno, Carolyn, Ott, Felix, Straub, Daniel, Graeff, Moritz, Seok Keun Cho, Seong Wook Yang, Stephan Wenkel, and Marcus G. Heisler
- Subjects
LEAF anatomy ,MICRORNA ,HOMEOBOX proteins ,LEUCINE zippers ,FOLIAR diagnosis ,PLANTS - Abstract
A defining feature of plant leaves is their flattened shape. This shape depends on an antagonism between the genes that specify adaxial (top) and abaxial (bottom) tissue identity; however, the molecular nature of this antagonism remains poorly understood. Class III homeodomain leucine zipper (HD-ZIP) transcription factors are key mediators in the regulation of adaxial-abaxial patterning. Their expression is restricted adaxially during early development by the abaxially expressed microRNA (MIR)165/166, yet the mechanism that restricts MIR165/166 expression to abaxial leaf tissues remains unknown. Here, we show that class III and class II HD-ZIP proteins act together to repress MIR165/166 via a conserved cis-element in their promoters. Organ morphology and tissue patterning in plants, therefore, depend on a bidirectional repressive circuit involving a set of miRNAs and its targets. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
48. Effect of salts, solvents and buffer on miRNA detection using DNA silver nanocluster (DNA/AgNCs) probes
- Author
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Sukwon Choi, Andreas Rørvig-Lund, Seok Keun Cho, Peter W. Thulstrup, Yong Joo Bhang, Pratik Shah, Jong Cheol Ahn, and Seong Wook Yang
- Subjects
Silver ,Materials science ,Metal Nanoparticles ,Bioengineering ,Nanotechnology ,Buffers ,Buffer (optical fiber) ,Nanoclusters ,Nucleic acid thermodynamics ,chemistry.chemical_compound ,microRNA ,General Materials Science ,A-DNA ,Electrical and Electronic Engineering ,Gene ,Fluorescent Dyes ,Mechanical Engineering ,Nucleic Acid Hybridization ,DNA ,General Chemistry ,Fluorescence ,MicroRNAs ,Spectrometry, Fluorescence ,chemistry ,Mechanics of Materials ,Solvents ,Biophysics ,Salts ,DNA Probes - Abstract
MicroRNAs (miRNAs) are small regulatory RNAs (size ~21 nt to ~25 nt) which regulate a variety of important cellular events in plants, animals and single cell eukaryotes. Especially because of their use in diagnostics of human diseases, efforts have been directed towards the invention of a rapid, simple and sequence selective detection method for miRNAs. Recently, we reported an innovative method for the determination of miRNA levels using the red fluorescent properties of DNA/silver nanoclusters (DNA/AgNCs). Our method is based on monitoring the emission drop of a DNA/AgNCs probe in the presence of its specific target miRNA. Accordingly, the accuracy and efficiency of the method relies on the sensitivity of hybridization between the probe and target. To gain specific and robust hybridization between probe and target, we investigated a range of diverse salts, organic solvents, and buffer to optimize target sensing conditions. Under the newly adjusted conditions, the target sensitivity and the formation of emissive DNA/AgNCs probes were significantly improved. Also, fortification of the Tris-acetate buffer with inorganic salts or organic solvents improved the sensitivity of the DNA/AgNC probes. On the basis of these optimizations, the versatility of the DNA/AgNCs-based miRNA detection method can be expanded.
- Published
- 2014
49. Post-Translational Regulation of miRNA Pathway Components, AGO1 and HYL1, in Plants.
- Author
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Seok Keun Cho, Moon Young Ryu, Shah, Pratik, Poulsen, Christian Peter, and Seong Wook Yang
- Abstract
Post-translational modifications (PTMs) of proteins are essential to increase the functional diversity of the proteome. By adding chemical groups to proteins, or degrading entire proteins by phosphorylation, glycosylation, ubiquitination, neddylation, acetylation, lipidation, and proteolysis, the complexity of the proteome increases, and this then influences most biological processes. Although small RNAs are crucial regulatory elements for gene expression in most eukaryotes, PTMs of small RNA microprocessor and RNA silencing components have not been extensively investigated in plants. To date, several studies have shown that the proteolytic regulation of AGOs is important for host-pathogen interactions. DRB4 is regulated by the ubiquitin-proteasome system, and the degradation of HYL1 is modulated by a de-etiolation repressor, COP1, and an unknown cytoplasmic protease. Here, we discuss current findings on the PTMs of microprocessor and RNA silencing components in plants. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
50. Locking-to-unlocking system is an efficient strategy to design DNA/silver nanoclusters (AgNCs) probe for human miRNAs.
- Author
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Shah, Pratik, Suk Won Choi, Ho-jin Kim, Seok Keun Cho, Yong-Joo Bhang, Moon Young Ryu, Thulstrup, Peter Waaben, Bjerrum, Morten Jannik, and Seong Wook Yang
- Published
- 2016
- Full Text
- View/download PDF
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