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Kwon Y, Kim C, Choi G. Phytochrome B photobody components. New Phytol 2024; 242:909-915. [PMID: 38477037 DOI: 10.1111/nph.19675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
Phytochrome B (phyB) is a red and far-red photoreceptor that promotes light responses. Upon photoactivation, phyB enters the nucleus and forms a molecular condensate called a photobody through liquid-liquid phase separation. Phytochrome B photobody comprises phyB, the main scaffold molecule, and at least 37 client proteins. These clients belong to diverse functional categories enriched with transcription regulators, encompassing both positive and negative light signaling factors, with the functional bias toward the negative factors. The functionally diverse clients suggest that phyB photobody acts either as a trap to capture proteins, including negatively acting transcription regulators, for processes such as sequestration, modification, or degradation or as a hub where proteins are brought into close proximity for interaction in a light-dependent manner.
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Affiliation(s)
- Yongmin Kwon
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Chanhee Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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2
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Kim H, Lee N, Kim Y, Choi G. The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins. Plant Cell 2024:koae110. [PMID: 38593049 DOI: 10.1093/plcell/koae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024]
Abstract
Phytochrome-interacting factors (PIFs) are basic helix-loop-helix transcription factors that regulate light responses downstream of phytochromes. In Arabidopsis (Arabidopsis thaliana), eight PIFs (PIF1-8) regulate light responses, either redundantly or distinctively. Distinctive roles of PIFs may be attributed to differences in mRNA expression patterns governed by promoters or variations in molecular activities of proteins. However, elements responsible for the functional diversification of PIFs have yet to be determined. Here, we investigated the role of promoters and proteins in the functional diversification of PIF1 and PIF4 by analyzing transgenic lines expressing promoter-swapped PIF1 and PIF4, as well as chimeric PIF1 and PIF4 proteins. For seed germination, PIF1 promoter played a major role, conferring dominance to PIF1 gene with a minor contribution from PIF1 protein. Conversely, for hypocotyl elongation under red light, PIF4 protein was the major element conferring dominance to PIF4 gene with the minor contribution from PIF4 promoter. In contrast, both PIF4 promoter and PIF4 protein were required for the dominant role of PIF4 in promoting hypocotyl elongation at high ambient temperatures. Together, our results support that the functional diversification of PIF1 and PIF4 genes resulted from contributions of both promoters and proteins, with their relative importance varying depending on specific light responses.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Yeojae Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
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3
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Hur YS, Oh J, Kim N, Kim S, Son O, Kim J, Um JH, Ji Z, Kim MH, Ko JH, Ohme-Takagi M, Choi G, Cheon CI. Arabidopsis transcription factor TCP13 promotes shade avoidance syndrome-like responses by directly targeting a subset of shade-responsive gene promoters. J Exp Bot 2024; 75:241-257. [PMID: 37824096 DOI: 10.1093/jxb/erad402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
TCP13 belongs to a subgroup of TCP transcription factors implicated in the shade avoidance syndrome (SAS), but its exact role remains unclear. Here, we show that TCP13 promotes the SAS-like response by enhancing hypocotyl elongation and suppressing flavonoid biosynthesis as a part of the incoherent feed-forward loop in light signaling. Shade is known to promote the SAS by activating PHYTOCHROME-INTERACTING FACTOR (PIF)-auxin signaling in plants, but we found no evidence in a transcriptome analysis that TCP13 activates PIF-auxin signaling. Instead, TCP13 mimics shade by activating the expression of a subset of shade-inducible and cell elongation-promoting SAUR genes including SAUR19, by direct targeting of their promoters. We also found that TCP13 and PIF4, a molecular proxy for shade, repress the expression of flavonoid biosynthetic genes by directly targeting both shared and distinct sets of biosynthetic gene promoters. Together, our results indicate that TCP13 promotes the SAS-like response by directly targeting a subset of shade-responsive genes without activating the PIF-auxin signaling pathway.
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Affiliation(s)
- Yoon-Sun Hur
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Jeonghwa Oh
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Namuk Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Sunghan Kim
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Ora Son
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Jiyoung Kim
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Ji-Hyun Um
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Zuowei Ji
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
| | - Min-Ha Kim
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Choong-Ill Cheon
- Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea
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Kim C, Choi G. Light-Dependent High Ambient Temperature-Induced Senescence Assay Using Whole Seedlings. Methods Mol Biol 2024; 2795:25-35. [PMID: 38594524 DOI: 10.1007/978-1-0716-3814-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
High ambient temperature affects various plant developmental and physiological processes, including senescence. Here, we present a protocol for assaying light-dependent high ambient temperature-induced senescence using whole seedlings. The protocol covers all steps, from inducing senescence by darkness at high ambient temperature to determining the degree of senescence, and includes experimental tips and notes. The onset of senescence is established by quantifying the increased expression of senescence marker genes by quantitative real-time PCR (RT-qPCR). The degree of senescence is determined by measuring the loss of chlorophyll and the increase of ion leakage. This protocol can be adapted to study light-dependent high ambient temperature-induced senescence in other plant species by adjusting the temperature and duration of darkness.
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Affiliation(s)
- Chanhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
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Kwon Y, Kim C, Choi G. Isolation of Phytochrome B Photobodies. Methods Mol Biol 2024; 2795:113-122. [PMID: 38594533 DOI: 10.1007/978-1-0716-3814-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Phytochrome B (phyB), a plant photoreceptor, forms a membraneless organelle known as a photobody. Here, we present a protocol for the isolation of phyB photobodies through fluorescence-activated particle sorting from mature transgenic Arabidopsis leaves expressing phyB-GFP. This protocol involves the isolation of nuclei from frozen ground leaves using sucrose gradient centrifugation, the disruption of nuclear envelopes by sonication, and the subsequent isolation of phyB photobodies through fluorescence-activated particle sorting. We include experimental tips and notes for each step.
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Affiliation(s)
- Yongmin Kwon
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - Chanhee Kim
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, South Korea.
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Jeon J, Rahman MM, Yang HW, Kim J, Gam HJ, Song JY, Jeong SW, Kim JI, Choi MG, Shin DH, Choi G, Shim D, Jung JH, Lee IJ, Jeon JS, Park YI. Modulation of warm temperature-sensitive growth using a phytochrome B dark reversion variant, phyB[G515E], in Arabidopsis and rice. J Adv Res 2023:S2090-1232(23)00324-7. [PMID: 37926145 DOI: 10.1016/j.jare.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/19/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023] Open
Abstract
INTRODUCTION Ambient temperature-induced hypocotyl elongation in Arabidopsis seedlings is sensed by the epidermis-localized phytochrome B (phyB) and transduced into auxin biosynthesis via a basic helix-loop-helix transcription factor, phytochrome-interacting factor 4 (PIF4). Once synthesized, auxin travels down from the cotyledons to the hypocotyl, triggering hypocotyl cell elongation. Thus, the phyB-PIF4 module involved in thermosensing and signal transduction is a potential genetic target for engineering warm temperature-insensitive plants. OBJECTIVES This study aims to manipulate warm temperature-induced elongation of plants at the post-translational level using phyB variants with dark reversion, the expression of which is subjected to heat stress. METHODS The thermosensitive growth response of Arabidopsis was manipulated by expressing the single amino acid substitution variant of phyB (phyB[G515E]), which exhibited a lower dark reversion rate than wild-type phyB. Other variants with slow (phyB[G564E]) or rapid (phyB[S584F]) dark reversion or light insensitivity (phyB[G767R]) were also included in this study for comparison. Warming-induced transient expression of phyB variants was achieved using heat shock-inducible promoters. Arabidopsis PHYB[G515E] and PHYB[G564E] were also constitutively expressed in rice in an attempt to manipulate the heat sensitivity of a monocotyledonous plant species. RESULTS At an elevated temperature, Arabidopsis seedlings transiently expressing PHYB[G515E] under the control of a heat shock-inducible promoter exhibited shorter hypocotyls than those expressing PHYB and other PHYB variant genes. This warm temperature-insensitive growth was related to the lowered PIF4 and auxin responses. In addition, transgenic rice seedlings expressing Arabidopsis PHYB[G515E] and PHYB[G564E] showed warm temperature-insensitive shoot growth. CONCLUSION Transient expression of phyB variants with altered dark reversion rates could serve as an effective optogenetic technique for manipulating PIF4-auxin-mediated thermomorphogenic responses in plants.
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Affiliation(s)
- Jin Jeon
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Md Mizanor Rahman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jaewook Kim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ho-Jun Gam
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ji Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seok Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jeong-Il Kim
- Department of Molecular Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Myoung-Goo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong-Ho Shin
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghwan Shim
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jae-Hoon Jung
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong-Seong Jeon
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea.
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Kim N, Jeong J, Kim J, Oh J, Choi G. Withdrawn as duplicate: Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1. Plant Physiol 2023; 192:680. [PMID: 36756693 PMCID: PMC10152669 DOI: 10.1093/plphys/kiad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 05/03/2023]
Abstract
AbstractThis article has been withdrawn due to an error that caused the article to be duplicated. The definitive version of this article is published under DOI https://doi.org/10.1093/plphys/kiad029
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Affiliation(s)
- Namuk Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jinkil Jeong
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jeongheon Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jeonghwa Oh
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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Kim N, Jeong J, Kim J, Oh J, Choi G. Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1. Plant Physiol 2023; 191:2334-2352. [PMID: 36702576 PMCID: PMC10069884 DOI: 10.1093/plphys/kiad029] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
PHYTOCHROME-INTERACTING FACTORs (PIFs) repress photosynthetic genes partly by upregulating REPRESSOR OF PHOTOSYNTHETIC GENES 1 (RPGE1) and RPGE2. However, it is unknown how RPGEs inhibit gene expression at the molecular level. Here, we show that Arabidopsis (Arabidopsis thaliana) RPGE overexpression lines display extensive similarities to the golden2-like 1 (glk1)/glk2 double mutant at the phenotypic and transcriptomic levels, prompting us to hypothesize that there is a close molecular relationship between RPGEs and chloroplast development-regulating GLK transcription factors. Indeed, we found that RPGE1 disrupts the homodimerization of GLK1 by interacting with its dimerization domain and debilitates the DNA-binding activity of GLK1. The interaction was not restricted to the Arabidopsis RPGE1-GLK1 pair, but rather extended to RPGE-GLK homolog pairs across species, providing a molecular basis for the pale green leaves of Arabidopsis transgenic lines expressing a rice (Oryza sativa) RPGE homolog. Our discovery of RPGE-GLK regulatory pairs suggests that any condition leading to an increase in RPGE levels would decrease the expression levels of GLK target genes. Consistently, we found that shade, which upregulates the RPGE mRNA by stabilizing PIFs, represses the expression of photosynthetic genes partly by inhibiting the DNA-binding activity of GLK1. Taken together, these results indicate that RPGE-GLK regulatory pairs regulate photosynthetic gene expression downstream of PIFs.
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Affiliation(s)
- Namuk Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jinkil Jeong
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jeongheon Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jeonghwa Oh
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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Kim H, Kim J, Choi G. Epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm. New Phytol 2023; 238:705-723. [PMID: 36651061 DOI: 10.1111/nph.18746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Phytochrome B (phyB) expressed in the epidermis is sufficient to promote red light responses, including the inhibition of hypocotyl elongation and hypocotyl negative gravitropism. Nonetheless, the downstream mechanism of epidermal phyB in promoting light responses had been elusive. Here, we mutagenized the epidermis-specific phyB-expressing line (MLB) using ethyl methanesulfonate (EMS) and characterized a novel mutant allele of RRC1 (rrc1-689), which causes reduced epidermal phyB-mediated red light responses. The rrc1-689 mutation increases the alternative splicing of major clock gene transcripts, including PRR7 and TOC1, disrupting the rhythmic expression of the entire clock and clock-controlled genes. Combined with the result that MLB/prr7 exhibits the same red-hyposensitive phenotypes as MLB/rrc1-689, our data support that the circadian clock is required for the ability of epidermal phyB to promote light responses. We also found that, unlike phyB, RRC1 preferentially acts in the endodermis to maintain the circadian rhythm by suppressing the alternative splicing of core clock genes. Together, our results suggest that epidermal phyB requires RRC1 to promote light responses by activating the circadian rhythm in Arabidopsis thaliana.
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Affiliation(s)
- Hanim Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
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Kim C, Kwon Y, Jeong J, Kang M, Lee GS, Moon JH, Lee HJ, Park YI, Choi G. Phytochrome B photobodies are comprised of phytochrome B and its primary and secondary interacting proteins. Nat Commun 2023; 14:1708. [PMID: 36973259 PMCID: PMC10042835 DOI: 10.1038/s41467-023-37421-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Phytochrome B (phyB) is a plant photoreceptor that forms a membraneless organelle called a photobody. However, its constituents are not fully known. Here, we isolated phyB photobodies from Arabidopsis leaves using fluorescence-activated particle sorting and analyzed their components. We found that a photobody comprises ~1,500 phyB dimers along with other proteins that could be classified into two groups: The first includes proteins that directly interact with phyB and localize to the photobody when expressed in protoplasts, while the second includes proteins that interact with the first group proteins and require co-expression of a first-group protein to localize to the photobody. As an example of the second group, TOPLESS interacts with PHOTOPERIODIC CONTROL OF HYPOCOTYL 1 (PCH1) and localizes to the photobody when co-expressed with PCH1. Together, our results support that phyB photobodies include not only phyB and its primary interacting proteins but also its secondary interacting proteins.
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Affiliation(s)
- Chanhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Yongmin Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Jaehoon Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Minji Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea
| | - Ga Seul Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk, 28160, Korea
| | - Jeong Hee Moon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Korea.
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Costigliolo Rojas C, Bianchimano L, Oh J, Romero Montepaone S, Tarkowská D, Minguet EG, Schön J, García Hourquet M, Flugel T, Blázquez MA, Choi G, Strnad M, Mora-García S, Alabadi D, Zurbriggen MD, Casal JJ. Organ-specific COP1 control of BES1 stability adjusts plant growth patterns under shade or warmth. Dev Cell 2022; 57:2009-2025.e6. [PMID: 35901789 DOI: 10.1016/j.devcel.2022.07.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 02/16/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022]
Abstract
Under adverse conditions such as shade or elevated temperatures, cotyledon expansion is reduced and hypocotyl growth is promoted to optimize plant architecture. The mechanisms underlying the repression of cotyledon cell expansion remain unknown. Here, we report that the nuclear abundance of the BES1 transcription factor decreased in the cotyledons and increased in the hypocotyl in Arabidopsis thaliana under shade or warmth. Brassinosteroid levels did not follow the same trend. PIF4 and COP1 increased their nuclear abundance in both organs under shade or warmth. PIF4 directly bound the BES1 promoter to enhance its activity but indirectly reduced BES1 expression. COP1 physically interacted with the BES1 protein, promoting its proteasome degradation in the cotyledons. COP1 had the opposite effect in the hypocotyl, demonstrating organ-specific regulatory networks. Our work indicates that shade or warmth reduces BES1 activity by transcriptional and post-translational regulation to inhibit cotyledon cell expansion.
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Affiliation(s)
- Cecilia Costigliolo Rojas
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | - Luciana Bianchimano
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | - Jeonghwa Oh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Sofía Romero Montepaone
- Institute of Synthetic Biology and Cluster of Excellence in Plant Sciences, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Dana Tarkowská
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czech Republic
| | - Eugenio G Minguet
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jonas Schön
- Institute of Synthetic Biology and Cluster of Excellence in Plant Sciences, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Mariano García Hourquet
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | - Timo Flugel
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | - Miguel A Blázquez
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, Olomouc, Czech Republic
| | - Santiago Mora-García
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | - David Alabadi
- Instituto de Biologίa Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence in Plant Sciences, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Jorge J Casal
- Fundaciόn Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina; Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina.
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12
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Kim DH, Lee SW, Moon H, Choi D, Kim S, Kang H, Kim J, Choi G, Huq E. ABI3- and PIF1-mediated regulation of GIG1 enhances seed germination by detoxification of methylglyoxal in Arabidopsis. Plant J 2022; 110:1578-1591. [PMID: 35365944 DOI: 10.1111/tpj.15755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/22/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Methylglyoxal (MG) is a toxic by-product of the glycolysis pathway in most living organisms and was previously shown to inhibit seed germination. MG is detoxified by glyoxalase I and II family proteins in plants. MG is abundantly produced during early embryogenesis in Arabidopsis seeds. However, the mechanism that alleviates the toxic effect of MG in maturing seeds is poorly understood. In this study, by T-DNA mutant population screening, we found that mutations in a glyoxalase I gene (named GERMINATION-IMPAIRED GLYOXALASE 1, GIG1) led to significantly impaired germination compared with wild-type seeds. Transformation of full-length GIG1 cDNA under the constitutively active cauliflower mosaic virus 35S promoter in the gig1 background completely recovered the seed germination phenotype. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses revealed that GIG1 is uniquely expressed in seeds and is upregulated by abscisic acid (ABA) and downregulated by gibberellic acid (GA) during seed germination. An ABA signaling component, ABI3, directly activated GIG1 in maturing seeds. In addition, PHYTOCHROME INTERACTING FACTOR 1 (PIF1) also plays cooperatively with ABI3 in the regulation of GIG1 expression in the early stage of imbibed seeds. Furthermore, GIG1 expression is stably silenced by epigenetic repressors such as polycomb repressor complexes. Altogether, our results indicate that light and ABA signaling cooperate to enhance seed germination by the upregulation of GIG1 to detoxify MG in maturing seeds.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Woo Lee
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heewon Moon
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sujeong Kim
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hajeong Kang
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Jungtae Kim
- Department of Plant Science and Technology, College of Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
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13
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Le DD, Kim W, Lim S, Kim SC, Choi G. Identification of three groups of ginsenoside biosynthetic UDP-glycosyltransferases from Gynostemma pentaphyllum. Plant Sci 2021; 313:111069. [PMID: 34763860 DOI: 10.1016/j.plantsci.2021.111069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/06/2021] [Accepted: 09/24/2021] [Indexed: 05/02/2023]
Abstract
Ginsenosides are glycosylated dammarene-type triterpenes that have been identified in distantly related Panax ginseng and Gynostemma pentaphyllum. The phylogenetic relatedness of the ginsenoside biosynthetic genes in the two species was previously unknown. The final steps of ginsenoside biosynthesis are the glycosylations of hydroxylated triterpenes, protopanaxadiol (PPD) and protopanaxatriol (PPT), and their glycosylated forms by UDP-glycosyltransferases (UGTs). Ginsenoside biosynthetic UGTs have been identified in Panax but not in Gynostemma. Through a biochemical screening of Gynostemma UGTs (GpUGTs), we herein identified three groups of ginsenoside biosynthetic GpUGTs. These groups comprise: two GpUGTs that belong to the UGT71 family and glucosylate the C20-OH positions of PPD- and PPT-type ginsenosides; one GpUGT that belongs to the UGT74 family and glucosylates the C3-OH position of PPD-type ginsenosides; and two GpUGTs that belong to the UGT94 family and add a glucose to the C3-O-glucosides of PPD-type ginsenosides. These GpUGTs belong to the same UGT families as the ginsenoside biosynthetic Panax UGTs (PgUGTs). However, GpUGTs and PgUGTs belong to different subfamilies. Furthermore, cucumber UGTs orthologous to GpUGTs do not glucosylate ginsenosides. These results collectively suggest that, during evolution, P. ginseng and G. pentaphyllum independently opted to use the same UGT families to synthesize ginsenosides.
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Affiliation(s)
- Duc Duy Le
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Woohyun Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Soohwan Lim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea.
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14
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Rafeek AD, Choi G, Evans LA. Controlled synthesis of dicalcium phosphate dihydrate (DCPD) from metastable solutions: insights into pathogenic calcification. J Mater Sci Mater Med 2021; 32:142. [PMID: 34817698 PMCID: PMC8613102 DOI: 10.1007/s10856-021-06617-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/24/2021] [Indexed: 05/14/2023]
Abstract
Calcium phosphate (CaP) compounds may occur in the body as abnormal pathogenic phases in addition to their normal occurrence as bones and teeth. Dicalcium phosphate dihydrate (DCPD; CaPO4·2H2O), along with other significant CaP phases, have been observed in pathogenic calcifications such as dental calculi, kidney stones and urinary stones. While other studies have shown that polar amino acids can inhibit the growth of CaPs, these studies have mainly focused on hydroxyapatite (HAp; Ca10(PO4)6(OH)2) formation from highly supersaturated solutions, while their effects on DCPD nucleation and growth from metastable solutions have been less thoroughly explored. By further elucidating the mechanisms of DCPD formation and the influence of amino acids on those mechanisms, insights may be gained into ways that amino acids could be used in treatment and prevention of unwanted calcifications. The current study involved seeded growth of DCPD from metastable solutions at constant pH in the presence of neutral, acidic and phosphorylated amino acid side chains. As a comparison, solutions were also seeded with calcium pyrophosphate (CPP; Ca2P2O7), a known calcium phosphate inhibitor. The results show that polar amino acids inhibit DCPD growth; this likely occurs due to electrostatic interactions between amino acid side groups and charged DCPD surfaces. Phosphoserine had the greatest inhibitory ability of the amino acids tested, with an effect equal to that of CPP. Clustering of DCPD crystals giving rise to a "chrysanthemum-like" morphology was noted with glutamic acid. This study concludes that molecules containing an increased number of polar side groups will enhance the inhibition of DCPD seeded growth from metastable solutions.
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Affiliation(s)
- A D Rafeek
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - G Choi
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - L A Evans
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia.
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15
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Toba T, Otake H, Roy A, Choi G, Gobi N, Schaap M, Takahashi Y, Fukuyama Y, Nakano S, Tanimura K, Matsuoka Y, Kawamori H, Taylor C, Ken-Ichi K. Diagnostic performance of fractional flow reserve derived from computed tomography in the stented coronary arteries. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The current system of HeartFlow fractional flow reserve derived from computed tomography (FFRCT) is not available for stented coronary arteries. However, the latest version of HeartFlow FFRCT has the potential of rendering an accurate assessment for stented coronary arteries.
Objectives
To evaluate the feasibility of FFRCT for the stented coronary arteries.
Methods
We retrospectively enrolled patients with a history of coronary stent implantation who underwent invasive fractional flow reserve (FFR) for the stented coronary arteries within 3 months after coronary computed tomographic angiography (cCTA). As a subgroup analysis, we analyzed optical coherence tomography (OCT) images in patients who underwent OCT for stented vessels. OCT was performed as a part of the Kobe University Hospital OCT registry, which is a single-centre registry of consecutive patients who underwent OCT for the coronary arteries. The diagnostic performance of HeartFlow FFRCT for stented vessels was evaluated by comparing with that of cCTA alone. Minimum lumen area (MLA) within stent segments derived from cCTA was also compared with MLA derived from optical coherence tomography (OCT).
Results
A total of 30 vessels in 23 patients were studied. The diagnostic accuracy, sensitivity, specificity, positive and negative predictive value of FFRCT for myocardial ischemia using invasive FFR as a reference standard was 73.3%, 88.9%, 67.7%, 53.3% and 93.3%, respectively. FFRCT provided superior diagnostic performance than cCTA alone (p=0.016). FFRCT was significantly correlated with the invasive FFR (r=0.620, p<0.001), and Bland-Altman plot showed a mean bias of −0.041 with 95% limit of agreement of −0.173 to 0.092 (Figure 1). Among a total of 30 studied vessels, OCT was available for 25 vessels. MLA derived from cCTA correlated significantly with that derived from OCT (r=0.695, p<0.001), and Bland-Altman plot showed a mean bias of −0.32 mm2 with 95% limit of agreement of −2.89 to 2.25 mm2 (Figure 2).
Conclusions
The latest version of the HeartFlow FFRCT has the potential to be available for stented coronary arteries. Further investigation is required to elaborate our results.
Funding Acknowledgement
Type of funding sources: None. Figure 1Figure 2
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Affiliation(s)
- T Toba
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - H Otake
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - A Roy
- HeartFlow, Inc., Redwood City, United States of America
| | - G Choi
- HeartFlow, Inc., Redwood City, United States of America
| | - N Gobi
- HeartFlow, Inc., Redwood City, United States of America
| | - M Schaap
- HeartFlow, Inc., Redwood City, United States of America
| | - Y Takahashi
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - Y Fukuyama
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - S Nakano
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - K Tanimura
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - Y Matsuoka
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - H Kawamori
- Kobe University Graduate School of Medicine, Kobe, Japan
| | - C Taylor
- HeartFlow, Inc., Redwood City, United States of America
| | - K Ken-Ichi
- Kobe University Graduate School of Medicine, Kobe, Japan
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16
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Song K, Lee DW, Kim J, Kim J, Guim H, Kim K, Jeon JS, Choi G. EARLY STARVATION 1 Is a Functionally Conserved Protein Promoting Gravitropic Responses in Plants by Forming Starch Granules. Front Plant Sci 2021; 12:628948. [PMID: 34367195 PMCID: PMC8343138 DOI: 10.3389/fpls.2021.628948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/29/2021] [Indexed: 05/29/2023]
Abstract
Starch granules in the endodermis of plant hypocotyls act as statoliths that promote hypocotyl negative gravitropism-the directional growth of hypocotyls against gravity-in the dark. To identify the molecular components that regulate hypocotyl negative gravitropism, we performed a mutagenesis screen and isolated reduced gravitropic 1 (rgv1) mutants that lack starch granules in their hypocotyl endodermis and show reduced hypocotyl negative gravitropism in the dark. Using whole genome sequencing, we identified three different rgv1 mutants that are allelic to the previously reported early starvation 1 mutant, which is rapidly depleted of starch just before the dawn. ESV1 orthologs are present in starch-producing green organisms, suggesting ESV1 is a functionally conserved protein necessary for the formation of starch granules. Consistent with this, we found that liverwort and rice ESV1 can complement the Arabidopsis ESV1 mutant phenotype for both starch granules and hypocotyl negative gravitropism. To further investigate the function of ESV1 in other plants, we isolated rice ESV1 mutants and found that they show reduced levels of starch in their leaves and loosely packed starch granules in their grains. Both Arabidopsis and rice ESV1 mutants also lack starch granules in root columella and show reduced root gravitropism. Together, these results indicate ESV1 is a functionally conserved protein that promotes gravitropic responses in plants via its role in starch granule formation.
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Affiliation(s)
- Kijong Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Dae-Woo Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si, South Korea
| | - Jeongheon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jaewook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hwanuk Guim
- Research Center for Materials Analysis, Korea Basic Science Institute, Daejeon, South Korea
| | - Keunhwa Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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17
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Kim DH, Yamaguchi S, Lim S, Oh E, Park J, Hanada A, Kamiya Y, Choi G. Corrigendum to: SOMNUS, a CCCH-Type Zinc Finger Protein in Arabidopsis, Negatively Regulates Light-Dependent Seed Germination Downstream of PIL5. Plant Cell 2021; 33:2093-2095. [PMID: 33764458 PMCID: PMC8290283 DOI: 10.1093/plcell/koab086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 03/21/2021] [Indexed: 06/01/2023]
Affiliation(s)
- Dong Hwan Kim
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | | | - Soohwan Lim
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Eunkyoo Oh
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Jeongmu Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Atsushi Hanada
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Yuji Kamiya
- RIKEN Plant Science Center, Yokohama, Kanagawa 230-0045, Japan
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
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18
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Kim C, Kim SJ, Jeong J, Park E, Oh E, Park YI, Lim PO, Choi G. High Ambient Temperature Accelerates Leaf Senescence via PHYTOCHROME-INTERACTING FACTOR 4 and 5 in Arabidopsis. Mol Cells 2020; 43:645-661. [PMID: 32732458 PMCID: PMC7398796 DOI: 10.14348/molcells.2020.0117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
Leaf senescence is a developmental process by which a plant actively remobilizes nutrients from aged and photosynthetically inefficient leaves to young growing ones by disassembling organelles and degrading macromolecules. Senescence is accelerated by age and environmental stresses such as prolonged darkness. Phytochrome B (phyB) inhibits leaf senescence by inhibiting phytochrome-interacting factor 4 (PIF4) and PIF5 in prolonged darkness. However, it remains unknown whether phyB mediates the temperature signal that regulates leaf senescence. We found the light-activated form of phyB (Pfr) remains active at least four days after a transfer to darkness at 20°C but is inactivated more rapidly at 28°C. This faster inactivation of Pfr further increases PIF4 protein levels at the higher ambient temperature. In addition, PIF4 mRNA levels rise faster after the transfer to darkness at high ambient temperature via a mechanism that depends on ELF3 but not phyB. Increased PIF4 protein then binds to the ORE1 promoter and activates its expression together with ABA and ethylene signaling, accelerating leaf senescence at high ambient temperature. Our results support a role for the phy-PIF signaling module in integrating not only light signaling but also temperature signaling in the regulation of leaf senescence.
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Affiliation(s)
- Chanhee Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Sun Ji Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu 4988, Korea
| | - Jinkil Jeong
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 9207, USA
| | - Eunae Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
| | - Eunkyoo Oh
- Division of Life Sciences, Korea University, Seoul 0281, Korea
| | - Youn-Il Park
- Department of Biological Sciences and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 34134, Korea
| | - Pyung Ok Lim
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 344, Korea
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Affiliation(s)
- L Ling
- The Chinese University of Hong Kong, China
| | - W T Wong
- The Chinese University of Hong Kong, China
| | - W T P Wan
- The Chinese University of Hong Kong, China
| | - G Choi
- The Chinese University of Hong Kong, China
| | - G M Joynt
- The Chinese University of Hong Kong, China
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20
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Abstract
Seed germination assays consist of counting the number of germinated seeds, defined as seeds in which the radicle has ruptured the endosperm and emerged from the seed coat. In Arabidopsis seed germination assays, Arabidopsis seeds are surface-sterilized, plated on agar plates containing test compounds, and incubated at specific temperatures under specific light conditions, after which the germinated seeds are counted, either with the naked eye or under a microscope. This chapter describes step-by-step protocols for Arabidopsis seed germination assays under phytochrome-dependent conditions.
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Affiliation(s)
- Kijong Song
- Department of Biological Sciences, KAIST, Daejeon, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, South Korea.
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21
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Oh J, Park E, Song K, Bae G, Choi G. PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis. Plant Cell 2020; 32:186-205. [PMID: 31732705 PMCID: PMC6961613 DOI: 10.1105/tpc.19.00515] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/25/2019] [Accepted: 11/14/2019] [Indexed: 05/04/2023]
Abstract
PHYTOCHROME INTERACTING FACTORs (PIFs) are a group of basic helix-loop-helix (bHLH) transcription factors that repress plant light responses. PIF8 is one of the less-characterized Arabidopsis (Arabidopsis thaliana) PIFs, whose putative orthologs are conserved in other plant species. PIF8 possesses a bHLH motif and an active phytochrome B motif but not an active phytochrome A motif. Consistent with this motif composition, PIF8 binds to G-box elements and interacts with the Pfr form of phyB but only very weakly, if at all, with that of phyA. PIF8 differs, however, from other PIFs in its protein accumulation pattern and functional roles in different light conditions. First, PIF8 inhibits phyA-induced seed germination, suppression of hypocotyl elongation, and randomization of hypocotyl growth orientation in far-red light, but it does not inhibit phyB-induced red light responses. Second, PIF8 protein accumulates more in far-red light than in darkness or red light. This is distinct from the pattern observed with PIF3, which accumulates more in darkness. This PIF8 accumulation pattern requires degradation of PIF8 by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in darkness, inhibition of COP1 by phyA in far-red light, and promotion of PIF8 degradation by phyB in red light. Together, our results indicate that PIF8 is a genuine PIF that represses phyA-mediated light responses.
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Affiliation(s)
- Jeonghwa Oh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Eunae Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kijong Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Gabyong Bae
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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Rahimi S, Kim J, Mijakovic I, Jung KH, Choi G, Kim SC, Kim YJ. Triterpenoid-biosynthetic UDP-glycosyltransferases from plants. Biotechnol Adv 2019; 37:107394. [PMID: 31078628 DOI: 10.1016/j.biotechadv.2019.04.016] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/20/2019] [Accepted: 04/30/2019] [Indexed: 01/22/2023]
Abstract
Triterpenoid saponins are naturally occurring structurally diverse glycosides of triterpenes that are widely distributed among plant species. Great interest has been expressed by pharmaceutical and agriculture industries for the glycosylation of triterpenes. Such modifications alter their taste and bio-absorbability, affect their intra-/extracellular transport and storage in plants, and induce novel biological activities in the human body. Uridine diphosphate (UDP)-glycosyltransferases (UGTs) catalyze glycosylation using UDP sugar donors. These enzymes belong to a multigene family and recognize diverse natural products, including triterpenes, as the acceptor molecules. For this review, we collected and analyzed all of the UGT sequences found in Arabidopsis thaliana as well as 31 other species of triterpene-producing plants. To identify potential UGTs with novel functions in triterpene glycosylation, we screened and classified those candidates based on similarity with UGTs from Panax ginseng, Glycine max, Medicago truncatula, Saponaria vaccaria, and Barbarea vulgaris that are known to function in glycosylate triterpenes. We highlight recent findings on UGT inducibility by methyl jasmonate, tissue-specific expression, and subcellular localization, while also describing their catalytic activity in terms of regioselectivity for potential key UGTs dedicated to triterpene glycosylation in plants. Discovering these new UGTs expands our capacity to manipulate the biological and physicochemical properties of such valuable molecules.
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Affiliation(s)
- Shadi Rahimi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Intelligent Synthetic Biology Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea; Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden.
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Ivan Mijakovic
- Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Sun-Chang Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea; Intelligent Synthetic Biology Center, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea.
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Lee Y, Won C, Jung K, Nam H, Choi G, Park Y, Park M, Kim B. PAC‐14028 cream for atopic dermatitis. Br J Dermatol 2019. [DOI: 10.1111/bjd.17802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Lee Y, Won C, Jung K, Nam H, Choi G, Park Y, Park M, Kim B. 用于特应性皮炎的 PAC‐14028 乳膏. Br J Dermatol 2019. [DOI: 10.1111/bjd.17814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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25
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Lee YW, Won CH, Jung K, Nam HJ, Choi G, Park YH, Park M, Kim B. Efficacy and safety of PAC-14028 cream - a novel, topical, nonsteroidal, selective TRPV1 antagonist in patients with mild-to-moderate atopic dermatitis: a phase IIb randomized trial. Br J Dermatol 2019; 180:1030-1038. [PMID: 30623408 PMCID: PMC6850419 DOI: 10.1111/bjd.17455] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/21/2022]
Abstract
Background Transient receptor potential vanilloid subfamily, member 1 (TRPV1) may play an important role in pruritus and inflammation induction in atopic dermatitis (AD). The treatment effect of TRPV1 antagonist via topical application in patients with AD remains unknown. Objectives To assess the clinical efficacy and safety of PAC‐14028, a TRPV1 antagonist, via topical application in patients with AD. Methods In this 8‐week, phase IIb, randomized, double‐blind, multicentre, vehicle‐controlled study, patients with mild‐to‐moderate AD were randomized to receive PAC‐14028 cream 0·1%, 0·3%, 1·0% or vehicle cream twice daily. The primary efficacy end point was the Investigator's Global Assessment (IGA) success rate defined as the percentage of patients with an IGA score of 0 or 1 at week 8. The secondary efficacy end points included the severity Scoring of Atopic Dermatitis (SCORAD) index and Eczema Area and Severity Index (EASI) 75/90. Results A total of 194 patients were enrolled. IGA success rates at week 8 were 14·58% for vehicle cream, 42·55% for PAC‐14028 cream 0·1% (P = 0·0025 vs. vehicle), 38·30% for PAC‐14028 cream 0·3% (P = 0·0087 vs. vehicle) and 57·45% for PAC‐14028 cream 1·0% (P < 0·001 vs. vehicle). In particular, statistically significant differences were found between the vehicle and treatment groups in the IGA success rates with two‐grade improvement. The SCORAD index, EASI 75/90, sleep disturbance score and pruritus visual analogue scale showed a trend towards improvement. No significant safety issues were reported. Conclusions PAC‐14028 cream may be an effective and safe treatment modality for the treatment of patients with mild‐to‐moderate AD. What is already known about this topic? Atopic dermatitis (AD) is one of the most common inflammatory skin diseases characterized by pruritic erythematous skin lesions and barrier dysfunction. Transient receptor potential vanilloid subfamily, member 1 (TRPV1) antagonists suppress the release of pruritic and proinflammatory mediators. The preclinical results demonstrate the feasibility of TRPV1 as a potential therapeutic target for the treatment of AD.
What does this study add? TRPV1 regulates inflammation and pruritus in patients with AD. PAC‐14028 cream, a novel TRPV1 antagonist, was superior to vehicle in improving clinical symptoms and signs with a favourable safety profile in adults with mild‐to‐moderate AD. TRPV1 antagonism may play a role as a promising nonsteroidal topical treatment target for AD with a new mechanism of action.
Linked Editorial:https://doi.org/10.1111/bjd.17777. https://doi.org/10.1111/bjd.17802 available online https://www.bjdonline.com/article/
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Affiliation(s)
- Y W Lee
- Department of Dermatology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - C-H Won
- Department of Dermatology, Ulsan University College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - K Jung
- Vital Beautie Research Institute, AmorePacific Corporation R&D Center, Yongin, Republic of Korea
| | - H-J Nam
- Vital Beautie Research Institute, AmorePacific Corporation R&D Center, Yongin, Republic of Korea
| | - G Choi
- Vital Beautie Research Institute, AmorePacific Corporation R&D Center, Yongin, Republic of Korea
| | - Y-H Park
- Vital Beautie Research Institute, AmorePacific Corporation R&D Center, Yongin, Republic of Korea
| | - M Park
- Vital Beautie Research Institute, AmorePacific Corporation R&D Center, Yongin, Republic of Korea
| | - B Kim
- Department of Dermatology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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Park E, Kim Y, Choi G. Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses across a Wide Range of Light Conditions. Plant Cell 2018; 30:1277-1292. [PMID: 29764986 PMCID: PMC6048787 DOI: 10.1105/tpc.17.00913] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/23/2018] [Accepted: 05/10/2018] [Indexed: 05/04/2023]
Abstract
Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyBG111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990G767R and phyBG111D, are equally capable of inducing light responses under continuous red light. However, phyBG111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions.
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Affiliation(s)
- Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Yeojae Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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Lee YK, Rhee JY, Lee SH, Chung GC, Park SJ, Segami S, Maeshima M, Choi G. Functionally redundant LNG3 and LNG4 genes regulate turgor-driven polar cell elongation through activation of XTH17 and XTH24. Plant Mol Biol 2018; 97:23-36. [PMID: 29616436 DOI: 10.1007/s11103-018-0722-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/25/2018] [Indexed: 05/03/2023]
Abstract
In this work, we genetically characterized the function of Arabidopsis thaliana, LONGIFOLIA (LNG1), LNG2, LNG3, LNG4, their contribution to regulate vegetative architecture in plant. We used molecular and biophysical approaches to elucidate a gene function that regulates vegetative architecture, as revealed by the leaf phenotype and later effects on flowering patterns in Arabidopsis loss-of-function mutants. As a result, LNG genes play an important role in polar cell elongation by turgor pressure controlling the activation of XTH17 and XTH24. Plant vegetative architecture is related to important traits that later influence the floral architecture involved in seed production. Leaf morphology is the primary key trait to compose plant vegetative architecture. However, molecular mechanism on leaf shape determination is not fully understood even in the model plant A. thaliana. We previously showed that LONGIFOLIA (LNG1) and LONGIFOLIA2 (LNG2) genes regulate leaf morphology by promoting longitudinal cell elongation in Arabidopsis. In this study, we further characterized two homologs of LNG1, LNG3, and LNG4, using genetic, biophysical, and molecular approaches. Single loss-of-function mutants, lng3 and lng4, do not show any phenotypic difference, but mutants of lng quadruple (lngq), and lng1/2/3 and lng1/2/4 triples, display reduced leaf length, compared to wild type. Using the paradermal analysis, we conclude that the reduced leaf size of lngq is due to decreased cell elongation in the direction of longitudinal leaf growth, and not decreased cell proliferation. This data indicate that LNG1/2/3/4 are functionally redundant, and are involved in polar cell elongation in Arabidopsis leaf. Using a biophysical approach, we show that the LNGs contribute to maintain high turgor pressure, thus regulating turgor pressure-dependent polar cell elongation. In addition, gene expression analysis showed that LNGs positively regulate the expression of the cell wall modifying enzyme encoded by a multi-gene family, xyloglucan endotransglucosylase/hydrolase (XTH). Taking all of these together, we propose that LNG related genes play an important role in polar cell elongation by changing turgor pressure and controlling the activation of XTH17 and XTH24.
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Affiliation(s)
- Young Koung Lee
- Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea.
- Division of Biological Sciences and Institute for Basic Science/Division of Biological Sciences and Research Institute for Glycoscience, Wonkwang University, Iksan, 54538, South Korea.
| | - Ji Ye Rhee
- Department of Plant Biotechnology, Agricultural Plant Stress Research Center, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Seong Hee Lee
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2E3, Canada
| | - Gap Chae Chung
- Department of Plant Biotechnology, Agricultural Plant Stress Research Center, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea
| | - Soon Ju Park
- Division of Biological Sciences and Institute for Basic Science/Division of Biological Sciences and Research Institute for Glycoscience, Wonkwang University, Iksan, 54538, South Korea
| | - Shoji Segami
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Masayohi Maeshima
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, South Korea
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Byun J, An H, Yeom S, Choi G. 127 NDRG1 regulates proliferation of endothelial cells of infantile hemangioma. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Raphael I, Almodovar K, Bedrosian A, Brandow C, Choi G, Saini R, Singh N, Ebrahimzadeh P, Abraham C, Keenan L. 1061 The FRESNO Project: Fresno Residents’ Experience in Sleep and Nighttime Optimization. Sleep 2018. [DOI: 10.1093/sleep/zsy061.1060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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30
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Choi G, Kwak S, Lee H, Chang M. Effect of high-frequency repetitive transcranial magnetic stimulation on chronic central pain after mild traumatic brain injury: A pilot study. J Rehabil Med 2018; 50:246-252. [PMID: 29392332 DOI: 10.2340/16501977-2321] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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31
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Sakuraba Y, Bülbül S, Piao W, Choi G, Paek NC. Arabidopsis EARLY FLOWERING3 increases salt tolerance by suppressing salt stress response pathways. Plant J 2017; 92:1106-1120. [PMID: 29032592 DOI: 10.1111/tpj.13747] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 05/03/2023]
Abstract
Arabidopsis EARLY FLOWERING3 (ELF3) functions in modulating light input to the circadian clock, as a component of ELF3-ELF4-LUX ARRHYTHMO (LUX) evening complex. However, the role of ELF3 in stress responses remains largely unknown. In this study, we show that ELF3 enhances plants' resilience to salt stress: ELF3-overexpressing (ELF3-OX) plants are salt-tolerant, while elf3 mutants are more sensitive to salt stress. The expressions of many salt stress- and senescence-associated genes are altered in elf3-1 and ELF3-OX plants compared with wild-type. During salt stress, ELF3 suppresses factors that promote salt stress response pathways, mainly GIGANTEA (GI), at the post-translational level, and PHYTOCHROME INTERACTING FACTOR4 (PIF4), at the transcriptional level. To enhance the salt stress response, PIF4 directly downregulates the transcription of JUNGBRUNNEN1 (JUB1/ANAC042), encoding a transcription factor that upregulates the expression of stress tolerance genes, DREB2A and DELLA. Furthermore, PIF4 directly upregulates the transcription of ORESARA1 (ORE1/ANAC092) and SAG29, positive regulators of salt stress response pathways. Based on our results, we propose that ELF3 modulates key regulatory components in salt stress response pathways at the transcriptional and post-translational levels.
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Affiliation(s)
- Yasuhito Sakuraba
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Selin Bülbül
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam-Golm, Germany
| | - Weilan Piao
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
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32
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Bates J, Choi G, Usuki K, Katz A, Milano M. The Impact of Right-Sided Initial Tumor Location Among Patients With Oligometastatic Colorectal Carcinoma Treated With Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Kim Hyo S, Lee AY, Choi G, Moon Byeong C. Development and validation of ultra-performance convergence chromatography method for quality control of Saposhnikoviae Radix. Am J Transl Res 2017. [DOI: 10.1055/s-0037-1608513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- S Kim Hyo
- K-Herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Korea, Republic of (South)
| | - AY Lee
- K-Herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Korea, Republic of (South)
| | - G Choi
- K-Herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Korea, Republic of (South)
| | - C Moon Byeong
- K-Herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Korea, Republic of (South)
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Abstract
A screening process for the germination and growth of seed is generally required for plant research. Such a repetitive screening process is costly and time-consuming, and its bulky setup requires a lot of space. In particular, the control of the variables, such as light, nutrients, hormones and temperature, is difficult due to the limited space for incubation. In addition, small seeds such as Arabidopsis thaliana are difficult to handle as they are hundreds of microns in diameter and require a more precisely controllable screening environment. However, conventional screening methods involve the seeding of multiple seeds on a single agarose plate without physical partitions. Such methods need to be improved because they lack control over the growth environment and the results are highly dependent on the researchers. To overcome the above-mentioned limitations, a novel seeding array chip has been developed which can be filled with conventional solid agarose while enabling more efficient screening. Individual seeds can be partitioned from each other and a number of different agarose conditions can be tested in a single plant array chip. As a demonstration, we tested the effect of various concentrations of Murashige and Skoog medium and a plant hormone (e.g., abscisic acid) on the growth of Arabidopsis. The chip can efficiently save the space required for screening by providing different conditions for ∼400 seeds in a 59 × 55 mm chip, and it also provides easy observation and analysis of seed growth. The proposed plant array chip is expected to contribute to more efficient screening of essential phenotypes such as germination and growth for both academic and industrial purposes.
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Affiliation(s)
- Youn-Hee Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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35
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Lee N, Choi G. Phytochrome-interacting factor from Arabidopsis to liverwort. Curr Opin Plant Biol 2017; 35:54-60. [PMID: 27875778 DOI: 10.1016/j.pbi.2016.11.004] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 10/29/2016] [Accepted: 11/02/2016] [Indexed: 05/08/2023]
Abstract
Phytochromes are red and far-red light photoreceptors that regulate the responses of plants to light throughout their life cycles. Phytochromes do this in part by inhibiting the function of a group of basic helix-loop-helix transcription factors called phytochrome-interacting factors (PIFs). Arabidopsis has eight PIFs that function sometimes redundantly and sometimes distinctively depending on their expression patterns and protein stability, as well as on variations in the promoters they target in vivo. PIF-like proteins exist in other seed plants and non-vascular plants where they also regulate light responses. The mechanism by which phytochrome regulates light responses by promoting the degradation of the PIFs is conserved in liverwort, suggesting it must have evolved some time before the last common ancestor shared by seed plants and non-vascular plants.
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Affiliation(s)
- Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Republic of Korea.
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36
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Park J, Oh DH, Dassanayake M, Nguyen KT, Ogas J, Choi G, Sun TP. Gibberellin Signaling Requires Chromatin Remodeler PICKLE to Promote Vegetative Growth and Phase Transitions. Plant Physiol 2017; 173:1463-1474. [PMID: 28057895 PMCID: PMC5291033 DOI: 10.1104/pp.16.01471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 05/20/2023]
Abstract
PICKLE (PKL) is an ATP-dependent chromodomain-helicase-DNA-binding domain (CHD3) chromatin remodeling enzyme in Arabidopsis (Arabidopsis thaliana). Previous studies showed that PKL promotes embryonic-to-vegetative transition by inhibiting expression of seed-specific genes during seed germination. The pkl mutants display a low penetrance of the "pickle root" phenotype, with a thick and green primary root that retains embryonic characteristics. The penetrance of this pickle root phenotype in pkl is dramatically increased in gibberellin (GA)-deficient conditions. At adult stages, the pkl mutants are semidwarfs with delayed flowering time, which resemble reduced GA-signaling mutants. These findings suggest that PKL may play a positive role in regulating GA signaling. A recent biochemical analysis further showed that PKL and GA signaling repressors DELLAs antagonistically regulate hypocotyl cell elongation genes by direct protein-protein interaction. To elucidate further the role of PKL in GA signaling and plant development, we studied the genetic interaction between PKL and DELLAs using the hextuple mutant containing pkl and della pentuple (dP) mutations. Here, we show that PKL is required for most of GA-promoted developmental processes, including vegetative growth such as hypocotyl, leaf, and inflorescence stem elongation, and phase transitions such as juvenile-to-adult leaf and vegetative-to-reproductive phase. The removal of all DELLA functions (in the dP background) cannot rescue these phenotypes in pkl RNA-sequencing analysis using the ga1 (a GA-deficient mutant), pkl, and the ga1 pkl double mutant further shows that expression of 80% of GA-responsive genes in seedlings is PKL dependent, including genes that function in cell elongation, cell division, and phase transitions. These results indicate that the CHD3 chromatin remodeler PKL is required for regulating gene expression during most of GA-regulated developmental processes.
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Affiliation(s)
- Jeongmoo Park
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Dong-Ha Oh
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Maheshi Dassanayake
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Khoa Thi Nguyen
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Joe Ogas
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Giltsu Choi
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.);
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.);
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
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Hendriks D, Choi G, de Bruyn M, Wiersma VR, Bremer E. Antibody-Based Cancer Therapy: Successful Agents and Novel Approaches. Int Rev Cell Mol Biol 2017; 331:289-383. [PMID: 28325214 DOI: 10.1016/bs.ircmb.2016.10.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Since their discovery, antibodies have been viewed as ideal candidates or "magic bullets" for use in targeted therapy in the fields of cancer, autoimmunity, and chronic inflammatory disorders. A wave of antibody-dedicated research followed, which resulted in the clinical approval of a first generation of monoclonal antibodies for cancer therapy such as rituximab (1997) and cetuximab (2004), and infliximab (2002) for the treatment of autoimmune diseases. More recently, the development of antibodies that prevent checkpoint-mediated inhibition of T cell responses invigorated the field of cancer immunotherapy. Such antibodies induced unprecedented long-term remissions in patients with advanced stage malignancies, most notably melanoma and lung cancer, that do not respond to conventional therapies. In this review, we will recapitulate the development of antibody-based therapy, and detail recent advances and new functions, particularly in the field of cancer immunotherapy. With the advent of recombinant DNA engineering, a number of rationally designed molecular formats of antibodies and antibody-derived agents have become available, and we will discuss various molecular formats including antibodies with improved effector functions, bispecific antibodies, antibody-drug conjugates, antibody-cytokine fusion proteins, and T cells genetically modified with chimeric antigen receptors. With these exciting advances, new antibody-based treatment options will likely enter clinical practice and pave the way toward more successful control of malignant diseases.
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Affiliation(s)
- D Hendriks
- Department of Surgery, Translational Surgical Oncology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - G Choi
- Department of Hematology, Section Immunohematology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - M de Bruyn
- Department of Obstetrics & Gynecology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - V R Wiersma
- Department of Hematology, Section Immunohematology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands.
| | - E Bremer
- Department of Hematology, Section Immunohematology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands; University of Exeter Medical School, Exeter, UK.
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Kim J, Song K, Park E, Kim K, Bae G, Choi G. Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously. Plant Cell 2016; 28:2770-2785. [PMID: 27758895 PMCID: PMC5155346 DOI: 10.1105/tpc.16.00487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/27/2016] [Accepted: 10/06/2016] [Indexed: 05/20/2023]
Abstract
Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Kijong Song
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Keunhwa Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Gabyong Bae
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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Kim K, Jeong J, Kim J, Lee N, Kim ME, Lee S, Chang Kim S, Choi G. PIF1 Regulates Plastid Development by Repressing Photosynthetic Genes in the Endodermis. Mol Plant 2016; 9:1415-1427. [PMID: 27591813 DOI: 10.1016/j.molp.2016.08.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/14/2023]
Abstract
Mutations in Phytochrome Interacting Factors (PIFs) induce a conversion of the endodermal amyloplasts necessary for gravity sensing to plastids with developed thylakoids accompanied by abnormal activation of photosynthetic genes in the dark. In this study, we investigated how PIFs regulate endodermal plastid development by performing comparative transcriptome analysis. We show that both endodermal expression of PIF1 and global expression of the PIF quartet induce transcriptional changes in genes enriched for nuclear-encoded photosynthetic genes such as LHCA and LHCB. Among the 94 shared differentially expressed genes identified from the comparative transcriptome analysis, only 14 genes are demonstrated to be direct targets of PIF1, and most photosynthetic genes are not. Using a co-expression analysis, we identified a direct target of PIF, whose expression pattern shows a strong negative correlation with many photosynthetic genes. We have named this gene REPRESSOR OF PHOTOSYNTHETIC GENES1 (RPGE1). Endodermal expression of RPGE1 rescued the elevated expression of photosynthetic genes found in the pif quadruple (pifQ) mutant and partly restored amyloplast development and hypocotyl negative gravitropism. Taken together, our results indicate that RPGE1 acts downstream of PIF1 in the endodermis to repress photosynthetic genes and regulate plastid development.
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Affiliation(s)
- Keunhwa Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Jeongheon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Mi Eon Kim
- Center for Gas Analysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Republic of Korea
| | - Sangil Lee
- Center for Gas Analysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science (KRISS), Daejeon 305-340, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
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Choi G, Bates J, Milano M. Myxopapillary Ependymoma: A Surveillance, Epidemiology, and End Results Analysis of Epidemiology and Outcomes. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Kim WJ, Ji Y, Choi G, Kang YM, Yang S, Moon BC. Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences. Genet Mol Res 2016; 15:gmr8472. [PMID: 27525917 DOI: 10.4238/gmr.15038472] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study was performed to identify and analyze the phylogenetic relationship among four herbaceous species of the genus Paeonia, P. lactiflora, P. japonica, P. veitchii, and P. suffruticosa, using DNA barcodes. These four species, which are commonly used in traditional medicine as Paeoniae Radix and Moutan Radicis Cortex, are pharmaceutically defined in different ways in the national pharmacopoeias in Korea, Japan, and China. To authenticate the different species used in these medicines, we evaluated rDNA-internal transcribed spacers (ITS), matK and rbcL regions, which provide information capable of effectively distinguishing each species from one another. Seventeen samples were collected from different geographic regions in Korea and China, and DNA barcode regions were amplified using universal primers. Comparative analyses of these DNA barcode sequences revealed species-specific nucleotide sequences capable of discriminating the four Paeonia species. Among the entire sequences of three barcodes, marker nucleotides were identified at three positions in P. lactiflora, eleven in P. japonica, five in P. veitchii, and 25 in P. suffruticosa. Phylogenetic analyses also revealed four distinct clusters showing homogeneous clades with high resolution at the species level. The results demonstrate that the analysis of these three DNA barcode sequences is a reliable method for identifying the four Paeonia species and can be used to authenticate Paeoniae Radix and Moutan Radicis Cortex at the species level. Furthermore, based on the assessment of amplicon sizes, inter/intra-specific distances, marker nucleotides, and phylogenetic analysis, rDNA-ITS was the most suitable DNA barcode for identification of these species.
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Affiliation(s)
- W J Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
| | - Y Ji
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
| | - G Choi
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
| | - Y M Kang
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
| | - S Yang
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
| | - B C Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, Yuseong-daero, Yuseong-gu, Daejeon, Republic of Korea
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Choi G, Lee H, Alqathami M, Ibbott G. TH-AB-BRA-11: Using 3D Dosimeters for the Investigation of the Electron Return Effect (ERE) in MR-Guided Radiation Therapy: A Feasibility Study. Med Phys 2016. [DOI: 10.1118/1.4958062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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43
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Kim J, Kang H, Park J, Kim W, Yoo J, Lee N, Kim J, Yoon TY, Choi G. PIF1-Interacting Transcription Factors and Their Binding Sequence Elements Determine the in Vivo Targeting Sites of PIF1. Plant Cell 2016; 28:1388-405. [PMID: 27303023 PMCID: PMC4944412 DOI: 10.1105/tpc.16.00125] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 05/18/2023]
Abstract
The bHLH transcription factor PHYTOCHROME INTERACTING FACTOR1 (PIF1) binds G-box elements in vitro and inhibits light-dependent germination in Arabidopsis thaliana A previous genome-wide analysis of PIF1 targeting indicated that PIF1 binds 748 sites in imbibed seeds, only 59% of which possess G-box elements. This suggests the G-box is not the sole determinant of PIF1 targeting. The targeting of PIF1 to specific sites could be stabilized by PIF1-interacting transcription factors (PTFs) that bind other nearby sequence elements. Here, we report PIF1 targeting sites are enriched with not only G-boxes but also with other hexameric sequence elements we named G-box coupling elements (GCEs). One of these GCEs possesses an ACGT core and serves as a binding site for group A bZIP transcription factors, including ABSCISIC ACID INSENSITIVE5 (ABI5), which inhibits seed germination in abscisic acid signaling. PIF1 interacts with ABI5 and other group A bZIP transcription factors and together they target a subset of PIF1 binding sites in vivo. In vitro single-molecule fluorescence imaging confirms that ABI5 facilitates PIF1 binding to DNA fragments possessing multiple G-boxes or the GCE alone. Thus, we show in vivo PIF1 targeting to specific binding sites is determined by its interaction with PTFs and their binding to GCEs.
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Affiliation(s)
- Junghyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Hyojin Kang
- Department of Convergence Technology Research, KISTI, Daejeon 34141, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Woohyun Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Janghyun Yoo
- Department of Physics, KAIST, Daejeon 34141, Korea
| | - Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | | | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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44
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Moon BC, Kim WJ, Ji Y, Lee YM, Kang YM, Choi G. Molecular identification of the traditional herbal medicines, Arisaematis Rhizoma and Pinelliae Tuber, and common adulterants via universal DNA barcode sequences. Genet Mol Res 2016; 15:gmr7064. [PMID: 26909979 DOI: 10.4238/gmr.15017064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Methods to identify Pinelliae Tuber and Arisaematis Rhizoma are required because of frequent reciprocal substitution between these two herbal medicines and the existence of several closely related plant materials. As a result of the morphological similarity of dried tubers, correct discrimination of authentic herbal medicines is difficult by conventional methods. Therefore, we analyzed DNA barcode sequences to identify each herbal medicine and the common adulterants at a species level. To verify the identity of these herbal medicines, we collected five authentic species (Pinellia ternata for Pinelliae Tuber, and Arisaema amurense, A. amurense var. serratum, A. erubescens, and A. heterophyllum for Arisaematis Rhizoma) and six common adulterant plant species. Maturase K (matK) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) genes were then amplified using universal primers. In comparative analyses of two DNA barcode sequences, we obtained 45 species-specific nucleotides sufficient to identify each species (except A. erubescens with matK) and 28 marker nucleotides for each species (except P. pedatisecta with rbcL). Sequence differences at corresponding positions of the two combined DNA barcodes provided genetic marker nucleotides that could be used to identify specimens of the correct species among the analyzed medicinal plants. Furthermore, we generated a phylogenetic tree showing nine distinct groups depending on the species. These results can be used to authenticate Pinelliae Tuber and Arisaematis Rhizoma from their adulterants and to identify each species. Thus, comparative analyses of plant DNA barcode sequences identified useful genetic markers for the authentication of Pinelliae Tuber and Arisaematis Rhizoma from several adulterant herbal materials.
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Affiliation(s)
- B C Moon
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - W J Kim
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Y Ji
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Y M Lee
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - Y M Kang
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
| | - G Choi
- K-herb Research Center, Korea Institute of Oriental Medicine, Daejeon, Republic of Korea
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Jeong J, Kim K, Kim ME, Kim HG, Heo GS, Park OK, Park YI, Choi G, Oh E. Phytochrome and Ethylene Signaling Integration in Arabidopsis Occurs via the Transcriptional Regulation of Genes Co-targeted by PIFs and EIN3. Front Plant Sci 2016; 7:1055. [PMID: 27486469 PMCID: PMC4949226 DOI: 10.3389/fpls.2016.01055] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/05/2016] [Indexed: 05/20/2023]
Abstract
Plant seedlings germinating under the soil are challenged by rough soil grains that can induce physical damage and sudden exposure to light, which can induce photobleaching. Seedlings overcome these challenges by developing apical hooks and by suppressing chlorophyll precursor biosynthesis. These adaptive responses are, respectively, regulated by the phytochrome and ethylene signaling pathways via the PHYTOCHROME-INTERACTING FACTORs (PIFs) and the ETHYLENE INSENSITIVE 3 (EIN3)/EIN3-LIKE transcription factors. Although many processes downstream of phytochrome and ethylene signaling are similar, it remains unclear if and where these pathways converge. Here, we show PIFs and EIN3 induce similar changes in the transcriptome without robustly regulating each other's signaling pathways. PIFs and EIN3 target highly overlapped gene promoters and activate subsets of the co-target genes either interdependently or additively to induce plant responses. For chlorophyll biosynthesis, PIFs and EIN3 target and interdependently activate the expression of HOOKLESS1. HOOKLESS1, in turn, represses chlorophyll synthesis genes to prevent photobleaching. Thus, our results indicate an integration of the phytochrome and ethylene signaling pathways at the level of transcriptional gene regulation by two core groups of transcription factors, PIFs and EIN3.
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Affiliation(s)
- Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Keunhwa Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
| | - Mi E. Kim
- Center for Gas Analysis, Korea Research Institute of Standards and ScienceDaejeon, South Korea
| | - Hye G. Kim
- School of Life Sciences and Biotechnology, Korea UniversitySeoul, South Korea
| | - Gwi S. Heo
- Center for Gas Analysis, Korea Research Institute of Standards and ScienceDaejeon, South Korea
| | - Ohkmae K. Park
- School of Life Sciences and Biotechnology, Korea UniversitySeoul, South Korea
| | - Youn-Il Park
- Department of Bioscience and Biotechnology, Chungnam National UniversityDaejeon, South Korea
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and TechnologyDaejeon, South Korea
- *Correspondence: Giltsu Choi, Eunkyoo Oh,
| | - Eunkyoo Oh
- Department of Bioenergy Science and Technology, Chonnam National UniversityGwangju, South Korea
- *Correspondence: Giltsu Choi, Eunkyoo Oh,
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46
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Nguyen KT, Park J, Park E, Lee I, Choi G. The Arabidopsis RING Domain Protein BOI Inhibits Flowering via CO-dependent and CO-independent Mechanisms. Mol Plant 2015; 8:1725-36. [PMID: 26298008 DOI: 10.1016/j.molp.2015.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 07/24/2015] [Accepted: 08/12/2015] [Indexed: 05/25/2023]
Abstract
BOTRYTIS SUSCEPTIBLE1 INTERACTOR (BOI) and its three homologs (BOIs) are RING domain-containing proteins that repress flowering. Here, we investigated how BOIs repress flowering. Genetic analysis of the boiQ quadruple mutant indicates that BOIs repress flowering mainly through FLOWERING LOCUS T (FT). BOIs repress the expression of FT by CONSTANS (CO)-dependent and -independent mechanisms: in the CO-dependent mechanism, BOIs bind to CO, inhibit the targeting of CO to the FT locus, and thus repress the expression of FT; in the CO-independent mechanism, BOIs target the FT locus via a mechanism that requires DELLAs but not CO. This dual repression of FT makes BOIs strong repressors of flowering in both CO-dependent and CO-independent pathways in Arabidopsis thaliana. Our finding that BOIs inhibit CO targeting further suggests that, in addition to modulating CO mRNA expression and CO protein stability, flowering regulation can also modulate the targeting of CO to FT.
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Affiliation(s)
- Khoa Thi Nguyen
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Ilha Lee
- School of Biological Sciences, Seoul National University, Seoul 151-747, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea.
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Lee N, Park J, Kim K, Choi G. The Transcriptional Coregulator LEUNIG_HOMOLOG Inhibits Light-Dependent Seed Germination in Arabidopsis. Plant Cell 2015; 27:2301-13. [PMID: 26276832 PMCID: PMC4568510 DOI: 10.1105/tpc.15.00444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/27/2015] [Indexed: 05/11/2023]
Abstract
PHYTOCHROME-INTERACTING FACTOR1 (PIF1) is a basic helix-loop-helix transcription factor that inhibits light-dependent seed germination in Arabidopsis thaliana. However, it remains unclear whether PIF1 requires other factors to regulate its direct targets. Here, we demonstrate that LEUNIG_HOMOLOG (LUH), a Groucho family transcriptional corepressor, binds to PIF1 and coregulates its targets. Not only are the transcriptional profiles of the luh and pif1 mutants remarkably similar, more than 80% of the seeds of both genotypes germinate in the dark. We show by chromatin immunoprecipitation that LUH binds a subset of PIF1 targets in a partially PIF1-dependent manner. Unexpectedly, we found LUH binds and coregulates not only PIF1-activated targets but also PIF1-repressed targets. Together, our results indicate LUH functions with PIF1 as a transcriptional coregulator to inhibit seed germination.
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Affiliation(s)
- Nayoung Lee
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Keunhwa Kim
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
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48
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Jung JH, Park BH, Oh SJ, Choi G, Seo TS. Integration of reverse transcriptase loop-mediated isothermal amplification with an immunochromatographic strip on a centrifugal microdevice for influenza A virus identification. Lab Chip 2015; 15:718-25. [PMID: 25426967 DOI: 10.1039/c4lc01033g] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A novel centrifugal microdevice which could perform reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and immunochromatographic strip (ICS) based amplicon detection was demonstrated for simple and cost-effective influenza A virus identification. The proposed centrifugal microdevice consists of the sample and running buffer loading reservoirs, the RT-LAMP chamber, and the ICS for detecting gene expression. The entire process could be completed sequentially and automatically by simply controlling the rotation speed and by optimizing the microfluidic design. Monoplex and multiplex RT-LAMP reactions targeting H1 and/or M gene were executed at 66 °C for 40 min, and the resultant amplicons were successfully analysed on the ICS within 15 min. Influenza A H1N1 virus was subtyped by detecting H1 and M gene on the ICS even with 10 copies of viral RNAs. Highly specific and multiplex viral typing of the integrated RT-LAMP-ICS microdevice was also demonstrated. The combination of the rapid isothermal amplification with the simple colorimetric detection on a strip in a single centrifugal microdevice will provide an advanced genetic analysis platform in the field of on-site pathogen diagnostics.
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Affiliation(s)
- J H Jung
- Department of Chemical and Biomolecular Engineering (BK21 Plus program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea.
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49
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Gomersall CD, Tian Q, Reynolds D, Ip M, Choi G, Joynt G. Adsorption of amikacin during continuous venovenous haemofiltration in a swine model of acute renal failure. Crit Care 2015. [PMCID: PMC4472770 DOI: 10.1186/cc14197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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50
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Shahgaldi K, Hegner T, Da Silva C, Fukuyama A, Takeuchi M, Uema A, Kado Y, Nagata Y, Hayashi A, Otani K, Fukuda S, Yoshitani H, Otsuji Y, Morhy S, Lianza A, Afonso T, Oliveira W, Tavares G, Rodrigues A, Vieira M, Warth A, Deutsch A, Fischer C, Tezynska-Oniszk I, Turska-Kmiec A, Kawalec W, Dangel J, Maruszewski B, Bokiniec R, Burczynski P, Borszewska-Kornacka K, Ziolkowska L, Zuk M, Troshina A, Dzhalilova D, Poteshkina N, Hamitov F, Warita S, Kawasaki M, Tanaka R, Yagasaki H, Minatoguchi S, Wanatabe T, Ono K, Noda T, Wanatabe S, Minatoguchi S, Angelis A, Ageli K, Vlachopoulos C, Felekos I, Ioakimidis N, Aznaouridis K, Vaina S, Abdelrasoul M, Tsiamis E, Stefanadis C, Cameli M, Sparla S, D'ascenzi F, Fineschi M, Favilli R, Pierli C, Henein M, Mondillo S, Lindqvist P, Tossavainen E, Gonzalez M, Soderberg S, Henein M, Holmgren A, Strachinaru M, Catez E, Jousten I, Pavel O, Janssen C, Morissens M, Chatzistamatiou E, Moustakas G, Memo G, Konstantinidis D, Mpampatzeva Vagena I, Manakos K, Traxanas K, Vergi N, Feretou A, Kallikazaros I, Tsai WC, Sun YT, Lee WH, Yang LT, Liu YW, Lee CH, Li WT, Mizariene V, Bieseviciene M, Karaliute R, Verseckaite R, Vaskelyte J, Lesauskaite V, Chatzistamatiou E, Mpampatseva Vagena I, Manakos K, Moustakas G, Konstantinidis D, Memo G, Mitsakis O, Kasakogias A, Syros P, Kallikazaros I, Hristova K, Cornelissen G, Singh R, Shiue I, Coisne D, Madjalian AM, Tchepkou C, Raud Raynier P, Degand B, Christiaens L, Baldenhofer G, Spethmann S, Dreger H, Sanad W, Baumann G, Stangl K, Stangl V, Knebel F, Azzaz S, Kacem S, Ouali S, Risos L, Dedobbeleer C, Unger P, Sinem Cakal S, Elif Eroglu E, Baydar O, Beytullah Cakal B, Mehmet Vefik Yazicioglu M, Mustafa Bulut M, Cihan Dundar C, Kursat Tigen K, Birol Ozkan B, Ali Metin Esen A, Tournoux F, Chequer R, Sroussi M, Hyafil F, Rouzet F, Leguludec D, Baum P, Stoebe S, Pfeiffer D, Hagendorff A, Fang F, Lau M, Zhang Q, Luo X, Wang X, Chen L, Yu C, Zaborska B, Smarz K, Makowska E, Kulakowski P, Budaj A, Bengrid TM, Zhao Y, Henein MY, Caminiti G, D'antoni V, Cardaci V, Conti V, Volterrani M, Warita S, Kawasaki M, Yagasaki H, Minatoguchi S, Nagaya M, Ono K, Noda T, Watanabe S, Houle H, Minatoguchi S, Gillebert TC, Chirinos JA, Claessens TC, Raja MW, De Buyzere ML, Segers P, Rietzschel ER, Kim K, Cha J, Chung H, Kim J, Yoon Y, Lee B, Hong B, Rim S, Kwon H, Choi E, Pyankov V, Aljaroudi W, Matta S, Al-Shaar L, Habib R, Gharzuddin W, Arnaout S, Skouri H, Jaber W, Abchee A, Bouzas Mosquera A, Peteiro J, Broullon F, Constanso Conde I, Bescos Galego H, Martinez Ruiz D, Yanez Wonenburger J, Vazquez Rodriguez J, Alvarez Garcia N, Castro Beiras A, Gunyeli E, Oliveira Da Silva C, Shahgaldi K, Manouras A, Winter R, Meimoun P, Abouth S, Martis S, Boulanger J, Elmkies F, Zemir H, Detienne J, Luycx-Bore A, Clerc J, Rodriguez Palomares JF, Gutierrez L, Maldonado G, Garcia G, Galuppo V, Gruosso D, Teixido G, Gonzalez Alujas M, Evangelista A, Garcia Dorado D, Rechcinski T, Wierzbowska-Drabik K, Wejner-Mik P, Szymanska B, Jerczynska H, Lipiec P, Kasprzak J, El-Touny K, El-Fawal S, Loutfi M, El-Sharkawy E, Ashour S, Boniotti C, Carminati M, Fusini L, Andreini D, Pontone G, Pepi M, Caiani E, Oryshchyn N, Kramer B, Hermann S, Liu D, Hu K, Ertl G, Weidemann F, Ancona F, Miyazaki S, Slavich M, Figini F, Latib A, Chieffo A, Montorfano M, Alfieri O, Colombo A, Agricola E, Nogueira M, Branco L, Rosa S, Portugal G, Galrinho A, Abreu J, Cacela D, Patricio L, Fragata J, Cruz Ferreira R, Igual Munoz B, Erdociain Perales M, Maceira Gonzalez A, Estornell Erill Jordi J, Donate Bertolin L, Vazquez Sanchez Alejandro A, Miro Palau Vicente V, Cervera Zamora A, Piquer Gil M, Montero Argudo A, Girgis HYA, Illatopa V, Cordova F, Espinoza D, Ortega J, Khan U, Islam A, Majumder A, Girgis HYA, Bayat F, Naghshbandi E, Naghshbandi E, Samiei N, Samiei N, Malev E, Omelchenko M, Vasina L, Zemtsovsky E, Piatkowski R, Kochanowski J, Budnik M, Scislo P, Opolski G, Kochanowski J, Piatkowski R, Scislo P, Budnik M, Marchel M, 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Poster session 3: Thursday 4 December 2014, 14:00-18:00 * Location: Poster area. Eur Heart J Cardiovasc Imaging 2014. [DOI: 10.1093/ehjci/jeu253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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