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Kannan P, Oh J, Yeon YJ, Park YI, Seo MH, Park K. Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome. Proteins 2024; 92:106-116. [PMID: 37646483 DOI: 10.1002/prot.26586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.
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Affiliation(s)
- Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jisung Oh
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Convergence Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of 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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Park YI, Choi SH, Hong CS, Cho MS, Son J, Han MC, Kim J, Kim H, Kim DW, Kim JS. A Photograph-Based Visualization and Prediction Framework for Radiation-Induced Dermatitis. Int J Radiat Oncol Biol Phys 2023; 117:e480-e481. [PMID: 37785522 DOI: 10.1016/j.ijrobp.2023.06.1701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) This study aimed to suggest a photograph-based prediction system for acute radiation-induced dermatitis (RID), which can be applied to notify patients about the risk of the development of skin discomfort during radiotherapy. MATERIALS/METHODS The proposed system compared the spatial dose distribution with the RID region using the following methods. Skin photographs of patients were taken using an RGB-depth camera to acquire the shape information of RID. The skin surface data measured from the camera was registered with the shape of the external body contour using an iterative closest point algorithm. Spatial dose distribution of skin was extracted from the external body contour to a depth of 2 mm and projected onto the plane of the skin photograph using a transformation matrix for skin depth data. To compare the spatial distribution of skin dose with the shape of RID, the region of RID in patients' skin was delineated on photographs into three toxicity symptoms referring to the CTCAE criteria grade 1 (skin redness), grade 2 (dry desquamation), and grade 3 (moist desquamation). The degree of overlap between the shape of each RID and skin dose distribution was evaluated using the dice similarity coefficient (DSC). Threshold doses for predicting RID occurrence were estimated by skin isodose lines with the highest DSC. The developed system was validated using data from 19 patients who received volumetric modulated arc therapy for head-neck cancer at a single institution. RESULTS Threshold doses for RID grades 1, 2, and 3 were estimated using 18, 18, and 2 individual RID labels delineated on skin photographs, respectively. Isodose lines with the highest DSC for RID grades 1, 2, and 3 were calculated as 26.0 Gy, 36.5 Gy, and 54.0 Gy, respectively. A strong overlap (average DSC > 0.6) was observed between isodose skin lines and the shape of RID labels in all RID grades. CONCLUSION Assessing the spatial information of skin dose can be helpful in predicting acute RID. The region of RID shows a strong similarity with the skin dose distribution in head-neck patients. Visualization of skin dose on the patient photograph is potent to patient education for preparing the cosmetic discomfort during radiotherapy, which may lead to the improvement of the patient satisfaction in treatment.
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Affiliation(s)
- Y I Park
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - S H Choi
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - C S Hong
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - M S Cho
- Department of Radiation Oncology, Yongin Severance Hospital, Yonsei University College of Medicine, Gyeonggi-do, Korea, Republic of (South) Korea
| | - J Son
- Department of Radiation Oncology, Yongin Severance Hospital, Yonsei University College of Medicine, Gyeonggi-do, Korea, Republic of (South) Korea
| | - M C Han
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - H Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - D W Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
| | - J S Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea; Department of Radiation Oncology, Yonsei Cancer Center, Heavy Ion Therapy Research Institute, Yonsei University College of Medicine, Seoul, Korea, Republic of (South) Korea
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Han MH, Yang HW, Yoon J, Villafani Y, Song JY, Pan CH, Park K, Cho Y, Song JJ, Kim SJ, Park YI, Park J. Color-Tuning Mechanism of the Lit Form of Orange Carotenoid Protein. Mol Cells 2023; 46:513-525. [PMID: 37587751 PMCID: PMC10440265 DOI: 10.14348/molcells.2023.2186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.
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Affiliation(s)
- Man-Hyuk Han
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jungmin Yoon
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Yvette Villafani
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Cheol Ho Pan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea
| | - Youngmoon Cho
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, KI for the BioCentury, KAIST, Daejeon 34141, Korea
| | - Seung Joong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
- Quantum Intelligence Corp., Seoul 07326, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Jiyong Park
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Korea
- Department of Chemistry, KAIST, Daejeon 34141, Korea
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Moon KB, Park SJ, Park JS, Lee HJ, Shin SY, Lee SM, Choi GJ, Kim SG, Cho HS, Jeon JH, Kim YS, Park YI, Kim HS. Corrigendum: Editing of StSR4 by Cas9-RNPs confers resistance to Phytophthora infestans in potato. Front Plant Sci 2023; 13:1063362. [PMID: 37293182 PMCID: PMC10245271 DOI: 10.3389/fpls.2022.1063362] [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] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 06/10/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.997888.].
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Seung Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- GenKOre, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of 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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Lim JM, Jung S, In JS, Park YI, Jeong WJ. Heterologous overexpression of the cyanobacterial alcohol dehydrogenase sysr1 confers cold tolerance to the oleaginous alga Nannochloropsis salina. Front Plant Sci 2023; 14:1045917. [PMID: 36760652 PMCID: PMC9905847 DOI: 10.3389/fpls.2023.1045917] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Temperature is an important regulator of growth in algae and other photosynthetic organisms. Temperatures above or below the optimal growth temperature could cause oxidative stress to algae through accumulation of oxidizing compounds such as reactive oxygen species (ROS). Thus, algal temperature stress tolerance could be attained by enhancing oxidative stress resistance. In plants, alcohol dehydrogenase (ADH) has been implicated in cold stress tolerance, eliciting a signal for the synthesis of antioxidant enzymes that counteract oxidative damage associated with several abiotic stresses. Little is known whether temperature stress could be alleviated by ADH in algae. Here, we generated transgenic lines of the unicellular oleaginous alga Nannochloropsis salina that heterologously expressed sysr1, which encodes ADH in the cyanobacterium Synechocystis sp. PCC 6906. To drive sysr1 expression, the heat shock protein 70 (HSP70) promoter isolated from N. salina was used, as its transcript levels were significantly increased under either cold or heat stress growth conditions. When subjected to cold stress, transgenic N. salina cells were more cold-tolerant than wild-type cells, showing less ROS production but increased activity of antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, and catalase. Thus, we suggest that reinforcement of alcohol metabolism could be a target for genetic manipulation to endow algae with cold temperature stress tolerance.
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Affiliation(s)
- Jong-Min Lim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Sokyong Jung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jae-Sun In
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Won-Joong Jeong
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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Park YI, Choi SH, Hong CS, Cho MS, Son J, Han MC, Kim J, Kim H, Kim DW, Kim JS. A New Approach to Quantify and Grade Radiation Dermatitis Using Deep-Learning Segmentation in Skin Photographs. Clin Oncol (R Coll Radiol) 2023; 35:e10-e19. [PMID: 35918275 DOI: 10.1016/j.clon.2022.07.001] [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: 12/08/2021] [Revised: 06/15/2022] [Accepted: 07/06/2022] [Indexed: 01/04/2023]
Abstract
AIMS Objective evaluation of radiation dermatitis is important for analysing the correlation between the severity of radiation dermatitis and dose distribution in clinical practice and for reliable reporting in clinical trials. We developed a novel radiation dermatitis segmentation system based on convolutional neural networks (CNNs) to consistently evaluate radiation dermatitis. MATERIALS AND METHODS The radiation dermatitis segmentation system is designed to segment the radiation dermatitis occurrence area using skin photographs and skin-dose distribution. A CNN architecture with a dilated convolution layer and skip connection was designed to estimate the radiation dermatitis area. Seventy-three skin photographs obtained from patients undergoing radiotherapy were collected for training and testing. The ground truth of radiation dermatitis segmentation is manually delineated from the skin photograph by an experienced radiation oncologist and medical physicist. We converted the skin photographs to RGB (red-green-blue) and CIELAB (lightness (L∗), red-green (a∗) and blue-yellow (b∗)) colour information and trained the network to segment faint and severe radiation dermatitis using three different input combinations: RGB, RGB + CIELAB (RGBLAB) and RGB + CIELAB + skin-dose distribution (RGBLAB_D). The proposed system was evaluated using the Dice similarity coefficient (DSC), sensitivity, specificity and normalised Matthews correlation coefficient (nMCC). A paired t-test was used to compare the results of different segmentation performances. RESULTS Optimal data composition was observed in the network trained for radiation dermatitis segmentation using skin photographs and skin-dose distribution. The average DSC, sensitivity, specificity and nMCC values of RGBLAB_D were 0.62, 0.61, 0.91 and 0.77, respectively, in faint radiation dermatitis, and 0.69, 0.78, 0.96 and 0.83, respectively, in severe radiation dermatitis. CONCLUSION Our study showed that CNN-based radiation dermatitis segmentation in skin photographs of patients undergoing radiotherapy can describe radiation dermatitis severity and pattern. Our study could aid in objectifying the radiation dermatitis grading and analysing the reliable correlation between dosimetric factors and the morphology of radiation dermatitis.
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Affiliation(s)
- Y I Park
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea; Medical Physics and Biomedical Engineering Lab (MPBEL), Yonsei University College of Medicine, Seoul, South Korea
| | - S H Choi
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea; Department of Radiation Oncology, Yongin Severance Hospital, Yongin, South Korea
| | - C-S Hong
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea.
| | - M-S Cho
- Department of Radiation Oncology, Yongin Severance Hospital, Yongin, South Korea
| | - J Son
- Department of Radiation Oncology, Yongin Severance Hospital, Yongin, South Korea
| | - M C Han
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea
| | - J Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea
| | - H Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea
| | - D W Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea
| | - J S Kim
- Department of Radiation Oncology, Yonsei University College of Medicine, Seoul, South Korea; Medical Physics and Biomedical Engineering Lab (MPBEL), Yonsei University College of Medicine, Seoul, South Korea.
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Moon KB, Park SJ, Park JS, Lee HJ, Shin SY, Lee SM, Choi GJ, Kim SG, Cho HS, Jeon JH, Kim YS, Park YI, Kim HS. Editing of StSR4 by Cas9-RNPs confers resistance to Phytophthora infestans in potato. Front Plant Sci 2022; 13:997888. [PMID: 36212382 PMCID: PMC9539116 DOI: 10.3389/fpls.2022.997888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/06/2022] [Indexed: 06/10/2023]
Abstract
Potato (Solanum tuberosum L.) cultivation is threatened by various environmental stresses, especially disease. Genome editing technologies are effective tools for generating pathogen-resistant potatoes. Here, we established an efficient RNP-mediated CRISPR/Cas9 genome editing protocol in potato to develop Phytophthora infestans resistant mutants by targeting the susceptibility gene, Signal Responsive 4 (SR4), in protoplasts. Mutations in StSR4 were efficiently introduced into the regenerated potato plants, with a maximum efficiency of 34%. High co-expression of StEDS1 and StPAD4 in stsr4 mutants induced the accumulation of salicylic acid (SA), and enhanced the expression of the pathogen resistance marker StPR1. In addition, increased SA content in the stsr4 mutant enhanced its resistance to P. infestans more than that in wild type. However, the growth of stsr4_3-19 and stsr4_3-698 mutants with significantly high SA was strongly inhibited, and a dwarf phenotype was induced. Therefore, it is important to adequate SA accumulation in order to overcome StSR4 editing-triggered growth inhibition and take full advantages of the improved pathogen resistance of stsr4 mutants. This RNP-mediated CRISPR/Cas9-based potato genome editing protocol will accelerate the development of pathogen-resistant Solanaceae crops via molecular breeding.
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Seung Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Soo Min Lee
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Gyung Ja Choi
- Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, Republic of Korea
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- GenKOre, Daejeon, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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10
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Timilsina R, Kim Y, Park S, Park H, Park SJ, Kim JH, Park JH, Kim D, Park YI, Hwang D, Lee JC, Woo HR. ORESARA 15, a PLATZ transcription factor, controls root meristem size through auxin and cytokinin signalling-related pathways. J Exp Bot 2022; 73:2511-2524. [PMID: 35139177 DOI: 10.1093/jxb/erac050] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/08/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
An optimal size of post-embryonic root apical meristem (RAM) is achieved by a balance between cell division and differentiation. Despite extensive research, molecular mechanisms underlying the coordination of cell division and differentiation are still fragmentary. Here, we report that ORESARA 15 (ORE15), an Arabidopsis PLANT A/T-RICH SEQUENCE-AND ZINC-BINDING PROTEIN (PLATZ) transcription factor preferentially expressed in the RAM, determines RAM size. Primary root length, RAM size, cell division rate, and stem cell niche activity were reduced in an ore15 loss-of-function mutant but enhanced in an activation-tagged line overexpressing ORE15, compared with wild type. ORE15 forms mutually positive and negative feedback loops with auxin and cytokinin signalling, respectively. Collectively, our findings imply that ORE15 controls RAM size by mediating the antagonistic interaction between auxin and cytokinin signalling-related pathways.
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Affiliation(s)
- Rupak Timilsina
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Yongmin Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Sanghoon Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hyunsoo Park
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Sung-Jin Park
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Ji-Hwan Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Doa Kim
- Center for Plant Aging Research, Institute for Basic Science, Daegu, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Hye Ryun Woo
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
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11
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Ryu AJ, Jeong BR, Kang NK, Jeon S, Sohn MG, Yun HJ, Lim JM, Jeong SW, Park YI, Jeong WJ, Park S, Chang YK, Jeong KJ. Safe-Harboring based novel genetic toolkit for Nannochloropsis salina CCMP1776: Efficient overexpression of transgene via CRISPR/Cas9-Mediated Knock-in at the transcriptional hotspot. Bioresour Technol 2021; 340:125676. [PMID: 34365302 DOI: 10.1016/j.biortech.2021.125676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/30/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Transgene expression in microalgae can be hampered by transgene silencing and unstable expression due to position effects. To overcome this, "safe harboring" transgene expression system was established for Nannochloropsis. Initially, transformants were obtained expressing a sfGFP reporter, followed by screening for high expression of sfGFP with fluorescence-activated cell sorter (FACS). 'T1' transcriptional hotspot was identified from a mutant showing best expression of sfGFP, but did not affect growth or lipid contents. By using a Cas9 editor strain, FAD12 gene, encoding Δ12-fatty acid desaturase (FAD12), was successfully knocked-in at the T1 locus, resulting in significantly higher expression of FAD12 than those of random integration. Importantly, the "safe harbored" FAD12 transformants showed four-fold higher production of linoleic acid (LA), the product of FAD12, leading to 1.5-fold increase in eicosapentaenoic acid (EPA). This safe harboring principle provide excellent proof of the concept for successful genetic/metabolic engineering of microalgae and other organisms.
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Affiliation(s)
- Ae Jin Ryu
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Byeong-Ryool Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; Single-Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Qingdao, Shandong 266101, China
| | - Nam Kyu Kang
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Min Gi Sohn
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyo Jin Yun
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jong Min Lim
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seok Won Jeong
- Department of Biological Sciences, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Won Joong Jeong
- Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Institute for the BioCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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12
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Gong Y, Kang NK, Kim YU, Wang Z, Wei L, Xin Y, Shen C, Wang Q, You W, Lim JM, Jeong SW, Park YI, Oh HM, Pan K, Poliner E, Yang G, Li-Beisson Y, Li Y, Hu Q, Poetsch A, Farre EM, Chang YK, Jeong WJ, Jeong BR, Xu J. The NanDeSyn database for Nannochloropsis systems and synthetic biology. Plant J 2020; 104:1736-1745. [PMID: 33103271 DOI: 10.1111/tpj.15025] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 05/25/2020] [Revised: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 06/11/2023]
Abstract
Nannochloropsis species, unicellular industrial oleaginous microalgae, are model organisms for microalgal systems and synthetic biology. To facilitate community-based annotation and mining of the rapidly accumulating functional genomics resources, we have initiated an international consortium and present a comprehensive multi-omics resource database named Nannochloropsis Design and Synthesis (NanDeSyn; http://nandesyn.single-cell.cn). Via the Tripal toolkit, it features user-friendly interfaces hosting genomic resources with gene annotations and transcriptomic and proteomic data for six Nannochloropsis species, including two updated genomes of Nannochloropsis oceanica IMET1 and Nannochloropsis salina CCMP1776. Toolboxes for search, Blast, synteny view, enrichment analysis, metabolic pathway analysis, a genome browser, etc. are also included. In addition, functional validation of genes is indicated based on phenotypes of mutants and relevant bibliography. Furthermore, epigenomic resources are also incorporated, especially for sequencing of small RNAs including microRNAs and circular RNAs. Such comprehensive and integrated landscapes of Nannochloropsis genomics and epigenomics will promote and accelerate community efforts in systems and synthetic biology of these industrially important microalgae.
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Affiliation(s)
- Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Nam K Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, 61801, USA
| | - Young U Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Zengbin Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Wuxin You
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Suk-Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Kehou Pan
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Laboratory of Applied Microalgae, College of Fisheries, Ocean University of China, Qingdao, 266003, China
| | - Eric Poliner
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Guanpin Yang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
- Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Yonghua Li-Beisson
- Aix Marseille Univ, CEA, CNRS, Institut de Biosciences et Biotechnologies Aix-Marseille, CEA Cadarache, 13108, Saint Paul-Lez-Durance, France
| | - Yantao Li
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, University of Maryland, Baltimore County, Baltimore, MD, 21202, USA
| | - Qiang Hu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ansgar Poetsch
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
- Department of Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, 266003, China
| | - Eva M Farre
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Yong K Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Byeong-Ryool Jeong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Shandong Institute of Energy Research, Qingdao Institute of BioEnergy and Bioprocess Technology (QIBEBT), Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
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13
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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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14
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Villafani Y, Yang HW, Park YI. Color Sensing and Signal Transmission Diversity of Cyanobacterial Phytochromes and Cyanobacteriochromes. Mol Cells 2020; 43:509-516. [PMID: 32438780 PMCID: PMC7332365 DOI: 10.14348/molcells.2020.0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
To perceive fluctuations in light quality, quantity, and timing, higher plants have evolved diverse photoreceptors including UVR8 (a UV-B photoreceptor), cryptochromes, phototropins, and phytochromes (Phys). In contrast to plants, prokaryotic oxygen-evolving photosynthetic organisms, cyanobacteria, rely mostly on bilin-based photoreceptors, namely, cyanobacterial phytochromes (Cphs) and cyanobacteriochromes (CBCRs), which exhibit structural and functional differences compared with plant Phys. CBCRs comprise varying numbers of light sensing domains with diverse color-tuning mechanisms and signal transmission pathways, allowing cyanobacteria to respond to UV-A, visible, and far-red lights. Recent genomic surveys of filamentous cyanobacteria revealed novel CBCRs with broader chromophore-binding specificity and photocycle protochromicity. Furthermore, a novel Cph lineage has been identified that absorbs blue-violet/yellow-orange light. In this minireview, we briefly discuss the diversity in color sensing and signal transmission mechanisms of Cphs and CBCRs, along with their potential utility in the field of optogenetics.
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Affiliation(s)
- Yvette Villafani
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
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15
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Choi MG, Kim EJ, Song JY, Choi SB, Cho SW, Park CS, Kang CS, Park YI. Peptide transporter2 (PTR2) enhances water uptake during early seed germination in Arabidopsis thaliana. Plant Mol Biol 2020; 102:615-624. [PMID: 31997111 PMCID: PMC7062858 DOI: 10.1007/s11103-020-00967-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/28/2019] [Accepted: 01/10/2020] [Indexed: 05/12/2023]
Abstract
PTR2 in Arabidopsis thaliana is negatively regulated by ABI4 and plays a key role in water uptake by seeds, ensuring that imbibed seeds proceed to germination. Peptide transporters (PTRs) transport nitrogen-containing substrates in a proton-dependent manner. Among the six PTRs in Arabidopsis thaliana, the physiological role of the tonoplast-localized, seed embryo abundant PTR2 is unknown. In the present study, a molecular physiological analysis of PTR2 was conducted using ptr2 mutants and PTR2CO complementation lines. Compared with the wild type, the ptr2 mutant showed ca. 6 h delay in testa rupture and consequently endosperm rupture because of 17% lower water content and 10% higher free abscisic acid (ABA) content. Constitutive overexpression of the PTR2 gene under the control of the Cauliflower mosaic virus (CaMV) 35S promoter in ptr2 mutants rescued the mutant phenotypes. After cold stratification, a transient increase in ABA INSENSITIVE4 (ABI4) transcript levels during induction of testa rupture was followed by a similar increase in PTR2 transcript levels, which peaked prior to endosperm rupture. The PTR2 promoter region containing multiple CCAC motifs was recognized by ABI4 in electrophoretic mobility shift assays, and PTR2 expression was repressed by 67% in ABI4 overexpression lines compared with the wild type, suggesting that PTR2 is an immediate downstream target of ABI4. Taken together, the results suggest that ABI4-dependent temporal regulation of PTR2 expression may influence water status during seed germination to promote the post-germinative growth of imbibed seeds.
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Affiliation(s)
- Myoung-Goo Choi
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Eui Joong Kim
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, 17058, Gyunggi-do, Republic of Korea
| | - Seong-Woo Cho
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Chul Soo Park
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju, 54896, Republic of Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Song JY, Lee HY, Yang HW, Song JJ, Lagarias JC, Park YI. Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes. J Biol Chem 2020; 295:6754-6766. [PMID: 32184354 DOI: 10.1074/jbc.ra120.012950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 02/06/2020] [Revised: 03/13/2020] [Indexed: 11/06/2022] Open
Abstract
The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, here we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue-absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical "second" cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.
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Affiliation(s)
- Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ha Yong Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Joon Song
- Department of Biological Science and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
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Vikramathithan J, Hwangbo K, Lim JM, Lim KM, Kang DY, Park YI, Jeong WJ. Overexpression of Chlamydomonas reinhardtii LCIA (CrLCIA) gene increases growth of Nannochloropsis salina CCMP1776. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101807] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Moon KB, Park JS, Park YI, Song IJ, Lee HJ, Cho HS, Jeon JH, Kim HS. Development of Systems for the Production of Plant-Derived Biopharmaceuticals. Plants (Basel) 2019; 9:plants9010030. [PMID: 31878277 PMCID: PMC7020158 DOI: 10.3390/plants9010030] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022]
Abstract
Over the last several decades, plants have been developed as a platform for the production of useful recombinant proteins due to a number of advantages, including rapid production and scalability, the ability to produce unique glycoforms, and the intrinsic safety of food crops. The expression methods used to produce target proteins are divided into stable and transient systems depending on applications that use whole plants or minimally processed forms. In the early stages of research, stable expression systems were mostly used; however, in recent years, transient expression systems have been preferred. The production of the plant itself, which produces recombinant proteins, is currently divided into two major approaches, open-field cultivation and closed-indoor systems. The latter encompasses such regimes as greenhouses, vertical farming units, cell bioreactors, and hydroponic systems. Various aspects of each system will be discussed in this review, which focuses mainly on practical examples and commercially feasible approaches.
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Affiliation(s)
- Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
- Department of Biological Sciences, Chungnam National University, 99 Deahank-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, 99 Deahank-ro, Yuseong-gu, Daejeon 34134, Korea
| | - In-Ja Song
- National Research Safety Headquarters, Korea Research Institute of Bioscience and Biotechnology, 30 Yeongudanji-ro, Ochang, Chungbuk-do 28116, Korea;
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
| | - Hye Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea; (K.-B.M.); (J.-S.P.); (H.-J.L.); (H.S.C.); (J.-H.J.)
- Correspondence: ; Tel.: +82-42-860-4493
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Lee K, Park SJ, Park YI, Kang H. CFM9, a Mitochondrial CRM Protein, Is Crucial for Mitochondrial Intron Splicing, Mitochondria Function and Arabidopsis Growth and Stress Responses. Plant Cell Physiol 2019; 60:2538-2548. [PMID: 31359042 DOI: 10.1093/pcp/pcz147] [Citation(s) in RCA: 8] [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: 06/07/2019] [Accepted: 07/18/2019] [Indexed: 05/24/2023]
Abstract
Although the importance of chloroplast RNA splicing and ribosome maturation (CRM) domain-containing proteins has been established for chloroplast RNA metabolism and plant development, the functional role of CRM proteins in mitochondria remains largely unknown. Here, we investigated the role of a mitochondria-targeted CRM protein (At3g27550), named CFM9, in Arabidopsis thaliana. Confocal analysis revealed that CFM9 is localized in mitochondria. The cfm9 mutant exhibited delayed seed germination, retarded growth and shorter height compared with the wild type under normal conditions. The growth-defect phenotypes were more manifested upon high salinity, dehydration or ABA application. Complementation lines expressing CFM9 in the mutant background fully recovered the wild-type phenotypes. Notably, the mutant had abnormal mitochondria, increased hydrogen peroxide and reduced respiration activity, implying that CFM9 is indispensable for normal mitochondrial function. More important, the splicing of many intron-containing genes in mitochondria was defective in the mutant, suggesting that CFM9 plays a crucial role in the splicing of mitochondrial introns. Collectively, our results provide clear evidence emphasizing that CFM9 is an essential factor in the splicing of mitochondrial introns, which is crucial for mitochondrial biogenesis and function and the growth and development of Arabidopsis.
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Affiliation(s)
- Kwanuk Lee
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, Korea
| | - Su Jung Park
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju, Korea
- AgriBio Institute of Climate Change Management, Chonnam National University, Gwangju, Korea
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20
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Hwangbo K, Lim JM, Jeong SW, Vikramathithan J, Park YI, Jeong WJ. Elevated Inorganic Carbon Concentrating Mechanism Confers Tolerance to High Light in an Arctic Chlorella sp. ArM0029B. Front Plant Sci 2018; 9:590. [PMID: 29868055 PMCID: PMC5949578 DOI: 10.3389/fpls.2018.00590] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/16/2018] [Indexed: 05/29/2023]
Abstract
Microalgae and higher plants employ an inorganic carbon (Ci) concentrating mechanism (CCM) to increase CO2 availability to Rubisco. Operation of the CCM should enhance the activity of the Calvin cycle, which could act as an electron sink for electrons generated by photosynthesis, and lower the redox status of photosynthetic electron transport chains. In this study, a hypothesis that microalgal cells with fully operating CCM are less likely to be photodamaged was tested by comparing a Chlorella mutant with its wild type (WT). The mutant acquired by screening gamma-ray-induced mutant libraries of Chlorella sp. ArM0029B exhibited constitutively active CCM (CAC) even in the presence of additional Ci sources under mixotrophic growth conditions. In comparison to the WT alga, the mutant named to constitutively active CCM1 (CAC1) showed more transcript levels for genes coding proteins related to CCM such as Ci transporters and carbonic anhydrases (CA), and greater levels of intracellular Ci content and CA activity regardless of whether growth is limited by light or not. Under photoinhibitory conditions, CAC1 mutant showed faster growth than WT cells with more PSII reaction center core component D1 protein (encoded by psbA), higher photochemical efficiency as estimated by the chlorophyll fluorescence parameter (Fv/Fm), and fewer reactive oxygen species (ROS). Interestingly, high light (HL)-induced increase in ROS contents in WT cells was significantly inhibited by bicarbonate supplementation. It is concluded that constitutive operation of CCM endows Chlorella cells with resistance to HL partly by reducing the endogenous generation of ROS. These results will provide useful information on the interaction between CCM expression, ROS production, and photodamage in Chlorella and related microalgae.
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Affiliation(s)
- Kwon Hwangbo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Seok-Won Jeong
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Jayaraman Vikramathithan
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, South Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
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21
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An CH, Nazki S, Park SC, Jeong YJ, Lee JH, Park SJ, Khatun A, Kim WI, Park YI, Jeong JC, Kim CY. Plant synthetic GP4 and GP5 proteins from porcine reproductive and respiratory syndrome virus elicit immune responses in pigs. Planta 2018; 247:973-985. [PMID: 29313103 DOI: 10.1007/s00425-017-2836-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 09/06/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
We demonstrated successful overexpression of porcine reproductive and respiratory syndrome virus (PRRSV)-derived GP4D and GP5D antigenic proteins in Arabidopsis. Pigs immunized with transgenic plants expressing GP4D and GP5D proteins generated both humoral and cellular immune responses to PRRSV. Porcine reproductive and respiratory syndrome virus (PRRSV) causes PRRS, the most economically significant disease affecting the swine industry worldwide. However, current commercial PRRSV vaccines (killed virus or modified live vaccines) show poor efficacy and safety due to concerns such as reversion of virus to wild type and lack of cross protection. To overcome these problems, plants are considered a promising alternative to conventional platforms and as a vehicle for large-scale production of recombinant proteins. Here, we demonstrate successful production of recombinant protein vaccine by expressing codon-optimized and transmembrane-deleted recombinant glycoproteins (GP4D and GP5D) from PRRSV in planta. We generated transgenic Arabidopsis plants expressing GP4D and GP5D proteins as candidate antigens. To examine immunogenicity, pigs were fed transgenic Arabidopsis leaves expressing the GP4D and GP5D antigens (three times at 2-week intervals) and then challenged with PRRSV at 6-week post-initial treatment. Immunized pigs showed significantly lower lung lesion scores and reduced viremia and viral loads in the lung than pigs fed Arabidopsis leaves expressing mYFP (control). Immunized pigs also had higher titers of PRRSV-specific antibodies and significantly higher levels of pro-inflammatory cytokines (TNF-α and IL-12). Furthermore, the numbers of IFN-γ+-producing cells were higher, and those of regulatory T cells were lower, in GP4D and GP5D immunized pigs than in control pigs. Thus, plant-derived GP4D and GP5D proteins provide an alternative platform for producing an effective subunit vaccine against PRRSV.
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MESH Headings
- Animals
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Blotting, Western
- Enzyme-Linked Immunosorbent Assay
- Flow Cytometry
- Immunity, Cellular
- Immunity, Humoral
- Leukocytes, Mononuclear/immunology
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Porcine respiratory and reproductive syndrome virus/immunology
- Reverse Transcriptase Polymerase Chain Reaction
- Swine/immunology
- Swine/virology
- Vaccines, Synthetic/biosynthesis
- Vaccines, Synthetic/immunology
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Affiliation(s)
- Chul Han An
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea
- Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Salik Nazki
- College of Veterinary Medicine and College of Environmental and Biosource Science, Chonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Sung-Chul Park
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea
| | - Yu Jeong Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea
| | - Ju Huck Lee
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea
| | - Su-Jin Park
- Natural Product Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea
| | - Amina Khatun
- College of Veterinary Medicine and College of Environmental and Biosource Science, Chonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Won-Il Kim
- College of Veterinary Medicine and College of Environmental and Biosource Science, Chonbuk National University, Iksan, Jeonbuk, 54596, Republic of Korea
| | - Youn-Il Park
- Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jae Cheol Jeong
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea.
| | - Cha Young Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 181 Ipsin-gil, Jeongeup, Jeonbuk, 56212, Republic of Korea.
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22
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Choe J, Kim JE, Lee BW, Lee JH, Nam M, Park YI, Jo SH. A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae. Database (Oxford) 2018; 2018:5032609. [PMID: 29873704 PMCID: PMC6007222 DOI: 10.1093/database/bay047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 04/23/2018] [Indexed: 11/20/2022]
Abstract
It is necessary for molecular breeders to overcome the difficulties in applying abundant genomic information to crop breeding. Candidate orthologs would be discovered more efficiently in less-studied crops if the information gained from studies of related crops were used. We developed a comparative analysis tool and web-based genome viewer to identify orthologous genes based synteny as well as sequence similarity between tomato, pepper and potato. The tool has a step-by-step interface with multiple viewing levels to support the easy and accurate exploration of functional orthologs. Furthermore, it provides access to single nucleotide-polymorphism markers from the massive genetic resource pool in order to accelerate the development of molecular markers for candidate orthologs in the Solanaceae. This tool provides a bridge between genome data and breeding by supporting effective marker development, data utilization and communication. Database URL: http://tgsol.seeders.co.kr/scomp/
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Affiliation(s)
- Junkyoung Choe
- SEEDERS Inc, Daejeon 34015, Republic of Korea.,School of Medicine, Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Ji-Eun Kim
- SEEDERS Inc, Daejeon 34015, Republic of Korea
| | | | | | - Moon Nam
- SEEDERS Inc, Daejeon 34015, Republic of Korea
| | - Youn-Il Park
- School of Medicine, Biological Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
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23
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Shanmugam T, Abbasi N, Kim HS, Kim HB, Park NI, Park GT, Oh SA, Park SK, Muench DG, Choi Y, Park YI, Choi SB. An Arabidopsis divergent pumilio protein, APUM24, is essential for embryogenesis and required for faithful pre-rRNA processing. Plant J 2017; 92:1092-1105. [PMID: 29031033 DOI: 10.1111/tpj.13745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 12/15/2016] [Revised: 09/28/2017] [Accepted: 10/03/2017] [Indexed: 05/06/2023]
Abstract
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization. Additionally, the mutant embryos displayed defects in cell patterning from pro-embryo through globular stages. The mutant embryos were marked by altered auxin maxima, which were substantiated by the mislocalization of PIN1 and PIN7 transporters in the defective embryos. Homozygous apum24 callus accumulates rRNA processing intermediates, including uridylated and adenylated 5.8S and 25S rRNA precursors. An RNA-protein interaction assay showed that the histidine-tagged recombinant APUM24 binds RNAin vitro with no apparent specificity. Overall, our results demonstrated that APUM24 is required for rRNA processing and early embryogenesis in Arabidopsis.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nazia Abbasi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Hyung-Sae Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Ho Bang Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Nam-Il Park
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
| | - Guen Tae Park
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Sung Aeong Oh
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 702-701, South Korea
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Yeonhee Choi
- School of Biological Sciences, Seoul National University, Seoul, 151-747, South Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, South Korea
| | - Sang-Bong Choi
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyunggi-do, 449-728, South Korea
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Jeon S, Lim JM, Lee HG, Shin SE, Kang NK, Park YI, Oh HM, Jeong WJ, Jeong BR, Chang YK. Current status and perspectives of genome editing technology for microalgae. Biotechnol Biofuels 2017; 10:267. [PMID: 29163669 PMCID: PMC5686953 DOI: 10.1186/s13068-017-0957-z] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
Genome editing techniques are critical for manipulating genes not only to investigate their functions in biology but also to improve traits for genetic engineering in biotechnology. Genome editing has been greatly facilitated by engineered nucleases, dubbed molecular scissors, including zinc-finger nuclease (ZFN), TAL effector endonuclease (TALEN) and clustered regularly interspaced palindromic sequences (CRISPR)/Cas9. In particular, CRISPR/Cas9 has revolutionized genome editing fields with its simplicity, efficiency and accuracy compared to previous nucleases. CRISPR/Cas9-induced genome editing is being used in numerous organisms including microalgae. Microalgae have been subjected to extensive genetic and biological engineering due to their great potential as sustainable biofuel and chemical feedstocks. However, progress in microalgal engineering is slow mainly due to a lack of a proper transformation toolbox, and the same problem also applies to genome editing techniques. Given these problems, there are a few reports on successful genome editing in microalgae. It is, thus, time to consider the problems and solutions of genome editing in microalgae as well as further applications of this exciting technology for other scientific and engineering purposes.
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Affiliation(s)
- Seungjib Jeon
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Jong-Min Lim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Hyung-Gwan Lee
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Sung-Eun Shin
- LG Chem, 188 Munji-ro, Yuseong-gu, Daejeon, 34122 Republic of Korea
| | - Nam Kyu Kang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 34134 Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Byeong-ryool Jeong
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
| | - Yong Keun Chang
- Advanced Biomass Research and Development Center (ABC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141 Republic of Korea
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25
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Lee K, Han JH, Park YI, Colas des Francs-Small C, Small I, Kang H. The mitochondrial pentatricopeptide repeat protein PPR19 is involved in the stabilization of NADH dehydrogenase 1 transcripts and is crucial for mitochondrial function and Arabidopsis thaliana development. New Phytol 2017; 215:202-216. [PMID: 28332713 DOI: 10.1111/nph.14528] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 12/20/2016] [Accepted: 02/19/2017] [Indexed: 05/06/2023]
Abstract
Despite the importance of pentatricopeptide repeat (PPR) proteins in organellar RNA metabolism and plant development, the functions of many PPR proteins remain unknown. Here, we determined the role of a mitochondrial PPR protein (At1g52620) comprising 19 PPR motifs, thus named PPR19, in Arabidopsis thaliana. The ppr19 mutant displayed abnormal seed development, reduced seed yield, delayed seed germination, and retarded growth, indicating that PPR19 is indispensable for normal growth and development of Arabidopsis thaliana. Splicing pattern analysis of mitochondrial genes revealed that PPR19 specifically binds to the specific sequence in the 3'-terminus of the NADH dehydrogenase 1 (nad1) transcript and stabilizes transcripts containing the second and third exons of nad1. Loss of these transcripts in ppr19 leads to multiple secondary effects on accumulation and splicing of other nad1 transcripts, from which we can infer the order in which cis- and trans-spliced nad1 transcripts are normally processed. Improper splicing of nad1 transcripts leads to the absence of mitochondrial complex I and alteration of the nuclear transcriptome, notably influencing the alternative splicing of a variety of nuclear genes. Our results indicate that the mitochondrial PPR19 is an essential component in the splicing of nad1 transcripts, which is crucial for mitochondrial function and plant development.
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Affiliation(s)
- Kwanuk Lee
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Ji Hoon Han
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 306-764, Korea
| | - Catherine Colas des Francs-Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Ian Small
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, Korea
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Osanai T, Park YI, Nakamura Y. Editorial: Biotechnology of Microalgae, Based on Molecular Biology and Biochemistry of Eukaryotic Algae and Cyanobacteria. Front Microbiol 2017; 8:118. [PMID: 28203229 PMCID: PMC5285351 DOI: 10.3389/fmicb.2017.00118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/17/2017] [Indexed: 11/30/2022] Open
Affiliation(s)
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University Daejeon, South Korea
| | - Yuki Nakamura
- Institute of Plant and Microbial Biology, Academia Sinica Taipei, Taiwan
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Kupriyanova EV, Cho SM, Park YI, Pronina NA, Los DA. The complete genome of a cyanobacterium from a soda lake reveals the presence of the components of CO 2-concentrating mechanism. Photosynth Res 2016; 130:151-165. [PMID: 26908147 DOI: 10.1007/s11120-016-0235-0] [Citation(s) in RCA: 8] [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: 12/31/2015] [Accepted: 02/12/2016] [Indexed: 06/05/2023]
Abstract
At present geological epoch, the carbon concentrating mechanism (CCM) of cyanobacteria represents the obligatory tool for adaptation to low content of CO2 in the atmosphere and for the maintenance of sufficient photosynthetic activity. Functional CCM was found in modern cyanobacteria from different ecological niches. However, the presence of such mechanism in species that inhabit soda lakes is not obvious due to high content of inorganic carbon (C i) in the environment. Here we analyze CCM components that have been identified by sequencing of the whole genome of the alkaliphilic cyanobacterium Microcoleus sp. IPPAS B-353. The composition of the CCM components of Microcoleus is similar to that of 'model' β-cyanobacteria, freshwater and marine Synechococcus or Synechocystis spp. However, CahB1 protein of Microcoleus, which is the homolog of CcaA, the carboxysomal β-type carbonic anhydrase (CA) of β-cyanobacteria, appeared to be the only active CA located in cell envelopes. The conservative regions of CcmM, CahG (a homolog of archeal γ-CAs, Cam/CamH), and ChpX of Microcoleus possess single amino acid substitutions that may cause a lack of CA activities. Unlike model cyanobacteria, Microcoleus induces only one BicA-type bicarbonate transporter in response to C i limitation. The differences in the appearance of CCM components and in their characteristics between alkaliphilic Microcoleus and freshwater or marine cyanobacteria are described. The possible reasons for the maintenance of CCM components in cyanobacteria, which permanently live at high concentrations of C i in soda lakes, are discussed.
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Affiliation(s)
- Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276.
| | - Sung Mi Cho
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Natalia A Pronina
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
| | - Dmitry A Los
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya street 35, Moscow, Russia, 127276
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Kim HB, Cho JI, Ryoo N, Shin DH, Park YI, Hwang YS, Lee SK, An G, Jeon JS. Role of rice cytosolic hexokinase OsHXK7 in sugar signaling and metabolism. J Integr Plant Biol 2016; 58:127-35. [PMID: 25951042 DOI: 10.1111/jipb.12366] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 01/23/2015] [Accepted: 05/03/2015] [Indexed: 05/23/2023]
Abstract
We characterized the function of the rice cytosolic hexokinase OsHXK7 (Oryza sativa Hexokinase7), which is highly upregulated when seeds germinate under O2 -deficient conditions. According to transient expression assays that used the promoter:luciferase fusion construct, OsHXK7 enhanced the glucose (Glc)-dependent repression of a rice α-amylase gene (RAmy3D) in the mesophyll protoplasts of maize, but its catalytically inactive mutant alleles did not. Consistently, the expression of OsHXK7, but not its catalytically inactive alleles, complemented the Arabidopsis glucose insensitive2-1 (gin2-1) mutant, thereby resulting in the wild type characteristics of Glc-dependent repression, seedling development, and plant growth. Interestingly, OsHXK7-mediated Glc-dependent repression was abolished in the O2 -deficient mesophyll protoplasts of maize. This result provides compelling evidence that OsHXK7 functions in sugar signaling via a glycolysis-dependent manner under normal conditions, but its signaling role is suppressed when O2 is deficient. The germination of two null OsHXK7 mutants, oshxk7-1 and oshxk7-2, was affected by O2 deficiency, but overexpression enhanced germination in rice. This result suggests the distinct role that OsHXK7 plays in sugar metabolism and efficient germination by enforcing glycolysis-mediated fermentation in O2 -deficient rice.
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Affiliation(s)
- Hyun-Bi Kim
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Jung-Il Cho
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Nayeon Ryoo
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Dong-Ho Shin
- Department of Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Youn-Il Park
- Department of Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Yong-Sic Hwang
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Korea
| | - Sang-Kyu Lee
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Gynheung An
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Jong-Seong Jeon
- Crop Biotech Institute & Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea
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29
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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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30
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Cho SM, Jeoung SC, Song JY, Kupriyanova EV, Pronina NA, Lee BW, Jo SW, Park BS, Choi SB, Song JJ, Park YI. Genomic Survey and Biochemical Analysis of Recombinant Candidate Cyanobacteriochromes Reveals Enrichment for Near UV/Violet Sensors in the Halotolerant and Alkaliphilic Cyanobacterium Microcoleus IPPAS B353. J Biol Chem 2015; 290:28502-28514. [PMID: 26405033 DOI: 10.1074/jbc.m115.669150] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [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: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs), which are exclusive to and widespread among cyanobacteria, are photoproteins that sense the entire range of near-UV and visible light. CBCRs are related to the red/far-red phytochromes that utilize linear tetrapyrrole (bilin) chromophores. Best characterized from the unicellular cyanobacterium Synechocystis sp. PCC 6803 and the multicellular heterocyst forming filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120, CBCRs have been poorly investigated in mat-forming, nonheterocystous cyanobacteria. In this study, we sequenced the genome of one of such species, Microcoleus IPPAS B353 (Microcoleus B353), and identified two phytochromes and seven CBCRs with one or more bilin-binding cGMP-specific phosphodiesterase, adenylyl cyclase and FhlA (GAF) domains. Biochemical and spectroscopic measurements of 23 purified GAF proteins from phycocyanobilin (PCB) producing recombinant Escherichia coli indicated that 13 of these proteins formed near-UV and visible light-absorbing covalent adducts: 10 GAFs contained PCB chromophores, whereas three contained the PCB isomer, phycoviolobilin (PVB). Furthermore, the complement of Microcoleus B353 CBCRs is enriched in near-UV and violet sensors, but lacks red/green and green/red CBCRs that are widely distributed in other cyanobacteria. We hypothesize that enrichment in short wavelength-absorbing CBCRs is critical for acclimation to high-light environments where this organism is found.
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Affiliation(s)
- Sung Mi Cho
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Sae Chae Jeoung
- Center for Advanced Measurement and Instrumentation, Korea Research Institute of Standards and Science, Daejeon 305-340, Korea
| | - Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
| | - Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | - Natalia A Pronina
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow 127276, Russia
| | | | | | - Beom-Seok Park
- The Agricultural Genome Center, National Academy of Agricultural Science, Rural Development Administration, Wanju 565-851, Korea.
| | - Sang-Bong Choi
- School of Biotechnology and Environmental Engineering, Myongji University, Yongin 449-728, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, 305-764, Korea
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31
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Ryu MH, Baba E, Lee KH, Park YI, Boku N, Hyodo I, Nam BH, Esaki T, Yoo C, Ryoo BY, Song EK, Cho SH, Kang WK, Yang SH, Zang DY, Shin DB, Park SR, Shinozaki K, Takano T, Kang YK. Comparison of two different S-1 plus cisplatin dosing schedules as first-line chemotherapy for metastatic and/or recurrent gastric cancer: a multicenter, randomized phase III trial (SOS). Ann Oncol 2015. [PMID: 26216386 DOI: 10.1093/annonc/mdv316] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Five-weekly S-1 plus cisplatin (SP5) is one of the standard first-line regimens for advanced gastric cancer (GC), proven in a Japanese phase III study. To enhance the dose intensity of cisplatin, 3-weekly S-1 plus cisplatin (SP3) was developed. PATIENTS AND METHODS This multicenter, randomized, open-label, phase III study evaluated whether SP3 (S-1 80 mg/m(2)/day on days 1-14 and cisplatin 60 mg/m(2) on day 1) was noninferior/superior to SP5 (S-1 80-120 mg/day on days 1-21 and cisplatin 60 mg/m(2) on day 1 or 8) in terms of progression-free survival (PFS). Chemotherapy-naive patients with metastatic, recurrent gastric or gastroesophageal junction adenocarcinoma were randomized 1 : 1 to receive either SP3 or SP5. The trial is registered at ClinicalTrials.gov (NCT00915382). RESULTS Between February 2009 and January 2012, 625 patients were randomized at 42 sites in Korea and Japan. With a median follow-up duration of 32.4 months (range, 13.3-48.6 months) in surviving patients, SP3 was not only noninferior but also superior to SP5 in terms of PFS [median 5.5 versus 4.9 months; hazard ratio (HR) = 0.82; 95% confidence interval (CI) 0.68-0.99; P = 0.0418 for superiority). There was no difference in overall survival (OS) between the groups (median 14.1 versus 13.9 months; HR = 0.99; 95% CI 0.81-1.21; P = 0.9068). In patients with measurable disease, the response rates were 60% in the SP3 arm and 50% in the SP5 arm (P = 0.065). Both regimens were generally well tolerated, but grade 3 or higher anemia (19% versus 9%) and neutropenia (39% versus 9%) were more frequent in SP3. CONCLUSIONS SP3 is superior to SP5 in terms of PFS. However, since the improvement in PFS was only slight and there was no difference in OS, both SP3 and SP5 can be recommended as first-line treatments for patients with advanced GC.
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Affiliation(s)
- M-H Ryu
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - E Baba
- Department of Comprehensive Clinical Oncology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - K H Lee
- Department of Hemato-oncology, Yeungnam University Hospital, Daegu
| | - Y I Park
- Center for Gastric Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Gyeonggi, Korea
| | - N Boku
- Department of Clinical Oncology, St Marianna University School of Medicine, Kawasaki
| | - I Hyodo
- Division of Gastroenterology, University of Tsukuba, Tsukuba, Japan
| | - B-H Nam
- Biometric Research Branch, National Cancer Center, Goyang, Gyeonggi, Korea
| | - T Esaki
- Department of Gastrointestinal and Medical Oncology, National Kyushu Cancer Center, Fukuoka, Japan
| | - C Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - B-Y Ryoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - E-K Song
- Division of Hematology/Oncology, Department of Internal Medicine, Chonbuk National University Medical School, Jeonju
| | - S-H Cho
- Department of Hematology-Oncology, Chonnam National University Hwasun Hospital, Gwangju
| | - W K Kang
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School Medicine, Seoul
| | - S H Yang
- Department of Internal Medicine, Korea Cancer Center Hospital, Seoul
| | - D Y Zang
- Division of Hematology-Oncology, Department of Internal Medicine, Hallym University Medical Center, Hallym University College of Medicine, Anyang
| | - D B Shin
- Division of Hematology/Oncology, Department of Internal Medicine, Gachon University Gil Hospital, Incheon, Korea
| | - S R Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - K Shinozaki
- Division of Clinical Oncology, Hiroshima Prefectural Hospital, Hiroshima
| | - T Takano
- Department of Medical Oncology, Toranomon Hospital, Minato-ku, Japan
| | - Y-K Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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32
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Shin DH, Cho M, Choi MG, Das PK, Lee SK, Choi SB, Park YI. Identification of genes that may regulate the expression of the transcription factor production of anthocyanin pigment 1 (PAP1)/MYB75 involved in Arabidopsis anthocyanin biosynthesis. Plant Cell Rep 2015; 34:805-15. [PMID: 25604992 DOI: 10.1007/s00299-015-1743-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 05/10/2023]
Abstract
A putative RNA-binding protein with a single RNA Recognition Motif (At3G63450) is involved in anthocyanin biosynthesis via its ability to modulate the transcript level of a major positive regulator PAP1 in Arabidopsis. The R2R3 MYB-activator production of anthocyanin pigment 1 (PAP1)/MYB75 plays a major role in anthocyanin biosynthesis in Arabidopsis in combination with one of three bHLH activators including transparent test 8 (TT8), enhancer of glabra3 (EGL3), glabra3 (GL3), and the WD-repeat transcription factor transparent testa 1 (TTG1), forming ternary MYB-basic HLH-WD40 complexes. Transcriptional activation of PAP1 expression is largely triggered by changes in light color and intensity, temperature fluctuations, nutrient status, and sugar and hormone treatments. However, the immediate upstream and downstream regulatory factors for PAP1 transcription are largely unknown. In the present study, using a T-DNA insertional mutagenesis approach, we transformed pap1-Dominant (pap1D) plants to modulate the levels of endogenous PAP1 transcripts. We employed Restriction Site Extension (RSE)-PCR analysis of 247 homogenous T3 genetic mutant lines exhibiting variations in anthocyanin accumulation compared to pap1D and identified 92 lines with T-DNA integrated in either intra- or inter-genic locations. This analysis revealed 80 novel candidate proteins, including a putative RNA-binding protein with a single RNA Recognition Motif (At3G63450), which may directly or indirectly regulate PAP1 expression at the transcriptional level.
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Affiliation(s)
- Dong Ho Shin
- Department of Biological Sciences, Chungnam National University, 99 Daehagro, Youseong, Daejeon, 305-764, Korea
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33
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Shin DH, Cho M, Choi MG, Das PK, Lee SK, Choi SB, Park YI. Identification of genes that may regulate the expression of the transcription factor production of anthocyanin pigment 1 (PAP1)/MYB75 involved in Arabidopsis anthocyanin biosynthesis. Plant Cell Rep 2015; 34:805-815. [PMID: 25604992 DOI: 10.1007/s00299-015-1743-1747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 05/25/2023]
Abstract
A putative RNA-binding protein with a single RNA Recognition Motif (At3G63450) is involved in anthocyanin biosynthesis via its ability to modulate the transcript level of a major positive regulator PAP1 in Arabidopsis. The R2R3 MYB-activator production of anthocyanin pigment 1 (PAP1)/MYB75 plays a major role in anthocyanin biosynthesis in Arabidopsis in combination with one of three bHLH activators including transparent test 8 (TT8), enhancer of glabra3 (EGL3), glabra3 (GL3), and the WD-repeat transcription factor transparent testa 1 (TTG1), forming ternary MYB-basic HLH-WD40 complexes. Transcriptional activation of PAP1 expression is largely triggered by changes in light color and intensity, temperature fluctuations, nutrient status, and sugar and hormone treatments. However, the immediate upstream and downstream regulatory factors for PAP1 transcription are largely unknown. In the present study, using a T-DNA insertional mutagenesis approach, we transformed pap1-Dominant (pap1D) plants to modulate the levels of endogenous PAP1 transcripts. We employed Restriction Site Extension (RSE)-PCR analysis of 247 homogenous T3 genetic mutant lines exhibiting variations in anthocyanin accumulation compared to pap1D and identified 92 lines with T-DNA integrated in either intra- or inter-genic locations. This analysis revealed 80 novel candidate proteins, including a putative RNA-binding protein with a single RNA Recognition Motif (At3G63450), which may directly or indirectly regulate PAP1 expression at the transcriptional level.
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Affiliation(s)
- Dong Ho Shin
- Department of Biological Sciences, Chungnam National University, 99 Daehagro, Youseong, Daejeon, 305-764, Korea
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34
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An CH, Lee KW, Lee SH, Jeong YJ, Woo SG, Chun H, Park YI, Kwak SS, Kim CY. Heterologous expression of IbMYB1a by different promoters exhibits different patterns of anthocyanin accumulation in tobacco. Plant Physiol Biochem 2015; 89:1-10. [PMID: 25681576 DOI: 10.1016/j.plaphy.2015.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 11/25/2014] [Accepted: 02/05/2015] [Indexed: 05/18/2023]
Abstract
We previously reported that the transient and stable expression of IbMYB1a produced anthocyanin pigmentation in tobacco leaves and transgenic Arabidopsis plants, respectively. To further determine the effects of different promoters on the expression of IbMYB1a and anthocyanin production, we generated and characterized stably transformed tobacco (Nicotiana tabacum SR1) plants expressing IbMYB1a under the control of three different promoters. We compared the differences in anthocyanin accumulation patterns and phenotypic features of the leaves of these transgenic tobacco plants during growth. Expression of IbMYB1a under the control of these three different promoters led to a remarkable variation in anthocyanin pigmentation in tobacco leaves. The anthocyanin contents of the leaves of the SPO-IbMYB1a-OX (SPO-M) line were higher than those of the SWPA2-IbMYB1a-OX (SPA-M) and 35S-IbMYB1a-OX (35S-M) lines. High levels of anthocyanin pigments negatively affected plant growth in the SPO-M lines, resulting delayed growth and, occasionally, a stunted phenotype. Furthermore, HPLC analysis revealed that transcriptional regulation of IbMYB1a led to the production of cyanidin-based anthocyanins in the tobacco plants. In addition, RT-PCR analysis revealed that IbMYB1a expression induced the up-regulation of several structural genes in the anthocyanin biosynthetic pathway, including DFR and ANS. Differential expression levels of IbMYB1a under the control of different promoters were highly correlated with the expression levels of the structural genes, thereby affecting anthocyanin production levels. These results indicate that IbMYB1a positively controls the expression of multiple anthocyanin biosynthetic genes and anthocyanin accumulation in heterologous tobacco plants.
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Affiliation(s)
- Chul Han An
- Eco-friendly Bio-Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 580-185, Republic of Korea; Department of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-806, Republic of Korea
| | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 331-801, Republic of Korea
| | - Sang-Hoon Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan 331-801, Republic of Korea
| | - Yu Jeong Jeong
- Eco-friendly Bio-Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 580-185, Republic of Korea
| | - Su Gyoung Woo
- Eco-friendly Bio-Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 580-185, Republic of Korea
| | - Hyokon Chun
- Eco-friendly Bio-Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 580-185, Republic of Korea
| | - Youn-Il Park
- Department of Bioscience and Biotechnology, Chungnam National University, Daejeon 305-806, Republic of Korea
| | - Sang-Soo Kwak
- Plant Systems Engineering Research Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Cha Young Kim
- Eco-friendly Bio-Material Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 580-185, Republic of Korea.
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Lim JM, Vikramathithan J, Hwangbo K, Ahn JW, Park YI, Choi DW, Jeong WJ. Threonine 286 of fatty acid desaturase 7 is essential for ω-3 fatty acid desaturation in the green microalga Chlamydomonas reinhardtii. Front Microbiol 2015; 6:66. [PMID: 25699037 PMCID: PMC4318421 DOI: 10.3389/fmicb.2015.00066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/19/2015] [Indexed: 12/21/2022] Open
Abstract
Omega-3 fatty acid desaturases catalyze the conversion of dienoic fatty acids (C18:2 and C16:2) into trienoic fatty acids (C18:3 and C16:3), accounting for more than 50% of the total fatty acids in higher plants and the green microalga Chlamydomonas reinhardtii. Here, we describe a Thr residue located in the fourth transmembrane domain of fatty acid desaturase 7 (FAD7) that is essential for the biosynthesis of ω-3 fatty acids in C. reinhardtii. The ω-3 fatty acid deficiency in strain CC-620, which contains a putative missense mutation at Thr286 of CrFAD7, was recovered by the overexpression of CC-125 CrFAD7. A Ser substitution in position 286 was able to partially complement the phenotype of the ω-3 fatty acid deficiency, but other substitution variants, such as Tyr, His, Cys, and Gly, failed to do so. Prediction of the phosphorylation target site revealed that Thr286 may be phosphorylated. Analysis of the structural conformation of CC-620 CrFAD7 via topology prediction (and bends in the helix) shows that this missense mutation may collapse the catalytic structure of CrFAD7. Taken together, this study suggests that Thr286 is essential for the maintaining the catalytic structure of CrFAD7.
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Affiliation(s)
- Jong-Min Lim
- Sustainable Bioresource Center, Korea Institute of Bioscience and Biotechnology Daejeon, South Korea
| | - Jayaraman Vikramathithan
- Sustainable Bioresource Center, Korea Institute of Bioscience and Biotechnology Daejeon, South Korea
| | - Kwon Hwangbo
- Sustainable Bioresource Center, Korea Institute of Bioscience and Biotechnology Daejeon, South Korea ; Department of Biological Science, Chungnam National University Daejeon, South Korea
| | - Joon-Woo Ahn
- Advanced Radiation Technology Institute - Korea Atomic Energy Research Institute Jeonbuk, South Korea
| | - Youn-Il Park
- Department of Biological Science, Chungnam National University Daejeon, South Korea
| | - Dong-Woog Choi
- Department of Biology Education, Chonnam National University South Korea
| | - Won-Joong Jeong
- Sustainable Bioresource Center, Korea Institute of Bioscience and Biotechnology Daejeon, South Korea
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Park YI, Postupna O, Zhugayevych A, Shin H, Park YS, Kim B, Yen HJ, Cheruku P, Martinez JS, Park JW, Tretiak S, Wang HL. A new pH sensitive fluorescent and white light emissive material through controlled intermolecular charge transfer. Chem Sci 2015; 6:789-797. [PMID: 28936321 PMCID: PMC5592806 DOI: 10.1039/c4sc01911c] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [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] [Received: 06/27/2014] [Accepted: 09/07/2014] [Indexed: 11/21/2022] Open
Abstract
A new, pH dependent and water-soluble, conjugated oligomer (amino, trimethylammonium oligophenylene vinylene, ATAOPV) was synthesized with a quaternary ammonium salt and an aromatic amine at the two ends of a π-conjugated oligomer, thus creating a strong dipole across the molecule. A unique white light LED is successfully fabricated from a stimuli responsive organic molecule whose emission properties are dominated by the pH value of the solution through controlled intermolecular charge transfer.
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Affiliation(s)
- Y I Park
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - O Postupna
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - A Zhugayevych
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - H Shin
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - Y-S Park
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - B Kim
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - H-J Yen
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - P Cheruku
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - J S Martinez
- Center for Integrated Nanotechnologies , Materials Physics and Applications Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA
| | - J W Park
- Department of Chemistry/Display Research Center , Catholic University of Korea , Bucheon 420-743 , Republic of Korea
| | - S Tretiak
- Theoretical Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
| | - H-L Wang
- Physical Chemistry and Applied Spectroscopy (C-PCS) , Chemistry Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , USA .
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Lee SK, Eom JS, Voll LM, Prasch CM, Park YI, Hahn TR, Ha SH, An G, Jeon JS. Analysis of a triose phosphate/phosphate translocator-deficient mutant reveals a limited capacity for starch synthesis in rice leaves. Mol Plant 2014; 7:1705-1708. [PMID: 25038232 DOI: 10.1093/mp/ssu082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Sang-Kyu Lee
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Korea
| | - Joon-Seob Eom
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Korea
| | - Lars M Voll
- Friedrich-Alexander Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - Christian M Prasch
- Friedrich-Alexander Universität Erlangen-Nürnberg, Lehrstuhl für Biochemie, Staudtstrasse 5, D-91058 Erlangen, Germany
| | - Youn-Il Park
- Department of Biology, Chungnam National University, Daejeon 305-764, Korea
| | - Tae-Ryong Hahn
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Korea
| | - Sun-Hwa Ha
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Gynheung An
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea; Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea; Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Korea; Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 446-701, Korea.
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Kupriyanova EV, Sinetova MA, Cho SM, Park YI, Los DA, Pronina NA. CO2-concentrating mechanism in cyanobacterial photosynthesis: organization, physiological role, and evolutionary origin. Photosynth Res 2013; 117:133-146. [PMID: 23733616 DOI: 10.1007/s11120-013-9860-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/25/2013] [Indexed: 06/02/2023]
Abstract
The cellular and molecular organization of the CO2-concentrating mechanism (CCM) of cyanobacteria is reviewed. The primary processes of uptake, translocation, and accumulation of inorganic carbon (Ci) near the active site of carbon assimilation by the enzyme ribulose-1,5-bisphosphate carboxylase in the C3 cycle in cyanobacteria are described as one of the specialized forms of CO2 concentration which occurs in some photoautotrophic cells. The existence of this form of CO2 concentration expands our understanding of photosynthetic Ci assimilation. The means of supplying Ci to the C3 cycle in cyanobacteria is not by simple diffusion into the cell, but it is the result of coordinated functions of high-affinity systems for the uptake of CO2 and bicarbonate, as well as intracellular CO2/HCO3 (-) interconversions by carbonic anhydrases. These biochemical events are under genetic control, and they serve to maintain cellular homeostasis and adaptation to CO2 limitation. Here we describe the organization of the CCM in cyanobacteria with a special focus on the CCM of relict halo- and alkaliphilic cyanobacteria of soda lakes. We also assess the role of the CCM at the levels of the organism, the biosphere, and evolution.
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Affiliation(s)
- Elena V Kupriyanova
- Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street, 35, Moscow, 127276, Russia
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Byeon Y, Lee K, Park YI, Park S, Back K. Molecular cloning and functional analysis of serotonin N-acetyltransferase from the cyanobacterium Synechocystis sp. PCC 6803. J Pineal Res 2013; 55:371-6. [PMID: 23952748 DOI: 10.1111/jpi.12080] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 07/19/2013] [Indexed: 01/13/2023]
Abstract
Serotonin N-acetyltransferase (SNAT) catalyzes conversion of serotonin into N-acetylserotonin, which is a direct precursor for melatonin biosynthesis in all organisms. Molecular cloning of plant SNAT from rice led to a screening for SNAT homolog genes in other species. We identified a cyanobacterium SNAT-like gene (cSNAT) that showed 56% amino acid homology with the rice SNAT. To confirm whether cSNAT encoded SNAT enzyme activity, we expressed cSNAT DNA in Escherichia coli and purified the cSNAT protein as a C-terminal His-tagged form. The purified cSNAT protein exhibited SNAT enzyme activities, transferring the acetyl group into either serotonin or tryptamine substrates. The optimum temperature was 55°C, but it was still highly active at 70°C, suggesting that cSNAT is a thermotolerant enzyme. The Km and Vmax were 823 μm and 1.6 nmol/min/mg protein, respectively. The cSNAT gene is highly conserved in all cyanobacterial taxa and seems to be an origin of SNAT in higher plants. The thermotolerance of cSNAT suggests that melatonin plays a role in the response to high-temperature stress. Further analysis of this role of melatonin in higher plants is needed.
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Affiliation(s)
- Yeong Byeon
- Department of Biotechnology, Bioenergy Research Center, Chonnam National University, Gwangju, Korea
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40
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Lee JY, Lee HS, Song JY, Jung YJ, Reinbothe S, Park YI, Lee SY, Pai HS. Cell growth defect factor1/chaperone-like protein of POR1 plays a role in stabilization of light-dependent protochlorophyllide oxidoreductase in Nicotiana benthamiana and Arabidopsis. Plant Cell 2013; 25:3944-60. [PMID: 24151298 PMCID: PMC3877821 DOI: 10.1105/tpc.113.111096] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 09/11/2013] [Accepted: 09/30/2013] [Indexed: 05/20/2023]
Abstract
Angiosperms require light for chlorophyll biosynthesis because one reaction in the pathway, the reduction of protochlorophyllide (Pchlide) to chlorophyllide, is catalyzed by the light-dependent protochlorophyllide oxidoreductase (POR). Here, we report that Cell growth defect factor1 (Cdf1), renamed here as chaperone-like protein of POR1 (CPP1), an essential protein for chloroplast development, plays a role in the regulation of POR stability and function. Cdf1/CPP1 contains a J-like domain and three transmembrane domains, is localized in the thylakoid and envelope membranes, and interacts with POR isoforms in chloroplasts. CPP1 can stabilize POR proteins with its holdase chaperone activity. CPP1 deficiency results in diminished POR protein accumulation and defective chlorophyll synthesis, leading to photobleaching and growth inhibition of plants under light conditions. CPP1 depletion also causes reduced POR accumulation in etioplasts of dark-grown plants and as a result impairs the formation of prolamellar bodies, which subsequently affects chloroplast biogenesis upon illumination. Furthermore, in cyanobacteria, the CPP1 homolog critically regulates POR accumulation and chlorophyll synthesis under high-light conditions, in which the dark-operative Pchlide oxidoreductase is repressed by its oxygen sensitivity. These findings and the ubiquitous presence of CPP1 in oxygenic photosynthetic organisms suggest the conserved nature of CPP1 function in the regulation of POR.
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Affiliation(s)
- Jae-Yong Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Ho-Seok Lee
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
| | - Ji-Young Song
- Department of Biological Science and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Young Jun Jung
- Division of Applied Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Steffen Reinbothe
- Biologie Environnementale et Systémique, Université Joseph Fourier LBFA, BP53F 38041 Grenoble cedex 9 France
| | - Youn-Il Park
- Department of Biological Science and Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon 305-764, Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences, Gyeongsang National University, Jinju 660-701, Korea
| | - Hyun-Sook Pai
- Department of Systems Biology, Yonsei University, Seoul 120-749, Korea
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41
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Shin DH, Choi MG, Lee HK, Cho M, Choi SB, Choi G, Park YI. Calcium dependent sucrose uptake links sugar signaling to anthocyanin biosynthesis in Arabidopsis. Biochem Biophys Res Commun 2012; 430:634-9. [PMID: 23220235 DOI: 10.1016/j.bbrc.2012.11.100] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 11/25/2012] [Indexed: 10/27/2022]
Abstract
Sugars enhance light signaling-induced anthocyanin accumulation in Arabidopsis seedlings via differential regulation of several positive and negative transcription factors. Ca(2+) plays a role as a second messenger in sugar signaling in grape and wheat. However, whether anthocyanin pigmentation is modulated by changes in intracellular Ca(2+) level in Arabidopsis is not known. Here, we used a pharmaceutical approach that Ca(2+) antagonists strongly interfered with sucrose uptake and anthocyanin accumulation by downregulating the expression of sucrose transporter 1 (SUC1) and transcriptional regulatory factors, such as PAP1. Time course analysis of the effect of Ca(2+) antagonists showed the early inhibition of sucrose-induced sugar uptake leading to decreased anthocyanin accumulation, indicating that Ca(2+) signals play a role in sugar uptake rather than in anthocyanin biosynthesis. An early increase in cytosolic Ca(2+) level in Arabidopsis roots in response to sucrose feeding was significantly inhibited by Ca(2+) antagonists. Taken together, these results indicate that sucrose-induced sugar uptake in Arabidopsis is modulated by changes in endogenous Ca(2+) levels, which in turn regulate anthocyanin accumulation.
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Affiliation(s)
- Dong Ho Shin
- Department of Biological Sciences, Chungnam National University, Daejeon 305-764, Republic of Korea
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Ahn JW, Hwangbo K, Lee SY, Choi HG, Park YI, Liu JR, Jeong WJ. A new Arctic Chlorella species for biodiesel production. Bioresour Technol 2012; 125:340-3. [PMID: 23069611 DOI: 10.1016/j.biortech.2012.09.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 09/07/2012] [Accepted: 09/09/2012] [Indexed: 05/04/2023]
Abstract
Microalgae are a potential resource for biodiesel production. A green alga, Chlorella sp., was isolated from Arctic sea ice, which was named ArM0029B. These algae displayed faster growth at a wide temperature range of 4-32°C compared to Chlorella vulgaris. ArM0029B also accumulated high levels of total fatty acids under nitrogen starvation conditions, reaching 39% of dry cell weight, with the proportion of oleic acid (18:1) and linoleic acid (18:2) reaching 54% of total fatty acids. Taken together, these results indicate that the newly identified Chlorella species, ArM0029B, is a promising candidate for biodiesel production.
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Affiliation(s)
- Joon-Woo Ahn
- Green Bio Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Abstract
Anthocyanins, a class of flavonoids, are recognized for their diverse functions in plant development and beneficial effects on human health. Many of the genes encoding anthocyanin biosynthesis enzymes and the transcription factors that activate or repress them have been identified. Regulatory proteins that control anthocyanin biosynthesis by regulating the expression of different structural genes at the transcriptional and post-transcriptional levels are differentially modulated by environmental and biological factors such as light, temperature, sugar and hormones. This minireview summarizes the recent findings contributing to our understanding of the role of sugars and hormones in the modulation of the anthocyanin biosynthesis pathway with emphasis on the coordinated regulation of the critical transcriptional R2R3-MYB/bHLH/WD40 (MBW) complex in Arabidopsis.
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Affiliation(s)
- Prasanta Kumar Das
- Department of Biological Sciences, College of Biological Science and Technology, Chungnam National University, Daejeon 305-764,
Korea
| | - Dong Ho Shin
- Department of Biological Sciences, College of Biological Science and Technology, Chungnam National University, Daejeon 305-764,
Korea
| | | | - Youn-Il Park
- Department of Biological Sciences, College of Biological Science and Technology, Chungnam National University, Daejeon 305-764,
Korea
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Chung Y, Choe V, Fujioka S, Takatsuto S, Han M, Jeon JS, Park YI, Lee KO, Choe S. Constitutive activation of brassinosteroid signaling in the Arabidopsis elongated-D/bak1 mutant. Plant Mol Biol 2012; 80:489-501. [PMID: 22961663 DOI: 10.1007/s11103-012-9963-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/24/2012] [Indexed: 05/10/2023]
Abstract
Defects in brassinosteroid (BR) biosynthetic or signaling genes result in dwarfed plants, whereas overexpression of these genes increases overall stature. An Arabidopsis elongated-D (elg-D) mutant shares phenotypic similarities with BR overexpression lines, suggesting its implication in BR pathways. Here, we determine how elg-D affects BR signaling. Since elg-D rescued dwarfism in bri1-5 plants, a BR receptor mutant, but not in BR-insensitive bin2/dwf12-1D plants, elg-D appears to act between bri1-5 and bin2/dwf12-1D in BR signaling. We found that elg-D had an increased response to epi-brassinolide (epi-BL); that the BES1 transcription factor was shifted toward the dephosphorylated form in elg-D; that the expression of a BR responsive gene, SAUR-AC1, was upregulated in elg-D; and that transcription of BR biosynthetic genes, DWF4 and CPD, was downregulated by feedback inhibition. Thus, endogenous levels of CS and BL as well as biosynthetic intermediates were reduced by the elg-D mutation, whereas basal levels of BR signaling were elevated. Map-based cloning and sequencing revealed that elg-D is allelic to the BR co-receptor protein, BAK1, and has an Asp(122) to Asn substitution in the third repeat of the extracellular leucine-rich repeat (LRR) domain. In agreement with the finding that BAK1/ELG is involved in the perception of pathogen-associated molecular patterns (PAMPs), the bak1/elg-D plants exhibited increased Pseudomonas syringae growth. Therefore, bak1/elg-D promotes Arabidopsis growth by stimulating BR signaling at the expense of its readiness to respond to biotic stress factors. The BAK1/ELG BR co-receptor thus plays an important role in BR signaling that is mediated by its LRR domain.
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Affiliation(s)
- Yuhee Chung
- School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, Korea
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46
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Chow WS, Fan DY, Oguchi R, Jia H, Losciale P, Park YI, He J, Oquist G, Shen YG, Anderson JM. Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments: approaches and approximations. Photosynth Res 2012; 113:63-74. [PMID: 22638914 DOI: 10.1007/s11120-012-9740-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/04/2012] [Indexed: 05/12/2023]
Abstract
Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. (1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. (2) The gross O(2) yield per single-turnover flash in CO(2)-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O(2) molecule after four flashes. However, the gross O(2) yield per single-turnover flash (multiplied by four) could over-estimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. (3) The cumulative delivery of electrons from PS II to P700(+) (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field.
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Affiliation(s)
- Wah Soon Chow
- Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, 0200, Australia.
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Kim CG, Park SR, Choi IJ, Lee JY, Cho SJ, Park YI, Nam BH, Kim YW. Effect of chemotherapy on the outcome of self-expandable metallic stents in gastric cancer patients with malignant outlet obstruction. Endoscopy 2012; 44:807-12. [PMID: 22752892 DOI: 10.1055/s-0032-1309893] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [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: 02/07/2023]
Abstract
BACKGROUND AND STUDY AIM Chemotherapy has been suggested to affect the outcome of pyloric stent placement. This study aimed to investigate the association between the response to chemotherapy and pyloric stent outcome. PATIENTS AND METHODS Data from 113 patients with inoperable gastric cancer who received chemotherapy after pyloric stent placement at the National Cancer Center hospital were analyzed retrospectively. Chemotherapy response was assessed using the Response Evaluation Criteria in Solid Tumors. A Cox proportional hazards model was used to evaluate the effect of chemotherapy response on the complications of stents. RESULTS The stent migration rate was 15.9% (18/113) and the re-stenosis rate was 30.1% (34/113). The response rates to chemotherapy were higher in the first-line group than in the salvage chemotherapy group (second-line or more) (44.8% [26/58] vs. 3.6% [2/55], respectively; P < 0.001). The proportion of patients with long time-to-progression (> 8 weeks) was also higher in the first-line than the salvage chemotherapy group (81.0% [47 /58] vs. 61.8% [34 /55], respectively; P = 0.036). Although, the response to chemotherapy was not associated with stent migration or re-stenosis, a long time-to-progression (adjusted hazard ratio [aHR] = 0.29, 95% confidence interval [CI] 0.13-0.67) and first-line chemotherapy (aHR = 0.45, 95%CI 0.22-0.93) were protective factors against re-stenosis in the multivariate analysis. In patients who received first-line chemotherapy, the median duration of patency of covered and uncovered stents was 20 weeks (95%CI 11-29) and 33 weeks (95 %CI 18-48), respectively (P = 0.317). CONCLUSIONS A long time-to-progression and first-line chemotherapy were significant protective factors against re-stenosis. In chemotherapy-naïve gastric cancer patients with pyloric obstruction, placement of an uncovered stent followed by chemotherapy can be considered to increase stent patency.
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Affiliation(s)
- C G Kim
- Center for Gastric Cancer, National Cancer Center, Goyang, Republic of Korea
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Park KS, Ryu SB, Park YI, Ahn KY. Retraction: Effects of Estrogen Deprivation on the Rabbit Clitoral Cavernosal Fibrosis. Korean J Urol 2012; 53:890. [PMID: 23301138 PMCID: PMC3531647 DOI: 10.4111/kju.2012.53.12.890] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- KS Park
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
| | - SB Ryu
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
| | - YI Park
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
| | - KY Ahn
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
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49
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Jung J, Kumar K, Lee HY, Park YI, Cho HT, Ryu SB. Translocation of phospholipase A2α to apoplasts is modulated by developmental stages and bacterial infection in Arabidopsis. Front Plant Sci 2012; 3:126. [PMID: 22719742 PMCID: PMC3376726 DOI: 10.3389/fpls.2012.00126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 05/25/2012] [Indexed: 05/21/2023]
Abstract
Phospholipase A(2) (PLA(2)) hydrolyzes phospholipids at the sn-2 position to yield lysophospholipids and free fatty acids. Of the four paralogs expressed in Arabidopsis, the cellular functions of PLA(2)α in planta are poorly understood. The present study shows that PLA(2)α possesses unique characteristics in terms of spatiotemporal subcellular localization, as compared with the other paralogs that remain in the ER and/or Golgi apparatus during secretory processes. Only PLA(2)α is secreted out to extracellular spaces, and its secretion to apoplasts is modulated according to the developmental stages of plant tissues. Observation of PLA(2)α-RFP transgenic plants suggests that PLA(2)α localizes mostly at the Golgi bodies in actively growing leaf tissues, but is gradually translocated to apoplasts as the leaves become mature. When Pseudomonas syringae pv.~tomato DC3000 carrying the avirulent factor avrRpm1 infects the apoplasts of host plants, PLA(2)α rapidly translocates to the apoplasts where bacteria attempt to become established. PLA(2)α promoter::GUS assays show that PLA(2)α gene expression is controlled in a developmental stage- and tissue-specific manner. It would be interesting to investigate if PLA(2)α functions in plant defense responses at apoplasts where secreted PLA(2)α confronts with invading pathogens.
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Affiliation(s)
- Jihye Jung
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB),Daejeon, Korea
- Division of Biosystems and Bioengineering, University of Science and Technology,Daejeon, Korea
| | - Krishna Kumar
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB),Daejeon, Korea
- Department of Biological Sciences, Chungnam National University,Daejeon, Korea
| | - Hyoung Yool Lee
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB),Daejeon, Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University,Daejeon, Korea
| | - Hyung-Taeg Cho
- School of Biological Sciences and Genomics and Breeding Institute, Seoul National University,Seoul, Korea
| | - Stephen Beungtae Ryu
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB),Daejeon, Korea
- Division of Biosystems and Bioengineering, University of Science and Technology,Daejeon, Korea
- *Correspondence: Stephen Beungtae Ryu, Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 306-809, Korea. e-mail:
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Jeon Y, Jung HJ, Kang H, Park YI, Lee SH, Pai HS. S1 domain-containing STF modulates plastid transcription and chloroplast biogenesis in Nicotiana benthamiana. New Phytol 2012; 193:349-63. [PMID: 22050604 DOI: 10.1111/j.1469-8137.2011.03941.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
• In this study, we examined the biochemical and physiological functions of Nicotiana benthamiana S1 domain-containing Transcription-Stimulating Factor (STF) using virus-induced gene silencing (VIGS), cosuppression, and overexpression strategies. • STF : green fluorescent protein (GFP) fusion protein colocalized with sulfite reductase (SiR), a chloroplast nucleoid-associated protein also present in the stroma. Full-length STF and its S1 domain preferentially bound to RNA, probably in a sequence-nonspecific manner. • STF silencing by VIGS or cosuppression resulted in severe leaf yellowing caused by disrupted chloroplast development. STF deficiency significantly perturbed plastid-encoded multimeric RNA polymerase (PEP)-dependent transcript accumulation. Chloroplast transcription run-on assays revealed that the transcription rate of PEP-dependent plastid genes was reduced in the STF-silenced leaves. Conversely, the exogenously added recombinant STF protein increased the transcription rate, suggesting a direct role of STF in plastid transcription. Etiolated seedlings of STF cosuppression lines showed defects in the light-triggered transition from etioplasts to chloroplasts, accompanied by reduced light-induced expression of plastid-encoded genes. • These results suggest that STF plays a critical role as an auxiliary factor of the PEP transcription complex in the regulation of plastid transcription and chloroplast biogenesis in higher plants.
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Affiliation(s)
- Young Jeon
- Department of Systems Biology, Yonsei University, Seoul, Korea
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